Mark M. Davis

All Publications

• Human Coronary Plaque T Cells Are Clonal and Cross-React to Virus and Self. Circulation research Roy Chowdhury, R., D'Addabbo, J., Huang, X., Veizades, S., Sasagawa, K., Louis, D. M., Cheng, P., Sokol, J., Jensen, A., Tso, A., Shankar, V., Wendel, B. S., Bakerman, I., Liang, G., Koyano, T., Fong, R., Nau, A., Ahmad, H., Gopakumar, J. K., Wirka, R., Lee, A., Boyd, J., Woo, Y. J., Quertermous, T., Gulati, G., Jaiswal, S., Chien, Y. H., Chan, C., Davis, M. M., Nguyen, P. K. 2022: 101161CIRCRESAHA121320090

  Abstract

  Once considered primarily a disorder of lipid deposition, coronary artery disease is an incurable, life-threatening disease that is now also characterized by chronic inflammation notable for the buildup of atherosclerotic plaques containing immune cells in various states of activation and differentiation. Understanding how these immune cells contribute to disease progression may lead to the development of novel therapeutic strategies.We used single-cell technology and in vitro assays to interrogate the immune microenvironment of human coronary atherosclerotic plaque at different stages of maturity.In addition to macrophages, we found a high proportion of αβ T cells in the coronary plaques. Most of these T cells lack high expression of CCR7 and L-selectin, indicating that they are primarily antigen-experienced, memory cells. Notably, nearly one-third of these cells express the HLA-DRA surface marker, signifying activation through their TCRs (T-cell receptors). Consistent with this, TCR repertoire analysis confirmed the presence of activated αβ T cells (CD4

  View details for DOI 10.1161/CIRCRESAHA.121.320090

  View details for PubMedID 35430876

• KIR+CD8+ T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19. Science (New York, N.Y.) Li, J., Zaslavsky, M., Su, Y., Guo, J., Sikora, M. J., van Unen, V., Christophersen, A., Chiou, S., Chen, L., Li, J., Ji, X., Wilhelmy, J., McSween, A. M., Palanski, B. A., Mallajosyula, V. V., Bracey, N. A., Dhondalay, G. K., Bhamidipati, K., Pai, J., Kipp, L. B., Dunn, J. E., Hauser, S. L., Oksenberg, J. R., Satpathy, A. T., Robinson, W. H., Dekker, C. L., Steinmetz, L. M., Khosla, C., Utz, P. J., Sollid, L. M., Chien, Y., Heath, J. R., Fernandez-Becker, N. Q., Nadeau, K. C., Saligrama, N., Davis, M. M. 2022: eabi9591

  Abstract

  Here we find that CD8+ T cells expressing inhibitory killer cell immunoglobulin-like receptors (KIRs) are the human equivalent of Ly49+CD8+ regulatory T cells in mice and are increased in the blood and inflamed tissues of patients with a variety of autoimmune diseases. Moreover, these CD8+ T cells efficiently eliminated pathogenic gliadin-specific CD4+ T cells from celiac disease patients' leukocytes in vitro. We also find elevated levels of KIR+CD8+ T cells, but not CD4+ regulatory T cells, in COVID-19 patients, which correlated with disease severity and vasculitis. Selective ablation of Ly49+CD8+ T cells in virus-infected mice led to autoimmunity post infection. Our results indicate that in both species, these regulatory CD8+ T cells act uniquely to suppress pathogenic T cells in autoimmune and infectious diseases.

  View details for DOI 10.1126/science.abi9591

  View details for PubMedID 35258337

• Minimal Information about MHC Multimers (MIAMM). Journal of immunology (Baltimore, Md. : 1950) Vita, R., Mody, A., Overton, J. A., Buus, S., Haley, S. T., Sette, A., Mallajosyula, V., Davis, M. M., Long, D. L., Willis, R. A., Peters, B., Altman, J. D. 1800; 208 (3): 531-537

  Abstract

  With the goal of improving the reproducibility and annotatability of MHC multimer reagent data, we present the establishment of a new data standard: Minimal Information about MHC Multimers (https://miamm.lji.org/). Multimers are engineered reagents composed of a ligand and a MHC, which can be represented in a standardized format using ontology terminology. We provide an online Web site to host the details of the standard, as well as a validation tool to assist with the adoption of the standard. We hope that this publication will bring increased awareness of Minimal Information about MHC Multimers and drive acceptance, ultimately improving the quality and documentation of multimer data in the scientific literature.

  View details for DOI 10.4049/jimmunol.2100961

  View details for PubMedID 35042788

• Multiple early factors anticipate post-acute COVID-19 sequelae. Cell Su, Y., Yuan, D., Chen, D. G., Ng, R. H., Wang, K., Choi, J., Li, S., Hong, S., Zhang, R., Xie, J., Kornilov, S. A., Scherler, K., Pavlovitch-Bedzyk, A. J., Dong, S., Lausted, C., Lee, I., Fallen, S., Dai, C. L., Baloni, P., Smith, B., Duvvuri, V. R., Anderson, K. G., Li, J., Yang, F., Duncombe, C. J., McCulloch, D. J., Rostomily, C., Troisch, P., Zhou, J., Mackay, S., DeGottardi, Q., May, D. H., Taniguchi, R., Gittelman, R. M., Klinger, M., Snyder, T. M., Roper, R., Wojciechowska, G., Murray, K., Edmark, R., Evans, S., Jones, L., Zhou, Y., Rowen, L., Liu, R., Chour, W., Algren, H. A., Berrington, W. R., Wallick, J. A., Cochran, R. A., Micikas, M. E., ISB-Swedish COVID-19 Biobanking Unit, Wrin, T., Petropoulos, C. J., Cole, H. R., Fischer, T. D., Wei, W., Hoon, D. S., Price, N. D., Subramanian, N., Hill, J. A., Hadlock, J., Magis, A. T., Ribas, A., Lanier, L. L., Boyd, S. D., Bluestone, J. A., Chu, H., Hood, L., Gottardo, R., Greenberg, P. D., Davis, M. M., Goldman, J. D., Heath, J. R. 2022

  Abstract

  Post-acute sequelae of COVID-19 (PASC) represent an emerging global crisis. However, quantifiable risk factors for PASC and their biological associations are poorly resolved. We executed a deep multi-omic, longitudinal investigation of 309 COVID-19 patients from initial diagnosis to convalescence (2-3months later), integrated with clinical data and patient-reported symptoms. We resolved four PASC-anticipating risk factors at the time of initial COVID-19 diagnosis: type 2 diabetes, SARS-CoV-2 RNAemia, Epstein-Barr virus viremia, and specific auto-antibodies. In patients with gastrointestinal PASC, SARS-CoV-2-specific and CMV-specific CD8+ Tcells exhibited unique dynamics during recovery from COVID-19. Analysis of symptom-associated immunological signatures revealed coordinated immunity polarization into four endotypes, exhibiting divergent acute severity and PASC. We find that immunological associations between PASC factors diminish over time, leading to distinct convalescent immune states. Detectability of most PASC factors at COVID-19 diagnosis emphasizes the importance of early disease measurements for understanding emergent chronic conditions and suggests PASC treatment strategies.

  View details for DOI 10.1016/j.cell.2022.01.014

  View details for PubMedID 35216672

• Early non-neutralizing, afucosylated antibody responses are associated with COVID-19 severity. Science translational medicine Chakraborty, S., Gonzalez, J. C., Sievers, B. L., Mallajosyula, V., Chakraborty, S., Dubey, M., Ashraf, U., Cheng, B. Y., Kathale, N., Tran, K. Q., Scallan, C., Sinnott, A., Cassidy, A., Chen, S. T., Gelbart, T., Gao, F., Golan, Y., Ji, X., Kim-Schulze, S., Prahl, M., Gaw, S. L., Gnjatic, S., Marron, T. U., Merad, M., Arunachalam, P. S., Boyd, S. D., Davis, M. M., Holubar, M., Khosla, C., Maecker, H. T., Maldonado, Y., Mellins, E. D., Nadeau, K. C., Pulendran, B., Singh, U., Subramanian, A., Utz, P. J., Sherwood, R., Zhang, S., Jagannathan, P., Tan, G. S., Wang, T. T. 1800: eabm7853

  Abstract

  A damaging inflammatory response is implicated in the pathogenesis of severe coronavirus disease 2019 (COVID-19), but mechanisms contributing to this response are unclear. In two prospective cohorts, early non-neutralizing, afucosylated IgG antibodies specific to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were associated with progression from mild to more severe COVID-19. In contrast to the antibody structures that were associated with disease progression, antibodies that were elicited by mRNA SARS-CoV-2 vaccines were instead highly fucosylated and enriched in sialylation, both modifications that reduce the inflammatory potential of IgG. To study the biology afucosylated IgG immune complexes, we developed an in vivo model that revealed that human IgG-Fc gamma receptor (FcgammaR) interactions could regulate inflammation in the lung. Afucosylated IgG immune complexes isolated from COVID-19 patients induced inflammatory cytokine production and robust infiltration of the lung by immune cells. By contrast, vaccine-elicited IgG did not promote an inflammatory lung response. Together, these results show that IgG-FcgammaR interactions are able to regulate inflammation in the lung and may define distinct lung activities associated with the IgG that are associated with severe COVID-19 and protection against infection with SARS-CoV-2.

  View details for DOI 10.1126/scitranslmed.abm7853

  View details for PubMedID 35040666

• Durability of immune responses to the BNT162b2 mRNA vaccine MED Suthar, M. S., Arunachalam, P. S., Hu, M., Reis, N., Trisal, M., Raeber, O., Chinthrajah, S., Davis-Gardner, M. E., Manning, K., Mudvari, P., Boritz, E., Godbole, S., Henry, A. R., Douek, D. C., Halfmann, P., Kawaoka, Y., Boyd, S. D., Davis, M. M., Zarnitsyna, V. I., Nadeau, K., Pulendran, B. 2022; 3 (1): 25-27

  View details for DOI 10.1016/j.medj.2021.12.005

  View details for Web of Science ID 000758831100004

• Antibodies elicited by SARS-CoV-2 infection or mRNA vaccines have reduced neutralizing activity against Beta and Omicron pseudoviruses. Science translational medicine Sievers, B. L., Chakraborty, S., Xue, Y., Gelbart, T., Gonzalez, J. C., Cassidy, A. G., Golan, Y., Prahl, M., Gaw, S. L., Arunachalam, P. S., Blish, C. A., Boyd, S. D., Davis, M. M., Jagannathan, P., Nadeau, K. C., Pulendran, B., Singh, U., Scheuermann, R. H., Frieman, M. B., Vashee, S., Wang, T. T., Tan, G. S. 1800: eabn7842

  Abstract

  Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that possess mutations associated with increased transmission and antibody escape have arisen over the course of the current pandemic. Although the current vaccines have largely been effective against past variants, the number of mutations found on the Omicron (B.1.1.529) spike protein appear to diminish the protection conferred by pre-existing immunity. Using vesicular stomatitis virus (VSV) pseudoparticles expressing the spike protein of several SARS-CoV-2 variants, we evaluated the magnitude and breadth of the neutralizing antibody response over time in individuals after infection and in mRNA-vaccinated individuals. We observed that boosting increases the magnitude of the antibody response to wildtype (D614), Beta, Delta, and Omicron variants; however, the Omicron variant was the most resistant to neutralization. We further observed that vaccinated healthy adults had robust and broad antibody responses whereas responses may have been reduced in vaccinated pregnant women, underscoring the importance of learning how to maximize mRNA vaccine responses in pregnant populations. Findings from this study show substantial heterogeneity in the magnitude and breadth of responses after infection and mRNA vaccination and may support the addition of more conserved viral antigens to existing SARS-CoV-2 vaccines.

  View details for DOI 10.1126/scitranslmed.abn7842

  View details for PubMedID 35025672

• Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination. Cell Röltgen, K., Nielsen, S. C., Silva, O., Younes, S. F., Zaslavsky, M., Costales, C., Yang, F., Wirz, O. F., Solis, D., Hoh, R. A., Wang, A., Arunachalam, P. S., Colburg, D., Zhao, S., Haraguchi, E., Lee, A. S., Shah, M. M., Manohar, M., Chang, I., Gao, F., Mallajosyula, V., Li, C., Liu, J., Shoura, M. J., Sindher, S. B., Parsons, E., Dashdorj, N. J., Dashdorj, N. D., Monroe, R., Serrano, G. E., Beach, T. G., Chinthrajah, R. S., Charville, G. W., Wilbur, J. L., Wohlstadter, J. N., Davis, M. M., Pulendran, B., Troxell, M. L., Sigal, G. B., Natkunam, Y., Pinsky, B. A., Nadeau, K. C., Boyd, S. D. 2022

  Abstract

  During the SARS-CoV-2 pandemic, novel and traditional vaccine strategies have been deployed globally. We investigated whether antibodies stimulated by mRNA vaccination (BNT162b2), including third-dose boosting, differ from those generated by infection or adenoviral (ChAdOx1-S and Gam-COVID-Vac) or inactivated viral (BBIBP-CorV) vaccines. We analyzed human lymph nodes after infection or mRNA vaccination for correlates of serological differences. Antibody breadth against viral variants is lower after infection compared with all vaccines evaluated but improves over several months. Viral variant infection elicits variant-specific antibodies, but prior mRNA vaccination imprints serological responses toward Wuhan-Hu-1 rather than variant antigens. In contrast to disrupted germinal centers (GCs) in lymph nodes during infection, mRNA vaccination stimulates robust GCs containing vaccine mRNA and spike antigen up to 8 weeks postvaccination in some cases. SARS-CoV-2 antibody specificity, breadth, and maturation are affected by imprinting from exposure history and distinct histological and antigenic contexts in infection compared with vaccination.

  View details for DOI 10.1016/j.cell.2022.01.018

  View details for PubMedID 35148837

• Treatment With Simvastatin and Rifaximin Restores the Plasma Metabolomic Profile in Patients With Decompensated Cirrhosis. Hepatology communications Pose, E., Sola, E., Lozano, J. J., Juanola, A., Sidorova, J., Zaccherini, G., de Wit, K., Uschner, F., Tonon, M., Kazankov, K., Jimenez, C., Campion, D., Napoleone, L., Ma, A. T., Carol, M., Morales-Ruiz, M., Alessandria, C., Beuers, U., Caraceni, P., Francoz, C., Durand, F., Mookerjee, R. P., Trebicka, J., Vargas, V., Piano, S., Watson, H., Abraldes, J. G., Kamath, P. S., Davis, M. M., Gines, P., investigators of the LIVERHOPE Consortium, Schulz, M., Ferstl, P., Giovo, I., Roux, O., Simon-Talero, M., Perez-Guasch, M., Rubio, A. B., Cervera, M., Martinez, S., Fabrellas, N., Pich, J., Vives, A., Avitabile, E., Graupera, I., Sole, C., Bassegoda, O., Gratacos-Gines, J., Joyera, M., Palacio, E., Aban, M., Lanzillotti, T., Nicolao, G., Chiappa, M. T., Esnault, V., Andrade, R., Pavesi, M., Korenjak, M., Farres, J., Serra-Burriel, M., Angeli, P. 1800

  Abstract

  Patients with decompensated cirrhosis, particularly those with acute-on-chronic liver failure (ACLF), show profound alterations in plasma metabolomics. The aim of this study was to investigate the effect of treatment with simvastatin and rifaximin on plasma metabolites of patients with decompensated cirrhosis, specifically on compounds characteristic of the ACLF plasma metabolomic profile. Two cohorts of patients were investigated. The first was a descriptive cohort of patients with decompensated cirrhosis (n=42), with and without ACLF. The second was an intervention cohort from the LIVERHOPE-SAFETY randomized, double-blind, placebo-controlled trial treated with simvastatin 20mg/day plus rifaximin 1,200mg/day (n=12) or matching placebo (n=13) for 3months. Plasma samples were analyzed using ultrahigh performance liquid chromatography-tandem mass spectroscopy for plasma metabolomics characterization. ACLF was characterized by intense proteolysis and lipid alterations, specifically in pathways associated with inflammation and mitochondrial dysfunction, such as the tryptophan-kynurenine and carnitine beta-oxidation pathways. An ACLF-specific signature was identified. Treatment with simvastatin and rifaximin was associated with changes in 161 of 985 metabolites in comparison to treatment with placebo. A remarkable reduction in levels of metabolites from the tryptophan-kynurenine and carnitine pathways was found. Notably, 18 of the 32 metabolites of the ACLF signature were affected by the treatment. Conclusion: Treatment with simvastatin and rifaximin modulates some of the pathways that appear to be key in ACLF development. This study unveils some of the mechanisms involved in the effects of treatment with simvastatin and rifaximin in decompensated cirrhosis and sets the stage for the use of metabolomics to investigate new targeted therapies in cirrhosis to prevent ACLF development.

  View details for DOI 10.1002/hep4.1881

  View details for PubMedID 34964311

• Alloantigen-specific type 1 regulatory T cells suppress through CTLA-4 and PD-1 pathways and persist long-term in patients. Science translational medicine Chen, P. P., Cepika, A., Agarwal-Hashmi, R., Saini, G., Uyeda, M. J., Louis, D. M., Cieniewicz, B., Narula, M., Amaya Hernandez, L. C., Harre, N., Xu, L., Thomas, B. C., Ji, X., Shiraz, P., Tate, K. M., Margittai, D., Bhatia, N., Meyer, E., Bertaina, A., Davis, M. M., Bacchetta, R., Roncarolo, M. G. 2021; 13 (617): eabf5264

  Abstract

  [Figure: see text].

  View details for DOI 10.1126/scitranslmed.abf5264

  View details for PubMedID 34705520

• Single-cell sequencing unveils distinct immune microenvironments with CCR6-CCL20 crosstalk in human chronic pancreatitis. Gut Lee, B., Namkoong, H., Yang, Y., Huang, H., Heller, D., Szot, G. L., Davis, M. M., Husain, S. Z., Pandol, S. J., Bellin, M. D., Habtezion, A. 2021

  Abstract

  OBJECTIVE: Chronic pancreatitis (CP) is a potentially fatal disease of the exocrine pancreas, with no specific or effective approved therapies. Due to difficulty in accessing pancreas tissues, little is known about local immune responses or pathogenesis in human CP. We sought to characterise pancreatic immune responses using tissues derived from patients with different aetiologies of CP and non-CP organ donors in order to identify key signalling molecules associated with human CP.DESIGN: We performed single-cell level cellular indexing of transcriptomes and epitopes by sequencing and T-cell receptor (TCR) sequencing of pancreatic immune cells isolated from organ donors, hereditary and idiopathic patients with CP who underwent total pancreatectomy. We validated gene expression data by performing flow cytometry and functional assays in a second patient with CP cohort.RESULTS: Deep single-cell sequencing revealed distinct immune characteristics and significantly enriched CCR6+ CD4+ T cells in hereditary compared with idiopathic CP. In hereditary CP, a reduction in T-cell clonality was observed due to the increased CD4+ T (Th) cells that replaced tissue-resident CD8+ T cells. Shared TCR clonotype analysis among T-cell lineages also unveiled unique interactions between CCR6+ Th and Th1 subsets, and TCR clustering analysis showed unique common antigen binding motifs in hereditary CP. In addition, we observed a significant upregulation of the CCR6 ligand (CCL20) expression among monocytes in hereditary CP as compared with those in idiopathic CP. The functional significance of CCR6 expression in CD4+ T cells was confirmed by flow cytometry and chemotaxis assay.CONCLUSION: Single-cell sequencing with pancreatic immune cells in human CP highlights pancreas-specific immune crosstalk through the CCR6-CCL20 axis, a signalling pathway that might be leveraged as a potential future target in human hereditary CP.

  View details for DOI 10.1136/gutjnl-2021-324546

  View details for PubMedID 34702715

• CD4+ T cells contribute to neurodegeneration in Lewy body dementia. Science (New York, N.Y.) Gate, D., Tapp, E., Leventhal, O., Shahid, M., Nonninger, T. J., Yang, A. C., Strempfl, K., Unger, M. S., Fehlmann, T., Oh, H., Channappa, D., Henderson, V. W., Keller, A., Aigner, L., Galasko, D. R., Davis, M. M., Poston, K. L., Wyss-Coray, T. 2021: eabf7266

  Abstract

  [Figure: see text].

  View details for DOI 10.1126/science.abf7266

  View details for PubMedID 34648304

• Functional Consequences of Memory Inflation after Solid Organ Transplantation. Journal of immunology (Baltimore, Md. : 1950) Higdon, L. E., Schaffert, S., Cohen, R. H., Montez-Rath, M. E., Lucia, M., Saligrama, N., Margulies, K. B., Martinez, O. M., Tan, J. C., Davis, M. M., Khatri, P., Maltzman, J. S. 2021

  Abstract

  CMV is a major infectious complication following solid organ transplantation. Reactivation of CMV leads to memory inflation, a process in which CD8 T cells expand over time. Memory inflation is associated with specific changes in T cell function, including increased oligoclonality, decreased cytokine production, and terminal differentiation. To address whether memory inflation during the first year after transplantation in human subjects alters T cell differentiation and function, we employed single-cell-matched TCRalphabeta and targeted gene expression sequencing. Expanded T cell clones exhibited a terminally differentiated, immunosenescent, and polyfunctional phenotype whereas rare clones were less differentiated. Clonal expansion occurring between pre- and 3 mo posttransplant was accompanied by enhancement of polyfunctionality. In contrast, polyfunctionality and differentiation state were largely maintained between 3 and 12 mo posttransplant. Highly expanded clones had a higher degree of polyfunctionality than rare clones. Thus, CMV-responsive CD8 T cells differentiated during the pre- to posttransplant period then maintained their differentiation state and functional capacity despite posttransplant clonal expansion.

  View details for DOI 10.4049/jimmunol.2100405

  View details for PubMedID 34551963

• Evolution of Cytomegalovirus-Responsive T Cell Clonality following Solid Organ Transplantation. Journal of immunology (Baltimore, Md. : 1950) Higdon, L. E., Schaffert, S., Huang, H., Montez-Rath, M. E., Lucia, M., Jha, A., Saligrama, N., Margulies, K. B., Martinez, O. M., Davis, M. M., Khatri, P., Maltzman, J. S. 2021

  Abstract

  CMV infection is a significant complication after solid organ transplantation. We used single cell TCR alphabeta sequencing to determine how memory inflation impacts clonality and diversity of the CMV-responsive CD8 and CD4 T cell repertoire in the first year after transplantation in human subjects. We observed CD8 T cell inflation but no changes in clonal diversity, indicating homeostatic stability in clones. In contrast, the CD4 repertoire was diverse and stable over time, with no evidence of CMV-responsive CD4 T cell expansion. We identified shared CDR3 TCR motifs among patients but no public CMV-specific TCRs. Temporal changes in clonality in response to transplantation and in the absence of detectable viral reactivation suggest changes in the repertoire immediately after transplantation followed by an expansion with stable clonal competition that may mediate protection.

  View details for DOI 10.4049/jimmunol.2100404

  View details for PubMedID 34551964

• Effective Viral Vector SARS-CoV-2 Booster Vaccination in a Patient with Rheumatoid Arthritis after Initial Ineffective mRNA Vaccine Response. Arthritis & rheumatology (Hoboken, N.J.) Baker, M. C., Mallajosyula, V., Davis, M. M., Boyd, S. D., Nadeau, K. C., Robinson, W. H. 2021

  Abstract

  Managing patients with rheumatic disease during the COVID-19 pandemic has posed a unique challenge. Immunosuppressed patients are at an increased risk for developing severe COVID-19 and may not derive full protection from the vaccine (1-5). Thus, it is paramount we develop strategies whereby rheumatic disease patients can be protected from the pandemic virus and its variants.

  View details for DOI 10.1002/art.41978

  View details for PubMedID 34514750

• Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study SCIENCE IMMUNOLOGY Rouphael, N., Maecker, H., Montgomery, R. R., Diray-Arce, J., Kleinstein, S. H., Altman, M. C., Bosinger, S. E., Eckalbar, W., Guan, L., Hough, C. L., Krammer, F., Langelier, C., Levy, O., McEnaney, K., Peters, B., Rahman, A., Rajan, J., Sigelman, S., Steen, H., van Bakel, H., Ward, A., Wilson, M. R., Woodruff, P., Zamecnik, C. R., Augustine, A. D., Al Ozonoff, Reed, E. F., Becker, P. M., Higuita, N., Altman, M. C., Atkinson, M. A., Baden, L. R., Bime, C., Brakenridge, S. C., Calfee, C. S., Cairns, C. B., Corry, D., Davis, M. M., Ehrlich, L. R., Haddad, E. K., Erle, D. J., Fernandez-Sesma, A., Hafler, D. A., Kheradmand, F., Kraft, M., McComsey, G. A., Melamed, E., Messer, W., Metcalf, J., Nadeau, K. C., Pulendran, B., Rouphaell, N., Sarwal, M., Schaenman, J., Sekaly, R., Shaw, A. C., Simon, V., IMPACC Manuscript Writing Team, IMPACC Network Steering Comm 2021; 6 (62)

  Abstract

  The IMmunoPhenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective longitudinal study designed to enroll 1000 hospitalized patients with COVID-19 (NCT04378777). IMPACC collects detailed clinical, laboratory and radiographic data along with longitudinal biologic sampling of blood and respiratory secretions for in depth testing. Clinical and lab data are integrated to identify immunologic, virologic, proteomic, metabolomic and genomic features of COVID-19-related susceptibility, severity and disease progression. The goals of IMPACC are to better understand the contributions of pathogen dynamics and host immune responses to the severity and course of COVID-19 and to generate hypotheses for identification of biomarkers and effective therapeutics, including optimal timing of such interventions. In this report we summarize the IMPACC study design and protocols including clinical criteria and recruitment, multi-site standardized sample collection and processing, virologic and immunologic assays, harmonization of assay protocols, high-level analyses and the data sharing plans.

  View details for DOI 10.1126/sciimmunol.abf3733

  View details for Web of Science ID 000684294900003

  View details for PubMedID 34376480

• Single-cell Sequencing Unveils Distinct Immune Microenvironment in Human Chronic Pancreatitis Lee, B., Namkoong, H., Yang, Y., Huang, H., Heller, D., Szot, G., Davis, M., Pandol, S. J., Bellin, M. D., Husain, S., Habtezion, A. LIPPINCOTT WILLIAMS & WILKINS. 2021: 1073

  View details for Web of Science ID 000706786400147

• Association of Longitudinal Changes in Skeletal Muscle Mass With Survival in Patients With Pancreatic Cancer Lee, B., Namkoong, H., Yang, Y., Huang, H., Heller, D., Szot, G., Davis, M., Pandol, S. J., Bellin, M. D., Husain, S., Habtezion, A. LIPPINCOTT WILLIAMS & WILKINS. 2021: 1073

  View details for Web of Science ID 000706786400146

• CD8+ T cells specific for conserved coronavirus epitopes correlate with milder disease in COVID-19 patients. Science immunology Mallajosyula, V., Ganjavi, C., Chakraborty, S., McSween, A. M., Pavlovitch-Bedzyk, A. J., Wilhelmy, J., Nau, A., Manohar, M., Nadeau, K. C., Davis, M. M. 2021; 6 (61)

  Abstract

  A central feature of the SARS-CoV-2 pandemic is that some individuals become severely ill or die, whereas others have only a mild disease course or are asymptomatic. Here we report development of an improved multimeric alphabeta T cell staining reagent platform, with each maxi-ferritin "spheromer" displaying 12 peptide-MHC complexes. Spheromers stain specific T cells more efficiently than peptide-MHC tetramers and capture a broader portion of the sequence repertoire for a given peptide-MHC. Analyzing the response in unexposed individuals, we find that T cells recognizing peptides conserved amongst coronaviruses are more abundant and tend to have a "memory" phenotype, compared to those unique to SARS-CoV-2. Significantly, CD8+ T cells with these conserved specificities are much more abundant in COVID-19 patients with mild disease versus those with a more severe illness, suggesting a protective role.

  View details for DOI 10.1126/sciimmunol.abg5669

  View details for PubMedID 34210785

• An inflammatory aging clock (iAge) based on deep learning tracks multimorbidity, immunosenescence, frailty and cardiovascular aging. Nature aging Sayed, N., Huang, Y., Nguyen, K., Krejciova-Rajaniemi, Z., Grawe, A. P., Gao, T., Tibshirani, R., Hastie, T., Alpert, A., Cui, L., Kuznetsova, T., Rosenberg-Hasson, Y., Ostan, R., Monti, D., Lehallier, B., Shen-Orr, S. S., Maecker, H. T., Dekker, C. L., Wyss-Coray, T., Franceschi, C., Jojic, V., Haddad, F., Montoya, J. G., Wu, J. C., Davis, M. M., Furman, D. 2021; 1: 598-615

  Abstract

  While many diseases of aging have been linked to the immunological system, immune metrics capable of identifying the most at-risk individuals are lacking. From the blood immunome of 1,001 individuals aged 8-96 years, we developed a deep-learning method based on patterns of systemic age-related inflammation. The resulting inflammatory clock of aging (iAge) tracked with multimorbidity, immunosenescence, frailty and cardiovascular aging, and is also associated with exceptional longevity in centenarians. The strongest contributor to iAge was the chemokine CXCL9, which was involved in cardiac aging, adverse cardiac remodeling and poor vascular function. Furthermore, aging endothelial cells in human and mice show loss of function, cellular senescence and hallmark phenotypes of arterial stiffness, all of which are reversed by silencing CXCL9. In conclusion, we identify a key role of CXCL9 in age-related chronic inflammation and derive a metric for multimorbidity that can be utilized for the early detection of age-related clinical phenotypes.

  View details for DOI 10.1038/s43587-021-00082-y

  View details for PubMedID 34888528

• Humans with inherited Tcell CD28 deficiency are susceptible to skin papillomaviruses but are otherwise healthy. Cell Beziat, V., Rapaport, F., Hu, J., Titeux, M., Bonnet des Claustres, M., Bourgey, M., Griffin, H., Bandet, E., Ma, C. S., Sherkat, R., Rokni-Zadeh, H., Louis, D. M., Changi-Ashtiani, M., Delmonte, O. M., Fukushima, T., Habib, T., Guennoun, A., Khan, T., Bender, N., Rahman, M., About, F., Yang, R., Rao, G., Rouzaud, C., Li, J., Shearer, D., Balogh, K., Al Ali, F., Ata, M., Dabiri, S., Momenilandi, M., Nammour, J., Alyanakian, M., Leruez-Ville, M., Guenat, D., Materna, M., Marcot, L., Vladikine, N., Soret, C., Vahidnezhad, H., Youssefian, L., Saeidian, A. H., Uitto, J., Catherinot, E., Navabi, S. S., Zarhrate, M., Woodley, D. T., Jeljeli, M., Abraham, T., Belkaya, S., Lorenzo, L., Rosain, J., Bayat, M., Lanternier, F., Lortholary, O., Zakavi, F., Gros, P., Orth, G., Abel, L., Pretet, J., Fraitag, S., Jouanguy, E., Davis, M. M., Tangye, S. G., Notarangelo, L. D., Marr, N., Waterboer, T., Langlais, D., Doorbar, J., Hovnanian, A., Christensen, N., Bossuyt, X., Shahrooei, M., Casanova, J. 2021

  Abstract

  We study a patient with the human papilloma virus (HPV)-2-driven "tree-man" phenotype and two relatives with unusually severe HPV4-driven warts. The giant horns form an HPV-2-driven multifocal benign epithelial tumor overexpressing viral oncogenes in the epidermis basal layer. The patients are unexpectedly homozygous for a private CD28 variant. They have no detectable CD28 on their Tcells, with the exception of a small contingent of revertant memory CD4+ Tcells. Tcell development is barely affected, and Tcells respond to CD3 and CD2, but not CD28, costimulation. Although the patients do not display HPV-2- and HPV-4-reactive CD4+ Tcells invitro, they make antibodies specific for both viruses invivo. CD28-deficient mice are susceptible to cutaneous infections with the mouse papillomavirus MmuPV1. The control of HPV-2 and HPV-4 in keratinocytes is dependent on the Tcell CD28 co-activation pathway. Surprisingly, human CD28-dependent Tcell responses are largely redundant for protective immunity.

  View details for DOI 10.1016/j.cell.2021.06.004

  View details for PubMedID 34214472

• Nanoparticle-enabled innate immune stimulation activates endogenous tumor-infiltrating T cells with broad antigen specificities PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Yin, Q., Yu, W., Grzeskowiak, C. L., Li, J., Huang, H., Guo, J., Chen, L., Wang, F., Zhao, F., von Boehmer, L., Metzner, T. J., Leppert, J. T., Chien, Y., Kuo, C. J., Davis, M. M. 2021; 118 (21)

  View details for DOI 10.1073/pnas.2016168118|1of11

  View details for Web of Science ID 000659437300004

• Nanoparticle-enabled innate immune stimulation activates endogenous tumor-infiltrating T cells with broad antigen specificities. Proceedings of the National Academy of Sciences of the United States of America Yin, Q., Yu, W., Grzeskowiak, C. L., Li, J., Huang, H., Guo, J., Chen, L., Wang, F., Zhao, F., von Boehmer, L., Metzner, T. J., Leppert, J. T., Chien, Y., Kuo, C. J., Davis, M. M. 2021; 118 (21)

  Abstract

  Tumors are often infiltrated by T lymphocytes recognizing either self- or mutated antigens but are generally inactive, although they often show signs of prior clonal expansion. Hypothesizing that this may be due to peripheral tolerance, we formulated nanoparticles containing innate immune stimulants that we found were sufficient to activate self-specific CD8+ T cells and injected them into two different mouse tumor models, B16F10 and MC38. These nanoparticles robustly activated and/or expanded antigen-specific CD8+ tumor-infiltrating T cells, along with a decrease in regulatory CD4+ T cells and an increase in Interleukin-17 producers, resulting in significant tumor growth retardation or elimination and the establishment of immune memory in surviving mice. Furthermore, nanoparticles with modification of stimulating human T cells enabled the robust activation of endogenous T cells in patient-derived tumor organoids. These results indicate that breaking peripheral tolerance without regard to the antigen specificity creates a promising pathway for cancer immunotherapy.

  View details for DOI 10.1073/pnas.2016168118

  View details for PubMedID 34021082

• Systems Immunology: Revealing Influenza Immunological Imprint. Viruses Tomic, A., Pollard, A. J., Davis, M. M. 2021; 13 (5)

  Abstract

  Understanding protective influenza immunity and identifying immune correlates of protection poses a major challenge and requires an appreciation of the immune system in all of its complexity. While adaptive immune responses such as neutralizing antibodies and influenza-specific T lymphocytes are contributing to the control of influenza virus, key factors of long-term protection are not well defined. Using systems immunology, an approach that combines experimental and computational methods, we can capture the systems-level state of protective immunity and reveal the essential pathways that are involved. New approaches and technological developments in systems immunology offer an opportunity to examine roles and interrelationships of clinical, biological, and genetic factors in the control of influenza infection and have the potential to lead to novel discoveries about influenza immunity that are essential for the development of more effective vaccines to prevent future pandemics. Here, we review recent developments in systems immunology that help to reveal key factors mediating protective immunity.

  View details for DOI 10.3390/v13050948

  View details for PubMedID 34065617

• Adoptively Transferred, In Vitro-Generated Alloantigen-Specific Type 1 Regulatory T (Tr1) Cells Persist Long-Term In Vivo Cepika, A., Chen, P. P., Agarwal, R., Saini, G., Louis, D. M., Amaya-Hernandez, L. C., Xu, L., Shiraz, P., Tate, K. M., Margittai, D., Bhatia, N., Meyer, E., Bertaina, A., Davis, M. M., Bacchetta, R., Roncarolo, M. CELL PRESS. 2021: 73

  View details for Web of Science ID 000645188700142

• CRIPSR/Cas9 Technology: Hypoimmunogenic Pluripotent Stem Cells Evade Immune Rejection in Fully Immunocompetent Allogeneic Recipients Hu, X., Deuse, T., Gravina, A., Wang, D., Tediashvili, G., Reichenspurner, H., Davis, M. M., Lanier, L. L., Schrepfer, S. ELSEVIER SCIENCE INC. 2021: S28–S29

  View details for Web of Science ID 000631254400042

• Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-COV-2. iScience Gao, A., Chen, Z., Amitai, A., Doelger, J., Mallajosyula, V., Sundquist, E., Segal, F. P., Carrington, M., Davis, M. M., Streeck, H., Chakraborty, A. K., Julg, B. 2021: 102311

  Abstract

  We describe a physics-based learning model for predicting the immunogenicity of Cytotoxic-T-Lymphocyte (CTL) epitopes derived from diverse pathogens including SARS-CoV-2. The model was trained and optimized on the relative immunodominance of CTL epitopes in Human Immunodeficiency Virus infection. Its accuracy was tested against experimental data from COVID-19 patients. Our model predicts that only some SARS-CoV-2 epitopes predicted to bind to HLA molecules are immunogenic. The immunogenic CTL epitopes across all SARS-CoV-2 proteins are predicted to provide broad population coverage, but those from the SARS-CoV-2 spike protein alone are unlikely to do so. Our model also predicts that several immunogenic SARS-CoV-2 CTL epitopes are identical to seasonal coronaviruses circulating in the population and such cross-reactive CD8+ T cells can indeed be detected in prepandemic blood donors, suggesting that some level of CTL immunity against COVID-19 may be present in some individuals prior to SARS-CoV-2 infection.

  View details for DOI 10.1016/j.isci.2021.102311

  View details for PubMedID 33748696

• Aging and CMV discordance are associated with increased immune diversity between monozygotic twins. Immunity & ageing : I & A Yan, Z., Maecker, H. T., Brodin, P., Nygaard, U. C., Lyu, S. C., Davis, M. M., Nadeau, K. C., Andorf, S. 2021; 18 (1): 5

  Abstract

  BACKGROUND: Broadly, much of variance in immune system phenotype has been linked to the influence of non-heritable factors rather than genetics. In particular, two non-heritable factors: aging and human cytolomegavirus (CMV) infection, have been known to account for significant inter-individual immune variance. However, many specific relationships between them and immune composition remain unclear, especially between individuals over narrower age ranges. Further exploration of these relationships may be useful for informing personalized intervention development.RESULTS: To address this need, we evaluated 41 different cell type frequencies by mass cytometry and identified their relationships with aging and CMV seropositivity. Analyses were done using 60 healthy individuals, including 23 monozygotic twin pairs, categorized into young (12-31years) and middle-aged (42-59years). Aging and CMV discordance were associated with increased immune diversity between monozygotic twins overall, and particularly strongly in various T cell populations. Notably, we identified 17 and 11 cell subset frequencies as relatively influenced and uninfluenced by non-heritable factors, respectively, with results that largely matched those from studies on older-aged cohorts. Next, CD4+ T cell frequency was shown to diverge with age in twins, but with lower slope than in demographically similar non-twins, suggesting that much inter-individual variance in this cell type can be attributed to interactions between genetic and environmental factors. Several cell frequencies previously associated with memory inflation, such as CD27- CD8+ T cells and CD161+ CD4+ T cells, were positively correlated with CMV seropositivity, supporting findings that CMV infection may incur rapid aging of the immune system.CONCLUSIONS: Our study confirms previous findings that aging, even within a relatively small age range and by mid-adulthood, and CMV seropositivity, both contribute significantly to inter-individual immune diversity. Notably, we identify several key immune cell subsets that vary considerably with aging, as well as others associated with memory inflation which correlate with CMV seropositivity.

  View details for DOI 10.1186/s12979-021-00216-1

  View details for PubMedID 33461563

• SIMON: Open-Source Knowledge Discovery Platform. Patterns (New York, N.Y.) Tomic, A., Tomic, I., Waldron, L., Geistlinger, L., Kuhn, M., Spreng, R. L., Dahora, L. C., Seaton, K. E., Tomaras, G., Hill, J., Duggal, N. A., Pollock, R. D., Lazarus, N. R., Harridge, S. D., Lord, J. M., Khatri, P., Pollard, A. J., Davis, M. M. 2021; 2 (1): 100178

  Abstract

  Data analysis and knowledge discovery has become more and more important in biology and medicine with the increasing complexity of biological datasets, but the necessarily sophisticated programming skills and in-depth understanding of algorithms needed pose barriers to most biologists and clinicians to perform such research. We have developed a modular open-source software, SIMON, to facilitate the application of 180+ state-of-the-art machine-learning algorithms to high-dimensional biomedical data. With an easy-to-use graphical user interface, standardized pipelines, and automated approach for machine learning and other statistical analysis methods, SIMON helps to identify optimal algorithms and provides a resource that empowers non-technical and technical researchers to identify crucial patterns in biomedical data.

  View details for DOI 10.1016/j.patter.2020.100178

  View details for PubMedID 33511368

• Antigen-specific T Cell Activation Distinguishes Between Recent and Remote Tuberculosis Infection. American journal of respiratory and critical care medicine Mpande, C. A., Musvosvi, M., Rozot, V., Mosito, B., Reid, T. D., Schreuder, C., Lloyd, T., Bilek, N., Huang, H., Obermoser, G., Davis, M. M., Ruhwald, M., Hatherill, M., Scriba, T. J., Nemes, E., ACS Study Team 2021

  Abstract

  RATIONALE: Current diagnostic tests fail to identify individuals at higher risk of progression to tuberculosis disease, such as those with recent Mycobacterium tuberculosis infection, who should be prioritized for targeted preventive treatment.OBJECTIVES: To define a blood-based biomarker, measured with a simple flow cytometry assay, that can stratify different stages of tuberculosis infection to infer risk of disease.METHODS: South African adolescents were serially tested with QuantiFERON-TB Gold to define recent (QuantiFERON-TB conversion <6 months) and persistent (QuantiFERON-TB+ for >1 year) infection. We defined the DeltaHLA-DR median fluorescence intensity biomarker as the difference in HLA-DR expression between IFN-gamma+TNF+ Mycobacterium tuberculosis-specific and total CD3+ T cells. Biomarker performance was assessed by blinded prediction in untouched test cohorts with recent versus persistent infection or tuberculosis disease, and unblinded analysis of asymptomatic adolescents with tuberculosis infection who remained healthy (non-progressors) or who progressed to microbiologically-confirmed disease (progressors).MEASUREMENTS AND MAIN RESULTS: In the test cohorts, frequencies of Mycobacterium tuberculosis-specific T cells differentiated between QuantiFERON-TB- (n=25) and QuantiFERON-TB+ (n=47) individuals (area under the ROC curve and 95% confidence intervals: 0.94; 0.87-1.00). DeltaHLA-DR significantly discriminated between recent (n=20) and persistent (n=22) QuantiFERON-TB+ (0.91; 0.83-1.00); persistent QuantiFERON-TB+ and newly diagnosed tuberculosis (n=19, 0.99; 0.96-1.00); and tuberculosis progressors (n=22) and non-progressors (n=34, 0.75; 0.63-0.87). However, DeltaHLA-DR MFI could not discriminate between recent QuantiFERON-TB+ and tuberculosis (0.67; 0.50-0.84).CONCLUSION: The DeltaHLA-DR biomarker can identify individuals with recent QuantiFERON-TB conversion and those with disease progression, allowing targeted provision of preventive treatment to those at highest risk of tuberculosis. Further validation studies of this novel immune biomarker in various settings and populations at risk are warranted.

  View details for DOI 10.1164/rccm.202007-2686OC

  View details for PubMedID 33406011

• Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery. Immunity Chiou, S. H., Tseng, D. n., Reuben, A. n., Mallajosyula, V. n., Molina, I. S., Conley, S. n., Wilhelmy, J. n., McSween, A. M., Yang, X. n., Nishimiya, D. n., Sinha, R. n., Nabet, B. Y., Wang, C. n., Shrager, J. B., Berry, M. F., Backhus, L. n., Lui, N. S., Wakelee, H. A., Neal, J. W., Padda, S. K., Berry, G. J., Delaidelli, A. n., Sorensen, P. H., Sotillo, E. n., Tran, P. n., Benson, J. A., Richards, R. n., Labanieh, L. n., Klysz, D. D., Louis, D. M., Feldman, S. A., Diehn, M. n., Weissman, I. L., Zhang, J. n., Wistuba, I. I., Futreal, P. A., Heymach, J. V., Garcia, K. C., Mackall, C. L., Davis, M. M. 2021; 54 (3): 586–602.e8

  Abstract

  To identify disease-relevant T cell receptors (TCRs) with shared antigen specificity, we analyzed 778,938 TCRβ chain sequences from 178 non-small cell lung cancer patients using the GLIPH2 (grouping of lymphocyte interactions with paratope hotspots 2) algorithm. We identified over 66,000 shared specificity groups, of which 435 were clonally expanded and enriched in tumors compared to adjacent lung. The antigenic epitopes of one such tumor-enriched specificity group were identified using a yeast peptide-HLA A∗02:01 display library. These included a peptide from the epithelial protein TMEM161A, which is overexpressed in tumors and cross-reactive epitopes from Epstein-Barr virus and E. coli. Our findings suggest that this cross-reactivity may underlie the presence of virus-specific T cells in tumor infiltrates and that pathogen cross-reactivity may be a feature of multiple cancers. The approach and analytical pipelines generated in this work, as well as the specificity groups defined here, present a resource for understanding the T cell response in cancer.

  View details for DOI 10.1016/j.immuni.2021.02.014

  View details for PubMedID 33691136

• Single-cell epigenomic landscape of peripheral immune cells reveals establishment of trained immunity in individuals convalescing from COVID-19. Nature cell biology You, M., Chen, L., Zhang, D., Zhao, P., Chen, Z., Qin, E., Gao, Y., Davis, M. M., Yang, P. 2021; 23 (6): 620-630

  Abstract

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection often causes severe complications and even death. However, asymptomatic infection has also been reported, highlighting the difference in immune responses among individuals. Here we performed single-cell chromatin accessibility and T cell-receptor analyses of peripheral blood mononuclear cells collected from individuals convalescing from COVID-19 and healthy donors. Chromatin remodelling was observed in both innate and adaptive immune cells in the individuals convalescing from COVID-19. Compared with healthy donors, recovered individuals contained abundant TBET-enriched CD16+ and IRF1-enriched CD14+ monocytes with sequential trained and activated epigenomic states. The B-cell lineage in recovered individuals exhibited an accelerated developmental programme from immature B cells to antibody-producing plasma cells. Finally, an integrated analysis of single-cell T cell-receptor clonality with the chromatin accessibility landscape revealed the expansion of putative SARS-CoV-2-specific CD8+ T cells with epigenomic profiles that promote the differentiation of effector or memory cells. Overall, our data suggest that immune cells of individuals convalescing from COVID-19 exhibit global remodelling of the chromatin accessibility landscape, indicative of the establishment of immunological memory.

  View details for DOI 10.1038/s41556-021-00690-1

  View details for PubMedID 34108657

• Systems vaccinology of the BNT162b2 mRNA vaccine in humans. Nature Arunachalam, P. S., Scott, M. K., Hagan, T., Li, C., Feng, Y., Wimmers, F., Grigoryan, L., Trisal, M., Edara, V. V., Lai, L., Chang, S. E., Feng, A., Dhingra, S., Shah, M., Lee, A. S., Chinthrajah, S., Sindher, S. B., Mallajosyula, V., Gao, F., Sigal, N., Kowli, S., Gupta, S., Pellegrini, K., Tharp, G., Maysel-Auslender, S., Hamilton, S., Aoued, H., Hrusovsky, K., Roskey, M., Bosinger, S. E., Maecker, H. T., Boyd, S. D., Davis, M. M., Utz, P. J., Suthar, M. S., Khatri, P., Nadeau, K. C., Pulendran, B. 2021

  Abstract

  The emergency use authorization of two mRNA vaccines in less than a year since the emergence of SARS-CoV-2 represents a landmark in vaccinology1,2. Yet, how mRNA vaccines stimulate the immune system to elicit protective immune responses is unknown. Here we used a systems vaccinology approach to comprehensively profile the innate and adaptive immune responses of 56 healthy volunteers vaccinated with the Pfizer-BioNTech mRNA vaccine. Vaccination resulted in robust production of neutralizing antibodies (nAbs) against the parent Wuhan strain and, to a lesser extent, the B.1.351 strain, and significant increases in antigen-specific polyfunctional CD4 and CD8 T cells after the second dose. Booster vaccination stimulated a strikingly enhanced innate immune response compared to primary vaccination, evidenced by a greater: (i) frequency of CD14+CD16+ inflammatory monocytes; (ii) concentration of plasma IFN-g; (iii) transcriptional signature of innate antiviral immunity. Consistent with these observations, single-cell transcriptomics analysis demonstrated a ~100-fold increase in the frequency of a myeloid cell cluster, enriched in interferon-response transcription factors (TFs) and reduced in AP-1 TFs, following secondary immunization. Finally, we identified distinct innate pathways associated with CD8 T cell and nAb responses, and show that a monocyte-related signature correlates with the nAb response against the B.1.351 variant strain. Collectively, these data provide insights into immune responses induced by mRNA vaccination and demonstrate its capacity to prime the innate immune system to mount a more potent response following booster immunization.

  View details for DOI 10.1038/s41586-021-03791-x

  View details for PubMedID 34252919

• Signatures of immune dysfunction in HIV and HCV infection share features with chronic inflammation in aging and persist after viral reduction or elimination. Proceedings of the National Academy of Sciences of the United States of America Lopez Angel, C. J., Pham, E. A., Du, H. n., Vallania, F. n., Fram, B. J., Perez, K. n., Nguyen, T. n., Rosenberg-Hasson, Y. n., Ahmed, A. n., Dekker, C. L., Grant, P. M., Khatri, P. n., Maecker, H. T., Glenn, J. S., Davis, M. M., Furman, D. n. 2021; 118 (14)

  Abstract

  Chronic inflammation is thought to be a major cause of morbidity and mortality in aging, but whether similar mechanisms underlie dysfunction in infection-associated chronic inflammation is unclear. Here, we profiled the immune proteome, and cellular composition and signaling states in a cohort of aging individuals versus a set of HIV patients on long-term antiretroviral therapy therapy or hepatitis C virus (HCV) patients before and after sofosbuvir treatment. We found shared alterations in aging-associated and infection-associated chronic inflammation including T cell memory inflation, up-regulation of intracellular signaling pathways of inflammation, and diminished sensitivity to cytokines in lymphocytes and myeloid cells. In the HIV cohort, these dysregulations were evident despite viral suppression for over 10 y. Viral clearance in the HCV cohort partially restored cellular sensitivity to interferon-α, but many immune system alterations persisted for at least 1 y posttreatment. Our findings indicate that in the HIV and HCV cohorts, a broad remodeling and degradation of the immune system can persist for a year or more, even after the removal or drastic reduction of the pathogen load and that this shares some features of chronic inflammation in aging.

  View details for DOI 10.1073/pnas.2022928118

  View details for PubMedID 33811141

• Modeling human adaptive immune responses with tonsil organoids. Nature medicine Wagar, L. E., Salahudeen, A. n., Constantz, C. M., Wendel, B. S., Lyons, M. M., Mallajosyula, V. n., Jatt, L. P., Adamska, J. Z., Blum, L. K., Gupta, N. n., Jackson, K. J., Yang, F. n., Röltgen, K. n., Roskin, K. M., Blaine, K. M., Meister, K. D., Ahmad, I. N., Cortese, M. n., Dora, E. G., Tucker, S. N., Sperling, A. I., Jain, A. n., Davies, D. H., Felgner, P. L., Hammer, G. B., Kim, P. S., Robinson, W. H., Boyd, S. D., Kuo, C. J., Davis, M. M. 2021

  Abstract

  Most of what we know about adaptive immunity has come from inbred mouse studies, using methods that are often difficult or impossible to confirm in humans. In addition, vaccine responses in mice are often poorly predictive of responses to those same vaccines in humans. Here we use human tonsils, readily available lymphoid organs, to develop a functional organotypic system that recapitulates key germinal center features in vitro, including the production of antigen-specific antibodies, somatic hypermutation and affinity maturation, plasmablast differentiation and class-switch recombination. We use this system to define the essential cellular components necessary to produce an influenza vaccine response. We also show that it can be used to evaluate humoral immune responses to two priming antigens, rabies vaccine and an adenovirus-based severe acute respiratory syndrome coronavirus 2 vaccine, and to assess the effects of different adjuvants. This system should prove useful for studying critical mechanisms underlying adaptive immunity in much greater depth than previously possible and to rapidly test vaccine candidates and adjuvants in an entirely human system.

  View details for DOI 10.1038/s41591-020-01145-0

  View details for PubMedID 33432170

• Mass Cytometry Defines Virus-Specific CD4+ T Cells in Influenza Vaccination. ImmunoHorizons Subrahmanyam, P. B., Holmes, T. H., Lin, D., Su, L. F., Obermoser, G., Banchereau, J., Pascual, V., Garcia-Sastre, A., Albrecht, R. A., Palucka, K., Davis, M. M., Maecker, H. T. 2020; 4 (12): 774–88

  Abstract

  The antiviral response to influenza virus is complex and multifaceted, involving many immune cell subsets. There is an urgent need to understand the role of CD4+ T cells, which orchestrate an effective antiviral response, to improve vaccine design strategies. In this study, we analyzed PBMCs from human participants immunized with influenza vaccine, using high-dimensional single-cell proteomic immune profiling by mass cytometry. Data were analyzed using a novel clustering algorithm, denoised ragged pruning, to define possible influenza virus-specific clusters of CD4+ T cells. Denoised ragged pruning identified six clusters of cells. Among these, one cluster (Cluster 3) was found to increase in abundance following stimulation with influenza virus peptide ex vivo. A separate cluster (Cluster 4) was found to expand in abundance between days 0 and 7 postvaccination, indicating that it is vaccine responsive. We examined the expression profiles of all six clusters to characterize their lineage, functionality, and possible role in the response to influenza vaccine. Clusters 3 and 4 consisted of effector memory cells, with high CD154 expression. Cluster 3 expressed cytokines like IL-2, IFN-gamma, and TNF-alpha, whereas Cluster 4 expressed IL-17. Interestingly, some participants had low abundance of Clusters 3 and 4, whereas others had higher abundance of one of these clusters compared with the other. Taken together, we present an approach for identifying novel influenza virus-reactive CD4+ T cell subsets, a method that could help advance understanding of the immune response to influenza, predict responsiveness to vaccines, and aid in better vaccine design.

  View details for DOI 10.4049/immunohorizons.1900097

  View details for PubMedID 33310880

• Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. Nature Salahudeen, A. A., Choi, S. S., Rustagi, A., Zhu, J., van Unen, V., de la O, S. M., Flynn, R. A., Margalef-Catala, M., Santos, A. J., Ju, J., Batish, A., Usui, T., Zheng, G. X., Edwards, C. E., Wagar, L. E., Luca, V., Anchang, B., Nagendran, M., Nguyen, K., Hart, D. J., Terry, J. M., Belgrader, P., Ziraldo, S. B., Mikkelsen, T. S., Harbury, P. B., Glenn, J. S., Garcia, K. C., Davis, M. M., Baric, R. S., Sabatti, C., Amieva, M. R., Blish, C. A., Desai, T. J., Kuo, C. J. 2020

  Abstract

  The distal lung contains terminal bronchioles and alveoli that facilitate gas exchange. Three-dimensional in vitro human distal lung culture systems would strongly facilitate investigation of pathologies including interstitial lung disease, cancer, and SARS-CoV-2-associated COVID-19 pneumonia. We generated long-term feeder-free, chemically defined culture of distal lung progenitors as organoids derived from single adult human alveolar epithelial type II (AT2) or KRT5+ basal cells. AT2 organoids exhibited AT1 transdifferentiation potential while basal cell organoids developed lumens lined by differentiated club and ciliated cells. Single cell analysis of basal organoid KRT5+ cells revealed a distinct ITGA6+ITGB4+ mitotic population whose proliferation further segregated to a TNFRSF12Ahi subfraction comprising ~10% of KRT5+ basal cells, residing in clusters within terminal bronchioles and exhibiting enriched clonogenic organoid growth activity. Distal lung organoids were created with apical-out polarity to display ACE2 on the exposed external surface, facilitating SARS-CoV-2 infection of AT2 and basal cultures and identifying club cells as a novel target population. This long-term, feeder-free organoid culture of human distal lung, coupled with single cell analysis, identifies unsuspected basal cell functional heterogeneity and establishes a facile in vitro organoid model for human distal lung infections including COVID-19-associated pneumonia.

  View details for DOI 10.1038/s41586-020-3014-1

  View details for PubMedID 33238290

• Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19. Cell Su, Y., Chen, D., Yuan, D., Lausted, C., Choi, J., Dai, C. L., Voillet, V., Duvvuri, V. R., Scherler, K., Troisch, P., Baloni, P., Qin, G., Smith, B., Kornilov, S. A., Rostomily, C., Xu, A., Li, J., Dong, S., Rothchild, A., Zhou, J., Murray, K., Edmark, R., Hong, S., Heath, J. E., Earls, J., Zhang, R., Xie, J., Li, S., Roper, R., Jones, L., Zhou, Y., Rowen, L., Liu, R., Mackay, S., O'Mahony, D. S., Dale, C. R., Wallick, J. A., Algren, H. A., Zager, M. A., ISB-Swedish COVID19 Biobanking Unit, Wei, W., Price, N. D., Huang, S., Subramanian, N., Wang, K., Magis, A. T., Hadlock, J. J., Hood, L., Aderem, A., Bluestone, J. A., Lanier, L. L., Greenberg, P. D., Gottardo, R., Davis, M. M., Goldman, J. D., Heath, J. R. 2020

  Abstract

  We present an integrated analysis of the clinical measurements, immune cells, and plasma multi-omics of 139 COVID-19 patients representing all levels of disease severity, from serial blood draws collected during the first week of infection following diagnosis. We identify a major shift between mild and moderate disease, at which point elevated inflammatory signaling is accompanied by the loss of specific classes of metabolites and metabolic processes. Within this stressed plasma environment at moderate disease, multiple unusual immune cell phenotypes emerge and amplify with increasing disease severity. We condensed over 120,000 immune features into a single axis to capture how different immune cell classes coordinate in response to SARS-CoV-2. This immune-response axis independently aligns with the major plasma composition changes, with clinical metrics of blood clotting, and with the sharp transition between mild and moderate disease. This study suggests that moderate disease may provide the most effective setting for therapeutic intervention.

  View details for DOI 10.1016/j.cell.2020.10.037

  View details for PubMedID 33171100

• Bifidobacterium alters the gut microbiota and modulates the functional metabolism of T regulatory cells in the context of immune checkpoint blockade. Proceedings of the National Academy of Sciences of the United States of America Sun, S., Luo, L., Liang, W., Yin, Q., Guo, J., Rush, A. M., Lv, Z., Liang, Q., Fischbach, M. A., Sonnenburg, J. L., Dodd, D., Davis, M. M., Wang, F. 2020

  Abstract

  Immune checkpoint-blocking antibodies that attenuate immune tolerance have been used to effectively treat cancer, but they can also trigger severe immune-related adverse events. Previously, we found that Bifidobacterium could mitigate intestinal immunopathology in the context of CTLA-4 blockade in mice. Here we examined the mechanism underlying this process. We found that Bifidobacterium altered the composition of the gut microbiota systematically in a regulatory T cell (Treg)-dependent manner. Moreover, this altered commensal community enhanced both the mitochondrial fitness and the IL-10-mediated suppressive functions of intestinal Tregs, contributing to the amelioration of colitis during immune checkpoint blockade.

  View details for DOI 10.1073/pnas.1921223117

  View details for PubMedID 33077598

• The Power of Single Cell Technologies; from T Cell Receptor to Antigen(s) in Multiple Sclerosis Saligrama, N., Fernandes, R. A., Pai, J., Oksenberg, J., Satpathy, A., Davis, M. M. WILEY. 2020: S198

  View details for Web of Science ID 000572509100353

• The science and medicine of human immunology. Science (New York, N.Y.) Pulendran, B., Davis, M. M. 2020; 369 (6511)

  Abstract

  Although the development of effective vaccines has saved countless lives from infectious diseases, the basic workings of the human immune system are complex and have required the development of animal models, such as inbred mice, to define mechanisms of immunity. More recently, new strategies and technologies have been developed to directly explore the human immune system with unprecedented precision. We discuss how these approaches are advancing our mechanistic understanding of human immunology and are facilitating the development of vaccines and therapeutics for infection, autoimmune diseases, and cancer.

  View details for DOI 10.1126/science.aay4014

  View details for PubMedID 32973003

• HYPOIMMUNOGENIC DERIVATIVES OF INDUCED PLURIPOTENT STEM CELLS EVADE IMMUNE REJECTION IN FULLY IMMUNOCOMPETENT ALLOGENEIC RECIPIENTS Hu, X., Deuse, T., Gravina, A., Wang, D., Tediashvili, G., De, C., Thayer, W., Wahl, A., Garcia, V., Reichenspurner, H., Davis, M., Lanier, L., Schrepfer, S. LIPPINCOTT WILLIAMS & WILKINS. 2020: S200

  View details for Web of Science ID 000618872100289

• Immune Profiling and Causal Antigen Discovery in Mouse and Human Models of Immune Checkpoint Inhibitor-induced Myocarditis Zhu, H., Lee, D., Sarah, W., Galdos, F. X., D'Addabbo, J., Fowler, M. B., Reddy, S., Heather, W., Neal, J. W., Witteles, R., Maecker, H. T., Davis, M., Nguyen, P. K., Wu, S. M. LIPPINCOTT WILLIAMS & WILKINS. 2020

  View details for DOI 10.1161/res.127.suppl_1.350

  View details for Web of Science ID 000606541500116

• Systems immunology. Current opinion in immunology Davis, M. M. 2020; 65: 79–82

  Abstract

  Systems biological approaches to immunology have grown exponentially in the past decade, especially as broad approaches to data collection have become more accessible. It is still in its infancy; however, largely descriptive, and looking for the main drivers of particular phenomena, such as vaccination effects or pregnancy. But this lays the ground work for an increasingly sophisticated appreciation of subsystems and interactions and will lead to predictive modeling and a deeper understanding of human diseases and interactions with pathogens.

  View details for DOI 10.1016/j.coi.2020.06.006

  View details for PubMedID 32738786

• Discovery of a novel shared tumor antigen in human lung cancer. Tseng, D., Chiou, S., Yang, X., Reuben, A., Wilhelmy, J., McSween, A., Conley, S., Sinha, R., Nabet, B., Wang, C., Shrager, J. B., Berry, M. F., Backhus, L., Lui, n., Wakelee, H. A., Neal, J. W., Zhang, J., Garcia, K., Mackall, C., Davis, M. AMER SOC CLINICAL ONCOLOGY. 2020

  View details for Web of Science ID 000560368301343

• Correction to: Cardiovascular Complications in Patients with COVID-19: Consequences of Viral Toxicities and Host Immune Response. Current cardiology reports Zhu, H., Rhee, J., Cheng, P., Waliany, S., Chang, A., Witteles, R. M., Maecker, H., Davis, M. M., Nguyen, P. K., Wu, S. M. 2020; 22 (5): 36

  Abstract

  It has been pointed out that the second paragraph of the section "Treatments for SARS-CoV-2 Infection" contains an error. The original article has been corrected.

  View details for DOI 10.1007/s11886-020-01302-4

  View details for PubMedID 32405913

• The Power Of Single Cell Technologies; From T Cell Receptor To Antigen(s) In Multiple Sclerosis Saligrama, N., Fernandes, R. A., Pai, J., Yao, W., Louis, D. M., Oksenberg, J., Kipp, L., Dunn, J. E., Satpathy, A., Garcia, K. C., Davis, M. M. SAGE PUBLICATIONS LTD. 2020: 5–6

  View details for Web of Science ID 000532412600007

• Hemagglutinin as potential in vivo driver of DQ6-restricted clonal expansion of CD4(+) T cells cross-reactive with hypocretin in narcolepsy Jiang, W., Birtley, J. R., Hung, S., Wang, W., Chiou, S., Davis, M. M., Stern, L. J., Mellins, E. D. AMER ASSOC IMMUNOLOGISTS. 2020

  View details for Web of Science ID 000589972402368

• Clonally expanded CD8 T cells patrol Alzheimer's cerebrospinal fluid Gate, D., Saligrama, N., Leventhal, O., Davis, M. M., Wyss-Coray, T. AMER ASSOC IMMUNOLOGISTS. 2020

  View details for Web of Science ID 000589972400098

• The Power Of Single Cell Technologies; From T Cell Receptor To Antigen(s) In Multiple Sclerosis Saligrama, N., Fernandes, R. A., Pai, J., Yao, W., Louis, D. M., Oksenberg, J., Kipp, L., Dunn, J. E., Satpathy, A., Garcia, K. C., Davis, M. M. SAGE PUBLICATIONS LTD. 2020: 126

  View details for Web of Science ID 000532412600273

• Hypoimmunogenic Derivatives of Induced Pluripotent Stem Cells Evade Immune Rejection in Fully Immunocompetent Allogeneic Recipients Hu, X., Deuse, T., Gravina, A., Wang, D., Tediashvili, G., De, C., Thayer, W., Wahl, A., Garcia, V., Reichenspurner, H., Davis, M., Lanier, L., Schrepfer, S. ELSEVIER SCIENCE INC. 2020: S176–S177

  View details for Web of Science ID 000522637201108

• Towards the identification of novel tumor antigens in human lung cancer. Chiou, S., Tseng, D., Wang, C., Reuben, A., Yang, X., Wilhelmy, J., McSween, A., Zhang, J., Shrager, J., Garcia, K., Davis, M. AMER ASSOC CANCER RESEARCH. 2020: 44–45

  View details for Web of Science ID 000518188200060

• Distinct immune characteristics distinguish hereditary and idiopathic chronic pancreatitis. The Journal of clinical investigation Lee, B., Adamska, J. Z., Namkoong, H., Bellin, M. D., Wilhelm, J. J., Szot, G. L., Louis, D. M., Davis, M. M., Pandol, S., Habtezion, A. 2020

  Abstract

  Chronic pancreatitis (CP) is considered an irreversible fibroinflammatory pancreatic disease. Despite numerous animal model studies, questions remain about local immune characteristics in human CP. We profiled pancreatic immune cell characteristics in control organ donors and CP patients that included hereditary and idiopathic CP undergoing total pancreatectomy with islet auto-transplantation. Flow cytometric analysis revealed a significant increase in the frequency of CD68+ macrophages in idiopathic CP. In contrast, hereditary CP showed a significant increase in CD3+ T cell frequency, which prompted us to investigate the T cell receptor beta (TCRbeta) repertoire in CP and controls. TCRbeta-sequencing revealed a significant increase in TCRbeta repertoire diversity and reduced clonality in both CP groups versus controls. Interestingly, we observed differences in Vbeta-Jbeta gene family usage between hereditary and idiopathic CP and a positive correlation of TCRbeta rearrangements with disease severity scores. Immunophenotyping analyses in hereditary and idiopathic CP pancreata indicate differences in innate and adaptive immune responses, which highlights differences in immunopathogenic mechanism of disease among subtypes of CP. TCR repertoire analysis further suggests a role for specific T cell responses in hereditary versus idiopathic CP pathogenesis providing new insights into immune responses associated with human CP.

  View details for DOI 10.1172/JCI134066

  View details for PubMedID 32053120

• Comprehensive T cell repertoire characterization of non-small cell lung cancer. Nature communications Reuben, A., Zhang, J., Chiou, S., Gittelman, R. M., Li, J., Lee, W., Fujimoto, J., Behrens, C., Liu, X., Wang, F., Quek, K., Wang, C., Kheradmand, F., Chen, R., Chow, C., Lin, H., Bernatchez, C., Jalali, A., Hu, X., Wu, C., Eterovic, A. K., Parra, E. R., Yusko, E., Emerson, R., Benzeno, S., Vignali, M., Wu, X., Ye, Y., Little, L. D., Gumbs, C., Mao, X., Song, X., Tippen, S., Thornton, R. L., Cascone, T., Snyder, A., Wargo, J. A., Herbst, R., Swisher, S., Kadara, H., Moran, C., Kalhor, N., Zhang, J., Scheet, P., Vaporciyan, A. A., Sepesi, B., Gibbons, D. L., Robins, H., Hwu, P., Heymach, J. V., Sharma, P., Allison, J. P., Baladandayuthapani, V., Lee, J. J., Davis, M. M., Wistuba, I. I., Futreal, P. A., Zhang, J. 2020; 11 (1): 603

  Abstract

  Immunotherapy targeting T cells is increasingly utilized to treat solid tumors including non-small cell lung cancer (NSCLC). This requires a better understanding of the T cells in the lungs of patients with NSCLC. Here, we report T cell repertoire analysis in a cohort of 236 early-stage NSCLC patients. T cell repertoire attributes are associated with clinicopathologic features, mutational and immune landscape. A considerable proportion of the most prevalent T cells in tumors are also prevalent in the uninvolved tumor-adjacent lungs and appear specific to shared background mutations or viral infections. Patients with higher T cell repertoire homology between the tumor and uninvolved tumor-adjacent lung, suggesting a less tumor-focused T cell response, exhibit inferior survival. These findings indicate that a concise understanding of antigens and T cells in NSCLC is needed to improve therapeutic efficacy and reduce toxicity with immunotherapy, particularly adoptive T cell therapy.

  View details for DOI 10.1038/s41467-019-14273-0

  View details for PubMedID 32001676

• Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer's disease. Nature Gate, D., Saligrama, N., Leventhal, O., Yang, A. C., Unger, M. S., Middeldorp, J., Chen, K., Lehallier, B., Channappa, D., De Los Santos, M. B., McBride, A., Pluvinage, J., Elahi, F., Tam, G. K., Kim, Y., Greicius, M., Wagner, A. D., Aigner, L., Galasko, D. R., Davis, M. M., Wyss-Coray, T. 2020

  Abstract

  Alzheimer's disease is an incurable neurodegenerative disorder in which neuroinflammation has a critical function1. However, little is known about the contribution of the adaptive immune response in Alzheimer's disease2. Here, using integrated analyses of multiple cohorts, we identify peripheral and central adaptive immune changes in Alzheimer's disease. First, we performed mass cytometry of peripheral blood mononuclear cells and discovered an immune signature of Alzheimer's disease that consists of increased numbers of CD8+ T effector memory CD45RA+ (TEMRA) cells. In a second cohort, we found that CD8+ TEMRA cells were negatively associated with cognition. Furthermore, single-cell RNA sequencing revealed that T cell receptor (TCR) signalling was enhanced in these cells. Notably, by using several strategies of single-cell TCR sequencing in a third cohort, we discovered clonally expanded CD8+ TEMRA cells in the cerebrospinal fluid of patients with Alzheimer's disease. Finally, we used machine learning, cloning and peptide screens to demonstrate the specificity of clonally expanded TCRs in the cerebrospinal fluid of patients with Alzheimer's disease to two separate Epstein-Barr virus antigens. These results reveal an adaptive immune response in the blood and cerebrospinal fluid in Alzheimer's disease and provide evidence of clonal, antigen-experienced T cells patrolling the intrathecal space of brains affected by age-related neurodegeneration.

  View details for DOI 10.1038/s41586-019-1895-7

  View details for PubMedID 31915375

• Author Correction: In vivo clonal expansion and phenotypes of hypocretin-specific CD4+ T cells in narcolepsy patients and controls. Nature communications Jiang, W. n., Birtley, J. R., Hung, S. C., Wang, W. n., Chiou, S. H., Macaubas, C. n., Kornum, B. n., Tian, L. n., Huang, H. n., Adler, L. n., Weaver, G. n., Lu, L. n., Ilstad-Minnihan, A. n., Somasundaram, S. n., Ayyangar, S. n., Davis, M. M., Stern, L. J., Mellins, E. D. 2020; 11 (1): 242

  Abstract

  An amendment to this paper has been published and can be accessed via a link at the top of the paper.

  View details for DOI 10.1038/s41467-019-13776-0

  View details for PubMedID 31913263

• Cardiovascular Complications in Patients with COVID-19: Consequences of Viral Toxicities and Host Immune Response Curr Cardiol Rep Zhu, H., Rhee, J., Cheng, P., Waliany, S., Chang, A., Witteles, R. M., Maecker, H., Davis, M. M., Nguyen, P. K., Wu, S. M. 2020; 22 (5)

  View details for DOI 10.1007/s11886-020-01292-3

• T cell analysis in vaccination. Current opinion in immunology Davis, M. M. 2020; 65: 70–73

  Abstract

  A major problem in the analysis of vaccine candidates is the lack of any agreed upon surrogates of efficacy, which means that for diseases that depend on a strong T cell response (HIV, TB especially) the only option is to perform an efficacy trial, involving thousands of subjects, enormous costs, and years before the results are known [1]. We also know that T cell responses are an important part of most pathogen responses, and so identifying key T cell response metrics in early vaccine trials would be generally useful. Given our ignorance of what the most important variables are, what would we like to measure and how can this be accomplished, especially given the explosion of new technologies that are available? What follows is a consideration of what should be measured, with the caveat that some of these will be more important than others.

  View details for DOI 10.1016/j.coi.2020.05.002

  View details for PubMedID 32604000

• Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening. Nature biotechnology Huang, H. n., Wang, C. n., Rubelt, F. n., Scriba, T. J., Davis, M. M. 2020

  Abstract

  CD4+ T cells are critical to fighting pathogens, but a comprehensive analysis of human T-cell specificities is hindered by the diversity of HLA alleles (>20,000) and the complexity of many pathogen genomes. We previously described GLIPH, an algorithm to cluster T-cell receptors (TCRs) that recognize the same epitope and to predict their HLA restriction, but this method loses efficiency and accuracy when >10,000 TCRs are analyzed. Here we describe an improved algorithm, GLIPH2, that can process millions of TCR sequences. We used GLIPH2 to analyze 19,044 unique TCRβ sequences from 58 individuals latently infected with Mycobacterium tuberculosis (Mtb) and to group them according to their specificity. To identify the epitopes targeted by clusters of Mtb-specific T cells, we carried out a screen of 3,724 distinct proteins covering 95% of Mtb protein-coding genes using artificial antigen-presenting cells (aAPCs) and reporter T cells. We found that at least five PPE (Pro-Pro-Glu) proteins are targets for T-cell recognition in Mtb.

  View details for DOI 10.1038/s41587-020-0505-4

  View details for PubMedID 32341563

• Injectable Hydrogels for Sustained Codelivery of Subunit Vaccines Enhance Humoral Immunity. ACS central science Roth, G. A., Gale, E. C., Alcántara-Hernández, M. n., Luo, W. n., Axpe, E. n., Verma, R. n., Yin, Q. n., Yu, A. C., Lopez Hernandez, H. n., Maikawa, C. L., Smith, A. A., Davis, M. M., Pulendran, B. n., Idoyaga, J. n., Appel, E. A. 2020; 6 (10): 1800–1812

  Abstract

  Vaccines aim to elicit a robust, yet targeted, immune response. Failure of a vaccine to elicit such a response arises in part from inappropriate temporal control over antigen and adjuvant presentation to the immune system. In this work, we sought to exploit the immune system's natural response to extended pathogen exposure during infection by designing an easily administered slow-delivery vaccine platform. We utilized an injectable and self-healing polymer-nanoparticle (PNP) hydrogel platform to prolong the codelivery of vaccine components to the immune system. We demonstrated that these hydrogels exhibit unique delivery characteristics, whereby physicochemically distinct compounds (such as antigen and adjuvant) could be codelivered over the course of weeks. When administered in mice, hydrogel-based sustained vaccine exposure enhanced the magnitude, duration, and quality of the humoral immune response compared to standard PBS bolus administration of the same model vaccine. We report that the creation of a local inflammatory niche within the hydrogel, coupled with sustained exposure of vaccine cargo, enhanced the magnitude and duration of germinal center responses in the lymph nodes. This strengthened germinal center response promoted greater antibody affinity maturation, resulting in a more than 1000-fold increase in antigen-specific antibody affinity in comparison to bolus immunization. In summary, this work introduces a simple and effective vaccine delivery platform that increases the potency and durability of subunit vaccines.

  View details for DOI 10.1021/acscentsci.0c00732

  View details for PubMedID 33145416

  View details for PubMedCentralID PMC7596866

• Upregulation of CD47 Is a Host Checkpoint Response to Pathogen Recognition. mBio Tal, M. C., Torrez Dulgeroff, L. B., Myers, L. n., Cham, L. B., Mayer-Barber, K. D., Bohrer, A. C., Castro, E. n., Yiu, Y. Y., Lopez Angel, C. n., Pham, E. n., Carmody, A. B., Messer, R. J., Gars, E. n., Kortmann, J. n., Markovic, M. n., Hasenkrug, M. n., Peterson, K. E., Winkler, C. W., Woods, T. A., Hansen, P. n., Galloway, S. n., Wagh, D. n., Fram, B. J., Nguyen, T. n., Corey, D. n., Kalluru, R. S., Banaei, N. n., Rajadas, J. n., Monack, D. M., Ahmed, A. n., Sahoo, D. n., Davis, M. M., Glenn, J. S., Adomati, T. n., Lang, K. S., Weissman, I. L., Hasenkrug, K. J. 2020; 11 (3)

  Abstract

  It is well understood that the adaptive immune response to infectious agents includes a modulating suppressive component as well as an activating component. We now show that the very early innate response also has an immunosuppressive component. Infected cells upregulate the CD47 "don't eat me" signal, which slows the phagocytic uptake of dying and viable cells as well as downstream antigen-presenting cell (APC) functions. A CD47 mimic that acts as an essential virulence factor is encoded by all poxviruses, but CD47 expression on infected cells was found to be upregulated even by pathogens, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that encode no mimic. CD47 upregulation was revealed to be a host response induced by the stimulation of both endosomal and cytosolic pathogen recognition receptors (PRRs). Furthermore, proinflammatory cytokines, including those found in the plasma of hepatitis C patients, upregulated CD47 on uninfected dendritic cells, thereby linking innate modulation with downstream adaptive immune responses. Indeed, results from antibody-mediated CD47 blockade experiments as well as CD47 knockout mice revealed an immunosuppressive role for CD47 during infections with lymphocytic choriomeningitis virus and Mycobacterium tuberculosis Since CD47 blockade operates at the level of pattern recognition receptors rather than at a pathogen or antigen-specific level, these findings identify CD47 as a novel potential immunotherapeutic target for the enhancement of immune responses to a broad range of infectious agents.IMPORTANCE Immune responses to infectious agents are initiated when a pathogen or its components bind to pattern recognition receptors (PRRs). PRR binding sets off a cascade of events that activates immune responses. We now show that, in addition to activating immune responses, PRR signaling also initiates an immunosuppressive response, probably to limit inflammation. The importance of the current findings is that blockade of immunomodulatory signaling, which is mediated by the upregulation of the CD47 molecule, can lead to enhanced immune responses to any pathogen that triggers PRR signaling. Since most or all pathogens trigger PRRs, CD47 blockade could be used to speed up and strengthen both innate and adaptive immune responses when medically indicated. Such immunotherapy could be done without a requirement for knowing the HLA type of the individual, the specific antigens of the pathogen, or, in the case of bacterial infections, the antimicrobial resistance profile.

  View details for DOI 10.1128/mBio.01293-20

  View details for PubMedID 32576678

• Regulation of peanut-specific CD8+ T cells from nonallergic individuals. The Journal of allergy and clinical immunology Yu, W. n., Zhou, X. n., Davis, M. M., Nadeau, K. C. 2020

  Abstract

  Peanut-specific CD8+ T cells in nonallergic individuals are not deleted, but have an expansion block that can be released by impairing regulatory T cell associated signaling pathways.

  View details for DOI 10.1016/j.jaci.2020.07.032

  View details for PubMedID 32835695

• Immune Checkpoint Inhibitor Cardiotoxicity: Understanding Basic Mechanisms and Clinical Characteristics and Finding a Cure. Annual review of pharmacology and toxicology Waliany, S. n., Lee, D. n., Witteles, R. M., Neal, J. W., Nguyen, P. n., Davis, M. M., Salem, J. E., Wu, S. M., Moslehi, J. J., Zhu, H. n. 2020

  Abstract

  Immune checkpoint inhibitors (ICIs) attenuate mechanisms of self-tolerance in the immune system, enabling T cell responses to cancerous tissues and revolutionizing care for cancer patients. However, by lowering barriers against self-reactivity, ICIs often result in varying degrees of autoimmunity. Cardiovascular complications, particularly myocarditis but also arrhythmias, pericarditis, and vasculitis, have emerged as significant complications associated with ICIs. In this review, we examine the clinical aspects and basic science principles that underlie ICI-associated myocarditis and other cardiovascular toxicities. In addition, we discuss current therapeutic approaches. We believe a better mechanistic understanding of ICI-associated toxicities can lead to improved patient outcomes by reducing treatment-related morbidity. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 61 is January 8, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  View details for DOI 10.1146/annurev-pharmtox-010919-023451

  View details for PubMedID 32776859

• Alloantigen-specific Tr1 cells designed to prevent GvHD have a distinct molecular identity and suppress through CTLA-4 and PD-1 Society for Immunotherapy of Cancer’s (SITC) 35th Anniversary Annual Meeting Cepika, A., Chen, P. P., Uyeda, M. J., Cieniewicz, B., Narula, M., Amaya, L., Louis, D. M., Xu, L., Ji, X., Bertaina, A., Agarwal-Hashmi, R., Davis, M. M., Meyer, E., Bacchetta, R., Roncarolo, M. 2020: A159–A159

  View details for DOI 10.1136/jitc-2020-SITC2020.0146

• An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity. Immunity Glass, D. R., Tsai, A. G., Oliveria, J. P., Hartmann, F. J., Kimmey, S. C., Calderon, A. A., Borges, L. n., Glass, M. C., Wagar, L. E., Davis, M. M., Bendall, S. C. 2020; 53 (1): 217–32.e5

  Abstract

  B cells are capable of a wide range of effector functions including antibody secretion, antigen presentation, cytokine production, and generation of immunological memory. A consistent strategy for classifying human B cells by using surface molecules is essential to harness this functional diversity for clinical translation. We developed a highly multiplexed screen to quantify the co-expression of 351 surface molecules on millions of human B cells. We identified differentially expressed molecules and aligned their variance with isotype usage, VDJ sequence, metabolic profile, biosynthesis activity, and signaling response. Based on these analyses, we propose a classification scheme to segregate B cells from four lymphoid tissues into twelve unique subsets, including a CD45RB+CD27- early memory population, a class-switched CD39+ tonsil-resident population, and a CD19hiCD11c+ memory population that potently responds to immune activation. This classification framework and underlying datasets provide a resource for further investigations of human B cell identity and function.

  View details for DOI 10.1016/j.immuni.2020.06.013

  View details for PubMedID 32668225

• In vivo clonal expansion and phenotypes of hypocretin-specific CD4+ T cells in narcolepsy patients and controls. Nature communications Jiang, W., Birtley, J. R., Hung, S., Wang, W., Chiou, S., Macaubas, C., Kornum, B., Tian, L., Huang, H., Adler, L., Weaver, G., Lu, L., Ilstad-Minnihan, A., Somasundaram, S., Ayyangar, S., Davis, M. M., Stern, L. J., Mellins, E. D. 2019; 10 (1): 5247

  Abstract

  Individuals with narcolepsy suffer from abnormal sleep patterns due to loss of neurons that uniquely supply hypocretin (HCRT). Previous studies found associations of narcolepsy with thehuman leukocyte antigen (HLA)-DQ6 allele and T-cell receptor alpha (TRA) J24 gene segment and also suggested that in vitro-stimulated T cells can target HCRT. Here, we present evidence of in vivo expansion of DQ6-HCRT tetramer+/TRAJ24+/CD4+ T cells in DQ6+ individuals with and without narcolepsy. We identify related TRAJ24+ TCRalphabeta clonotypes encoded by identical alpha/beta gene regions from two patients and two controls. TRAJ24-G allele+ clonotypes only expand in the two patients, whereas a TRAJ24-C allele+ clonotype expands in a control. A representative tetramer+/G-allele+ TCR shows signaling reactivity to the epitope HCRT87-97. Clonally expanded G-allele+ T cells exhibit an unconventional effector phenotype. Our analysis of in vivo expansion of HCRT-reactive TRAJ24+ cells opens an avenue for further investigation of the autoimmune contribution to narcolepsy development.

  View details for DOI 10.1038/s41467-019-13234-x

  View details for PubMedID 31748512

• Follicular Lymphoma Organoids for Investigating the Tumor Microenvironment Wagar, L. E., Sworder, B., Khodadoust, M. S., Davis, M. M., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2019

  View details for DOI 10.1182/blood-2019-131192

  View details for Web of Science ID 000577160406180

• Maria-I: A Deep-Learning Approach for Accurate Prediction of MHC Class I Tumor Neoantigen Presentation Kathuria, K. R., Chen, B., Khodadoust, M. S., Olsson, N., Davis, M. M., Elias, J. E., Levy, R., Altman, R. B., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2019

  View details for DOI 10.1182/blood-2019-129334

  View details for Web of Science ID 000518218500130

• Immune Profiling of the Human Pancreas in Hereditary and Idiopathic Chronic Pancreatitis Lee, B., Adamska, J. Z., Namkoong, H., Bellin, M. D., Wilhelm, J., Szot, G., Louis, D. M., Davis, M. M., Pandol, S. J., Habtezion, A. LIPPINCOTT WILLIAMS & WILKINS. 2019: 1471

  View details for Web of Science ID 000505712800304

• The FluPRINT dataset, a multidimensional analysis of the influenza vaccine imprint on the immune system. Scientific data Tomic, A., Tomic, I., Dekker, C. L., Maecker, H. T., Davis, M. M. 2019; 6 (1): 214

  Abstract

  Machine learning has the potential to identify novel biological factors underlying successful antibody responses to influenza vaccines. The first attempts have revealed a high level of complexity in establishing influenza immunity, and many different cellular and molecular components are involved. Of note is that the previously identified correlates of protection fail to account for the majority of individual responses across different age groups and influenza seasons. Challenges remain from the small sample sizes in most studies and from often limited data sets, such as transcriptomic data. Here we report the creation of a unified database, FluPRINT, to enable large-scale studies exploring the cellular and molecular underpinnings of successful antibody responses to influenza vaccines. Over 3,000 parameters were considered, including serological responses to influenza strains, serum cytokines, cell phenotypes, and cytokine stimulations. FluPRINT, facilitates the application of machine learning algorithms for data mining. The data are publicly available and represent a resource to uncover new markers and mechanisms that are important for influenza vaccine immunogenicity.

  View details for DOI 10.1038/s41597-019-0213-4

  View details for PubMedID 31636302

• UNTARGETED METABOLOMIC ANALYSIS OF PATIENTS WITH CIRRHOSIS REVEALS MARKED DIFFERENCES AT DIFFERENT DISEASE STAGES, FROM COMPENSATED, TO DECOMPENSATED CIRRHOSIS AND ACUTE-ON-CHRONIC LIVER FAILURE (ACLF) Sola, E., Juanola, A., Sole, C., Pose, E., Carol, M., Gines, P., Davis, M. M. WILEY. 2019: 163A

  View details for Web of Science ID 000488653500250

• Increased Frequency of Bystander T Cells in the Lungs Is Associated with Recurrence in Localized Non-Small Cell Lung Cancer Reuben, A., Zhang, J., Gittelman, R., Chiou, S., Li, J., Fujimoto, J., Behrens, C., Kheradmand, F., Chow, C., Bernatchez, C., Eterovic, A. K., Benzeno, S., Vignali, M., Wu, X., Ye, Y., Cascone, T., Herbst, R., Swisher, S., Kadara, H., Moran, C., Zhang, J., Scheet, P., Vaporciyan, A., Sepesi, B., Gibbons, D., Robins, H., Hwu, P., Heymach, J., Sharma, P., Allison, J., Lee, J., Davis, M., Wistuba, I., Futreal, P. A., Zhang, J. ELSEVIER SCIENCE INC. 2019: S293

  View details for Web of Science ID 000492162201274

• Increased T Cell Differentiation and Cytolytic Function in Bangladeshi Compared to American Children. Frontiers in immunology Wagar, L. E., Bolen, C. R., Sigal, N., Lopez Angel, C. J., Guan, L., Kirkpatrick, B. D., Haque, R., Tibshirani, R. J., Parsonnet, J., Petri, W. A., Davis, M. M. 2019; 10: 2239

  Abstract

  During the first 5 years of life, children are especially vulnerable to infection-related morbidity and mortality. Conversely, the Hygiene Hypothesis suggests that a lack of exposure to infectious agents early in life could explain the increasing incidence of allergies and autoimmunity in high-income countries. Understanding these phenomena, however, is hampered by a lack of comprehensive, direct immune monitoring in children with differing degrees of microbial exposure. Using mass cytometry, we provide an in-depth profile of the peripheral blood mononuclear cells (PBMCs) of children in regions at the extremes of exposure: the San Francisco Bay Area, USA and an economically poor district of Dhaka, Bangladesh. Despite variability in clinical health, functional characteristics of PBMCs were similar in Bangladeshi and American children at 1 year of age. However, by 2-3 years of age, Bangladeshi children's immune cells often demonstrated altered activation and cytokine production profiles upon stimulation with PMA-ionomycin, with an overall immune trajectory more in line with American adults. Conversely, immune responses in children from the US remained steady. Using principal component analysis, donor location, ethnic background, and cytomegalovirus infection status were found to account for some of the variation identified among samples. Within Bangladeshi 1-year-olds, stunting (as measured by height-for-age z-scores) was found to be associated with IL-8 and TGFβ expression in PMA-ionomycin stimulated samples. Combined, these findings provide important insights into the immune systems of children in high vs. low microbial exposure environments and suggest an important role for IL-8 and TGFβ in mitigating the microbial challenges faced by the Bangladeshi children.

  View details for DOI 10.3389/fimmu.2019.02239

  View details for PubMedID 31620139

  View details for PubMedCentralID PMC6763580

• Increased T Cell Differentiation and Cytolytic Function in Bangladeshi Compared to American Children FRONTIERS IN IMMUNOLOGY Wager, L. E., Bolen, C. R., Sigel, N., Angel, C., Guan, L., Kirkpatrick, B. D., Haque, R., Tibshirani, R. J., Parsonnet, J., Petri, W. A., Davis, M. M. 2019; 10

  View details for DOI 10.3389/fimmu.2019.02239

  View details for Web of Science ID 000487188500001

• Transplantation Alters Function and Clonality of Cytomegalovirus-Responsive T Cells Higdon, L. E., Schaffert, S., Saligrama, N., Davis, M. M., Khatri, P., Maltzman, J. S. LIPPINCOTT WILLIAMS & WILKINS. 2019

  View details for Web of Science ID 000511467800256

• Recent progress in the analysis of alphabetaT cell and B cell receptor repertoires. Current opinion in immunology Davis, M. M., Boyd, S. D. 2019; 59: 109–14

  Abstract

  T cell receptors (TCRs) and B cell receptors (BCRs) are vertebrate evolution's best answer to the threat of microbial pathogens that can evolve much faster than ourselves. These antigen receptors are generated during T cell or B cell development by combinatorial rearrangement of germline genome V, D and J gene segments, and with junctional residues capable of enormous diversity. For decades the complexity of these receptor repertoires has limited their analysis, but advances in DNA sequencing technology and an array of complementary tools have now made their study much more tractable, filling a major gap in our ability to understand immunology as a system. Here, we summarize the recent approaches and discoveries that are enabling these advances, with some suggestions as to what may lie ahead.

  View details for DOI 10.1016/j.coi.2019.05.012

  View details for PubMedID 31326777

• Computational and Systems Immunology: A Student's Perspective. Trends in immunology Good, Z., Glanville, J., Gee, M. H., Davis, M. M., Khatri, P. 2019

  Abstract

  The big data revolution has transformed the landscape of immunology research. As inaugural students of Stanford's new Computational and Systems Immunology PhD track, we share our experiences and advice with other institutions considering a similar program.

  View details for DOI 10.1016/j.it.2019.06.006

  View details for PubMedID 31288986

• Distinct phenotype of CD4(+) T cells driving celiac disease identified in multiple autoimmune conditions NATURE MEDICINE Christophersen, A., Lund, E. G., Snir, O., Sola, E., Kanduri, C., Dahal-Koirala, S., Zuhlke, S., Molberg, O., Utz, P. J., Rohani-Pichavant, M., Simard, J. F., Dekker, C. L., Lundin, K. A., Sollid, L. M., Davis, M. M. 2019; 25 (5): 734-+

  View details for DOI 10.1038/s41591-019-0403-9

  View details for Web of Science ID 000468247800015

• Allergen-specific CD8(+) T cells in peanut-allergic individuals JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY Yu, W., Zhou, X., Dunham, D., Lyu, S., Manohar, M., Zhang, W., Zhao, F., Davis, M. M., Nadeau, K. 2019; 143 (5): 1948–52

  View details for DOI 10.1016/j.jaci.2019.01.011

  View details for Web of Science ID 000466784600036

• Select sequencing of clonally expanded CD8(+) T cells reveals limits to clonal expansion PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Huang, H., Sikora, M. J., Islam, S., Chowdhury, R., Chien, Y., Scriba, T. J., Davis, M. M., Steinmetz, L. M. 2019; 116 (18): 8995–9001

  View details for DOI 10.1073/pnas.1902649116

  View details for Web of Science ID 000466446500053

• Select sequencing of clonally expanded CD8+ T cells reveals limits to clonal expansion. Proceedings of the National Academy of Sciences of the United States of America Huang, H., Sikora, M. J., Islam, S., Chowdhury, R. R., Chien, Y., Scriba, T. J., Davis, M. M., Steinmetz, L. M. 2019

  Abstract

  To permit the recognition of antigens, T cells generate a vast diversity of T cell receptor (TCR) sequences. Upon binding of the TCR to an antigen-MHC complex, T cells clonally expand to establish an immune response. To study antigen-specific T cell clonality, we have developed a method that allows selection of rare cells, based on RNA expression, before in-depth scRNA-seq (named SELECT-seq). We applied SELECT-seq to collect both TCR sequences and then transcriptomes from single cells of peripheral blood lymphocytes activated by a Mycobacterium tuberculosis (Mtb) lysate. TCR sequence analysis allowed us to preferentially select expanded conventional CD8+ T cells as well as invariant natural killer T (iNKT) cells and mucosal-associated invariant T (MAIT) cells. The iNKT and MAIT cells have a highly similar transcriptional pattern, indicating that they carry out similar immunological functions and differ considerably from conventional CD8+ T cells. While there is no relationship between expression profiles and clonal expansion in iNKT or MAIT cells, highly expanded conventional CD8+ T cells down-regulate the interleukin 2 (IL-2) receptor alpha (IL2RA, or CD25) protein and show signs of senescence. This suggests inherent limits to clonal expansion that act to diversify the T cell response repertoire.

  View details for PubMedID 30992377

• High-dimensional profiling of immune response in cirrhosis: Key role for activated CD8+T-cells and relationship with prognosis Sola, E., Pose, E., Juanola, A., Blaya, D., McSween, A., Wilhelmy, J., Louis, D., Carol, M., Sole, C., Sancho-Bru, P., Gines, P., Davis, M. M. ELSEVIER SCIENCE BV. 2019: E91

  View details for Web of Science ID 000463481700162

• Distinct phenotype of CD4+ T cells driving celiac disease identified in multiple autoimmune conditions. Nature medicine Christophersen, A., Lund, E. G., Snir, O., Sola, E., Kanduri, C., Dahal-Koirala, S., Zuhlke, S., Molberg, O., Utz, P. J., Rohani-Pichavant, M., Simard, J. F., Dekker, C. L., Lundin, K. E., Sollid, L. M., Davis, M. M. 2019

  Abstract

  Combining HLA-DQ-gluten tetramers with mass cytometry and RNA sequencing analysis, we find that gluten-specific CD4+ T cells in the blood and intestines of patients with celiac disease display a surprisingly rare phenotype. Cells with this phenotype are also elevated in patients with systemic sclerosis and systemic lupus erythematosus, suggesting a way to characterize CD4+ T cells specific for disease-driving antigens in multiple autoimmune conditions.

  View details for PubMedID 30911136

• A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring. Nature medicine Alpert, A., Pickman, Y., Leipold, M., Rosenberg-Hasson, Y., Ji, X., Gaujoux, R., Rabani, H., Starosvetsky, E., Kveler, K., Schaffert, S., Furman, D., Caspi, O., Rosenschein, U., Khatri, P., Dekker, C. L., Maecker, H. T., Davis, M. M., Shen-Orr, S. S. 2019

  Abstract

  Immune responses generally decline with age. However, the dynamics of this process at the individual level have not been characterized, hindering quantification of an individual's immune age. Here, we use multiple 'omics' technologies to capture population- and individual-level changes in the human immune system of 135 healthy adult individuals of different ages sampled longitudinally over a nine-year period. We observed high inter-individual variability in the rates of change of cellular frequencies that was dictated by their baseline values, allowing identification of steady-state levels toward which a cell subset converged and the ordered convergence of multiple cell subsets toward an older adult homeostasis. These data form a high-dimensional trajectory of immune aging (IMM-AGE) that describes a person's immune status better than chronological age. We show that the IMM-AGE score predicted all-cause mortality beyond well-established risk factors in the Framingham Heart Study, establishing its potential use in clinics for identification of patients at risk.

  View details for PubMedID 30842675

• LUNG DISEASE IN SYSTEMIC JIA: AN EMERGING PROBLEM LINKED WITH YOUNG AGE AND ANTI-IL-1/IL-6 Chen, G., Saper, V., Deutsch, G., Guillerman, R. P., Jagadeesh, K., Schulert, G., Canna, S., Lu, Y., Birgmeier, J., Leung, A., Grom, A., Bejerano, G., Davis, M., Khatri, P., Mellins, E., Consortium sJIA-LD Case Reporters BMJ PUBLISHING GROUP. 2019: A57

  View details for DOI 10.1136/annrheumdis-2018-EWRR2019.115

  View details for Web of Science ID 000466415300116

• Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients NATURE BIOTECHNOLOGY Deuse, T., Hu, X., Gravina, A., Wang, D., Tediashvili, G., De, C., Thayer, W. O., Wahl, A., Garcia, J., Reichenspurner, H., Davis, M. M., Lanier, L. L., Schrepfer, S. 2019; 37 (3): 252-+

  View details for DOI 10.1038/s41587-019-0016-3

  View details for Web of Science ID 000460155900015

• A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring NATURE MEDICINE Alpert, A., Pickman, Y., Leipold, M., Rosenberg-Hasson, Y., Ji, X., Gaujoux, R., Rabani, H., Starosvetsky, E., Kveler, K., Schaffert, S., Furman, D., Caspi, O., Rosenschein, U., Khatri, P., Dekker, C. L., Maecker, H. T., Davis, M. M., Shen-Orr, S. S. 2019; 25 (3): 487-+

  View details for DOI 10.1038/s41591-019-0381-y

  View details for Web of Science ID 000460643100028

• Shaping of infant B cell receptor repertoires by environmental factors and infectious disease. Science translational medicine Nielsen, S. C., Roskin, K. M., Jackson, K. J., Joshi, S. A., Nejad, P., Lee, J., Wagar, L. E., Pham, T. D., Hoh, R. A., Nguyen, K. D., Tsunemoto, H. Y., Patel, S. B., Tibshirani, R., Ley, C., Davis, M. M., Parsonnet, J., Boyd, S. D. 2019; 11 (481)

  Abstract

  Antigenic exposures at epithelial sites in infancy and early childhood are thought to influence the maturation of humoral immunity and modulate the risk of developing immunoglobulin E (IgE)-mediated allergic disease. How different kinds of environmental exposures influence B cell isotype switching to IgE, IgG, or IgA, and the somatic mutation maturation of these antibody pools, is not fully understood. We sequenced antibody repertoires in longitudinal blood samples in a birth cohort from infancy through the first 3 years of life and found that, whereas IgG and IgA show linear increases in mutational maturation with age, IgM and IgD mutations are more closely tied to pathogen exposure. IgE mutation frequencies are primarily increased in children with impaired skin barrier conditions such as eczema, suggesting that IgE affinity maturation could provide a mechanistic link between epithelial barrier failure and allergy development.

  View details for PubMedID 30814336

• Shaping of infant B cell receptor repertoires by environmental factors and infectious disease SCIENCE TRANSLATIONAL MEDICINE Nielsen, S. A., Roskin, K. M., Jackson, K. L., Joshi, S. A., Nejad, P., Lee, J., Wagar, L. E., Pham, T. D., Hoh, R. A., Nguyen, K. D., Tsunemoto, H. Y., Patel, S. B., Tibshirani, R., Ley, C., Davis, M. M., Parsonnet, J., Boyd, S. D. 2019; 11 (481)

  View details for DOI 10.1126/scitranslmed.aat2004

  View details for Web of Science ID 000460307000001

• B-cell lymphomas present immunoglobulin neoantigens BLOOD Khodadoust, M. S., Olsson, N., Chen, B., Sworder, B., Shree, T., Liu, C., Zhang, L., Czerwinski, D. K., Davis, M. M., Levy, R., Elias, J. E., Alizadeh, A. A. 2019; 133 (8): 878–81

  View details for DOI 10.1182/blood-2018-06-845156

  View details for Web of Science ID 000459264700019

• Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients. Nature biotechnology Deuse, T., Hu, X., Gravina, A., Wang, D., Tediashvili, G., De, C., Thayer, W. O., Wahl, A., Garcia, J. V., Reichenspurner, H., Davis, M. M., Lanier, L. L., Schrepfer, S. 2019

  Abstract

  Autologous induced pluripotent stem cells (iPSCs) constitute an unlimited cell source for patient-specific cell-based organ repair strategies. However, their generation and subsequent differentiation into specific cells or tissues entail cell line-specific manufacturing challenges and form a lengthy process that precludes acute treatment modalities. These shortcomings could be overcome by using prefabricated allogeneic cell or tissue products, but the vigorous immune response against histo-incompatible cells has prevented the successful implementation of this approach. Here we show that both mouse and human iPSCs lose their immunogenicity when major histocompatibility complex (MHC) class I and II genes are inactivated and CD47 is over-expressed. These hypoimmunogenic iPSCs retain their pluripotent stem cell potential and differentiation capacity. Endothelial cells, smooth muscle cells, and cardiomyocytes derived from hypoimmunogenic mouse or human iPSCs reliably evade immune rejection in fully MHC-mismatched allogeneic recipients and survive long-term without the use of immunosuppression. These findings suggest that hypoimmunogenic cell grafts can be engineered for universal transplantation.

  View details for PubMedID 30778232

• A functional subset of CD8+ T cells during chronic exhaustion is defined by SIRPalpha expression. Nature communications Myers, L. M., Tal, M. C., Torrez Dulgeroff, L. B., Carmody, A. B., Messer, R. J., Gulati, G., Yiu, Y. Y., Staron, M. M., Angel, C. L., Sinha, R., Markovic, M., Pham, E. A., Fram, B., Ahmed, A., Newman, A. M., Glenn, J. S., Davis, M. M., Kaech, S. M., Weissman, I. L., Hasenkrug, K. J. 2019; 10 (1): 794

  Abstract

  Prolonged exposure of CD8+ T cells to antigenic stimulation, as in chronic viral infections, leads to a state of diminished function termed exhaustion. We now demonstrate that even during exhaustion there is a subset of functional CD8+ T cells defined by surface expression of SIRPalpha, a protein not previously reported on lymphocytes. On SIRPalpha+ CD8+ T cells, expression of co-inhibitory receptors is counterbalanced by expression of co-stimulatory receptors and it is only SIRPalpha+ cells that actively proliferate, transcribe IFNgamma and show cytolytic activity. Furthermore, target cells that express the ligand for SIRPalpha, CD47, are more susceptible to CD8+ T cell-killing in vivo. SIRPalpha+ CD8+ T cells are evident in mice infected with Friend retrovirus, LCMV Clone 13, and in patients with chronic HCV infections. Furthermore, therapeutic blockade of PD-L1 to reinvigorate CD8+ T cells during chronic infection expands the cytotoxic subset of SIRPalpha+ CD8+ T cells.

  View details for PubMedID 30770827

• A functional subset of CD8(+) T cells during chronic exhaustion is defined by SIRP alpha expression NATURE COMMUNICATIONS Myers, L. M., Tal, M., Dulgeroff, L., Carmody, A. B., Messer, R. J., Gulati, G., Yiu, Y., Staron, M. M., Angel, C., Sinha, R., Markovic, M., Pham, E. A., Fram, B., Ahmed, A., Newman, A. M., Glenn, J. S., Davis, M. M., Kaech, S. M., Weissman, I. L., Hasenkrug, K. J. 2019; 10

  View details for DOI 10.1038/s41467-019-08637-9

  View details for Web of Science ID 000458755400008

• Identification of specificity TCR groups of tumor antigen specific T-cells Chen, L., Wang, C., Davis, M. AMER ASSOC CANCER RESEARCH. 2019

  View details for DOI 10.1158/2326-6074.CRICIMTEATIAACR18-PR14

  View details for Web of Science ID 000557035600437

• Allergen Specific CD8+ T cells in Peanut Allergic Individuals. The Journal of allergy and clinical immunology Yu, W., Zhou, X., Dunham, D., Lyu, S. C., Manohar, M., Zhang, W., Zhao, F., Davis, M. M., Nadeau, K. 2019

  Abstract

  CD8+ T cells are seldom considered in IgE mediated food allergy; we show that peanut specific CD8+ T cells are increased in peanut allergic human subjects.

  View details for PubMedID 30682458

• Prevalence and Severity of Food Allergies Among US Adults. JAMA network open Gupta, R. S., Warren, C. M., Smith, B. M., Jiang, J., Blumenstock, J. A., Davis, M. M., Schleimer, R. P., Nadeau, K. C. 2019; 2 (1): e185630

  Abstract

  Importance: Food allergy is a costly, potentially life-threatening condition. Although studies have examined the prevalence of childhood food allergy, little is known about prevalence, severity, or health care utilization related to food allergies among US adults.Objective: To provide nationally representative estimates of the distribution, severity, and factors associated with adult food allergies.Design, Setting, and Participants: In this cross-sectional survey study of US adults, surveys were administered via the internet and telephone from October 9, 2015, to September 18, 2016. Participants were first recruited from NORC at the University of Chicago's probability-based AmeriSpeak panel, and additional participants were recruited from the non-probability-based Survey Sampling International (SSI) panel.Exposures: Demographic and allergic participant characteristics.Main Outcomes and Measures: Self-reported food allergies were the main outcome and were considered convincing if reported symptoms to specific allergens were consistent with IgE-mediated reactions. Diagnosis history to specific allergens and food allergy-related health care use were also primary outcomes. Estimates were based on this nationally representative sample using small-area estimation and iterative proportional fitting methods. To increase precision, AmeriSpeak data were augmented by calibration-weighted, non-probability-based responses from SSI.Results: Surveys were completed by 40 443 adults (mean [SD] age, 46.6 [20.2] years), with a survey completion rate of 51.2% observed among AmeriSpeak panelists (n=7210) and 5.5% among SSI panelists (n=33 233). Estimated convincing food allergy prevalence among US adults was 10.8% (95% CI, 10.4%-11.1%), although 19.0% (95% CI, 18.5%-19.5%) of adults self-reported a food allergy. The most common allergies were shellfish (2.9%; 95% CI, 2.7%-3.1%), milk (1.9%; 95% CI, 1.8%-2.1%), peanut (1.8%; 95% CI, 1.7%-1.9%), tree nut (1.2%; 95% CI, 1.1%-1.3%), and fin fish (0.9%; 95% CI, 0.8%-1.0%). Among food-allergic adults, 51.1% (95% CI, 49.3%-52.9%) experienced a severe food allergy reaction, 45.3% (95% CI, 43.6%-47.1%) were allergic to multiple foods, and 48.0% (95% CI, 46.2%-49.7%) developed food allergies as an adult. Regarding health care utilization, 24.0% (95% CI, 22.6%-25.4%) reported a current epinephrine prescription, and 38.3% (95% CI, 36.7%-40.0%) reported at least 1 food allergy-related lifetime emergency department visit.Conclusions and Relevance: These data suggest that at least 10.8% (>26 million) of US adults are food allergic, whereas nearly 19% of adults believe that they have a food allergy. Consequently, these findings suggest that it is crucial that adults with suspected food allergy receive appropriate confirmatory testing and counseling to ensure food is not unnecessarily avoided and quality of life is not unduly impaired.

  View details for PubMedID 30646188

• Clonal replacement of tumor-specific T cells following PD-1 blockade. Nature medicine Yost, K. E., Satpathy, A. T., Wells, D. K., Qi, Y. n., Wang, C. n., Kageyama, R. n., McNamara, K. L., Granja, J. M., Sarin, K. Y., Brown, R. A., Gupta, R. K., Curtis, C. n., Bucktrout, S. L., Davis, M. M., Chang, A. L., Chang, H. Y. 2019

  Abstract

  Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of patients with cancer1. However, whether the T cell response to checkpoint blockade relies on reinvigoration of pre-existing tumor-infiltrating lymphocytes or on recruitment of novel T cells remains unclear2-4. Here we performed paired single-cell RNA and T cell receptor sequencing on 79,046 cells from site-matched tumors from patients with basal or squamous cell carcinoma before and after anti-PD-1 therapy. Tracking T cell receptor clones and transcriptional phenotypes revealed coupling of tumor recognition, clonal expansion and T cell dysfunction marked by clonal expansion of CD8+CD39+ T cells, which co-expressed markers of chronic T cell activation and exhaustion. However, the expansion of T cell clones did not derive from pre-existing tumor-infiltrating T lymphocytes; instead, the expanded clones consisted of novel clonotypes that had not previously been observed in the same tumor. Clonal replacement of T cells was preferentially observed in exhausted CD8+ T cells and evident in patients with basal or squamous cell carcinoma. These results demonstrate that pre-existing tumor-specific T cells may have limited reinvigoration capacity, and that the T cell response to checkpoint blockade derives from a distinct repertoire of T cell clones that may have just recently entered the tumor.

  View details for DOI 10.1038/s41591-019-0522-3

  View details for PubMedID 31359002

• Comparing consumer perceptions of appliances’ electricity use to appliances’ actual direct-metered consumption Environmental Research Communications Lesic, V., Glasgo, B., Krishnamurti, T., Bruine de Bruin, W., Davis, M., Azevedo, I. 2019; 1 (11)

  View details for DOI 10.1088/2515-7620/ab4a99

• Pregnancy-Induced Alterations in NK Cell Phenotype and Function. Frontiers in immunology Le Gars, M., Seiler, C., Kay, A. W., Bayless, N. L., Starosvetsky, E., Moore, L., Shen-Orr, S. S., Aziz, N., Khatri, P., Dekker, C. L., Swan, G. E., Davis, M. M., Holmes, S., Blish, C. A. 2019; 10: 2469

  Abstract

  Pregnant women are particularly susceptible to complications of influenza A virus infection, which may result from pregnancy-induced changes in the function of immune cells, including natural killer (NK) cells. To better understand NK cell function during pregnancy, we assessed the ability of the two main subsets of NK cells, CD56dim, and CD56bright NK cells, to respond to influenza-virus infected cells and tumor cells. During pregnancy, CD56dim and CD56bright NK cells displayed enhanced functional responses to both infected and tumor cells, with increased expression of degranulation markers and elevated frequency of NK cells producing IFN-gamma. To better understand the mechanisms driving this enhanced function, we profiled CD56dim and CD56bright NK cells from pregnant and non-pregnant women using mass cytometry. NK cells from pregnant women displayed significantly increased expression of several functional and activation markers such as CD38 on both subsets and NKp46 on CD56dim NK cells. NK cells also displayed diminished expression of the chemokine receptor CXCR3 during pregnancy. Overall, these data demonstrate that functional and phenotypic shifts occur in NK cells during pregnancy that can influence the magnitude of the immune response to both infections and tumors.

  View details for DOI 10.3389/fimmu.2019.02469

  View details for PubMedID 31708922

• Emergent high fatality lung disease in systemic juvenile arthritis. Annals of the rheumatic diseases Saper, V. E., Chen, G. n., Deutsch, G. H., Guillerman, R. P., Birgmeier, J. n., Jagadeesh, K. n., Canna, S. n., Schulert, G. n., Deterding, R. n., Xu, J. n., Leung, A. N., Bouzoubaa, L. n., Abulaban, K. n., Baszis, K. n., Behrens, E. M., Birmingham, J. n., Casey, A. n., Cidon, M. n., Cron, R. Q., De, A. n., De Benedetti, F. n., Ferguson, I. n., Fishman, M. P., Goodman, S. I., Graham, T. B., Grom, A. A., Haines, K. n., Hazen, M. n., Henderson, L. A., Ho, A. n., Ibarra, M. n., Inman, C. J., Jerath, R. n., Khawaja, K. n., Kingsbury, D. J., Klein-Gitelman, M. n., Lai, K. n., Lapidus, S. n., Lin, C. n., Lin, J. n., Liptzin, D. R., Milojevic, D. n., Mombourquette, J. n., Onel, K. n., Ozen, S. n., Perez, M. n., Phillippi, K. n., Prahalad, S. n., Radhakrishna, S. n., Reinhardt, A. n., Riskalla, M. n., Rosenwasser, N. n., Roth, J. n., Schneider, R. n., Schonenberg-Meinema, D. n., Shenoi, S. n., Smith, J. A., Sönmez, H. E., Stoll, M. L., Towe, C. n., Vargas, S. O., Vehe, R. K., Young, L. R., Yang, J. n., Desai, T. n., Balise, R. n., Lu, Y. n., Tian, L. n., Bejerano, G. n., Davis, M. M., Khatri, P. n., Mellins, E. D. 2019

  Abstract

  To investigate the characteristics and risk factors of a novel parenchymal lung disease (LD), increasingly detected in systemic juvenile idiopathic arthritis (sJIA).In a multicentre retrospective study, 61 cases were investigated using physician-reported clinical information and centralised analyses of radiological, pathological and genetic data.LD was associated with distinctive features, including acute erythematous clubbing and a high frequency of anaphylactic reactions to the interleukin (IL)-6 inhibitor, tocilizumab. Serum ferritin elevation and/or significant lymphopaenia preceded LD detection. The most prevalent chest CT pattern was septal thickening, involving the periphery of multiple lobes ± ground-glass opacities. The predominant pathology (23 of 36) was pulmonary alveolar proteinosis and/or endogenous lipoid pneumonia (PAP/ELP), with atypical features including regional involvement and concomitant vascular changes. Apparent severe delayed drug hypersensitivity occurred in some cases. The 5-year survival was 42%. Whole exome sequencing (20 of 61) did not identify a novel monogenic defect or likely causal PAP-related or macrophage activation syndrome (MAS)-related mutations. Trisomy 21 and young sJIA onset increased LD risk. Exposure to IL-1 and IL-6 inhibitors (46 of 61) was associated with multiple LD features. By several indicators, severity of sJIA was comparable in drug-exposed subjects and published sJIA cohorts. MAS at sJIA onset was increased in the drug-exposed, but was not associated with LD features.A rare, life-threatening lung disease in sJIA is defined by a constellation of unusual clinical characteristics. The pathology, a PAP/ELP variant, suggests macrophage dysfunction. Inhibitor exposure may promote LD, independent of sJIA severity, in a small subset of treated patients. Treatment/prevention strategies are needed.

  View details for DOI 10.1136/annrheumdis-2019-216040

  View details for PubMedID 31562126

• Opposing T cell responses in experimental autoimmune encephalomyelitis. Nature Saligrama, N. n., Zhao, F. n., Sikora, M. J., Serratelli, W. S., Fernandes, R. A., Louis, D. M., Yao, W. n., Ji, X. n., Idoyaga, J. n., Mahajan, V. B., Steinmetz, L. M., Chien, Y. H., Hauser, S. L., Oksenberg, J. R., Garcia, K. C., Davis, M. M. 2019

  Abstract

  Experimental autoimmune encephalomyelitis is a model for multiple sclerosis. Here we show that induction generates successive waves of clonally expanded CD4+, CD8+ and γδ+ T cells in the blood and central nervous system, similar to gluten-challenge studies of patients with coeliac disease. We also find major expansions of CD8+ T cells in patients with multiple sclerosis. In autoimmune encephalomyelitis, we find that most expanded CD4+ T cells are specific for the inducing myelin peptide MOG35-55. By contrast, surrogate peptides derived from a yeast peptide major histocompatibility complex library of some of the clonally expanded CD8+ T cells inhibit disease by suppressing the proliferation of MOG-specific CD4+ T cells. These results suggest that the induction of autoreactive CD4+ T cells triggers an opposing mobilization of regulatory CD8+ T cells.

  View details for DOI 10.1038/s41586-019-1467-x

  View details for PubMedID 31391585

• SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses. Journal of immunology (Baltimore, Md. : 1950) Tomic, A. n., Tomic, I. n., Rosenberg-Hasson, Y. n., Dekker, C. L., Maecker, H. T., Davis, M. M. 2019

  Abstract

  Machine learning holds considerable promise for understanding complex biological processes such as vaccine responses. Capturing interindividual variability is essential to increase the statistical power necessary for building more accurate predictive models. However, available approaches have difficulty coping with incomplete datasets which is often the case when combining studies. Additionally, there are hundreds of algorithms available and no simple way to find the optimal one. In this study, we developed Sequential Iterative Modeling "OverNight" (SIMON), an automated machine learning system that compares results from 128 different algorithms and is particularly suitable for datasets containing many missing values. We applied SIMON to data from five clinical studies of seasonal influenza vaccination. The results reveal previously unrecognized CD4+ and CD8+ T cell subsets strongly associated with a robust Ab response to influenza Ags. These results demonstrate that SIMON can greatly speed up the choice of analysis modalities. Hence, it is a highly useful approach for data-driven hypothesis generation from disparate clinical datasets. Our strategy could be used to gain biological insight from ever-expanding heterogeneous datasets that are publicly available.

  View details for DOI 10.4049/jimmunol.1900033

  View details for PubMedID 31201239

• Acute myeloid leukemia immunopeptidome reveals HLA presentation of mutated nucleophosmin. PloS one Narayan, R. n., Olsson, N. n., Wagar, L. E., Medeiros, B. C., Meyer, E. n., Czerwinski, D. n., Khodadoust, M. S., Zhang, L. n., Schultz, L. n., Davis, M. M., Elias, J. E., Levy, R. n. 2019; 14 (7): e0219547

  Abstract

  Somatic mutations in cancer are a potential source of cancer specific neoantigens. Acute myeloid leukemia (AML) has common recurrent mutations shared between patients in addition to private mutations specific to individuals. We hypothesized that neoantigens derived from recurrent shared mutations would be attractive targets for future immunotherapeutic approaches. Here we sought to study the HLA Class I and II immunopeptidome of thirteen primary AML tumor samples and two AML cell lines (OCI-AML3 and MV4-11) using mass spectrometry to evaluate for endogenous mutation-bearing HLA ligands from common shared AML mutations. We identified two endogenous, mutation-bearing HLA Class I ligands from nucleophosmin (NPM1). The ligands, AVEEVSLRK from two patient samples and C(cys)LAVEEVSL from OCI-AML3, are predicted to bind the common HLA haplotypes, HLA-A*03:01 and HLA-A*02:01 respectively. Since NPM1 is mutated in approximately one-third of patients with AML, the finding of endogenous HLA ligands from mutated NPM1 supports future studies evaluating immunotherapeutic approaches against this shared target, for this subset of patients with AML.

  View details for DOI 10.1371/journal.pone.0219547

  View details for PubMedID 31291378

• Single-cell analysis reveals T cell infiltration in old neurogenic niches. Nature Dulken, B. W., Buckley, M. T., Navarro Negredo, P. n., Saligrama, N. n., Cayrol, R. n., Leeman, D. S., George, B. M., Boutet, S. C., Hebestreit, K. n., Pluvinage, J. V., Wyss-Coray, T. n., Weissman, I. L., Vogel, H. n., Davis, M. M., Brunet, A. n. 2019

  Abstract

  The mammalian brain contains neurogenic niches that comprise neural stem cells and other cell types. Neurogenic niches become less functional with age, but how they change during ageing remains unclear. Here we perform single-cell RNA sequencing of young and old neurogenic niches in mice. The analysis of 14,685 single-cell transcriptomes reveals a decrease in activated neural stem cells, changes in endothelial cells and microglia, and an infiltration of T cells in old neurogenic niches. T cells in old brains are clonally expanded and are generally distinct from those in old blood, which suggests that they may experience specific antigens. T cells in old brains also express interferon-γ, and the subset of neural stem cells that has a high interferon response shows decreased proliferation in vivo. We find that T cells can inhibit the proliferation of neural stem cells in co-cultures and in vivo, in part by secreting interferon-γ. Our study reveals an interaction between T cells and neural stem cells in old brains, opening potential avenues through which to counteract age-related decline in brain function.

  View details for DOI 10.1038/s41586-019-1362-5

  View details for PubMedID 31270459

• Predicting HLA class II antigen presentation through integrated deep learning. Nature biotechnology Chen, B. n., Khodadoust, M. S., Olsson, N. n., Wagar, L. E., Fast, E. n., Liu, C. L., Muftuoglu, Y. n., Sworder, B. J., Diehn, M. n., Levy, R. n., Davis, M. M., Elias, J. E., Altman, R. B., Alizadeh, A. A. 2019

  Abstract

  Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II molecules would be valuable for vaccine development and cancer immunotherapies. Current computational methods trained on in vitro binding data are limited by insufficient training data and algorithmic constraints. Here we describe MARIA (major histocompatibility complex analysis with recurrent integrated architecture; https://maria.stanford.edu/ ), a multimodal recurrent neural network for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles. In addition to in vitro binding measurements, MARIA is trained on peptide HLA ligand sequences identified by mass spectrometry, expression levels of antigen genes and protease cleavage signatures. Because it leverages these diverse training data and our improved machine learning framework, MARIA (area under the curve = 0.89-0.92) outperformed existing methods in validation datasets. Across independent cancer neoantigen studies, peptides with high MARIA scores are more likely to elicit strong CD4+ T cell responses. MARIA allows identification of immunogenic epitopes in diverse cancers and autoimmune disease.

  View details for DOI 10.1038/s41587-019-0280-2

  View details for PubMedID 31611695

• Organoid Modeling of the Tumor Immune Microenvironment. Cell Neal, J. T., Li, X., Zhu, J., Giangarra, V., Grzeskowiak, C. L., Ju, J., Liu, I. H., Chiou, S., Salahudeen, A. A., Smith, A. R., Deutsch, B. C., Liao, L., Zemek, A. J., Zhao, F., Karlsson, K., Schultz, L. M., Metzner, T. J., Nadauld, L. D., Tseng, Y., Alkhairy, S., Oh, C., Keskula, P., Mendoza-Villanueva, D., De La Vega, F. M., Kunz, P. L., Liao, J. C., Leppert, J. T., Sunwoo, J. B., Sabatti, C., Boehm, J. S., Hahn, W. C., Zheng, G. X., Davis, M. M., Kuo, C. J. 2018; 175 (7): 1972

  Abstract

  Invitro cancer cultures, including three-dimensional organoids, typically contain exclusively neoplastic epithelium but require artificial reconstitution to recapitulate the tumor microenvironment (TME). The co-culture of primary tumor epithelia with endogenous, syngeneic tumor-infiltrating lymphocytes (TILs) as a cohesive unit has been particularly elusive. Here, an air-liquid interface (ALI) method propagated patient-derived organoids (PDOs) from >100 human biopsies or mouse tumors in syngeneic immunocompetent hosts as tumor epithelia with native embedded immune cells (T, B, NK, macrophages). Robust droplet-based, single-cell simultaneous determination of gene expression and immune repertoire indicated that PDO TILs accurately preserved the original tumor Tcell receptor (TCR) spectrum. Crucially, human and murine PDOs successfully modeled immune checkpoint blockade (ICB) with anti-PD-1- and/or anti-PD-L1 expanding and activating tumor antigen-specific TILs and eliciting tumor cytotoxicity. Organoid-based propagation of primary tumor epithelium en bloc with endogenous immune stroma should enable immuno-oncology investigations within the TME and facilitate personalized immunotherapy testing.

  View details for PubMedID 30550791

• Organoid Modeling of the Tumor Immune Microenvironment CELL Neal, J. T., Li, X., Zhu, J., Giangarra, V., Grzeskowiak, C. L., Ju, J., Liu, I. H., Chiou, S., Salahudeen, A. A., Smith, A. R., Deutsch, B. C., Liao, L., Zemek, A. J., Zhao, F., Karlsson, K., Schultz, L. M., Metzner, T. J., Nadauld, L. D., Tseng, Y., Alkhairy, S., Oh, C., Keskula, P., Mendoza-Villanueva, D., De La Vega, F. M., Kunz, P. L., Liao, J. C., Leppert, J. T., Sunwoo, J. B., Sabatti, C., Boehm, J. S., Hahn, W. C., Zheng, G. Y., Davis, M. M., Kuo, C. J. 2018; 175 (7): 1972-+

  View details for DOI 10.1016/j.cell.2018.11.021

  View details for Web of Science ID 000453242200023

• Allelic resolution NGS HLA typing of Class I and Class II loci and haplotypes in Cape Town, South Africa HUMAN IMMUNOLOGY Thorstenson, Y. R., Creary, L. E., Huang, H., Rozot, V., Nguyen, T. T., Babrzadeh, F., Kancharla, S., Fukushima, M., Kuehn, R., Wang, C., Li, M., Krishnakumar, S., Mindrinos, M., Vina, M., Scriba, T. J., Davis, M. M. 2018; 79 (12): 839-847

  View details for DOI 10.1016/j.humimm.2018.09.004

  View details for Web of Science ID 000453647700005

• Histone H3 lysine 4 methylation signature associated with human undernutrition PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Uchiyama, R., Kupkova, K., Shetty, S. J., Linford, A. S., Pray-Grant, M. G., Wagar, L. E., Davis, M. M., Haque, R., Gaultier, A., Mayo, M. W., Grant, P. A., Petri, W. A., Bekiranov, S., Auble, D. T. 2018; 115 (48): E11264-E11273

  View details for DOI 10.1073/pnas.1722125115

  View details for Web of Science ID 000451351000013

• Histone H3 lysine 4 methylation signature associated with human undernutrition. Proceedings of the National Academy of Sciences of the United States of America Uchiyama, R., Kupkova, K., Shetty, S. J., Linford, A. S., Pray-Grant, M. G., Wagar, L. E., Davis, M. M., Haque, R., Gaultier, A., Mayo, M. W., Grant, P. A., Petri, W. A., Bekiranov, S., Auble, D. T. 2018

  Abstract

  Chronically undernourished children become stunted during their first 2 years and thereafter bear burdens of ill health for the rest of their lives. Contributors to stunting include poor nutrition and exposure to pathogens, and parental history may also play a role. However, the epigenetic impact of a poor environment on young children is largely unknown. Here we show the unfolding pattern of histone H3 lysine 4 trimethylation (H3K4me3) in children and mothers living in an urban slum in Dhaka, Bangladesh. A pattern of chromatin modification in blood cells of stunted children emerges over time and involves a global decrease in methylation at canonical locations near gene start sites and increased methylation at ectopic sites throughout the genome. This redistribution occurs at metabolic and immune genes and was specific for H3K4me3, as it was not observed for histone H3 lysine 27 acetylation in the same samples. Methylation changes in stunting globally resemble changes that occur in vitro in response to altered methylation capacity, suggesting that reduced levels of one-carbon nutrients in the diet play a key role in stunting in this population. A network of differentially expressed genes in stunted children reveals effects on chromatin modification machinery, including turnover of H3K4me3, as well as posttranscriptional gene regulation affecting immune response pathways and lipid metabolism. Consistent with these changes, reduced expression of the endocytic receptor gene LDL receptor 1 (LRP1) is a driver of stunting in a mouse model, suggesting a target for intervention.

  View details for PubMedID 30420518

• Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases. Nature communications Vallania, F., Tam, A., Lofgren, S., Schaffert, S., Azad, T. D., Bongen, E., Haynes, W., Alsup, M., Alonso, M., Davis, M., Engleman, E., Khatri, P. 2018; 9 (1): 4735

  Abstract

  In silico quantification of cell proportions from mixed-cell transcriptomics data (deconvolution) requires a reference expression matrix, called basis matrix. We hypothesize that matrices created using only healthy samples from a single microarray platform would introduce biological and technical biases in deconvolution. We show presence of such biases in two existing matrices, IRIS and LM22, irrespective of deconvolution method. Here, we present immunoStates, a basis matrix built using 6160 samples with different disease states across 42 microarray platforms. We find that immunoStates significantly reduces biological and technical biases. Importantly, we find that different methods have virtually no or minimal effect once the basis matrix is chosen. We further show that cellular proportion estimates using immunoStates are consistently more correlated with measured proportions than IRIS and LM22, across all methods. Our results demonstrate the need and importance of incorporating biological and technical heterogeneity in a basis matrix for achieving consistently high accuracy.

  View details for PubMedID 30413720

• Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases NATURE COMMUNICATIONS Vallania, F., Tam, A., Lofgren, S., Schaffert, S., Azad, T. D., Bongen, E., Haynes, W., Alsup, M., Alonso, M., Davis, M., Engleman, E., Khatri, P. 2018; 9

  View details for DOI 10.1038/s41467-018-07242-6

  View details for Web of Science ID 000449628200006

• Author Correction: A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes. Nature Roy Chowdhury, R., Vallania, F., Yang, Q., Lopez Angel, C. J., Darboe, F., Penn-Nicholson, A., Rozot, V., Nemes, E., Malherbe, S. T., Ronacher, K., Walzl, G., Hanekom, W., Davis, M. M., Winter, J., Chen, X., Scriba, T. J., Khatri, P., Chien, Y. 2018

  Abstract

  The spelling of author Qianting Yang was corrected; the affiliation of author Stephanus T. Malherbe was corrected; and graphs in Fig. 4b and c were corrected owing to reanalysis of the data into the correct timed intervals.

  View details for PubMedID 30377311

• Advanced model systems and tools for basic and translational human immunology. Genome medicine Wagar, L. E., DiFazio, R. M., Davis, M. M. 2018; 10 (1): 73

  Abstract

  There are fundamental differences between humans and the animals we typically use to study the immune system. We have learned much from genetically manipulated and inbred animal models, but instances in which these findings have been successfully translated to human immunity have been rare. Embracing the genetic and environmental diversity of humans can tell us about the fundamental biology of immune cell types and the elasticity of the immune system. Although people are much more immunologically diverse than conventionally housed animal models, tools and technologies are now available that permit high-throughput analysis of human samples, including both blood and tissues, which will give us deep insights into human immunity in health and disease. As we gain a more detailed picture of the human immune system, we can build more sophisticated models to better reflect this complexity, both enabling the discovery of new immunological mechanisms and facilitating translation into the clinic.

  View details for PubMedID 30266097

• Advanced model systems and tools for basic and translational human immunology GENOME MEDICINE Wagar, L. E., DiFazio, R. M., Davis, M. M. 2018; 10

  View details for DOI 10.1186/s13073-018-0584-8

  View details for Web of Science ID 000446302400001

• Allelic resolution NGS HLA typing of Class I and Class II loci and haplotypes in Cape Town, South Africa. Human immunology Thorstenson, Y. R., Creary, L. E., Huang, H., Rozot, V., Nguyen, T. T., Babrzadeh, F., Kancharla, S., Fukushima, M., Kuehn, R., Wang, C., Li, M., Krishnakumar, S., Mindrinos, M., Fernandez Vina, M. A., Scriba, T. J., Davis, M. M. 2018

  Abstract

  The development of next-generation sequencing (NGS) methods for HLA genotyping has already had an impact on the scope and precision of HLA research. In this study, allelic resolution HLA typing was obtained for 402 individuals from Cape Town, South Africa. The data were produced by high-throughput NGS sequencing as part of a study of T-cell responses to Mycobacterium tuberculosis in collaboration with the University of Cape Town and Stanford University. All samples were genotyped for 11 HLA loci, namely HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4, and -DRB5. NGS HLA typing of samples from Cape Town inhabitants revealed a unique cohort, including unusual haplotypes, and 22 novel alleles not previously reported in the IPD-IMGT/HLA Database. Eight novel alleles were in Class I loci and 14 were in Class II. There were 62 different alleles of HLA-A, 72 of HLA-B, and 47 of HLA-C. Alleles A23:17, A43:01, A29:11, A68:27:01, A01:23, B14:01:01, B15:10:01, B39:10:01, B45:07, B82:02:01 and C08:04:01 were notably more frequent in Cape Town compared to other populations reported in the literature. Class II loci had 21 different alleles of DPA1, 46 of DPB1, 27 of DQA1, 26 of DQB1, 41 of DRB1, 5 of DRB3, 4 of DRB4 and 6 of DRB5. The Cape Town cohort exhibited high degrees of HLA diversity and relatively high heterozygosity at most loci. Genetic distances between Cape Town and five other sub-Saharan African populations were also calculated and compared to European Americans.

  View details for PubMedID 30240896

• Assessing functional and structural cardiotoxicity in cultured human iPSC-cardiomyocytes in a single plate format Guo, L., Furniss, M., Hamre, J., Batista, L., Bastogne, T., Yan, Z., Wu, J. C., Eldridge, S., Davis, M. ELSEVIER SCIENCE INC. 2018: 163–64

  View details for DOI 10.1016/j.vascn.2018.01.532

  View details for Web of Science ID 000444523000172

• A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes NATURE Chowdhury, R., Vallania, F., Yang, Q., Angel, C., Darboe, F., Penn-Nicholson, A., Rozot, V., Nemes, E., Malherbe, S. T., Ronacher, K., Walzl, G., Hanekom, W., Davis, M. M., Winter, J., Chen, X., Scriba, T. J., Khatri, P., Chien, Y. 2018; 560 (7720): 644-+

  View details for DOI 10.1038/s41586-018-0439-x

  View details for Web of Science ID 000443218600050

• A multi-cohort study of the immune factors associated with M. tuberculosis infection outcomes. Nature Roy Chowdhury, R., Vallania, F., Yang, Q., Lopez Angel, C. J., Darboe, F., Penn-Nicholson, A., Rozot, V., Nemes, E., Malherbe, S. T., Ronacher, K., Walzl, G., Hanekom, W., Davis, M. M., Winter, J., Chen, X., Scriba, T. J., Khatri, P., Chien, Y. 2018

  Abstract

  Most infections with Mycobacterium tuberculosis (Mtb) manifest as a clinically asymptomatic, contained state, known as latent tuberculosis infection, that affects approximately one-quarter of the global population1. Although fewer than one in ten individuals eventually progress to active disease2, tuberculosis is a leading cause of death from infectious disease worldwide3. Despite intense efforts, immune factors that influence the infection outcomes remain poorly defined. Here we used integrated analyses of multiple cohorts to identify stage-specific host responses to Mtb infection. First, using high-dimensional mass cytometry analyses and functional assays of a cohort of South African adolescents, we show that latent tuberculosis is associated with enhanced cytotoxic responses, which are mostly mediated by CD16 (also known as FcgammaRIIIa) and natural killer cells, and continuous inflammation coupled with immune deviations in both T and B cell compartments.Next, using cell-type deconvolution of transcriptomic data from several cohorts of different ages, genetic backgrounds, geographical locations and infection stages, we show that although deviations in peripheral B and T cell compartments generally start at latency, they are heterogeneous across cohorts. However, an increase in the abundance of circulating natural killer cells in tuberculosis latency, with a corresponding decrease during active disease and a return to baseline levels upon clinical cure are features that are common to all cohorts. Furthermore, by analysing three longitudinal cohorts, we find that changes inperipheral levels of natural killer cells can inform disease progression and treatment responses, and inversely correlate with the inflammatory state of the lungs of patients with active tuberculosis. Together, our findings offer crucial insights into the underlying pathophysiology of tuberculosis latency, and identify factors that may influence infection outcomes.

  View details for PubMedID 30135583

• Plasmablast antibody repertoires in elderly influenza vaccine responders exhibit restricted diversity but increased breadth of binding across influenza strains CLINICAL IMMUNOLOGY Ju, C., Blum, L. K., Kongpachith, S., Lingampalli, N., Mao, R., Brodin, P., Dekker, C. L., Davis, M. M., Robinson, W. H. 2018; 193: 70–79

  View details for DOI 10.1016/j.clim.2018.01.011

  View details for Web of Science ID 000440126900010

• Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? Seeing the Forest Rather than a Few Trees COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY Davis, M. M., Tato, C. M. 2018; 10 (8)

  View details for DOI 10.1101/cshperspect.a028886

  View details for Web of Science ID 000440493200006

• Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding. Cell Sibener, L. V., Fernandes, R. A., Kolawole, E. M., Carbone, C. B., Liu, F., McAffee, D., Birnbaum, M. E., Yang, X., Su, L. F., Yu, W., Dong, S., Gee, M. H., Jude, K. M., Davis, M. M., Groves, J. T., Goddard, W. A., Heath, J. R., Evavold, B. D., Vale, R. D., Garcia, K. C. 2018; 174 (3): 672

  Abstract

  TCR-signaling strength generally correlates with peptide-MHC binding affinity; however, exceptions exist. We find high-affinity, yet non-stimulatory, interactions occur with high frequency in the human Tcell repertoire. Here, we studied human TCRs that are refractory to activation by pMHC ligands despite robust binding. Analysis of 3D affinity, 2D dwell time, and crystal structures of stimulatory versus non-stimulatory TCR-pMHC interactions failed to account for their different signaling outcomes. Using yeast pMHC display, we identified peptide agonists of a formerly non-responsive TCR. Single-molecule force measurements demonstrated the emergence of catch bonds in the activating TCR-pMHC interactions, correlating with exclusion of CD45 from the TCR-APC contact site. Molecular dynamics simulations of TCR-pMHC disengagement distinguished agonist from non-agonist ligands based on the acquisition of catch bonds withinthe TCR-pMHC interface. The isolation of catch bonds as a parameter mediating the coupling of TCR binding and signaling has important implications for TCR and antigen engineering for immunotherapy.

  View details for PubMedID 30053426

• Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding CELL Sibener, L. V., Fernandes, R. A., Kolawole, E. M., Carbone, C. B., Liu, F., McAffee, D., Birnbaum, M. E., Yang, X., Su, L. F., Yu, W., Dong, S., Gee, M. H., Jude, K. M., Davis, M. M., Groves, J. T., Goddard, W. A., Heath, J. R., Evavold, B. D., Vale, R. D., Garcia, K. 2018; 174 (3): 672-+

  View details for DOI 10.1016/j.cell.2018.06.017

  View details for Web of Science ID 000439870500016

• Altered Function of Cytomegalovirus Specific T Cells in Transplant Recipients. Higdon, L., Trofe-Clark, J., Liu, S., Saligrama, N., Margulies, K., Davis, M., Maltzman, J. WILEY. 2018: 436

  View details for Web of Science ID 000431965401493

• Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging CELL Cheung, P., Vallania, F., Warsinske, H. C., Donato, M., Schaffert, S., Chang, S. E., Dvorak, M., Dekker, C. L., Davis, M. M., Utz, P. J., Khatri, P., Kuo, A. J. 2018; 173 (6): 1385-+

  View details for DOI 10.1016/j.cell.2018.03.079

  View details for Web of Science ID 000433989100012

• CyTOF analysis allows characterization of Axl-Expressing Dendritic cells in healthy human donors Leylek, R., Alcantara-Hernandez, M., Wagar, L. E., Engleman, E. G., Marinkovich, M. P., Davis, M. M., Nolan, G. P., Idoyaga, J. WILEY. 2018: 29

  View details for Web of Science ID 000434106700041

• Bifidobacterium can mitigate intestinal immunopathology in the context of immune checkpoint blockade Wang, F., Sun, S., Yin, Q., Chen, L., Davis, M. M. AMER ASSOC IMMUNOLOGISTS. 2018

  View details for Web of Science ID 000459977702091

• Novel M-CSF-producing gamma delta T cells protect against recurrent malaria Mamedov, M. R., Scholzen, A., Nair, R. V., Cumnock, K., Kenkel, J. A., Oliveira, J. M., Trujillo, D. L., Saligrama, N., Zhang, Y., Rubelt, F., Schneider, D. S., Chien, Y., Sauerwein, R., Davis, M. M. AMER ASSOC IMMUNOLOGISTS. 2018

  View details for Web of Science ID 000459977700312

• A high-dimensional phenotypic map of human Dendritic cells paves the way for therapeutics Alcantara-Hernandez, M., Leylek, R., Wagar, L. E., Engleman, E. G., Keler, T., Marinkovich, M. P., Davis, M. M., Nolan, G. P., Idoyaga, J. WILEY. 2018: 25–26

  View details for Web of Science ID 000434106700035

• Rebooting Human Immunology. Annual review of immunology Davis, M. M., Brodin, P. 2018; 36: 843–64

  Abstract

  Recent progress in both conceptual and technological approaches to human immunology have rejuvenated a field that has long been in the shadow of the inbred mouse model. This is a healthy development both for the clinical relevance of immunology and for the fact that it is a way to gain access to the wealth of phenomenology in the many human diseases that involve the immune system. This is where we are likely to discover new immunological mechanisms and principals, especially those involving genetic heterogeneity or environmental influences that are difficult to model effectively in inbred mice. We also suggest that there are likely to be novel immunological mechanisms in long-lived, less fecund mammals such as human beings since they must remain healthy far longer than short-lived rodents in order for the species to survive.

  View details for PubMedID 29490162

• Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging. Cell Cheung, P., Vallania, F., Warsinske, H. C., Donato, M., Schaffert, S., Chang, S. E., Dvorak, M., Dekker, C. L., Davis, M. M., Utz, P. J., Khatri, P., Kuo, A. J. 2018

  Abstract

  Post-translational modifications of histone proteins and exchanges of histone variants of chromatin are central to the regulation of nearly all DNA-templated biological processes. However, the degree and variability of chromatin modifications in specific human immune cells remain largely unknown. Here, we employ a highly multiplexed mass cytometry analysis to profile the global levels of a broad array of chromatin modifications in primary human immune cells at the single-cell level. Our data reveal markedly different cell-type- and hematopoietic-lineage-specific chromatin modification patterns. Differential analysis between younger and older adults shows that aging is associated with increased heterogeneity between individuals and elevated cell-to-cell variability in chromatin modifications. Analysis of a twin cohort unveils heritability of chromatin modifications and demonstrates that aging-related chromatin alterations are predominantly driven by non-heritable influences. Together, we present a powerful platform for chromatin and immunology research. Our discoveries highlight the profound impacts of aging on chromatin modifications.

  View details for PubMedID 29706550

• IMMUNE PROFILE OF HEALTHY CARDIOVASCULAR AGING: INSIGHTS FROM A POPULATION-BASED STUDY AND NETWORK MODELING Bouajila, S., Moneghetti, K., Kobayashi, Y., Gomari, F. A., Abbasi, F., Davis, M. M., Wu, J. C., Kuznetsova, T., Sayed, N., Haddad, F. ELSEVIER SCIENCE INC. 2018: 1657

  View details for Web of Science ID 000429659703307

• Plasmablast antibody repertoires in elderly influenza vaccine responders exhibit restricted diversity but increased breadth of binding across influenza strains. Clinical immunology (Orlando, Fla.) Ju, C., Blum, L. K., Kongpachith, S., Lingampalli, N., Mao, R., Brodin, P., Dekker, C. L., Davis, M. M., Robinson, W. H. 2018

  Abstract

  Seasonal influenza vaccines elicit antibody responses that can prevent infection, but their efficacy is reduced in the elderly. While a subset of elderly individuals can still mount sufficient vaccine-induced antibody responses, little is known about the properties of the vaccine-induced antibody repertoires in elderly as compared to young responders. To gain insights into the effects of aging on influenza vaccine-induced antibody responses, we used flow cytometry and a cell-barcoding method to sequence antibody heavy and light chain gene pairs expressed by individual blood plasmablasts generated in response to influenza vaccination in elderly (aged 70-89) and young (aged 20-29) responders. We found similar blood plasmablast levels in the elderly and young responders seven days post vaccination. Informatics analysis revealed increased clonality, but similar heavy chain V(D)J gene usage in the elderly as compared to young vaccine responders. Although the elderly responders exhibited decreased antibody sequence diversity and fewer consequential mutations relative to young responders, recombinant antibodies from elderly responders bound a broader range of influenza strain HAs. Thus elderly influenza vaccine responders mount plasmablast responses with restricted diversity but with an increased breadth of binding across influenza strains. Our results suggest that the ability to generate plasmablast responses encoding cross-strain binding antibodies likely represents a mechanism important to vaccine responses in the elderly.

  View details for PubMedID 29410330

• From T Cell Receptor to Antigen, Systems Approach to Discovering T Cell Antigen(s) in Multiple Sclerosis and Experimental Autoimmune Encephalomyelitis Saligrama, N., Zhao, F., Fernandes, R. A., Serratelli, W. S., Louis, D. M., Chien, Y., Garcia, C. K., Oksenberg, J., Davis, M. M. SAGE PUBLICATIONS LTD. 2018: 5

  View details for Web of Science ID 000429034600007

• Comparison of CyTOF assays across sites: Results of a six-center pilot study JOURNAL OF IMMUNOLOGICAL METHODS Leipold, M. D., Obermoser, G., Fenwick, C., Kleinstuber, K., Rashidi, N., McNevin, J. P., Nau, A. N., Wagar, L. E., Rozot, V., Davis, M. M., DeRosa, S., Pantaleo, G., Scriba, T. J., Walker, B. D., Olsen, L. R., Maecker, H. T. 2018; 453: 37–43

  Abstract

  For more than five years, high-dimensional mass cytometry has been employed to study immunology. However, these studies have typically been performed in one laboratory on one or few instruments. We present the results of a six-center study using healthy control human peripheral blood mononuclear cells (PBMCs) and commercially available reagents to test the intra-site and inter-site variation of mass cytometers and operators. We used prestained controls generated by the primary center as a reference to compare against samples stained at each individual center. Data were analyzed at the primary center, including investigating the effects of two normalization methods. All six sites performed similarly, with CVs for both Frequency of Parent and median signal intensity (MSI) values<30%. Increased background was seen when using the premixed antibody cocktail aliquots at each site, suggesting that cocktails are best made fresh. Both normalization methods tested performed adequately for normalizing MSI values between centers. Clustering algorithms revealed slight differences between the prestained and the sites-stained samples, due mostly to the increased background of a few antibodies. Therefore, we believe that multicenter mass cytometry assays are feasible.

  View details for PubMedID 29174717

  View details for PubMedCentralID PMC5805584

• From T Cell Receptor to Antigen, Systems Approach to Discovering T Cell Antigen(s) in Multiple Sclerosis and Experimental Autoimmune Encephalomyelitis Saligrama, N., Zhao, F., Fernandes, R. A., Serratelli, W. S., Louis, D. M., Chien, Y., Garcia, C. K., Oksenberg, J., Davis, M. M. SAGE PUBLICATIONS LTD. 2018: 85

  View details for Web of Science ID 000429034600188

• Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes CELL Gee, M. H., Han, A., Lofgren, S. M., Beausang, J. F., Mendoza, J. L., Birnbaum, M. E., Bethune, M. T., Fischer, S., Yang, X., Gomez-Eerland, R., Bingham, D. B., Sibener, L. V., Fernandes, R. A., Velasco, A., Baltimore, D., Schumacher, T. N., Khatri, P., Quake, S. R., Davis, M. M., Garcia, K. 2018; 172 (3): 549-+

  Abstract

  The immune system can mount T cell responses against tumors; however, the antigen specificities of tumor-infiltrating lymphocytes (TILs) are not well understood. We used yeast-display libraries of peptide-human leukocyte antigen (pHLA) to screen for antigens of "orphan" T cell receptors (TCRs) expressed on TILs from human colorectal adenocarcinoma. Four TIL-derived TCRs exhibited strong selection for peptides presented in a highly diverse pHLA-A∗02:01 library. Three of the TIL TCRs were specific for non-mutated self-antigens, two of which were present in separate patient tumors, and shared specificity for a non-mutated self-antigen derived from U2AF2. These results show that the exposed recognition surface of MHC-bound peptides accessible to the TCR contains sufficient structural information to enable the reconstruction of sequences of peptide targets for pathogenic TCRs of unknown specificity. This finding underscores the surprising specificity of TCRs for their cognate antigens and enables the facile indentification of tumor antigens through unbiased screening.

  View details for PubMedID 29275860

  View details for PubMedCentralID PMC5786495

• Bifidobacterium can mitigate intestinal immunopathology in the context of CTLA-4 blockade PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wang, F., Yin, Q., Chen, L., Davis, M. M. 2018; 115 (1): 157–61

  Abstract

  Antibodies that attenuate immune tolerance have been used to effectively treat cancer, but they can also trigger severe autoimmunity. To investigate this, we combined anti-CTLA-4 treatment with a standard colitis model to give mice a more severe form of the disease. Pretreatment with an antibiotic, vancomycin, provoked an even more severe, largely fatal form, suggesting that a Gram-positive component of the microbiota had a mitigating effect. We then found that a commonly used probiotic, Bifidobacterium, could largely rescue the mice from immunopathology without an apparent effect on antitumor immunity, and this effect may be dependent on regulatory T cells.

  View details for PubMedID 29255057

• Transcript-indexed ATAC-seq for precision immune profiling. Nature medicine Satpathy, A. T., Saligrama, N. n., Buenrostro, J. D., Wei, Y. n., Wu, B. n., Rubin, A. J., Granja, J. M., Lareau, C. A., Li, R. n., Qi, Y. n., Parker, K. R., Mumbach, M. R., Serratelli, W. S., Gennert, D. G., Schep, A. N., Corces, M. R., Khodadoust, M. S., Kim, Y. H., Khavari, P. A., Greenleaf, W. J., Davis, M. M., Chang, H. Y. 2018

  Abstract

  T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy.

  View details for PubMedID 29686426

• Rebooting Human Immunology ANNUAL REVIEW OF IMMUNOLOGY, VOL 36 Davis, M. M., Brodin, P., Littman, D. R., Yokoyama, W. M. 2018; 36: 843-864

  View details for DOI 10.1146/annurev-immunol-042617-053206

  View details for Web of Science ID 000433486000031

• Autologous iPSC-Based Vaccines Elicit Anti-tumor Responses In Vivo CELL STEM CELL Kooreman, N. G., Kim, Y., de Almeida, P. E., Termglinchan, V., Diecke, S., Shao, N., Wei, T., Yi, H., Dey, D., Nelakanti, R., Brouwer, T. P., Paik, D. T., Sagiv-Barfi, I., Han, A., Quax, P. H., Hamming, J. F., Levy, R., Davis, M. M., Wu, J. C. 2018

  View details for DOI 10.1016/j.stem.2018.01.016

• B cell lymphomas present immunoglobulin neoantigens. Blood Khodadoust, M. S., Olsson, N. n., Chen, B. n., Sworder, B. n., Shree, T. n., Liu, C. L., Zhang, L. n., Czerwinski, D. K., Davis, M. M., Levy, R. n., Elias, J. E., Alizadeh, A. A. 2018

  View details for PubMedID 30545830

• A Macrophage Colony-Stimulating-Factor-Producing γδ T Cell Subset Prevents Malarial Parasitemic Recurrence. Immunity Mamedov, M. R., Scholzen, A. n., Nair, R. V., Cumnock, K. n., Kenkel, J. A., Oliveira, J. H., Trujillo, D. L., Saligrama, N. n., Zhang, Y. n., Rubelt, F. n., Schneider, D. S., Chien, Y. H., Sauerwein, R. W., Davis, M. M. 2018; 48 (2): 350–63.e7

  Abstract

  Despite evidence that γδ T cells play an important role during malaria, their precise role remains unclear. During murine malaria induced by Plasmodium chabaudi infection and in human P. falciparum infection, we found that γδ T cells expanded rapidly after resolution of acute parasitemia, in contrast to αβ T cells that expanded at the acute stage and then declined. Single-cell sequencing showed that TRAV15N-1 (Vδ6.3) γδ T cells were clonally expanded in mice and had convergent complementarity-determining region 3 sequences. These γδ T cells expressed specific cytokines, M-CSF, CCL5, CCL3, which are known to act on myeloid cells, indicating that this γδ T cell subset might have distinct functions. Both γδ T cells and M-CSF were necessary for preventing parasitemic recurrence. These findings point to an M-CSF-producing γδ T cell subset that fulfills a specialized protective role in the later stage of malaria infection when αβ T cells have declined.

  View details for PubMedID 29426701

• Autologous iPSC-Based Vaccines Elicit Anti-tumor Responses In Vivo. Cell stem cell Kooreman, N. G., Kim, Y. n., de Almeida, P. E., Termglinchan, V. n., Diecke, S. n., Shao, N. Y., Wei, T. T., Yi, H. n., Dey, D. n., Nelakanti, R. n., Brouwer, T. P., Paik, D. T., Sagiv-Barfi, I. n., Han, A. n., Quax, P. H., Hamming, J. F., Levy, R. n., Davis, M. M., Wu, J. C. 2018

  Abstract

  Cancer cells and embryonic tissues share a number of cellular and molecular properties, suggesting that induced pluripotent stem cells (iPSCs) may be harnessed to elicit anti-tumor responses in cancer vaccines. RNA sequencing revealed that human and murine iPSCs express tumor-associated antigens, and we show here a proof of principle for using irradiated iPSCs in autologous anti-tumor vaccines. In a prophylactic setting, iPSC vaccines prevent tumor growth in syngeneic murine breast cancer, mesothelioma, and melanoma models. As an adjuvant, the iPSC vaccine inhibited melanoma recurrence at the resection site and reduced metastatic tumor load, which was associated with fewer Th17 cells and increased CD11b+GR1himyeloid cells. Adoptive transfer of T cells isolated from vaccine-treated tumor-bearing mice inhibited tumor growth in unvaccinated recipients, indicating that the iPSC vaccine promotes an antigen-specific anti-tumor T cell response. Our data suggest an easy, generalizable strategy for multiple types of cancer that could prove highly valuable in clinical immunotherapy.

  View details for PubMedID 29456158

• Value of Circulating Cytokine Profiling During Submaximal Exercise Testing in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Scientific reports Moneghetti, K. J., Skhiri, M. n., Contrepois, K. n., Kobayashi, Y. n., Maecker, H. n., Davis, M. n., Snyder, M. n., Haddad, F. n., Montoya, J. G. 2018; 8 (1): 2779

  Abstract

  Myalgic Encephalomyelitis or Chronic Fatigue Syndrome (ME/CFS) is a heterogeneous syndrome in which patients often experience severe fatigue and malaise following exertion. Immune and cardiovascular dysfunction have been postulated to play a role in the pathophysiology. We therefore, examined whether cytokine profiling or cardiovascular testing following exercise would differentiate patients with ME/CFS. Twenty-four ME/CFS patients were matched to 24 sedentary controls and underwent cardiovascular and circulating immune profiling. Cardiovascular analysis included echocardiography, cardiopulmonary exercise and endothelial function testing. Cytokine and growth factor profiles were analyzed using a 51-plex Luminex bead kit at baseline and 18 hours following exercise. Cardiac structure and exercise capacity were similar between groups. Sparse partial least square discriminant analyses of cytokine profiles 18 hours post exercise offered the most reliable discrimination between ME/CFS and controls (κ = 0.62(0.34,0.84)). The most discriminatory cytokines post exercise were CD40L, platelet activator inhibitor, interleukin 1-β, interferon-α and CXCL1. In conclusion, cytokine profiling following exercise may help differentiate patients with ME/CFS from sedentary controls.

  View details for PubMedID 29426834

• Mapping and quantification of over 2,000 O-linked glycopeptides in activated human T cells with isotope-targeted glycoproteomics (IsoTaG). Molecular & cellular proteomics : MCP Woo, C. M., Lund, P. J., Huang, A. C., Davis, M. M., Bertozzi, C. R., Pitteri, S. n. 2018

  Abstract

  Post-translational modifications (PTMs) on proteins often function to regulate signaling cascades, with the activation of T cells during an adaptive immune response being a classic example.  Mounting evidence indicates that the modification of proteins by O-linked N-acetylglucosamine (O-GlcNAc), the only mammalian glycan found on nuclear and cytoplasmic proteins, helps regulate T cell activation.  Yet, a mechanistic understanding of how O-GlcNAc functions in T cell activation remains elusive, partly because of the difficulties in mapping and quantifying O-GlcNAc sites.  Thus, to advance insight into the role of O-GlcNAc in T cell activation, we performed glycosite mapping studies via direct glycopeptide measurement on resting and activated primary human T cells with a technique termed Isotope Targeted Glycoproteomics.  This approach led to the identification of 2,219 intact O-linked glycopeptides across 1,045 glycoproteins.  A significant proportion (>45%) of the identified O-GlcNAc sites lie in close proximity to or coincide with a known phosphorylation site, supporting the potential for PTM crosstalk.  Consistent with other studies, we find that O-GlcNAc sites in T cells lack a strict consensus sequence.  To validate our results, we employed gel shift assays based on conjugating mass tags to O-GlcNAc groups.  Notably, we observed that the transcription factors c-JUN and JUNB show higher levels of O-GlcNAc glycosylation and higher levels of expression in activated T cells.  Overall, our findings provide a quantitative characterization of O-GlcNAc glycoproteins and their corresponding modification sites in primary human T cells, which will facilitate mechanistic studies into the function of O-GlcNAc in T cell activation.

  View details for PubMedID 29351928

• REPLY TO ROERINK ET AL: Methods for recruitment, serum separation, and storage were the same for patients and controls PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Montoya, J. G., Maecker, H. T., Rosenberg-Hasson, Y., Davis, M. M. 2017; 114 (45): E9436

  View details for PubMedID 29087345

• Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? Seeing the Forest Rather than a Few Trees. Cold Spring Harbor perspectives in biology Davis, M. M., Tato, C. M. 2017

  Abstract

  Preventing morbidity and mortality from infectious disease through the development and use of effective vaccines is one of medicine's greatest achievements and greatest frustrations. We are struggling with improving vaccine efficacy for some of the most globally widespread diseases, such as malaria and tuberculosis. In an effort to gain an edge, systems biology approaches have begun to be employed to more broadly investigate the pathways leading to protective vaccine responses. As such, we are now at a critical juncture, needing to evaluate how fruitful these approaches have been. Herein we discuss the level of success achieved as compared to the original promise of systems methodologies, and conclude that while we have indeed begun to make clear inroads into understanding the immune response to vaccines, we still have much to learn and gain from the more comprehensive approach of systems-level analysis.

  View details for PubMedID 29038119

• Concerted T cell response in experimental autoimmune encephalomyelitis and multiple sclerosis Saligrama, N., Zhao, F., Fernandes, R., Serratelli, W. S., Louis, D. M., Chien, Y. C., Garcia, C. K., Oksenberg, J., Davis, M. M. SAGE PUBLICATIONS LTD. 2017: 201

  View details for Web of Science ID 000413730201026

• Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis. Science immunology de Bourcy, C. F., Dekker, C. L., Davis, M. M., Nicolls, M. R., Quake, S. R. 2017; 2 (15)

  Abstract

  Systemic sclerosis with pulmonary arterial hypertension (SSc-PAH) is a debilitating and frequently lethal disease of unknown cause lacking effective treatment options. Lymphocyte anomalies and autoantibodies observed in systemic sclerosis have suggested an autoimmune character. We study the clonal structure of the B cell repertoire in SSc-PAH using immunoglobulin heavy chain (IGH) sequencing before and after B cell depletion. We found SSc-PAH to be associated with anomalies in B cell development, namely, altered VDJ rearrangement frequencies (reduced IGHV2-5 segment usage) and an increased somatic mutation-fixation probability in expanded B cell lineages. SSc-PAH was also characterized by anomalies in B cell homeostasis, namely, an expanded immunoglobulin D-positive (IgD(+)) proportion with reduced mutation loads and an expanded proportion of highly antibody-secreting cells. Disease signatures pertaining to IGHV2-5 segment usage, IgD proportions, and mutation loads were temporarily reversed after B cell depletion. Analyzing the time course of B cell depletion, we find that the kinetics of naïve replenishment are predictable from baseline measurements alone, that release of plasma cells into the periphery can precede naïve replenishment, and that modes of B cell receptor diversity are highly elastic. Our findings reveal humoral immune signatures of SSc-PAH and uncover determinism in the effects of B cell depletion on the antibody repertoire.

  View details for DOI 10.1126/sciimmunol.aan8289

  View details for PubMedID 28963118

• Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis SCIENCE IMMUNOLOGY de Bourcy, C. A., Dekker, C. L., Davis, M. M., Nicolls, M. R., Quake, S. R. 2017; 2 (15)

  View details for DOI 10.1126/sciimiunol.aan8289

  View details for Web of Science ID 000434327200005

• Clonal Expansion and Interrelatedness of Distinct B-Lineage Compartments in Multiple Myeloma Bone Marrow CANCER IMMUNOLOGY RESEARCH Hansmann, L., Han, A., Penter, L., Liedtke, M., Davis, M. M. 2017; 5 (9): 744–54

  Abstract

  Multiple myeloma is characterized by the clonal expansion of malignant plasma cells in the bone marrow. But the phenotypic diversity and the contribution of less predominant B-lineage clones to the biology of this disease have been controversial. Here, we asked whether cells bearing the dominant multiple myeloma immunoglobulin rearrangement occupy phenotypic compartments other than that of plasma cells. To accomplish this, we combined 13-parameter FACS index sorting and t-Stochastic Neighbor Embedding (t-SNE) visualization with high-throughput single-cell immunoglobulin sequencing to track selected B-lineage clones across different stages of human B-cell development. As expected, the predominant clones preferentially mapped to aberrant plasma cell compartments, albeit phenotypically altered from wild type. Interestingly, up to 1.2% of cells of the predominant clones colocalized with B-lineage cells of a normal phenotype. In addition, minor clones with distinct immunoglobulin sequences were detected in up to 9% of sequenced cells, but only 2 out of 12 of these clones showed aberrant immune phenotypes. The majority of these minor clones showed intraclonal silent nucleotide differences within the CDR3s and varying frequencies of somatic mutations in the immunoglobulin genes. Therefore, the phenotypic range of multiple myeloma cells in the bone marrow is not confined to aberrant-phenotype plasma cells but extends to low frequencies of normal-phenotype B cells, in line with the recently reported success of B cell-targeting cellular therapies in some patients. The majority of minor clones result from parallel nonmalignant expansion. Cancer Immunol Res; 5(9); 744-54. ©2017 AACR.

  View details for PubMedID 28768640

  View details for PubMedCentralID PMC5590392

• Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses SCIENCE IMMUNOLOGY Avey, S., Cheung, F., Fermin, D., Frelinger, J., Gaujoux, R., Gottardo, R., Khatri, P., Kleinstein, S. H., Kotliarov, Y., Meng, H., Sauteraud, R., Shen-Orr, S. S., Tsang, J. S., Vallania, F., Anguiano, E., Baisch, J., Baldwin, N., Belshe, R. B., Blevins, T. P., Chaussabel, D., Davis, M. M., Fikrig, E., Grill, D. E., Hafler, D. A., Henrich, E., Joshi, S. R., Kaech, S. M., Kennedy, R. B., Mohanty, S., Montgomery, R. R., Oberg, A. L., Obermoser, G., Ovsyannikova, I. G., Palucka, A., Pascual, V., Poland, G. A., Pulendran, B., Reinherz, E. L., Shaw, A. C., Siconolfi, B., Stuart, K. D., Tsang, S., Ueda, I., Wilson, J., Zapata, H. J., HIPC-CHI Signatures Project Team, HIPC-I Consortium 2017; 2 (14)

  View details for Web of Science ID 000434326500001

• On the hunt for cancer neoantigens: is mass spectrometry the solution? Elias, J., Olsson, N., Khodadoust, M., Wagar, L., Swaminathan, K., Green, M. R., Davis, M. M., Levy, R., Alizadeh, A. A. AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC. 2017: S65

  View details for Web of Science ID 000407623600102

• Continuous immunotypes describe human immune variation and predict diverse responses PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kaczorowski, K. J., Shekhar, K., Nkulikiyimfura, D., Dekker, C. L., Maecker, H., Davis, M. M., Chakraborty, A. K., Brodin, P. 2017; 114 (30): E6097–E6106

  Abstract

  The immune system consists of many specialized cell populations that communicate with each other to achieve systemic immune responses. Our analyses of various measured immune cell population frequencies in healthy humans and their responses to diverse stimuli show that human immune variation is continuous in nature, rather than characterized by discrete groups of similar individuals. We show that the same three key combinations of immune cell population frequencies can define an individual's immunotype and predict a diverse set of functional responses to cytokine stimulation. We find that, even though interindividual variations in specific cell population frequencies can be large, unrelated individuals of younger age have more homogeneous immunotypes than older individuals. Across age groups, cytomegalovirus seropositive individuals displayed immunotypes characteristic of older individuals. The conceptual framework for defining immunotypes suggested by our results could guide the development of better therapies that appropriately modulate collective immunotypes, rather than individual immune components.

  View details for PubMedID 28696306

• Systems immunology: just getting started NATURE IMMUNOLOGY Davis, M. M., Tato, C. M., Furman, D. 2017; 18 (7): 725–32

  Abstract

  Systems-biology approaches in immunology take various forms, but here we review strategies for measuring a broad swath of immunological functions as a means of discovering previously unknown relationships and phenomena and as a powerful way of understanding the immune system as a whole. This approach has rejuvenated the field of vaccine development and has fostered hope that new ways will be found to combat infectious diseases that have proven refractory to classical approaches. Systems immunology also presents an important new strategy for understanding human immunity directly, taking advantage of the many ways the immune system of humans can be manipulated.

  View details for PubMedID 28632713

  View details for PubMedCentralID PMC5790187

• Mass cytometry identifies a distinct monocyte cytokine signature shared by clinically heterogeneous pediatric SLE patients. Journal of autoimmunity O'Gorman, W. E., Kong, D. S., Balboni, I. M., Rudra, P., Bolen, C. R., Ghosh, D., DAVIS, M. M., Nolan, G. P., Hsieh, E. W. 2017

  Abstract

  Systemic Lupus Erythematosus (SLE) is a heterogeneous autoimmune disease with heightened disease severity in children. The incomplete understanding of the precise cellular and molecular events that drive disease activity pose a significant hurdle to the development of targeted therapeutic agents. Here, we performed single-cell phenotypic and functional characterization of pediatric SLE patients and healthy controls blood via mass cytometry. We identified a distinct CD14(hi) monocyte cytokine signature, with increased levels of monocyte chemoattractant protein-1 (MCP1), macrophage inflammatory protein-1β (Mip1β), and interleukin-1 receptor antagonist (IL-1RA). This signature was shared by every clinically heterogeneous patient, and reproduced in healthy donors' blood upon ex-vivo exposure to plasma from clinically active patients only. This SLE-plasma induced signature was abrogated by JAK1/JAK2 selective inhibition. This study demonstrates the utility of mass cytometry to evaluate immune dysregulation in pediatric autoimmunity, by identification of a multi-parametric immune signature that can be further dissected to delineate the events that drive disease pathogenesis.

  View details for DOI 10.1016/j.jaut.2017.03.010

  View details for PubMedID 28389038

• Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens NATURE Khodadoust, M. S., Olsson, N., Wagar, L. E., Haabeth, O. A., Chen, B., Swaminathan, K., Rawson, K., Liu, C. L., Steiner, D., Lund, P., Rao, S., Zhang, L., Marceau, C., Stehr, H., Newman, A. M., Czerwinski, D. K., Carlton, V. E., Moorhead, M., Faham, M., Kohrt, H. E., Carette, J., Green, M. R., Davis, M. M., Levy, R., Elias, J. E., Alizadeh, A. A. 2017; 543 (7647): 723-?

  Abstract

  Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients. Remarkably, all discovered neoantigenic peptides were exclusively derived from the lymphoma immunoglobulin heavy- or light-chain variable regions. Although we identified MHC presentation of private polymorphic germline alleles, no mutated peptides were recovered from non-immunoglobulin somatically mutated genes. Somatic mutations within the immunoglobulin variable region were almost exclusively presented by MHC class II. We isolated circulating CD4(+) T cells specific for immunoglobulin-derived neoantigens and found these cells could mediate killing of autologous lymphoma cells. These results demonstrate that an integrative approach combining MHC isolation, peptide identification, and exome sequencing is an effective platform to uncover tumour neoantigens. Application of this strategy to human lymphoma implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.

  View details for DOI 10.1038/nature21433

  View details for PubMedID 28329770

• Multicenter Systems Analysis of Human Blood Reveals Immature Neutrophils in Males and During Pregnancy. Journal of immunology Blazkova, J., Gupta, S., Liu, Y., Gaudilliere, B., Ganio, E. A., Bolen, C. R., Saar-Dover, R., Fragiadakis, G. K., Angst, M. S., Hasni, S., Aghaeepour, N., Stevenson, D., Baldwin, N., Anguiano, E., Chaussabel, D., Altman, M. C., Kaplan, M. J., Davis, M. M., Furman, D. 2017; 198 (6): 2479-2488

  Abstract

  Despite clear differences in immune system responses and in the prevalence of autoimmune diseases between males and females, there is little understanding of the processes involved. In this study, we identified a gene signature of immature-like neutrophils, characterized by the overexpression of genes encoding for several granule-containing proteins, which was found at higher levels (up to 3-fold) in young (20-30 y old) but not older (60 to >89 y old) males compared with females. Functional and phenotypic characterization of peripheral blood neutrophils revealed more mature and responsive neutrophils in young females, which also exhibited an elevated capacity in neutrophil extracellular trap formation at baseline and upon microbial or sterile autoimmune stimuli. The expression levels of the immature-like neutrophil signature increased linearly with pregnancy, an immune state of increased susceptibility to certain infections. Using mass cytometry, we also find increased frequencies of immature forms of neutrophils in the blood of women during late pregnancy. Thus, our findings show novel sex differences in innate immunity and identify a common neutrophil signature in males and in pregnant women.

  View details for DOI 10.4049/jimmunol.1601855

  View details for PubMedID 28179497

• The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires. BMC bioinformatics Bolen, C. R., Rubelt, F., Vander Heiden, J. A., Davis, M. M. 2017; 18 (1): 155-?

  Abstract

  The B and T cells of the human adaptive immune system leverage a highly diverse repertoire of antigen-specific receptors to protect the human body from pathogens. The sequencing and analysis of immune repertoires is emerging as an important tool to understand immune responses, whether beneficial or harmful (in the case of autoimmunity). However, methods for studying these repertoires, and for directly comparing different immune repertoires, are lacking.In this paper, we present a non-parametric method for directly comparing sequencing repertoires, with the goal of rigorously quantifying differences in V, D, and J gene segment utilization. This method, referred to as the Repertoire Dissimilarity Index (RDI), uses a bootstrapped subsampling approach to account for variance in sequencing depth, and, coupled with a data simulation approach, allows for direct quantification of the average variation between repertoires. We use the RDI method to recapitulate known differences in the formation of the CD4(+) and CD8(+) T cell repertoires, and further show that antigen-driven activation of naïve CD8(+) T cells is more selective than in the CD4(+) repertoire, resulting in a more specialized CD8(+) memory repertoire.We prove that the RDI method is an accurate and versatile method for comparisons of immune repertoires. The RDI method has been implemented as an R package, and is available for download through Bitbucket.

  View details for DOI 10.1186/s12859-017-1556-5

  View details for PubMedID 28264647

  View details for PubMedCentralID PMC5340033

• T-Cell Receptor (TCR) Clonotype-Specific Differences in Inhibitory Activity of HIV-1 Cytotoxic T-Cell Clones Is Not Mediated by TCR Alone JOURNAL OF VIROLOGY Flerin, N. C., Chen, H., Glover, T. D., Lamothe, P. A., Zheng, J., Fang, J. W., Ndhlovu, Z. M., Newell, E. W., Davis, M. M., Walker, B. D., Goldstein, H. 2017; 91 (6)

  Abstract

  Functional analysis of T-cell responses in HIV-infected individuals has indicated that virus-specific CD8+ T cells with superior antiviral efficacy are well represented in HIV-1 controllers but are rare or absent in HIV-1 progressors. To define the role of individual T-cell receptor (TCR) clonotypes in differential antiviral CD8+ T-cell function, we performed detailed functional and mass cytometric cluster analysis of multiple CD8+ T-cell clones recognizing the identical HLA-B*2705-restricted HIV-1 epitope KK10 (KRWIILGLNK). Effective and ineffective CD8+ T-cell clones segregated based on responses to HIV-1-infected and peptide-loaded target cells. Following cognate peptide stimulation, effective HIV-specific clones displayed significantly more rapid TCR signal propagation, more efficient initial lytic granule release, and more sustained nonlytic cytokine and chemokine secretion than ineffective clones. To evaluate the TCR clonotype contribution to CD8+ T-cell function, we cloned the TCR α and β chain genes from one effective and two ineffective CD8+ T-cell clones from an elite controller into TCR-expressing lentivectors. We show that Jurkat/MA cells and primary CD8+ T cells transduced with lentivirus expressing TCR from one of the ineffective clones exhibited a level of activation by cognate peptide and inhibition of in vitro HIV-1 infection, respectively, that were comparable to those of the effective clonotype. Taken together, these data suggest that the potent antiviral capacity of some HIV-specific CD8+ T cells is a consequence of factors in addition to TCR sequence that modulate functionality and contribute to the increased antiviral capacity of HIV-specific CD8+ T cells in elite controllers to inhibit HIV infection.IMPORTANCE The greater ex vivo antiviral inhibitory activity of CD8+ T cells from elite controllers than from HIV-1 progressors supports the crucial role of effective HIV-specific CD8+ T cells in controlling HIV-1 replication. The contribution of TCR clonotype to inhibitory potency was investigated by delineating the responsiveness of effective and ineffective CD8+ T-cell clones recognizing the identical HLA-B*2705-restricted HIV-1 Gag-derived peptide, KK10 (KRWIILGLNK). KK10-stimulated "effective" CD8+ T-cell clones displayed significantly more rapid TCR signal propagation, more efficient initial lytic granule release, and more sustained cytokine and chemokine secretion than "ineffective" CD8+ T-cell clones. However, TCRs cloned from an effective and one of two ineffective clones conferred upon primary CD8+ T cells the equivalent potent capacity to inhibit HIV-1 infection. Taken together, these data suggest that other factors aside from intrinsic TCR-peptide-major histocompatibility complex (TCR-peptide-MHC) reactivity can contribute to the potent antiviral capacity of some HIV-specific CD8+ T-cell clones.

  View details for PubMedID 28077649

  View details for PubMedCentralID PMC5331796

• Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states NATURE MEDICINE Furman, D., Chang, J., Lartigue, L., Bolen, C. R., Haddad, F., Gaudilliere, B., Ganio, E. A., Fragiadakis, G. K., Spitzer, M. H., Douchet, I., Daburon, S., Moreau, J., Nolan, G. P., Blanco, P., Dechanet-Merville, J., Dekker, C. L., Jojic, V., Kuo, C. J., Davis, M. M., Faustin, B. 2017; 23 (2): 174-184

  Abstract

  Low-grade, chronic inflammation has been associated with many diseases of aging, but the mechanisms responsible for producing this inflammation remain unclear. Inflammasomes can drive chronic inflammation in the context of an infectious disease or cellular stress, and they trigger the maturation of interleukin-1β (IL-1β). Here we find that the expression of specific inflammasome gene modules stratifies older individuals into two extremes: those with constitutive expression of IL-1β, nucleotide metabolism dysfunction, elevated oxidative stress, high rates of hypertension and arterial stiffness; and those without constitutive expression of IL-1β, who lack these characteristics. Adenine and N(4)-acetylcytidine, nucleotide-derived metabolites that are detectable in the blood of the former group, prime and activate the NLRC4 inflammasome, induce the production of IL-1β, activate platelets and neutrophils and elevate blood pressure in mice. In individuals over 85 years of age, the elevated expression of inflammasome gene modules was associated with all-cause mortality. Thus, targeting inflammasome components may ameliorate chronic inflammation and various other age-associated conditions.

  View details for DOI 10.1038/nm.4267

  View details for Web of Science ID 000393729000009

  View details for PubMedID 28092664

• Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA de Bourcy, C. F., Angel, C. J., Vollmers, C., Dekker, C. L., Davis, M. M., Quake, S. R. 2017; 114 (5): 1105-1110

  Abstract

  The elderly have reduced humoral immunity, as manifested by increased susceptibility to infections and impaired vaccine responses. To investigate the effects of aging on B-cell receptor (BCR) repertoire evolution during an immunological challenge, we used a phylogenetic distance metric to analyze Ig heavy-chain transcript sequences in both young and elderly individuals before and after influenza vaccination. We determined that BCR repertoires become increasingly specialized over a span of decades, but less plastic. In 50% of the elderly individuals, a large space in the repertoire was occupied by a small number of recall lineages that did not decline during vaccine response and contained hypermutated IgD(+) B cells. Relative to their younger counterparts, older subjects demonstrated a contracted naive repertoire and diminished intralineage diversification, signifying a reduced substrate for mounting novel responses and decreased fine-tuning of BCR specificities by somatic hypermutation. Furthermore, a larger proportion of the repertoire exhibited premature stop codons in some elderly subjects, indicating that aging may negatively affect the ability of B cells to discriminate between functional and nonfunctional receptors. Finally, we observed a decreased incidence of radical mutations compared with conservative mutations in elderly subjects' vaccine responses, which suggests that accumulating original antigenic sin may be limiting the accessible space for paratope evolution. Our findings shed light on the complex interplay of environmental and gerontological factors affecting immune senescence, and provide direct molecular characterization of the effects of senescence on the immune repertoire.

  View details for DOI 10.1073/pnas.1617959114

  View details for Web of Science ID 000393196300087

  View details for PubMedID 28096374

  View details for PubMedCentralID PMC5293037

• High-Dimensional Phenotypic Mapping of Human Dendritic Cells Reveals Interindividual Variation and Tissue Specialization. Immunity Alcántara-Hernández, M. n., Leylek, R. n., Wagar, L. E., Engleman, E. G., Keler, T. n., Marinkovich, M. P., Davis, M. M., Nolan, G. P., Idoyaga, J. n. 2017

  Abstract

  Given the limited efficacy of clinical approaches that rely on ex vivo generated dendritic cells (DCs), it is imperative to design strategies that harness specialized DC subsets in situ. This requires delineating the expression of surface markers by DC subsets among individuals and tissues. Here, we performed a multiparametric phenotypic characterization and unbiased analysis of human DC subsets in blood, tonsil, spleen, and skin. We uncovered previously unreported phenotypic heterogeneity of human cDC2s among individuals, including variable expression of functional receptors such as CD172a. We found marked differences in DC subsets localized in blood and lymphoid tissues versus skin, and a striking absence of the newly discovered Axl+ DCs in the skin. Finally, we evaluated the capacity of anti-receptor monoclonal antibodies to deliver vaccine components to skin DC subsets. These results offer a promising path for developing DC subset-specific immunotherapies that cannot be provided by transcriptomic analysis alone.

  View details for PubMedID 29221729

• Identifying specificity groups in the T cell receptor repertoire. Nature Glanville, J. n., Huang, H. n., Nau, A. n., Hatton, O. n., Wagar, L. E., Rubelt, F. n., Ji, X. n., Han, A. n., Krams, S. M., Pettus, C. n., Haas, N. n., Arlehamn, C. S., Sette, A. n., Boyd, S. D., Scriba, T. J., Martinez, O. M., Davis, M. M. 2017

  Abstract

  T cell receptor (TCR) sequences are very diverse, with many more possible sequence combinations than T cells in any one individual. Here we define the minimal requirements for TCR antigen specificity, through an analysis of TCR sequences using a panel of peptide and major histocompatibility complex (pMHC)-tetramer-sorted cells and structural data. From this analysis we developed an algorithm that we term GLIPH (grouping of lymphocyte interactions by paratope hotspots) to cluster TCRs with a high probability of sharing specificity owing to both conserved motifs and global similarity of complementarity-determining region 3 (CDR3) sequences. We show that GLIPH can reliably group TCRs of common specificity from different donors, and that conserved CDR3 motifs help to define the TCR clusters that are often contact points with the antigenic peptides. As an independent validation, we analysed 5,711 TCRβ chain sequences from reactive CD4 T cells from 22 individuals with latent Mycobacterium tuberculosis infection. We found 141 TCR specificity groups, including 16 distinct groups containing TCRs from multiple individuals. These TCR groups typically shared HLA alleles, allowing prediction of the likely HLA restriction, and a large number of M. tuberculosis T cell epitopes enabled us to identify pMHC ligands for all five of the groups tested. Mutagenesis and de novo TCR design confirmed that the GLIPH-identified motifs were critical and sufficient for shared-antigen recognition. Thus the GLIPH algorithm can analyse large numbers of TCR sequences and define TCR specificity groups shared by TCRs and individuals, which should greatly accelerate the analysis of T cell responses and expedite the identification of specific ligands.

  View details for PubMedID 28636589

• Cytokine signature associated with disease severity in chronic fatigue syndrome patients. Proceedings of the National Academy of Sciences of the United States of America Montoya, J. G., Holmes, T. H., Anderson, J. N., Maecker, H. T., Rosenberg-Hasson, Y. n., Valencia, I. J., Chu, L. n., Younger, J. W., Tato, C. M., Davis, M. M. 2017; 114 (34): E7150–E7158

  Abstract

  Although some signs of inflammation have been reported previously in patients with myalgic encephalomyelitis or chronic fatigue syndrome (ME/CFS), the data are limited and contradictory. High-throughput methods now allow us to interrogate the human immune system for multiple markers of inflammation at a scale that was not previously possible. To determine whether a signature of serum cytokines could be associated with ME/CFS and correlated with disease severity and fatigue duration, cytokines of 192 ME/CFS patients and 392 healthy controls were measured using a 51-multiplex array on a Luminex system. Each cytokine's preprocessed data were regressed on ME/CFS severity plus covariates for age, sex, race, and an assay property of newly discovered importance: nonspecific binding. On average, TGF-β was elevated (P = 0.0052) and resistin was lower (P = 0.0052) in patients compared with controls. Seventeen cytokines had a statistically significant upward linear trend that correlated with ME/CFS severity: CCL11 (Eotaxin-1), CXCL1 (GROα), CXCL10 (IP-10), IFN-γ, IL-4, IL-5, IL-7, IL-12p70, IL-13, IL-17F, leptin, G-CSF, GM-CSF, LIF, NGF, SCF, and TGF-α. Of the 17 cytokines that correlated with severity, 13 are proinflammatory, likely contributing to many of the symptoms experienced by patients and establishing a strong immune system component of the disease. Only CXCL9 (MIG) inversely correlated with fatigue duration.

  View details for PubMedID 28760971

• Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis Dynamics of the human antibody repertoire after B cell depletion in systemic sclerosis de Bourcy, C. F., Dekker, C. L., Davis, M. M., Nicolls, M. R., Quake, S. R. 2017; 2 (15)

  View details for DOI 10.1126/sciimmunol.aan8289

• Human immune system variation. Nature reviews. Immunology Brodin, P. n., Davis, M. M. 2017; 17 (1): 21–29

  Abstract

  The human immune system is highly variable between individuals but relatively stable over time within a given person. Recent conceptual and technological advances have enabled systems immunology analyses, which reveal the composition of immune cells and proteins in populations of healthy individuals. The range of variation and some specific influences that shape an individual's immune system is now becoming clearer. Human immune systems vary as a consequence of heritable and non-heritable influences, but symbiotic and pathogenic microbes and other non-heritable influences explain most of this variation. Understanding when and how such influences shape the human immune system is key for defining metrics of immunological health and understanding the risk of immune-mediated and infectious diseases.

  View details for PubMedID 27916977

  View details for PubMedCentralID PMC5328245

• Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data. Nature immunology Rubelt, F. n., Busse, C. E., Bukhari, S. A., Bürckert, J. P., Mariotti-Ferrandiz, E. n., Cowell, L. G., Watson, C. T., Marthandan, N. n., Faison, W. J., Hershberg, U. n., Laserson, U. n., Corrie, B. D., Davis, M. M., Peters, B. n., Lefranc, M. P., Scott, J. K., Breden, F. n., Luning Prak, E. T., Kleinstein, S. H. 2017; 18 (12): 1274–78

  View details for PubMedID 29144493

• Antigen Presentation Profiling Reveals T-Cell Recognition of Lymphoma Immunoglobulin Neoantigens Khodadoust, M., Olsson, N., Wagar, L., Chen, B., Rawson, K., Liu, C., Steiner, D., Rao, S., Zhang, L., Stehr, H., Newman, A. M., Czerwinski, D. K., Carlton, V., Moorhead, M., Faham, M., Kohrt, H., Green, M. R., Davis, M. M., Levy, R., Elias, J., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2016

  View details for Web of Science ID 000394446803106

• Increased Proinflammatory Responses of Monocytes and Plasmacytoid Dendritic Cells to Influenza A Virus Infection During Pregnancy JOURNAL OF INFECTIOUS DISEASES Le Gars, M., Kay, A. W., Bayless, N. L., Aziz, N., Dekker, C. L., Swan, G. E., Davis, M. M., Blish, C. A. 2016; 214 (11): 1666-1671

  Abstract

  Pregnancy-induced alterations in immunity may contribute to the increased morbidity associated with influenza A virus infection during pregnancy. We characterized the immune response of monocytes and plasmacytoid dendritic cells (pDCs) to influenza A virus infection in 21 pregnant and 21 nonpregnant women. In pregnant women, monocytes and pDCs exhibit an exaggerated proinflammatory immune response to 2 strains of influenza A virus, compared with nonpregnant women, characterized by increased expression of major histocompatibility complex class II (approximately 2.0-fold), CD69 (approximately 2.2-fold), interferon γ-induced protein 10 (approximately 2.0-fold), and macrophage inflammatory protein 1β (approximately 1.5-fold). This enhanced innate inflammatory response during pregnancy could contribute to pulmonary inflammation following influenza A virus infection.

  View details for DOI 10.1093/infdis/jiw448

  View details for Web of Science ID 000393128800008

  View details for PubMedID 27655870

  View details for PubMedCentralID PMC5144734

• Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination. Nature medicine Lee, J., Boutz, D. R., Chromikova, V., Joyce, M. G., Vollmers, C., Leung, K., Horton, A. P., DeKosky, B. J., Lee, C., Lavinder, J. J., Murrin, E. M., Chrysostomou, C., Hoi, K. H., Tsybovsky, Y., Thomas, P. V., Druz, A., Zhang, B., Zhang, Y., Wang, L., Kong, W., Park, D., Popova, L. I., Dekker, C. L., Davis, M. M., Carter, C. E., Ross, T. M., Ellington, A. D., Wilson, P. C., Marcotte, E. M., Mascola, J. R., Ippolito, G. C., Krammer, F., Quake, S. R., Kwong, P. D., Georgiou, G. 2016

  Abstract

  Molecular understanding of serological immunity to influenza has been confounded by the complexity of the polyclonal antibody response in humans. Here we used high-resolution proteomics analysis of immunoglobulin (referred to as Ig-seq) coupled with high-throughput sequencing of transcripts encoding B cell receptors (BCR-seq) to quantitatively determine the antibody repertoire at the individual clonotype level in the sera of young adults before and after vaccination with trivalent seasonal influenza vaccine. The serum repertoire comprised between 40 and 147 clonotypes that were specific to each of the three monovalent components of the trivalent influenza vaccine, with boosted pre-existing clonotypes accounting for ∼60% of the response. An unexpectedly high fraction of serum antibodies recognized both the H1 and H3 monovalent vaccines. Recombinant versions of these H1 + H3 cross-reactive antibodies showed broad binding to hemagglutinins (HAs) from previously circulating virus strains; several of these antibodies, which were prevalent in the serum of multiple donors, recognized the same conserved epitope in the HA head domain. Although the HA-head-specific H1 + H3 antibodies did not show neutralization activity in vitro, they protected mice against infection with the H1N1 and H3N2 virus strains when administered before or after challenge. Collectively, our data reveal unanticipated insights regarding the serological response to influenza vaccination and raise questions about the added benefits of using a quadrivalent vaccine instead of a trivalent vaccine.

  View details for DOI 10.1038/nm.4224

  View details for PubMedID 27820605

• MASS CYTOMETRY, A SINGLE CELL PROTEOMIC PLATFORM FOR COMPREHENSIVE IMMUNE ANALYSIS McGuire, H., Choi, C., Smith, A., Fazekas de St Groth, B., Davis, M. WILEY. 2016: A19

  View details for Web of Science ID 000392825000083

• Defective Signaling in the JAK-STAT Pathway Tracks with Chronic Inflammation and Cardiovascular Risk in Aging Humans. Cell systems Shen-Orr, S. S., Furman, D., Kidd, B. A., Hadad, F., Lovelace, P., Huang, Y., Rosenberg-Hasson, Y., Mackey, S., Grisar, F. A., Pickman, Y., Maecker, H. T., Chien, Y., Dekker, C. L., Wu, J. C., Butte, A. J., Davis, M. M. 2016; 3 (4): 374-384 e4

  Abstract

  Chronic inflammation, a decline in immune responsiveness, and reduced cardiovascular function are all associated with aging, but the relationships among these phenomena remain unclear. Here, we longitudinally profiled a total of 84 signaling conditions in 91 young and older adults and observed an age-related reduction in cytokine responsiveness within four immune cell lineages, most prominently T cells. The phenotype can be partially explained by elevated baseline levels of phosphorylated STAT (pSTAT) proteins and a different response capacity of naive versus memory T cell subsets to interleukin 6 (IL-6), interferon α (IFN-α), and, to a lesser extent, IL-21 and IFN-γ. Baseline pSTAT levels tracked with circulating levels of C-reactive protein (CRP), and we derived a cytokine response score that negatively correlates with measures of cardiovascular disease, specifically diastolic dysfunction and atherosclerotic burden, outperforming CRP. Thus, we identified an immunological link between inflammation, decreased cell responsiveness in the JAK-STAT pathway, and cardiovascular aging. Targeting chronic inflammation may ameliorate this deficiency in cellular responsiveness and improve cardiovascular function.

  View details for DOI 10.1016/j.cels.2016.09.009

  View details for PubMedID 27746093

• Global Analysis of O-GlcNAc Glycoproteins in Activated Human T Cells. Journal of immunology Lund, P. J., Elias, J. E., Davis, M. M. 2016; 197 (8): 3086-3098

  Abstract

  T cell activation in response to Ag is largely regulated by protein posttranslational modifications. Although phosphorylation has been extensively characterized in T cells, much less is known about the glycosylation of serine/threonine residues by O-linked N-acetylglucosamine (O-GlcNAc). Given that O-GlcNAc appears to regulate cell signaling pathways and protein activity similarly to phosphorylation, we performed a comprehensive analysis of O-GlcNAc during T cell activation to address the functional importance of this modification and to identify the modified proteins. Activation of T cells through the TCR resulted in a global elevation of O-GlcNAc levels and in the absence of O-GlcNAc, IL-2 production and proliferation were compromised. T cell activation also led to changes in the relative expression of O-GlcNAc transferase (OGT) isoforms and accumulation of OGT at the immunological synapse of murine T cells. Using a glycoproteomics approach, we identified >200 O-GlcNAc proteins in human T cells. Many of the identified proteins had a functional relationship to RNA metabolism, and consistent with a connection between O-GlcNAc and RNA, inhibition of OGT impaired nascent RNA synthesis upon T cell activation. Overall, our studies provide a global analysis of O-GlcNAc dynamics during T cell activation and the first characterization, to our knowledge, of the O-GlcNAc glycoproteome in human T cells.

  View details for PubMedID 27655845

• Antigen exposure shapes the ratio between antigen-specific Tregs and conventional T cells in human peripheral blood PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Su, L. F., del Alcazar, D., Stelekati, E., Wherry, E. J., Davis, M. M. 2016; 113 (41): E6192-E6198

  Abstract

  The T-cell receptor (TCR) is required for maturation and function of regulatory T cells (Tregs), but the ligand specificities of Tregs outside the context of transgenic TCRs are largely unknown. Using peptide-MHC tetramers, we isolated rare specific Foxp3(+) cells directly ex vivo from adult peripheral blood and defined their frequency and phenotype. We find that a proportion of circulating Tregs recognize foreign antigens and the frequency of these cells are similar to that of self-reactive Tregs in the absence of cognate infection. In contrast, the frequencies of Tregs that recognize some common microbial antigens are significantly reduced in the blood of most adults. Exposure to peripheral antigens likely has a major influence on the balance between Tregs and conventional T-cell subsets because a larger proportion of flu-specific T cells has a regulatory cell phenotype in the cord blood. Consistent with this finding, we show that lymphocytic choriomeningitis virus infection can directly modulate the ratio of virus-specific effectors and Tregs in mice. The resulting change in the balance within an antigen-specific T-cell population further correlates with the magnitude of effector response and the chronicity of infection. Taken together, our data highlight the importance of antigen specificity in the functional dynamics of the T-cell repertoire. Each specific population of CD4(+) T cells in human peripheral blood contains a subset of Tregs at birth, but the balance between regulatory and effector subsets changes in response to peripheral antigen exposure and this could impact the robustness of antipathogen immunity.

  View details for DOI 10.1073/pnas.1611723113

  View details for Web of Science ID 000384886900024

  View details for PubMedID 27681619

  View details for PubMedCentralID PMC5068288

• Defective T Memory Cell Differentiation after Varicella Zoster Vaccination in Older Individuals. PLoS pathogens Qi, Q., Cavanagh, M. M., Le Saux, S., Wagar, L. E., Mackey, S., Hu, J., Maecker, H., Swan, G. E., Davis, M. M., Dekker, C. L., Tian, L., Weyand, C. M., Goronzy, J. J. 2016; 12 (10)

  Abstract

  Vaccination with attenuated live varicella zoster virus (VZV) can prevent zoster reactivation, but protection is incomplete especially in an older population. To decipher the molecular mechanisms underlying variable vaccine responses, T- and B-cell responses to VZV vaccination were examined in individuals of different ages including identical twin pairs. Contrary to the induction of VZV-specific antibodies, antigen-specific T cell responses were significantly influenced by inherited factors. Diminished generation of long-lived memory T cells in older individuals was mainly caused by increased T cell loss after the peak response while the expansion of antigen-specific T cells was not affected by age. Gene expression in activated CD4 T cells at the time of the peak response identified gene modules related to cell cycle regulation and DNA repair that correlated with the contraction phase of the T cell response and consequently the generation of long-lived memory cells. These data identify cell cycle regulatory mechanisms as targets to reduce T cell attrition in a vaccine response and to improve the generation of antigen-specific T cell memory, in particular in an older population.

  View details for DOI 10.1371/journal.ppat.1005892

  View details for PubMedID 27764254

  View details for PubMedCentralID PMC5072604

• Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching ELIFE Horns, F., Vollmers, C., Croote, D., Mackey, S. F., Swan, G. E., Dekker, C. L., Davis, M. M., Quake, S. R. 2016; 5

  View details for DOI 10.7554/eLife.16578

  View details for Web of Science ID 000380927400001

• Immuno-proteomic interrogation of antigen presentation during dengue infection reveals novel and HLA haplotype-specific MHC-I antigens Swaminathan, K., Lund, P., Olsson, N., Marceau, C., Carette, J., Davis, M., Elias, J. WILEY-BLACKWELL. 2016: 889

  View details for Web of Science ID 000383610402178

• Distinctive differences in lymphocyte receptor repertoire and in cell frequencies results in an individual immune system Rubelt, F., Bolen, C. R., Vander Heiden, J., McGuire, M. H., Gadala-Maria, D., Euskirchen, G., Mamedov, M., Swan, G. E., Dekker, C. L., Levin, M., Cowell, L. G., Pulendran, B., Kleinstein, S. H., Davis, M. M. WILEY-BLACKWELL. 2016: 54-55

  View details for Web of Science ID 000383610400108

• How environment alters immunity: comparing immune systems of children from low- and high-income countries Wagar, L. E., Bolen, C. R., Sigal, N., Haque, R., Parsonnet, J., Petri, W. A., Davis, M. M. WILEY-BLACKWELL. 2016: 80-81

  View details for Web of Science ID 000383610400162

• Inhibition of T cell receptor signaling by cholesterol sulfate, a naturally occurring derivative of membrane cholesterol NATURE IMMUNOLOGY Wang, F., Beck-Garcia, K., Zorzin, C., Schamel, W. W., Davis, M. M. 2016; 17 (7): 844-?

  Abstract

  Most adaptive immune responses require the activation of specific T cells through the T cell antigen receptor (TCR)-CD3 complex. Here we show that cholesterol sulfate (CS), a naturally occurring analog of cholesterol, inhibits CD3 ITAM phosphorylation, a crucial first step in T cell activation. In biochemical studies, CS disrupted TCR multimers, apparently by displacing cholesterol, which is known to bind TCRβ. Moreover, CS-deficient mice showed heightened sensitivity to a self-antigen, whereas increasing CS content by intrathymic injection inhibited thymic selection, indicating that this molecule is an intrinsic regulator of thymocyte development. These results reveal a regulatory role for CS in TCR signaling and thymic selection, highlighting the importance of the membrane microenvironment in modulating cell surface receptor activation.

  View details for DOI 10.1038/ni.3462

  View details for Web of Science ID 000378283200017

  View details for PubMedID 27213689

  View details for PubMedCentralID PMC4916016

• Profiling system-wide immune signaling in chronic viral infection and its response to viral clearance Angel, C., Furman, D., Pham, E., Fram, B., Thai Nguyen, Ahmed, A., Grant, P., Maecker, H. T., Glenn, J., Davis, M. M. AMER ASSOC IMMUNOLOGISTS. 2016

  View details for Web of Science ID 000380288303330

• Immuno-proteomic interrogation of antigen presentation during Dengue infection reveals novel and HLA haplotype-specific MHC-I antigens Swaminathan, K., Lund, P. J., Olsson, N., Marceau, C., Carette, J., Davis, M. M., Elias, J. E. AMER ASSOC IMMUNOLOGISTS. 2016

  View details for Web of Science ID 000380288300110

• HIGH RESOLUTION NGS HLA TYPING OF 403 DONORS FROM CAPE TOWN, SOUTH AFRICA Thorstenson, Y., Huang, H., Davis, M. M., Scriba, T. J., Rozot, V., Wang, C., Li, M., Kancharla, S., Fukushima, M., Kuehn, R., Krishnakumar, S., Mindrinos, M. WILEY-BLACKWELL. 2016: 282-283

  View details for Web of Science ID 000383951500201

• Detection, phenotyping, and quantification of antigen-specific T cells using a peptide-MHC dodecamer PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Huang, J., Zeng, X., Sigal, N., Lund, P. J., Su, L. F., Huang, H., Chien, Y., Davis, M. M. 2016; 113 (13): E1890-E1897

  Abstract

  Here we report a peptide-MHC (pMHC) dodecamer as a "next generation" technology that is a significantly more sensitive and versatile alternative to pMHC tetramers for the detection, isolation, and phenotypic analysis of antigen-specific T cells. In particular, dodecamers are able to detect two- to fivefold more antigen-specific T cells in both human and murine CD4(+)and CD8(+)αβ T-cell compartments compared with the equivalent tetramers. The low-affinity, tetramer-negative, dodecamer-positive T cells showed comparable effector cytokine responses as those of high-affinity, tetramer-positive T cells. Dodecamers are able to detect early stage CD4(+)CD8(+)double-positive thymocytes on which T-cell receptors are 10- to 30-fold less dense than mature T cells. Dodecamers also show utility in the analysis of γδ T cells and in cytometry by time-of-flight applications. This construct has a simple structure with a central scaffold protein linked to four streptavidin molecules, each having three pMHC ligands or other molecules. The dodecamer is straightforward and inexpensive to produce and is compatible with current tetramer technology and commercially available streptavidin conjugates.

  View details for DOI 10.1073/pnas.1602488113

  View details for Web of Science ID 000372876400017

  View details for PubMedCentralID PMC4822615

• Detection, phenotyping, and quantification of antigen-specific T cells using a peptide-MHC dodecamer. Proceedings of the National Academy of Sciences of the United States of America Huang, J., Zeng, X., Sigal, N., Lund, P. J., Su, L. F., Huang, H., Chien, Y., Davis, M. M. 2016; 113 (13): E1890-7

  Abstract

  Here we report a peptide-MHC (pMHC) dodecamer as a "next generation" technology that is a significantly more sensitive and versatile alternative to pMHC tetramers for the detection, isolation, and phenotypic analysis of antigen-specific T cells. In particular, dodecamers are able to detect two- to fivefold more antigen-specific T cells in both human and murine CD4(+)and CD8(+)αβ T-cell compartments compared with the equivalent tetramers. The low-affinity, tetramer-negative, dodecamer-positive T cells showed comparable effector cytokine responses as those of high-affinity, tetramer-positive T cells. Dodecamers are able to detect early stage CD4(+)CD8(+)double-positive thymocytes on which T-cell receptors are 10- to 30-fold less dense than mature T cells. Dodecamers also show utility in the analysis of γδ T cells and in cytometry by time-of-flight applications. This construct has a simple structure with a central scaffold protein linked to four streptavidin molecules, each having three pMHC ligands or other molecules. The dodecamer is straightforward and inexpensive to produce and is compatible with current tetramer technology and commercially available streptavidin conjugates.

  View details for DOI 10.1073/pnas.1602488113

  View details for PubMedID 26979955

  View details for PubMedCentralID PMC4822615

• CXCL13 is a plasma biomarker of germinal center activity PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Havenar-Daughton, C., Lindqvist, M., Heit, A., Wu, J. E., Reiss, S. M., Kendric, K., Belanger, S., Kasturi, S. P., Landais, E., Akondy, R. S., McGuire, H. M., Bothwell, M., Vagefi, P. A., Scully, E., Tomaras, G. D., Davis, M. M., Poignard, P., Ahmed, R., Walker, B. D., Pulendran, B., McElrath, M. J., Kaufmann, D. E., Crotty, S. 2016; 113 (10): 2702-2707

  Abstract

  Significantly higher levels of plasma CXCL13 [chemokine (C-X-C motif) ligand 13] were associated with the generation of broadly neutralizing antibodies (bnAbs) against HIV in a large longitudinal cohort of HIV-infected individuals. Germinal centers (GCs) perform the remarkable task of optimizing B-cell Ab responses. GCs are required for almost all B-cell receptor affinity maturation and will be a critical parameter to monitor if HIV bnAbs are to be induced by vaccination. However, lymphoid tissue is rarely available from immunized humans, making the monitoring of GC activity by direct assessment of GC B cells and germinal center CD4(+) T follicular helper (GC Tfh) cells problematic. The CXCL13-CXCR5 [chemokine (C-X-C motif) receptor 5] chemokine axis plays a central role in organizing both B-cell follicles and GCs. Because GC Tfh cells can produce CXCL13, we explored the potential use of CXCL13 as a blood biomarker to indicate GC activity. In a series of studies, we found that plasma CXCL13 levels correlated with GC activity in draining lymph nodes of immunized mice, immunized macaques, and HIV-infected humans. Furthermore, plasma CXCL13 levels in immunized humans correlated with the magnitude of Ab responses and the frequency of ICOS(+) (inducible T-cell costimulator) Tfh-like cells in blood. Together, these findings support the potential use of CXCL13 as a plasma biomarker of GC activity in human vaccine trials and other clinical settings.

  View details for DOI 10.1073/pnas.1520112113

  View details for PubMedID 26908875

• Individual heritable differences result in unique cell lymphocyte receptor repertoires of naive and antigen-experienced cells NATURE COMMUNICATIONS Rubelt, F., Bolen, C. R., McGuire, H. M., Vander Heiden, J. A., Gadala-Maria, D., Levin, M., Euskirchen, G. M., Mamedov, M. R., Swan, G. E., Dekker, C. L., Cowell, L. G., Kleinstein, S. H., Davis, M. M. 2016; 7

  Abstract

  The adaptive immune system's capability to protect the body requires a highly diverse lymphocyte antigen receptor repertoire. However, the influence of individual genetic and epigenetic differences on these repertoires is not typically measured. By leveraging the unique characteristics of B, CD4(+) T and CD8(+) T-lymphocyte subsets from monozygotic twins, we quantify the impact of heritable factors on both the V(D)J recombination process and on thymic selection. We show that the resulting biases in both V(D)J usage and N/P addition lengths, which are found in naïve and antigen experienced cells, contribute to significant variation in the CDR3 region. Moreover, we show that the relative usage of V and J gene segments is chromosomally biased, with ∼1.5 times as many rearrangements originating from a single chromosome. These data refine our understanding of the heritable mechanisms affecting the repertoire, and show that biases are evident on a chromosome-wide level.

  View details for DOI 10.1038/ncomms11112

  View details for Web of Science ID 000372735600001

  View details for PubMedCentralID PMC5191574

• Successful immunotherapy induces previously unidentified allergen-specific CD4+ T-cell subsets. Proceedings of the National Academy of Sciences of the United States of America Ryan, J. F., Hovde, R., Glanville, J., Lyu, S., Ji, X., Gupta, S., Tibshirani, R. J., Jay, D. C., Boyd, S. D., Chinthrajah, R. S., Davis, M. M., Galli, S. J., Maecker, H. T., Nadeau, K. C. 2016; 113 (9): E1286-95

  Abstract

  Allergen immunotherapy can desensitize even subjects with potentially lethal allergies, but the changes induced in T cells that underpin successful immunotherapy remain poorly understood. In a cohort of peanut-allergic participants, we used allergen-specific T-cell sorting and single-cell gene expression to trace the transcriptional "roadmap" of individual CD4+ T cells throughout immunotherapy. We found that successful immunotherapy induces allergen-specific CD4+ T cells to expand and shift toward an "anergic" Th2 T-cell phenotype largely absent in both pretreatment participants and healthy controls. These findings show that sustained success, even after immunotherapy is withdrawn, is associated with the induction, expansion, and maintenance of immunotherapy-specific memory and naive T-cell phenotypes as early as 3 mo into immunotherapy. These results suggest an approach for immune monitoring participants undergoing immunotherapy to predict the success of future treatment and could have implications for immunotherapy targets in other diseases like cancer, autoimmune disease, and transplantation.

  View details for DOI 10.1073/pnas.1520180113

  View details for PubMedID 26811452

• Human B-cell isotype switching origins of IgE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY Looney, T. J., Lee, J., Roskin, K. M., Hoh, R. A., King, J., Glanville, J., Liu, Y., Pham, T. D., Dekker, C. L., Davis, M. M., Boyd, S. D. 2016; 137 (2): 579-?

  Abstract

  B cells expressing IgE contribute to immunity against parasites and venoms and are the source of antigen specificity in allergic patients, yet the developmental pathways producing these B cells in human subjects remain a subject of debate. Much of our knowledge of IgE lineage development derives from model studies in mice rather than from human subjects.We evaluate models for isotype switching to IgE in human subjects using immunoglobulin heavy chain (IGH) mutational lineage data.We analyzed IGH repertoires in 9 allergic and 24 healthy adults using high-throughput DNA sequencing of 15,843,270 IGH rearrangements to identify clonal lineages of B cells containing members expressing IgE. Somatic mutations in IGH inherited from common ancestors within the clonal lineage are used to infer the relationships between B cells.Data from 613,641 multi-isotype B-cell clonal lineages, of which 592 include an IgE member, are consistent with indirect switching to IgE from IgG- or IgA-expressing lineage members in human subjects. We also find that these inferred isotype switching frequencies are similar in healthy and allergic subjects.We found evidence that secondary isotype switching of mutated IgG1-expressing B cells is the primary source of IgE in human subjects, with lesser contributions from precursors expressing other switched isotypes and rarely IgM or IgD, suggesting that IgE is derived from previously antigen-experienced B cells rather than naive B cells that typically express low-affinity unmutated antibodies. These data provide a basis from which to evaluate allergen-specific human antibody repertoires in healthy and diseased subjects.

  View details for DOI 10.1016/j.jaci.2015.07.014

  View details for Web of Science ID 000369235500028

• High-dimensional immune profiling of total and rotavirus VP6-specific intestinal and circulating B cells by mass cytometry MUCOSAL IMMUNOLOGY Nair, N., Newell, E. W., Vollmers, C., Quake, S. R., Morton, J. M., DAVIS, M. M., He, X. S., Greenberg, H. B. 2016; 9 (1): 68-82

  Abstract

  In-depth phenotyping of human intestinal antibody secreting cells (ASCs) and their precursors is important for developing improved mucosal vaccines. We used single-cell mass cytometry to simultaneously analyze 34 differentiation and trafficking markers on intestinal and circulating B cells. In addition, we labeled rotavirus (RV) double-layered particles with a metal isotope and characterized B cells specific to the RV VP6 major structural protein. We describe the heterogeneity of the intestinal B-cell compartment, dominated by ASCs with some phenotypic and transcriptional characteristics of long-lived plasma cells. Using principal component analysis, we visualized the phenotypic relationships between major B-cell subsets in the intestine and blood, and revealed that IgM(+) memory B cells (MBCs) and naive B cells were phenotypically related as were CD27(-) MBCs and switched MBCs. ASCs in the intestine and blood were highly clonally related, but associated with distinct trajectories of phenotypic development. VP6-specific B cells were present among diverse B-cell subsets in immune donors, including naive B cells, with phenotypes representative of the overall B-cell pool. These data provide a high dimensional view of intestinal B cells and the determinants regulating humoral memory to a ubiquitous, mucosal pathogen at steady-state.Mucosal Immunology advance online publication, 22 April 2015; doi:10.1038/mi.2015.36.

  View details for DOI 10.1038/mi.2015.36

  View details for Web of Science ID 000367653800006

• HLA HAPLOTYPE DIVERSITY IN CAPE TOWN, SOUTH AFRICA Thorstenson, Y., Creary, L., Huang, H., Rozot, V., Wang, C., Li, M., Kancharla, S., Fukushima, M., Kuehn, R., Krishnakumar, S., Mindrinos, M., Scriba, T. J., Davis, M. M. ELSEVIER SCIENCE INC. 2016: 110

  View details for DOI 10.1016/j.humimm.2016.07.163

  View details for Web of Science ID 000383313500152

• Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells. Nature communications Rubelt, F., Bolen, C. R., McGuire, H. M., Heiden, J. A., Gadala-Maria, D., Levin, M., M Euskirchen, G., Mamedov, M. R., Swan, G. E., Dekker, C. L., Cowell, L. G., Kleinstein, S. H., Davis, M. M. 2016; 7: 11112-?

  Abstract

  The adaptive immune system's capability to protect the body requires a highly diverse lymphocyte antigen receptor repertoire. However, the influence of individual genetic and epigenetic differences on these repertoires is not typically measured. By leveraging the unique characteristics of B, CD4(+) T and CD8(+) T-lymphocyte subsets from monozygotic twins, we quantify the impact of heritable factors on both the V(D)J recombination process and on thymic selection. We show that the resulting biases in both V(D)J usage and N/P addition lengths, which are found in naïve and antigen experienced cells, contribute to significant variation in the CDR3 region. Moreover, we show that the relative usage of V and J gene segments is chromosomally biased, with ∼1.5 times as many rearrangements originating from a single chromosome. These data refine our understanding of the heritable mechanisms affecting the repertoire, and show that biases are evident on a chromosome-wide level.

  View details for DOI 10.1038/ncomms11112

  View details for PubMedID 27005435

• CD161(int)CD8+ T cells: a novel population of highly functional, memory CD8+ T cells enriched within the gut. Mucosal immunology Fergusson, J. R., Hühn, M. H., Swadling, L. n., Walker, L. J., Kurioka, A. n., Llibre, A. n., Bertoletti, A. n., Holländer, G. n., Newell, E. W., Davis, M. M., Sverremark-Ekström, E. n., Powrie, F. n., Capone, S. n., Folgori, A. n., Barnes, E. n., Willberg, C. B., Ussher, J. E., Klenerman, P. n. 2016; 9 (2): 401–13

  Abstract

  The C-type lectin-like receptor CD161 is expressed by lymphocytes found in human gut and liver, as well as blood, especially natural killer (NK) cells, T helper 17 (Th17) cells, and a population of unconventional T cells known as mucosal-associated invariant T (MAIT) cells. The association of high CD161 expression with innate T-cell populations including MAIT cells is established. Here we show that CD161 is also expressed, at intermediate levels, on a prominent subset of polyclonal CD8+ T cells, including antiviral populations that display a memory phenotype. These memory CD161(int)CD8+ T cells are enriched within the colon and express both CD103 and CD69, markers associated with tissue residence. Furthermore, this population was characterized by enhanced polyfunctionality, increased levels of cytotoxic mediators, and high expression of the transcription factors T-bet and eomesodermin (EOMES). Such populations were induced by novel vaccine strategies based on adenoviral vectors, currently in trial against hepatitis C virus. Thus, intermediate CD161 expression marks potent polyclonal, polyfunctional tissue-homing CD8+ T-cell populations in humans. As induction of such responses represents a major aim of T-cell prophylactic and therapeutic vaccines in viral disease and cancer, analysis of these populations could be of value in the future.

  View details for PubMedID 26220166

• In Praise of Descriptive Science: A Breath of Fresh AIRE. Cell Davis, M. M. 2016; 166 (3): 530–31

  Abstract

  Meyer et al. find that subjects lacking the AIRE gene, critical for self-tolerance in T lymphocytes, show a broad range of autoantibody specificities, which can have extremely high affinities. The data also suggest that some of these autoantibodies can, surprisingly, prevent some types of autoimmunity, particularly type I diabetes.

  View details for PubMedID 27471960

  View details for PubMedCentralID PMC5294994

• MHC-Peptide Tetramers to Visualize Antigen-Specific T Cells. Current protocols in immunology Altman, J. D., Davis, M. M. 2016; 115: 17.3.1–17.3.44

  Abstract

  Mature T lymphocytes of the CD8 or CD4 classes bear αβ T cell receptors (TCR) that are specific for a molecular complex consisting of a major histocompatibility complex class I or II (MHC class I or II) molecule bound to a unique self or foreign peptide. Until recently, methods for monitoring antigen-specific T cell immune responses were restricted primarily to functional assays based on limiting dilution analysis, because the lack of specific molecular reagents to identify clonal T cells obviated approaches to identify and enumerate specific T cells. Development of efficient methods to express and refold MHC class I molecules with synthetic peptides coincided with identification of specific protein sequences that provide the substrate for enzymatic biotinylation. This combination has led to the development of a straightforward method for generating synthetic TCR ligands, making them tetravalent to provide increased avidity, and labeling them through a streptavidin moiety with useful fluorescent tags such as allophycocyanin or R-phycoerythrin. This unit describes the preparation of MHC class I/peptide tetramers in detail, including bacterial expression and refolding of the MHC class I light chain, β2-microglobulin (β2m), as well as the formation of a complex consisting of the MHC class I heavy chain of interest, β2m, and a chosen peptide. © 2016 by John Wiley & Sons, Inc.

  View details for PubMedID 27801510

• Lineage tracing of human B cells reveals the in vivo landscape of human antibody class switching. eLife Horns, F., Vollmers, C., Croote, D., Mackey, S. F., Swan, G. E., Dekker, C. L., Davis, M. M., Quake, S. R. 2016; 5

  Abstract

  Antibody class switching is a feature of the adaptive immune system which enables diversification of the effector properties of antibodies. Even though class switching is essential for mounting a protective response to pathogens, the in vivo patterns and lineage characteristics of antibody class switching have remained uncharacterized in living humans. Here we comprehensively measured the landscape of antibody class switching in human adult twins using antibody repertoire sequencing. The map identifies how antibodies of every class are created and delineates a two-tiered hierarchy of class switch pathways. Using somatic hypermutations as a molecular clock, we discovered that closely related B cells often switch to the same class, but lose coherence as somatic mutations accumulate. Such correlations between closely related cells exist when purified B cells class switch in vitro, suggesting that class switch recombination is directed toward specific isotypes by a cell-autonomous imprinted state.

  View details for DOI 10.7554/eLife.16578

  View details for PubMedID 27481325

  View details for PubMedCentralID PMC4970870

• Adenoviral Vector Vaccination Induces a Conserved Program of CD8(+) T Cell Memory Differentiation in Mouse and Man CELL REPORTS Bolinger, B., Sims, S., Swadling, L., O'Hara, G., de Lara, C., Baban, D., Saghal, N., Lee, L., Marchi, E., Davis, M., Newell, E., Capone, S., Folgori, A., Barnes, E., Klenerman, P. 2015; 13 (8): 1578–88

  Abstract

  Following exposure to vaccines, antigen-specific CD8(+) T cell responses develop as long-term memory pools. Vaccine strategies based on adenoviral vectors, e.g., those developed for HCV, are able to induce and sustain substantial CD8(+) T cell populations. How such populations evolve following vaccination remains to be defined at a transcriptional level. We addressed the transcriptional regulation of divergent CD8(+) T cell memory pools induced by an adenovector encoding a model antigen (beta-galactosidase). We observe transcriptional profiles that mimic those following infection with persistent pathogens, murine and human cytomegalovirus (CMV). Key transcriptional hallmarks include upregulation of homing receptors and anti-apoptotic pathways, driven by conserved networks of transcription factors, including T-bet. In humans, an adenovirus vaccine induced similar CMV-like phenotypes and transcription factor regulation. These data clarify the core features of CD8(+) T cell memory following vaccination with adenovectors and indicate a conserved pathway for memory development shared with persistent herpesviruses.

  View details for PubMedID 26586434

• Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY O'Gorman, W. E., Hsieh, E. W., Savig, E. S., Gherardini, P. F., Hernandez, J. D., Hansmann, L., Balboni, I. M., Utz, P. J., Bendall, S. C., Fantl, W. J., Lewis, D. B., Nolan, G. P., Davis, M. M. 2015; 136 (5): 1326-1336

  Abstract

  Activation of Toll-like receptors (TLRs) induces inflammatory responses involved in immunity to pathogens and autoimmune pathogenesis, such as in patients with systemic lupus erythematosus (SLE). Although TLRs are differentially expressed across the immune system, a comprehensive analysis of how multiple immune cell subsets respond in a system-wide manner has not been described.We sought to characterize TLR activation across multiple immune cell subsets and subjects, with the goal of establishing a reference framework against which to compare pathologic processes.Peripheral whole-blood samples were stimulated with TLR ligands and analyzed by means of mass cytometry simultaneously for surface marker expression, activation states of intracellular signaling proteins, and cytokine production. We developed a novel data visualization tool to provide an integrated view of TLR signaling networks with single-cell resolution. We studied 17 healthy volunteer donors and 8 patients with newly diagnosed and untreated SLE.Our data revealed the diversity of TLR-induced responses within cell types, with TLR ligand specificity. Subsets of natural killer cells and T cells selectively induced nuclear factor κ light chain enhancer of activated B cells in response to TLR2 ligands. CD14(hi) monocytes exhibited the most polyfunctional cytokine expression patterns, with more than 80 distinct cytokine combinations. Monocytic TLR-induced cytokine patterns were shared among a group of healthy donors, with minimal intraindividual and interindividual variability. Furthermore, autoimmune disease altered baseline cytokine production; newly diagnosed untreated SLE patients shared a distinct monocytic chemokine signature, despite clinical heterogeneity.Mass cytometry defined a systems-level reference framework for human TLR activation, which can be applied to study perturbations in patients with inflammatory diseases, such as SLE.

  View details for DOI 10.1016/j.jaci.2015.04.008

  View details for Web of Science ID 000364787200023

  View details for PubMedID 26037552

• Distinct Roles of Cytoskeletal Components in Immunological Synapse Formation and Directed Secretion JOURNAL OF IMMUNOLOGY Ueda, H., Zhou, J., Xie, J., Davis, M. M. 2015; 195 (9): 4117-4125

  Abstract

  A hallmark of CD4(+) T cell activation and immunological synapse (IS) formation is the migration of the microtubule organization center and associated organelles toward the APCs. In this study, we found that when murine CD4(+) T cells were treated with a microtubule-destabilizing agent (vinblastine) after the formation of IS, the microtubule organization center dispersed and all of the major cellular organelles moved away from the IS. Cytokines were no longer directed toward the synapse but were randomly secreted in quantities similar to those seen in synaptic secretion. However, if the actin cytoskeleton was disrupted at the same time with cytochalasin D, the organelles did not shift away from the IS. These findings suggest that there is a complex interplay between the microtubules and actin cytoskeleton, where microtubules are important for directing particular cytokines into the synapse, but they are not involved in the amount of cytokines that are produced for at least 1 h after IS formation. In addition, we found that they play a critical role in mobilizing organelles to reorient toward the synapse during T cell activation and in stabilizing organelles against the force that is generated through actin polymerization so that they move toward the APCs. These findings show that there is a complex interplay between these major cytoskeletal components during synapse formation and maintenance.

  View details for DOI 10.4049/jimmunol.1402175

  View details for PubMedID 26392461

  View details for PubMedCentralID PMC4610857

• New approaches to understanding the immune response to vaccination and infection. Vaccine Furman, D., Davis, M. M. 2015; 33 (40): 5271-5281

  Abstract

  The immune system is a network of specialized cell types and tissues that communicates via cytokines and direct contact, to orchestrate specific types of defensive responses. Until recently, we could only study immune responses in a piecemeal, highly focused fashion, on major components like antibodies to the pathogen. But recent advances in technology and in our understanding of the many components of the system, innate and adaptive, have made possible a broader approach, where both the multiple responding cells and cytokines in the blood are measured. This systems immunology approach to a vaccine response or an infection gives us a more holistic picture of the different parts of the immune system that are mobilized and should allow us a much better understanding of the pathways and mechanisms of such responses, as well as to predict vaccine efficacy in different populations well in advance of efficacy studies. Here we summarize the different technologies and methods and discuss how they can inform us about the differences between diseases and vaccines, and how they can greatly accelerate vaccine development.

  View details for DOI 10.1016/j.vaccine.2015.06.117

  View details for PubMedID 26232539

• Pregnancy Does Not Attenuate the Antibody or Plasmablast Response to Inactivated Influenza Vaccine. journal of infectious diseases Kay, A. W., Bayless, N. L., Fukuyama, J., Aziz, N., Dekker, C. L., Mackey, S., Swan, G. E., Davis, M. M., Blish, C. A. 2015; 212 (6): 861-870

  Abstract

  Inactivated influenza vaccine (IIV) is recommended during pregnancy to prevent influenza infection and its complications in pregnant women and their infants. However, the extent to which pregnancy modifies the antibody response to vaccination remains unclear, and prior studies have focused primarily on hemagglutinin inhibition (HI) titers. A more comprehensive understanding of how pregnancy modifies the humoral immune response to influenza vaccination will aid in maximizing vaccine efficacy.Healthy pregnant women and control women were studied prior to, 7 days after, and 28 days after vaccination with IIV. HI titers, microneutralization (MN) titers, and the frequency of circulating plasmablasts were evaluated in pregnant versus control women.Pregnant women and control women mount similarly robust serologic immune responses to IIV, with no significant differences for any influenza strain in postvaccination geometric mean HI or MN titers. HI and MN titers correlate, though MN titers demonstrate more robust changes pre- versus postvaccination. The induction of circulating plasmablasts is increased in pregnant women versus controls (median fold-change 2.60 vs 1.49 [interquartile range, 0.94-7.53 vs 0.63-2.67]; P = .03).Pregnant women do not have impaired humoral immune responses to IIV and may have increased circulating plasmablast production compared to control women.

  View details for DOI 10.1093/infdis/jiv138

  View details for PubMedID 25740957

  View details for PubMedCentralID PMC4548461

• IgH sequences in common variable immune deficiency reveal altered B cell development and selection. Science translational medicine Roskin, K. M., Simchoni, N., Liu, Y., Lee, J., Seo, K., Hoh, R. A., Pham, T., Park, J. H., Furman, D., Dekker, C. L., Davis, M. M., James, J. A., Nadeau, K. C., Cunningham-Rundles, C., Boyd, S. D. 2015; 7 (302): 302ra135-?

  Abstract

  Common variable immune deficiency (CVID) is the most common symptomatic primary immune deficiency, affecting ~1 in 25,000 persons. These patients suffer from impaired antibody responses, autoimmunity, and susceptibility to lymphoid cancers. To explore the cellular basis for these clinical phenotypes, we conducted high-throughput DNA sequencing of immunoglobulin heavy chain gene rearrangements from 93 CVID patients and 105 control subjects and sorted naïve and memory B cells from 13 of the CVID patients and 10 of the control subjects. The CVID patients showed abnormal VDJ rearrangement and abnormal formation of complementarity-determining region 3 (CDR3). We observed a decreased selection against antibodies with long CDR3s in memory repertoires and decreased variable gene replacement, offering possible mechanisms for increased patient autoreactivity. Our data indicate that patient immunodeficiency might derive from both decreased diversity of the naïve B cell pool and decreased somatic hypermutation in memory repertoires. The CVID patients also exhibited an abnormal clonal expansion of unmutated B cells relative to the controls. Although impaired B cell germinal center activation is commonly viewed as causative in CVID, these data indicate that CVID B cells diverge from controls as early as the pro-B stage, cell and suggest possible explanations for the increased incidence of autoimmunity, immunodeficiency, and lymphoma CVID patients.

  View details for DOI 10.1126/scitranslmed.aab1216

  View details for PubMedID 26311730

• IgH sequences in common variable immune deficiency reveal altered B cell development and selection. Science translational medicine Roskin, K. M., Simchoni, N., Liu, Y., Lee, J., Seo, K., Hoh, R. A., Pham, T., Park, J. H., Furman, D., Dekker, C. L., Davis, M. M., James, J. A., Nadeau, K. C., Cunningham-Rundles, C., Boyd, S. D. 2015; 7 (302): 302ra135-?

  Abstract

  Common variable immune deficiency (CVID) is the most common symptomatic primary immune deficiency, affecting ~1 in 25,000 persons. These patients suffer from impaired antibody responses, autoimmunity, and susceptibility to lymphoid cancers. To explore the cellular basis for these clinical phenotypes, we conducted high-throughput DNA sequencing of immunoglobulin heavy chain gene rearrangements from 93 CVID patients and 105 control subjects and sorted naïve and memory B cells from 13 of the CVID patients and 10 of the control subjects. The CVID patients showed abnormal VDJ rearrangement and abnormal formation of complementarity-determining region 3 (CDR3). We observed a decreased selection against antibodies with long CDR3s in memory repertoires and decreased variable gene replacement, offering possible mechanisms for increased patient autoreactivity. Our data indicate that patient immunodeficiency might derive from both decreased diversity of the naïve B cell pool and decreased somatic hypermutation in memory repertoires. The CVID patients also exhibited an abnormal clonal expansion of unmutated B cells relative to the controls. Although impaired B cell germinal center activation is commonly viewed as causative in CVID, these data indicate that CVID B cells diverge from controls as early as the pro-B stage, cell and suggest possible explanations for the increased incidence of autoimmunity, immunodeficiency, and lymphoma CVID patients.

  View details for DOI 10.1126/scitranslmed.aab1216

  View details for PubMedID 26311730

  View details for PubMedCentralID PMC4584259

• Human B-cell isotype switching origins of IgE. The Journal of allergy and clinical immunology Looney, T. J., Lee, J. Y., Roskin, K. M., Hoh, R. A., King, J., Glanville, J., Liu, Y., Pham, T. D., Dekker, C. L., Davis, M. M., Boyd, S. D. 2015

  Abstract

  B cells expressing IgE contribute to immunity against parasites and venoms and are the source of antigen specificity in allergic patients, yet the developmental pathways producing these B cells in human subjects remain a subject of debate. Much of our knowledge of IgE lineage development derives from model studies in mice rather than from human subjects.We evaluate models for isotype switching to IgE in human subjects using immunoglobulin heavy chain (IGH) mutational lineage data.We analyzed IGH repertoires in 9 allergic and 24 healthy adults using high-throughput DNA sequencing of 15,843,270 IGH rearrangements to identify clonal lineages of B cells containing members expressing IgE. Somatic mutations in IGH inherited from common ancestors within the clonal lineage are used to infer the relationships between B cells.Data from 613,641 multi-isotype B-cell clonal lineages, of which 592 include an IgE member, are consistent with indirect switching to IgE from IgG- or IgA-expressing lineage members in human subjects. We also find that these inferred isotype switching frequencies are similar in healthy and allergic subjects.We found evidence that secondary isotype switching of mutated IgG1-expressing B cells is the primary source of IgE in human subjects, with lesser contributions from precursors expressing other switched isotypes and rarely IgM or IgD, suggesting that IgE is derived from previously antigen-experienced B cells rather than naive B cells that typically express low-affinity unmutated antibodies. These data provide a basis from which to evaluate allergen-specific human antibody repertoires in healthy and diseased subjects.

  View details for DOI 10.1016/j.jaci.2015.07.014

  View details for PubMedID 26309181

• mir-181a-1/b-1 Modulates Tolerance through Opposing Activities in Selection and Peripheral T Cell Function JOURNAL OF IMMUNOLOGY Schaffert, S. A., Loh, C., Wang, S., Arnold, C. P., Axtell, R. C., Newell, E. W., Nolan, G., Ansel, K. M., Davis, M. M., Steinman, L., Chen, C. 2015; 195 (4): 1470-1479

  Abstract

  Understanding the consequences of tuning TCR signaling on selection, peripheral T cell function, and tolerance in the context of native TCR repertoires may provide insight into the physiological control of tolerance. In this study, we show that genetic ablation of a natural tuner of TCR signaling, mir-181a-1/b-1, in double-positive thymocytes dampened TCR and Erk signaling and increased the threshold of positive selection. Whereas mir-181a-1/b-1 deletion in mice resulted in an increase in the intrinsic reactivity of naive T cells to self-antigens, it did not cause spontaneous autoimmunity. Loss of mir-181a-1/b-1 dampened the induction of experimental autoimmune encephalomyelitis and reduced basal TCR signaling in peripheral T cells and their migration from lymph nodes to pathogenic sites. Taken together, these results demonstrate that tolerance can be modulated by microRNA gene products through the control of opposing activities in T cell selection and peripheral T cell function.

  View details for DOI 10.4049/jimmunol.1401587

  View details for Web of Science ID 000360013200017

  View details for PubMedID 26163591

• A Population Response Analysis Approach To Assign Class II HLA-Epitope Restrictions JOURNAL OF IMMUNOLOGY Paul, S., Dillon, M. B., Arlehamn, C. S., Huang, H., Davis, M. M., McKinney, D. M., Scriba, T. J., Sidney, J., Peters, B., Sette, A. 2015; 194 (12): 6164-6176

  Abstract

  Identification of the specific HLA locus and allele presenting an epitope for recognition by specific TCRs (HLA restriction) is necessary to fully characterize the immune response to Ags. Experimental determination of HLA restriction is complex and technically challenging. As an alternative, the restricting HLA locus and allele can be inferred by genetic association, using response data in an HLA-typed population. However, simple odds ratio (OR) calculations can be problematic when dealing with large numbers of subjects and Ags, and because the same epitope can be presented by multiple alleles (epitope promiscuity). In this study, we develop a tool, denominated Restrictor Analysis Tool for Epitopes, to extract inferred restriction from HLA class II-typed epitope responses. This automated method infers HLA class II restriction from large datasets of T cell responses in HLA class II-typed subjects by calculating ORs and relative frequencies from simple data tables. The program is validated by: 1) analyzing data of previously determined HLA restrictions; 2) experimentally determining in selected individuals new HLA restrictions using HLA-transfected cell lines; and 3) predicting HLA restriction of particular peptides and showing that corresponding HLA class II tetramers efficiently bind to epitope-specific T cells. We further design a specific iterative algorithm to account for promiscuous recognition by calculation of OR values for combinations of different HLA molecules while incorporating predicted HLA binding affinity. The Restrictor Analysis Tool for Epitopes program streamlines the prediction of HLA class II restriction across multiple T cell epitopes and HLA types.

  View details for DOI 10.4049/jimmunol.1403074

  View details for PubMedID 25948811

• Mass Cytometry Analysis Shows That a Novel Memory Phenotype B Cell Is Expanded in Multiple Myeloma CANCER IMMUNOLOGY RESEARCH Hansmann, L., Blum, L., Ju, C., Liedtke, M., Robinson, W. H., Davis, M. M. 2015; 3 (6): 650-660

  Abstract

  It would be very beneficial if the status of cancers could be determined from a blood specimen. However, peripheral blood leukocytes are very heterogeneous between individuals, and thus high-resolution technologies are likely required. We used cytometry by time-of-flight and next-generation sequencing to ask whether a plasma cell cancer (multiple myeloma) and related precancerous states had any consistent effect on the peripheral blood mononuclear cell phenotypes of patients. Analysis of peripheral blood samples from 13 cancer patients, 9 precancer patients, and 9 healthy individuals revealed significant differences in the frequencies of the T-cell, B-cell, and natural killer-cell compartments. Most strikingly, we identified a novel B-cell population that normally accounts for 4.0% ± 0.7% (mean ± SD) of total B cells and is up to 13-fold expanded in multiple myeloma patients with active disease. This population expressed markers previously associated with both memory (CD27(+)) and naïve (CD24(lo)CD38(+)) phenotypes. Single-cell immunoglobulin gene sequencing showed polyclonality, indicating that these cells are not precursors to the myeloma, and somatic mutations, a characteristic of memory cells. SYK, ERK, and p38 phosphorylation responses, and the fact that most of these cells expressed isotypes other than IgM or IgD, confirmed the memory character of this population, defining it as a novel type of memory B cells.

  View details for DOI 10.1158/2326-6066.CIR-14-0236-T

  View details for Web of Science ID 000357430000010

  View details for PubMedID 25711758

  View details for PubMedCentralID PMC4457663

• Clonal Deletion Prunes but Does Not Eliminate Self-Specific alpha beta CD8(+) T Lymphocytes IMMUNITY Yu, W., Jiang, N., Ebert, P. J., Kidd, B. A., Mueller, S., Lund, P. J., Juang, J., Adachi, K., Tse, T., Birnbaum, M. E., Newell, E. W., Wilson, D. M., Grotenbreg, G. M., Valitutti, S., Quake, S. R., Davis, M. M. 2015; 42 (5): 929-941

  Abstract

  It has long been thought that clonal deletion efficiently removes almost all self-specific T cells from the peripheral repertoire. We found that self-peptide MHC-specific CD8(+) T cells in the blood of healthy humans were present in frequencies similar to those specific for non-self antigens. For the Y chromosome-encoded SMCY antigen, self-specific T cells exhibited only a 3-fold lower average frequency in males versus females and were anergic with respect to peptide activation, although this inhibition could be overcome by a stronger stimulus. We conclude that clonal deletion prunes but does not eliminate self-specific T cells and suggest that to do so would create holes in the repertoire that pathogens could readily exploit. In support of this hypothesis, we detected T cells specific for all 20 amino acid variants at the p5 position of a hepatitis C virus epitope in a random group of blood donors.

  View details for DOI 10.1016/j.immuni.2015.05.001

  View details for PubMedID 25992863

• The Immunological Synapse: A Molecular Machine Controlling T Cell Activation JOURNAL OF IMMUNOLOGY Grakoui, A., Bromley, S. K., Sumen, C., Davis, M. M., Shaw, A. S., Allen, P. M., Dustin, M. L. 2015; 194 (9): 221-227

  View details for DOI 10.1126/science.285.5425.221

  View details for Web of Science ID 000353727400004

• Pregnancy does not attenuate the antibody or plasmablast response to inactivated influenza vaccine Bayless, N., Kay, A., Fukuayama, J., Aziz, N., Dekker, C., Mackey, S., Swan, G., Davis, M., Holmes, S., Blish, C. AMER ASSOC IMMUNOLOGISTS. 2015

  View details for Web of Science ID 000379404501203

• High-dimensional immune profiling of total and rotavirus VP6-specific intestinal and circulating B cells by mass cytometry. Mucosal immunology Nair, N., Newell, E. W., Vollmers, C., Quake, S. R., Morton, J. M., Davis, M. M., He, X. S., Greenberg, H. B. 2015

  Abstract

  In-depth phenotyping of human intestinal antibody secreting cells (ASCs) and their precursors is important for developing improved mucosal vaccines. We used single-cell mass cytometry to simultaneously analyze 34 differentiation and trafficking markers on intestinal and circulating B cells. In addition, we labeled rotavirus (RV) double-layered particles with a metal isotope and characterized B cells specific to the RV VP6 major structural protein. We describe the heterogeneity of the intestinal B-cell compartment, dominated by ASCs with some phenotypic and transcriptional characteristics of long-lived plasma cells. Using principal component analysis, we visualized the phenotypic relationships between major B-cell subsets in the intestine and blood, and revealed that IgM(+) memory B cells (MBCs) and naive B cells were phenotypically related as were CD27(-) MBCs and switched MBCs. ASCs in the intestine and blood were highly clonally related, but associated with distinct trajectories of phenotypic development. VP6-specific B cells were present among diverse B-cell subsets in immune donors, including naive B cells, with phenotypes representative of the overall B-cell pool. These data provide a high dimensional view of intestinal B cells and the determinants regulating humoral memory to a ubiquitous, mucosal pathogen at steady-state.Mucosal Immunology advance online publication, 22 April 2015; doi:10.1038/mi.2015.36.

  View details for DOI 10.1038/mi.2015.36

  View details for PubMedID 25899688

• Cytomegalovirus infection enhances the immune response to influenza. Science translational medicine Furman, D., Jojic, V., Sharma, S., Shen-Orr, S. S., Angel, C. J., Onengut-Gumuscu, S., Kidd, B. A., Maecker, H. T., Concannon, P., Dekker, C. L., Thomas, P. G., Davis, M. M. 2015; 7 (281): 281ra43-?

  Abstract

  Cytomegalovirus (CMV) is a β-herpesvirus present in a latent form in most people worldwide. In immunosuppressed individuals, CMV can reactivate and cause serious clinical complications, but the effect of the latent state on healthy people remains elusive. We undertook a systems approach to understand the differences between seropositive and negative subjects and measured hundreds of immune system components from blood samples including cytokines and chemokines, immune cell phenotyping, gene expression, ex vivo cell responses to cytokine stimuli, and the antibody response to seasonal influenza vaccination. As expected, we found decreased responses to vaccination and an overall down-regulation of immune components in aged individuals regardless of CMV status. In contrast, CMV-seropositive young adults exhibited enhanced antibody responses to influenza vaccination, increased CD8(+) T cell sensitivity, and elevated levels of circulating interferon-γ compared to seronegative individuals. Experiments with young mice infected with murine CMV also showed significant protection from an influenza virus challenge compared with uninfected animals, although this effect declined with time. These data show that CMV and its murine equivalent can have a beneficial effect on the immune response of young, healthy individuals, which may explain the ubiquity of CMV infection in humans and many other species.

  View details for DOI 10.1126/scitranslmed.aaa2293

  View details for PubMedID 25834109

• Cytomegalovirus infection enhances the immune response to influenza SCIENCE TRANSLATIONAL MEDICINE Furman, D., Jojic, V., Sharma, S., Shen-Orr, S. S., Angel, C. J., Onengut-Gumuscu, S., Kidd, B. A., Maecker, H. T., Concannon, P., Dekker, C. L., Thomas, P. G., Davis, M. M. 2015; 7 (281)

  Abstract

  Cytomegalovirus (CMV) is a β-herpesvirus present in a latent form in most people worldwide. In immunosuppressed individuals, CMV can reactivate and cause serious clinical complications, but the effect of the latent state on healthy people remains elusive. We undertook a systems approach to understand the differences between seropositive and negative subjects and measured hundreds of immune system components from blood samples including cytokines and chemokines, immune cell phenotyping, gene expression, ex vivo cell responses to cytokine stimuli, and the antibody response to seasonal influenza vaccination. As expected, we found decreased responses to vaccination and an overall down-regulation of immune components in aged individuals regardless of CMV status. In contrast, CMV-seropositive young adults exhibited enhanced antibody responses to influenza vaccination, increased CD8(+) T cell sensitivity, and elevated levels of circulating interferon-γ compared to seronegative individuals. Experiments with young mice infected with murine CMV also showed significant protection from an influenza virus challenge compared with uninfected animals, although this effect declined with time. These data show that CMV and its murine equivalent can have a beneficial effect on the immune response of young, healthy individuals, which may explain the ubiquity of CMV infection in humans and many other species.

  View details for DOI 10.1126/scitranslmed.aaa2293

  View details for Web of Science ID 000352135800004

  View details for PubMedID 25834109

• Distinct patterns of B-cell activation and priming by natural influenza virus infection versus inactivated influenza vaccination. journal of infectious diseases He, X., Holmes, T. H., Sanyal, M., Albrecht, R. A., García-Sastre, A., Dekker, C. L., Davis, M. M., Greenberg, H. B. 2015; 211 (7): 1051-1059

  Abstract

  The human B-cell response to natural influenza virus infection has not been extensively investigated at the polyclonal level.The overall B-cell response of patients acutely infected with the 2009 pandemic influenza A(H1N1)pdm09 virus (A[H1N1]pdm09) was analyzed by determining the reactivity of plasmablast-derived polyclonal antibodies (PPAbs) to influenza proteins. Recipients of inactivated influenza vaccine containing the same A(H1N1)pdm09 strain were studied for comparison.During acute infection, robust plasmablast responses to the infecting virus were detected, characterized by a greater PPAb reactivity to the conserved influenza virus nuclear protein and to heterovariant and heterosubtypic hemagglutinins, in comparison to responses to the inactivated A(H1N1)pdm09 vaccine. In A(H1N1)pdm09 vaccinees, the presence of baseline serum neutralizing antibodies against A(H1N1)pdm09, suggesting previous exposure to natural A(H1N1)pdm09 infection, did not affect the plasmablast response to vaccination, whereas repeated immunization with inactivated A(H1N1)pdm09 vaccine resulted in significantly reduced vaccine-specific and cross-reactive PPAb responses.Natural A(H1N1)pdm09 infection and inactivated A(H1N1)pdm09 vaccination result in very distinct patterns of B-cell activation and priming. These differences are likely to be associated with differences in protective immunity, especially cross-protection against heterovariant and heterosubtypic influenza virus strains.

  View details for DOI 10.1093/infdis/jiu580

  View details for PubMedID 25336731

  View details for PubMedCentralID PMC4366605

• The coreceptor CD4 is expressed in distinct nanoclusters and does not colocalize with T-cell receptor and active protein tyrosine kinase p56lck PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Roh, K., Lillemeier, B. F., Wang, F., Davis, M. M. 2015; 112 (13): E1604-E1613

  Abstract

  CD4 molecules on the surface of T lymphocytes greatly augment the sensitivity and activation process of these cells, but how it functions is not fully understood. Here we studied the spatial organization of CD4, and its relationship to T-cell antigen receptor (TCR) and the active form of Src kinase p56lck (Lck) using single and dual-color photoactivated localization microscopy (PALM) and direct stochastic optical reconstruction microscopy (dSTORM). In nonactivated T cells, CD4 molecules are clustered in small protein islands, as are TCR and Lck. By dual-color imaging, we find that CD4, TCR, and Lck are localized in their separate clusters with limited interactions in the interfaces between them. Upon T-cell activation, the TCR and CD4 begin clustering together, developing into microclusters, and undergo a larger scale redistribution to form supramolecluar activation clusters (SMACs). CD4 and Lck localize in the inner TCR region of the SMAC, but this redistribution of disparate cluster structures results in enhanced segregation from each other. In nonactivated cells these preclustered structures and the limited interactions between them may serve to limit spontaneous and random activation events. However, the small sizes of these island structures also ensure large interfacial surfaces for potential interactions and signal amplification when activation is initiated. In the later activation stages, the increasingly larger clusters and their segregation from each other reduce the interfacial surfaces and could have a dampening effect. These highly differentiated spatial distributions of TCR, CD4, and Lck and their changes during activation suggest that there is a more complex hierarchy than previously thought.

  View details for DOI 10.1073/pnas.1503532112

  View details for Web of Science ID 000351914500016

  View details for PubMedID 25829544

  View details for PubMedCentralID PMC4386407

• Tetramers reveal IL-17-secreting CD4+ T cells that are specific for U1-70 in lupus and mixed connective tissue disease. Proceedings of the National Academy of Sciences of the United States of America Kattah, N. H., Newell, E. W., Jarrell, J. A., Chu, A. D., Xie, J., Kattah, M. G., Goldberger, O., Ye, J., Chakravarty, E. F., Davis, M. M., Utz, P. J. 2015; 112 (10): 3044-3049

  Abstract

  Antigen-specific CD4(+) T cells are implicated in the autoimmune disease systemic lupus erythematosus (SLE), but little is known about the peptide antigens that they recognize and their precise function in disease. We generated a series of MHC class II tetramers of I-E(k)-containing peptides from the spliceosomal protein U1-70 that specifically stain distinct CD4(+) T-cell populations in MRL/lpr mice. The T-cell populations recognize an epitope differing only by the presence or absence of a single phosphate residue at position serine(140). The frequency of CD4(+) T cells specific for U1-70(131-150):I-E(k) (without phosphorylation) correlates with disease severity and anti-U1-70 autoantibody production. These T cells also express RORγt and produce IL-17A. Furthermore, the U1-70-specific CD4(+) T cells that produce IL-17A are detected in a subset of patients with SLE and are significantly increased in patients with mixed connective tissue disease. These studies provide tools for studying antigen-specific CD4(+) T cells in lupus, and demonstrate an antigen-specific source of IL-17A in autoimmune disease.

  View details for DOI 10.1073/pnas.1424796112

  View details for PubMedID 25713364

  View details for PubMedCentralID PMC4364210

• Associations of toll-like receptor (TLR)-4 single nucleotide polymorphisms and rheumatoid arthritis disease progression: An observational cohort study INTERNATIONAL IMMUNOPHARMACOLOGY Davis, M. L., LeVan, T. D., Yu, F., Sayles, H., Sokolove, J., Robinson, W., Michaud, K., Thiele, G. M., Mikuls, T. R. 2015; 24 (2): 346-352

  Abstract

  To examine the associations of toll-like receptor (TLR)-4 single nucleotide polymorphisms (SNPs) with disease progression in rheumatoid arthritis (RA).A total of 1188 RA patients were genotyped for TLR4 SNPs (rs1927911, rs11536878, and rs4986790). Measures of disease activity were examined, including Disease Activity Score-28 (DAS28), Multidimensional Health Assessment Questionnaire (MD-HAQ), Clinical Disease Activity Index (CDAI), and Simplified Disease Activity Index (SDAI). Genetic associations with these longitudinal measures were examined using generalized estimating equations in both univariate and multivariate analyses. Analyses were then stratified by antigen specific anti-citrullinated peptide antibody (ACPA) status including antibody to citrullinated fibrinogen and citrullinated histone H2B.Disease activity measures progressed less over time in the homozygous minor allele group of rs1927911 including DAS28 (p<0.001), CDAI (p=0.008), and MD-HAQ (p=0.015) in univariate analysis and DAS28, CDAI and SDAI in multivariate analysis. Disease activity progression among those homozygous for the minor allele tended to be lower in the groups with positive ACPA though major differences by autoantibody status were not identified. There were no associations of TLR4 rs11536878 and rs4986790 SNPs with RA disease activity progression.In this population, TLR4 rs1927911 genotypes are associated with disease activity independent of other covariates.

  View details for DOI 10.1016/j.intimp.2014.12.030

  View details for PubMedID 25573402

• Variation in the human immune system is largely driven by non-heritable influences. Cell Brodin, P., Jojic, V., Gao, T., Bhattacharya, S., Angel, C. J., Furman, D., Shen-Orr, S., Dekker, C. L., Swan, G. E., Butte, A. J., Maecker, H. T., Davis, M. M. 2015; 160 (1-2): 37-47

  Abstract

  There is considerable heterogeneity in immunological parameters between individuals, but its sources are largely unknown. To assess the relative contribution of heritable versus non-heritable factors, we have performed a systems-level analysis of 210 healthy twins between 8 and 82 years of age. We measured 204 different parameters, including cell population frequencies, cytokine responses, and serum proteins, and found that 77% of these are dominated (>50% of variance) and 58% almost completely determined (>80% of variance) by non-heritable influences. In addition, some of these parameters become more variable with age, suggesting the cumulative influence of environmental exposure. Similarly, the serological responses to seasonal influenza vaccination are also determined largely by non-heritable factors, likely due to repeated exposure to different strains. Lastly, in MZ twins discordant for cytomegalovirus infection, more than half of all parameters are affected. These results highlight the largely reactive and adaptive nature of the immune system in healthy individuals.

  View details for DOI 10.1016/j.cell.2014.12.020

  View details for PubMedID 25594173

  View details for PubMedCentralID PMC4302727

• William Erwin Paul (1936-2015). Cell Davis, M. M., Glimcher, L. H. 2015; 163 (3): 529–30

  View details for PubMedID 26807452

• DRUG-INDUCED mRNA SIGNATURES ARE ENRICHED FOR THE MINORITY OF GENES THAT ARE HIGHLY HERITABLE Gao, T., Brodin, P., Davis, M. M., Jojic, V., Altman, R. B., Dunker, A. K., Hunter, L., Ritchie, M. D., Murray, T., Klein, T. E. WORLD SCIENTIFIC PUBL CO PTE LTD. 2015: 395-406

  Abstract

  The blood gene expression signatures are used as biomarkers for immunological and non- immunological diseases. Therefore, it is important to understand the variation in blood gene expression patterns and the factors (heritable/non-heritable) that underlie this variation. In this paper, we study the relationship between drug effects on the one hand, and heritable and non-heritable factors influencing gene expression on the other. Understanding of this relationship can help select appropriate targets for drugs aimed at reverting disease phenotypes to healthy states. In order to estimate heritable and non-heritable effects on gene expression, we use Twin-ACE model on a gene expression dataset MuTHER, measured in blood samples from monozygotic and dizygotic twins. In order to associate gene expression with drug effects, we use CMap database. We show that, even though the expressions of most genes are driven by non-heritable factors, drugs are more likely to influence expression of genes, driven by heritable rather than non-heritable factors. We further study this finding in the context of a gene regulatory network. We investigate the relationship between the drug effects on gene expression and propagation of heritable and non-heritable factors through regulatory networks. We find that the decisive factor in determining whether a gene will be influenced by a drug is the flow of heritable effects supplied to the gene through regulatory network.

  View details for Web of Science ID 000461835500038

  View details for PubMedID 25592599

• Immunology. Flexibility for specificity. Science (New York, N.Y.) Davis, M. M. 2015; 347 (6220): 371–72

  View details for PubMedID 25613876

• Not-So-Negative Selection. Immunity Davis, M. M. 2015; 43 (5): 833–35

  Abstract

  It once seemed clear that negative selection of self-specific T cells in the thymus was the major mechanism of central tolerance. But recent studies, including Legoux et al. (2015) in this issue of Immunity, show that this is not always the case.

  View details for PubMedID 26588773

• CD161 Defines a Transcriptional and Functional Phenotype across Distinct Human T Cell Lineages CELL REPORTS Fergusson, J. R., Smith, K. E., Fleming, V. M., Rajoriya, N., Newell, E. W., Simmons, R., Marchi, E., Bjorkander, S., Kang, Y., Swadling, L., Kurioka, A., Sahgal, N., Lockstone, H., Baban, D., Freeman, G. J., Sverremark-Ekstrom, E., Davis, M. M., Davenport, M. P., Venturi, V., Ussher, J. E., Willberg, C. B., Klenerman, P. 2014; 9 (3): 1075-1088

  Abstract

  The C-type lectin CD161 is expressed by a large proportion of human T lymphocytes of all lineages, including a population known as mucosal-associated invariant T (MAIT) cells. To understand whether different T cell subsets expressing CD161 have similar properties, we examined these populations in parallel using mass cytometry and mRNA microarray approaches. The analysis identified a conserved CD161++/MAIT cell transcriptional signature enriched in CD161+CD8+ T cells, which can be extended to CD161+ CD4+ and CD161+TCRγδ+ T cells. Furthermore, this led to the identification of a shared innate-like, TCR-independent response to interleukin (IL)-12 plus IL-18 by different CD161-expressing T cell populations. This response was independent of regulation by CD161, which acted as a costimulatory molecule in the context of T cell receptor stimulation. Expression of CD161 hence identifies a transcriptional and functional phenotype, shared across human T lymphocytes and independent of both T cell receptor (TCR) expression and cell lineage.

  View details for DOI 10.1016/j.celrep.2014.09.045

  View details for Web of Science ID 000344470000028

  View details for PubMedID 25437561

  View details for PubMedCentralID PMC4250839

• The Split Virus Influenza Vaccine rapidly activates immune cells through Fc gamma receptors VACCINE O'Gorman, W. E., Huang, H., Wei, Y., Davis, K. L., Leipold, M. D., Bendall, S. C., Kidd, B. A., Dekker, C. L., Maecker, H. T., Chien, Y., Davis, M. M. 2014; 32 (45): 5989-5997

  Abstract

  Seasonal influenza vaccination is one of the most common medical procedures and yet the extent to which it activates the immune system beyond inducing antibody production is not well understood. In the United States, the most prevalent formulations of the vaccine consist of degraded or "split" viral particles distributed without any adjuvants. Based on previous reports we sought to determine whether the split influenza vaccine activates innate immune receptors-specifically Toll-like receptors. High-dimensional proteomic profiling of human whole-blood using Cytometry by Time-of-Flight (CyTOF) was used to compare signaling pathway activation and cytokine production between the split influenza vaccine and a prototypical TLR response ex vivo. This analysis revealed that the split vaccine rapidly and potently activates multiple immune cell types but yields a proteomic signature quite distinct from TLR activation. Importantly, vaccine induced activity was dependent upon the presence of human sera indicating that a serum factor was necessary for vaccine-dependent immune activation. We found this serum factor to be human antibodies specific for influenza proteins and therefore immediate immune activation by the split vaccine is immune-complex dependent. These studies demonstrate that influenza virus "splitting" inactivates any potential adjuvants endogenous to influenza, such as RNA, but in previously exposed individuals can elicit a potent immune response by facilitating the rapid formation of immune complexes.

  View details for DOI 10.1016/j.vaccine.2014.07.115

  View details for Web of Science ID 000343629900016

  View details for PubMedCentralID PMC4191649

• The Split Virus Influenza Vaccine rapidly activates immune cells through Fc? receptors. Vaccine O'Gorman, W. E., Huang, H., Wei, Y., Davis, K. L., Leipold, M. D., Bendall, S. C., Kidd, B. A., Dekker, C. L., Maecker, H. T., Chien, Y., Davis, M. M. 2014; 32 (45): 5989-5997

  Abstract

  Seasonal influenza vaccination is one of the most common medical procedures and yet the extent to which it activates the immune system beyond inducing antibody production is not well understood. In the United States, the most prevalent formulations of the vaccine consist of degraded or "split" viral particles distributed without any adjuvants. Based on previous reports we sought to determine whether the split influenza vaccine activates innate immune receptors-specifically Toll-like receptors. High-dimensional proteomic profiling of human whole-blood using Cytometry by Time-of-Flight (CyTOF) was used to compare signaling pathway activation and cytokine production between the split influenza vaccine and a prototypical TLR response ex vivo. This analysis revealed that the split vaccine rapidly and potently activates multiple immune cell types but yields a proteomic signature quite distinct from TLR activation. Importantly, vaccine induced activity was dependent upon the presence of human sera indicating that a serum factor was necessary for vaccine-dependent immune activation. We found this serum factor to be human antibodies specific for influenza proteins and therefore immediate immune activation by the split vaccine is immune-complex dependent. These studies demonstrate that influenza virus "splitting" inactivates any potential adjuvants endogenous to influenza, such as RNA, but in previously exposed individuals can elicit a potent immune response by facilitating the rapid formation of immune complexes.

  View details for DOI 10.1016/j.vaccine.2014.07.115

  View details for PubMedID 25203448

• Enhanced natural killer-cell and T-cell responses to influenza A virus during pregnancy PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kay, A. W., Fukuyama, J., Aziz, N., Dekker, C. L., Mackey, S., Swan, G. E., Davis, M. M., Holmes, S., Blish, C. A. 2014; 111 (40): 14506-14511

  Abstract

  Pregnant women experience increased morbidity and mortality after influenza infection, for reasons that are not understood. Although some data suggest that natural killer (NK)- and T-cell responses are suppressed during pregnancy, influenza-specific responses have not been previously evaluated. Thus, we analyzed the responses of women that were pregnant (n = 21) versus those that were not (n = 29) immediately before inactivated influenza vaccination (IIV), 7 d after vaccination, and 6 wk postpartum. Expression of CD107a (a marker of cytolysis) and production of IFN-γ and macrophage inflammatory protein (MIP) 1β were assessed by flow cytometry. Pregnant women had a significantly increased percentage of NK cells producing a MIP-1β response to pH1N1 virus compared with nonpregnant women pre-IIV [median, 6.66 vs. 0.90% (P = 0.0149)] and 7 d post-IIV [median, 11.23 vs. 2.81% (P = 0.004)], indicating a heightened chemokine response in pregnant women that was further enhanced by the vaccination. Pregnant women also exhibited significantly increased T-cell production of MIP-1β and polyfunctionality in NK and T cells to pH1N1 virus pre- and post-IIV. NK- and T-cell polyfunctionality was also enhanced in pregnant women in response to the H3N2 viral strain. In contrast, pregnant women had significantly reduced NK- and T-cell responses to phorbol 12-myristate 13-acetate and ionomycin. This type of stimulation led to the conclusion that NK- and T-cell responses during pregnancy are suppressed, but clearly this conclusion is not correct relative to the more biologically relevant assays described here. Robust cellular immune responses to influenza during pregnancy could drive pulmonary inflammation, explaining increased morbidity and mortality.

  View details for DOI 10.1073/pnas.1416569111

  View details for Web of Science ID 000342633900054

• Enhanced natural killer-cell and T-cell responses to influenza A virus during pregnancy. Proceedings of the National Academy of Sciences of the United States of America Kay, A. W., Fukuyama, J., Aziz, N., Dekker, C. L., Mackey, S., Swan, G. E., Davis, M. M., Holmes, S., Blish, C. A. 2014; 111 (40): 14506-14511

  Abstract

  Pregnant women experience increased morbidity and mortality after influenza infection, for reasons that are not understood. Although some data suggest that natural killer (NK)- and T-cell responses are suppressed during pregnancy, influenza-specific responses have not been previously evaluated. Thus, we analyzed the responses of women that were pregnant (n = 21) versus those that were not (n = 29) immediately before inactivated influenza vaccination (IIV), 7 d after vaccination, and 6 wk postpartum. Expression of CD107a (a marker of cytolysis) and production of IFN-γ and macrophage inflammatory protein (MIP) 1β were assessed by flow cytometry. Pregnant women had a significantly increased percentage of NK cells producing a MIP-1β response to pH1N1 virus compared with nonpregnant women pre-IIV [median, 6.66 vs. 0.90% (P = 0.0149)] and 7 d post-IIV [median, 11.23 vs. 2.81% (P = 0.004)], indicating a heightened chemokine response in pregnant women that was further enhanced by the vaccination. Pregnant women also exhibited significantly increased T-cell production of MIP-1β and polyfunctionality in NK and T cells to pH1N1 virus pre- and post-IIV. NK- and T-cell polyfunctionality was also enhanced in pregnant women in response to the H3N2 viral strain. In contrast, pregnant women had significantly reduced NK- and T-cell responses to phorbol 12-myristate 13-acetate and ionomycin. This type of stimulation led to the conclusion that NK- and T-cell responses during pregnancy are suppressed, but clearly this conclusion is not correct relative to the more biologically relevant assays described here. Robust cellular immune responses to influenza during pregnancy could drive pulmonary inflammation, explaining increased morbidity and mortality.

  View details for DOI 10.1073/pnas.1416569111

  View details for PubMedID 25246558

• High Dimensional Single-Cell Characterization of Human Toll-Like-Receptor Activation: Potential Clinical Applications in Systemic Lupus Erythematosus (SLE) Hsieh, E., O'Gorman, W., Savig, E., Gherardini, P. F., Balboni, I., Davis, M., Nolan, G. P. SPRINGER/PLENUM PUBLISHERS. 2014: S213

  View details for Web of Science ID 000347389100147

• Antigen-Specificity Regulates Peripheral Homeostasis of Regulatory T Cells Su, L., Davis, M. WILEY-BLACKWELL. 2014: S765-S766

  View details for Web of Science ID 000344384903367

• Clinical recovery from surgery correlates with single-cell immune signatures SCIENCE TRANSLATIONAL MEDICINE Gaudilliere, B., Fragiadakis, G. K., Bruggner, R. V., Nicolau, M., Finck, R., Tingle, M., Silva, J., Ganio, E. A., Yeh, C. G., Maloney, W. J., Huddleston, J. I., Goodman, S. B., Davis, M. M., Bendall, S. C., Fantl, W. J., Angst, M. S., Nolan, G. P. 2014; 6 (255)

  Abstract

  Delayed recovery from surgery causes personal suffering and substantial societal and economic costs. Whether immune mechanisms determine recovery after surgical trauma remains ill-defined. Single-cell mass cytometry was applied to serial whole-blood samples from 32 patients undergoing hip replacement to comprehensively characterize the phenotypic and functional immune response to surgical trauma. The simultaneous analysis of 14,000 phosphorylation events in precisely phenotyped immune cell subsets revealed uniform signaling responses among patients, demarcating a surgical immune signature. When regressed against clinical parameters of surgical recovery, including functional impairment and pain, strong correlations were found with STAT3 (signal transducer and activator of transcription), CREB (adenosine 3',5'-monophosphate response element-binding protein), and NF-κB (nuclear factor κB) signaling responses in subsets of CD14(+) monocytes (R = 0.7 to 0.8, false discovery rate <0.01). These sentinel results demonstrate the capacity of mass cytometry to survey the human immune system in a relevant clinical context. The mechanistically derived immune correlates point to diagnostic signatures, and potential therapeutic targets, that could postoperatively improve patient recovery.

  View details for DOI 10.1126/scitranslmed.3009701

  View details for Web of Science ID 000343316800006

• Clinical recovery from surgery correlates with single-cell immune signatures. Science translational medicine Gaudillière, B., Fragiadakis, G. K., Bruggner, R. V., Nicolau, M., Finck, R., Tingle, M., Silva, J., Ganio, E. A., Yeh, C. G., Maloney, W. J., Huddleston, J. I., Goodman, S. B., Davis, M. M., Bendall, S. C., Fantl, W. J., Angst, M. S., Nolan, G. P. 2014; 6 (255): 255ra131-?

  Abstract

  Delayed recovery from surgery causes personal suffering and substantial societal and economic costs. Whether immune mechanisms determine recovery after surgical trauma remains ill-defined. Single-cell mass cytometry was applied to serial whole-blood samples from 32 patients undergoing hip replacement to comprehensively characterize the phenotypic and functional immune response to surgical trauma. The simultaneous analysis of 14,000 phosphorylation events in precisely phenotyped immune cell subsets revealed uniform signaling responses among patients, demarcating a surgical immune signature. When regressed against clinical parameters of surgical recovery, including functional impairment and pain, strong correlations were found with STAT3 (signal transducer and activator of transcription), CREB (adenosine 3',5'-monophosphate response element-binding protein), and NF-κB (nuclear factor κB) signaling responses in subsets of CD14(+) monocytes (R = 0.7 to 0.8, false discovery rate <0.01). These sentinel results demonstrate the capacity of mass cytometry to survey the human immune system in a relevant clinical context. The mechanistically derived immune correlates point to diagnostic signatures, and potential therapeutic targets, that could postoperatively improve patient recovery.

  View details for DOI 10.1126/scitranslmed.3009701

  View details for PubMedID 25253674

• Human B cell isotype switching to IgE occurs primarily from IgG precursors Looney, T., Hoh, R. A., Lee, J., King, J., Glanville, J., Liu, Y., Roskin, K. M., Pham, T. D., Xu, L. T., David, F., Mackey, S., Dekker, C. L., Davis, M. M., Nadeau, K. C., Fire, A. Z., Boyd, S. D. WILEY-BLACKWELL. 2014: 173

  View details for Web of Science ID 000341139400414

• Association between Latent Proviral Characteristics and Immune Activation in Antiretrovirus-Treated Human Immunodeficiency Virus Type 1-Infected Adults. Journal of virology Liang, E. C., Sceats, L., Bayless, N. L., Strauss-Albee, D. M., Kubo, J., Grant, P. M., Furman, D., Desai, M., Katzenstein, D. A., Davis, M. M., Zolopa, A. R., Blish, C. A. 2014; 88 (15): 8629-8639

  Abstract

  Generalized immune activation during HIV infection is associated with an increased risk of cardiovascular disease, neurocognitive disease, osteoporosis, metabolic disorders, and physical frailty. The mechanisms driving this immune activation are poorly understood, particularly for individuals effectively treated with antiretroviral medications. We hypothesized that viral characteristics such as sequence diversity may play a role in driving HIV-associated immune activation. We therefore sequenced proviral DNA isolated from peripheral blood mononuclear cells from HIV-infected individuals on fully suppressive antiretroviral therapy. We performed phylogenetic analyses, calculated viral diversity and divergence in the env and pol genes, and determined coreceptor tropism and the frequency of drug resistance mutations. Comprehensive immune profiling included quantification of immune cell subsets, plasma cytokine levels, and intracellular signaling responses in T cells, B cells, and monocytes. These antiretroviral therapy-treated HIV-infected individuals exhibited a wide range of diversity and divergence in both env and pol genes. However, proviral diversity and divergence in env and pol, coreceptor tropism, and the level of drug resistance did not significantly correlate with markers of immune activation. A clinical history of virologic failure was also not significantly associated with levels of immune activation, indicating that a history of virologic failure does not inexorably lead to increased immune activation as long as suppressive antiretroviral medications are provided. Overall, this study demonstrates that latent viral diversity is unlikely to be a major driver of persistent HIV-associated immune activation.Chronic immune activation, which is associated with cardiovascular disease, neurologic disease, and early aging, is likely to be a major driver of morbidity and mortality in HIV-infected individuals. Although treatment of HIV with antiretroviral medications decreases the level of immune activation, levels do not return to normal. The factors driving this persistent immune activation, particularly during effective treatment, are poorly understood. In this study, we investigated whether characteristics of the latent, integrated HIV provirus that persists during treatment are associated with immune activation. We found no relationship between latent viral characteristics and immune activation in treated individuals, indicating that qualities of the provirus are unlikely to be a major driver of persistent inflammation. We also found that individuals who had previously failed treatment but were currently effectively treated did not have significantly increased levels of immune activation, providing hope that past treatment failures do not have a lifelong "legacy" impact.

  View details for DOI 10.1128/JVI.01257-14

  View details for PubMedID 24850730

  View details for PubMedCentralID PMC4135944

• Retraction of the Research Article: "CD4+ T cell autoimmunity to hypocretin/orexin and cross-reactivity to a 2009 H1N1 influenza A epitope in narcolepsy". Science translational medicine De la Herrán-Arita, A. K., Kornum, B. R., Mahlios, J., Jiang, W., Lin, L., Hou, T., Macaubas, C., Einen, M., Plazzi, G., Crowe, C., Newell, E. W., Davis, M. M., Mellins, E. D., Mignot, E. 2014; 6 (247): 247rt1-?

  View details for DOI 10.1126/scitranslmed.3009995

  View details for PubMedID 25080479

• Bypassing Tetramers: Convergent Anti-Epstein Barr Virus (EBV) T Cell Repertoires Allow Specificities to Be Read From Primary Sequence Hatton, O., Glanville, J., Han, A., Davis, M., Esquivel, C., Krams, S., Martinez, O. LIPPINCOTT WILLIAMS & WILKINS. 2014: 223

  View details for Web of Science ID 000339104601186

• Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements. Cell host & microbe Jackson, K. J., Liu, Y., Roskin, K. M., Glanville, J., Hoh, R. A., Seo, K., Marshall, E. L., Gurley, T. C., Moody, M. A., Haynes, B. F., Walter, E. B., Liao, H., Albrecht, R. A., García-Sastre, A., Chaparro-Riggers, J., Rajpal, A., Pons, J., Simen, B. B., Hanczaruk, B., Dekker, C. L., Laserson, J., Koller, D., Davis, M. M., Fire, A. Z., Boyd, S. D. 2014; 16 (1): 105-114

  Abstract

  B cells produce a diverse antibody repertoire by undergoing gene rearrangements. Pathogen exposure induces the clonal expansion of B cells expressing antibodies that can bind the infectious agent. To assess human B cell responses to trivalent seasonal influenza and monovalent pandemic H1N1 vaccination, we sequenced gene rearrangements encoding the immunoglobulin heavy chain, a major determinant of epitope recognition. The magnitude of B cell clonal expansions correlates with an individual's secreted antibody response to the vaccine, and the expanded clones are enriched with those expressing influenza-specific monoclonal antibodies. Additionally, B cell responses to pandemic influenza H1N1 vaccination and infection in different people show a prominent family of convergent antibody heavy chain gene rearrangements specific to influenza antigens. These results indicate that microbes can induce specific signatures of immunoglobulin gene rearrangements and that pathogen exposure can potentially be assessed from B cell repertoires.

  View details for DOI 10.1016/j.chom.2014.05.013

  View details for PubMedID 24981332

  View details for PubMedCentralID PMC4158033

• Linking T-cell receptor sequence to functional phenotype at the single-cell level NATURE BIOTECHNOLOGY Han, A., Glanville, J., Hansmann, L., Davis, M. M. 2014; 32 (7): 684-?

  Abstract

  Although each T lymphocyte expresses a T-cell receptor (TCR) that recognizes cognate antigen and controls T-cell activation, different T cells bearing the same TCR can be functionally distinct. Each TCR is a heterodimer, and both α- and β-chains contribute to determining TCR antigen specificity. Here we present a methodology enabling integration of information about TCR specificity with information about T cell function. This method involves sequencing of TCRα and TCRβ genes, and amplifying functional genes characteristic of different T cell subsets, in single T cells. Because this approach retains information about individual TCRα-TCRβ pairs, TCRs of interest can be expressed and used in functional studies, for antigen discovery, or in therapeutic applications. We apply this approach to study the clonal ancestry and differentiation of T lymphocytes infiltrating a human colorectal carcinoma.

  View details for DOI 10.1038/nbt.2938

  View details for Web of Science ID 000338705900035

  View details for PubMedCentralID PMC4337815

• The role of the reporting framework MIATA within current efforts to advance immune monitoring JOURNAL OF IMMUNOLOGICAL METHODS Janetzki, S., Britten, C. M., Davis, M. M., Hoos, A., Huber, C., Kalos, M., Levitsky, H. I., Maecker, H. T., Melief, C. M., O'Donnell-Tormey, J., Odunsi, K., Old, L., Ottensmeier, C., Roep, B. O., Romero, P., van der Burg, S., Walter, S., MIATA Core Team 2014; 409: 6-8

  View details for DOI 10.1016/j.jim.2014.05.003

  View details for Web of Science ID 000341548700002

  View details for PubMedID 24816466

• Linking T-cell receptor sequence to functional phenotype at the single-cell level. Nature biotechnology Han, A., Glanville, J., Hansmann, L., Davis, M. M. 2014; 32 (7): 684-692

  Abstract

  Although each T lymphocyte expresses a T-cell receptor (TCR) that recognizes cognate antigen and controls T-cell activation, different T cells bearing the same TCR can be functionally distinct. Each TCR is a heterodimer, and both α- and β-chains contribute to determining TCR antigen specificity. Here we present a methodology enabling integration of information about TCR specificity with information about T cell function. This method involves sequencing of TCRα and TCRβ genes, and amplifying functional genes characteristic of different T cell subsets, in single T cells. Because this approach retains information about individual TCRα-TCRβ pairs, TCRs of interest can be expressed and used in functional studies, for antigen discovery, or in therapeutic applications. We apply this approach to study the clonal ancestry and differentiation of T lymphocytes infiltrating a human colorectal carcinoma.

  View details for DOI 10.1038/nbt.2938

  View details for PubMedID 24952902

  View details for PubMedCentralID PMC4337815

• Bypassing Tetramers: Convergent Anti-Epstein Barr Virus (EBV) T Cell Repertoires Allow Specificities to Be Read From Primary Sequence. Hatton, O., Glanville, J., Han, A., Davis, M., Esquivel, C., Krams, S., Martinez, O. WILEY-BLACKWELL. 2014: 223

  View details for Web of Science ID 000338033301009

• Deconstructing the Peptide-MHC Specificity of T Cell Recognition. Cell Birnbaum, M. E., Mendoza, J. L., Sethi, D. K., Dong, S., Glanville, J., Dobbins, J., Ozkan, E., Davis, M. M., Wucherpfennig, K. W., Garcia, K. C. 2014; 157 (5): 1073-1087

  Abstract

  In order to survey a universe of major histocompatibility complex (MHC)-presented peptide antigens whose numbers greatly exceed the diversity of the T cell repertoire, T cell receptors (TCRs) are thought to be cross-reactive. However, the nature and extent of TCR cross-reactivity has not been conclusively measured experimentally. We developed a system to identify MHC-presented peptide ligands by combining TCR selection of highly diverse yeast-displayed peptide-MHC libraries with deep sequencing. Although we identified hundreds of peptides reactive with each of five different mouse and human TCRs, the selected peptides possessed TCR recognition motifs that bore a close resemblance to their known antigens. This structural conservation of the TCR interaction surface allowed us to exploit deep-sequencing information to computationally identify activating microbial and self-ligands for human autoimmune TCRs. The mechanistic basis of TCR cross-reactivity described here enables effective surveillance of diverse self and foreign antigens without necessitating degenerate recognition of nonhomologous peptides.

  View details for DOI 10.1016/j.cell.2014.03.047

  View details for PubMedID 24855945

  View details for PubMedCentralID PMC4071348

• The split-virus influenza vaccine activates Fc gamma receptors instead of Toll-like receptors O'Gorman, W., Huang, H., Wei, Y., Davis, K., Leipold, M., Bendall, S., Kidd, B., Dekker, C., Maecker, H., Chien, Y., Davis, M. AMER ASSOC IMMUNOLOGISTS. 2014

  View details for Web of Science ID 000209765002128

• Modification of proteins by O-linked N-acetylglucosamine in activated T cells Lund, P., Elias, J., Davis, M. AMER ASSOC IMMUNOLOGISTS. 2014

  View details for Web of Science ID 000209765005095

• High Dimensional Single-Cell Characterization of Human Toll-Like-Receptor Activation: Potential Clinical Applications in Systemic Lupus Erythematosus Hsieh, E., O'Gorman, W., Balboni, I. M., Savig, E., Gherardini, P., Davis, M. M., Nolan, G. P. SPRINGER/PLENUM PUBLISHERS. 2014: 355

  View details for Web of Science ID 000336046800035

• Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells NATURE BIOTECHNOLOGY Newell, E. W., Davis, M. M. 2014; 32 (2): 149-157

  Abstract

  Adaptive immune responses often begin with the formation of a molecular complex between a T-cell receptor (TCR) and a peptide antigen bound to a major histocompatibility complex (MHC) molecule. These complexes are highly variable, however, due to the polymorphism of MHC genes, the random, inexact recombination of TCR gene segments, and the vast array of possible self and pathogen peptide antigens. As a result, it has been very difficult to comprehensively study the TCR repertoire or identify and track more than a few antigen-specific T cells in mice or humans. For mouse studies, this had led to a reliance on model antigens and TCR transgenes. The study of limited human clinical samples, in contrast, requires techniques that can simultaneously survey TCR phenotype and function, and TCR reactivity to many T-cell epitopes. Thanks to recent advances in single-cell and cytometry methodologies, as well as high-throughput sequencing of the TCR repertoire, we now have or will soon have the tools needed to comprehensively analyze T-cell responses in health and disease.

  View details for DOI 10.1038/nbt.2783

  View details for Web of Science ID 000331074000020

  View details for PubMedID 24441473

  View details for PubMedCentralID PMC4001742

• High Dimensional Single-Cell Mass Cytometry Demonstrates Conserved Human Toll-Like-Receptor Activation Signatures Hsieh, E., O'Gorman, W., Savig, E., Gherardini, P., Davis, M., Nolan, G. MOSBY-ELSEVIER. 2014: AB244

  View details for DOI 10.1016/j.jaci.2013.12.869

  View details for Web of Science ID 000330241301161

• Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium NATURE BIOTECHNOLOGY Brusic, V., Gottardo, R., Kleinstein, S. H., Davis, M. M., HIPC Steering Comm 2014; 32 (2): 146–48

  View details for DOI 10.1038/nbt.2777

  View details for Web of Science ID 000331074000019

  View details for PubMedID 24441472

  View details for PubMedCentralID PMC4294529

• Effects of Aging, Cytomegalovirus Infection, and EBV Infection on Human B Cell Repertoires JOURNAL OF IMMUNOLOGY Wang, C., Liu, Y., Xu, L. T., Jackson, K. J., Roskin, K. M., Pham, T. D., Laserson, J., Marshall, E. L., Seo, K., Lee, J., Furman, D., Koller, D., Dekker, C. L., Davis, M. M., Fire, A. Z., Boyd, S. D. 2014; 192 (2): 603-611

  Abstract

  Elderly humans show decreased humoral immunity to pathogens and vaccines, yet the effects of aging on B cells are not fully known. Chronic viral infection by CMV is implicated as a driver of clonal T cell proliferations in some aging humans, but whether CMV or EBV infection contributes to alterations in the B cell repertoire with age is unclear. We have used high-throughput DNA sequencing of IGH gene rearrangements to study the BCR repertoires over two successive years in 27 individuals ranging in age from 20 to 89 y. Some features of the B cell repertoire remain stable with age, but elderly subjects show increased numbers of B cells with long CDR3 regions, a trend toward accumulation of more highly mutated IgM and IgG Ig genes, and persistent clonal B cell populations in the blood. Seropositivity for CMV or EBV infection alters B cell repertoires, regardless of the individual's age: EBV infection correlates with the presence of persistent clonal B cell expansions, whereas CMV infection correlates with the proportion of highly mutated Ab genes. These findings isolate effects of aging from those of chronic viral infection on B cell repertoires and provide a baseline for understanding human B cell responses to vaccination or infectious stimuli.

  View details for DOI 10.4049/jimmunol.1301384

  View details for Web of Science ID 000329224000006

  View details for PubMedID 24337376

• Systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination. Proceedings of the National Academy of Sciences of the United States of America Furman, D., Hejblum, B. P., Simon, N., Jojic, V., Dekker, C. L., Thiébaut, R., Tibshirani, R. J., Davis, M. M. 2014; 111 (2): 869-874

  Abstract

  Females have generally more robust immune responses than males for reasons that are not well-understood. Here we used a systems analysis to investigate these differences by analyzing the neutralizing antibody response to a trivalent inactivated seasonal influenza vaccine (TIV) and a large number of immune system components, including serum cytokines and chemokines, blood cell subset frequencies, genome-wide gene expression, and cellular responses to diverse in vitro stimuli, in 53 females and 34 males of different ages. We found elevated antibody responses to TIV and expression of inflammatory cytokines in the serum of females compared with males regardless of age. This inflammatory profile correlated with the levels of phosphorylated STAT3 proteins in monocytes but not with the serological response to the vaccine. In contrast, using a machine learning approach, we identified a cluster of genes involved in lipid biosynthesis and previously shown to be up-regulated by testosterone that correlated with poor virus-neutralizing activity in men. Moreover, men with elevated serum testosterone levels and associated gene signatures exhibited the lowest antibody responses to TIV. These results demonstrate a strong association between androgens and genes involved in lipid metabolism, suggesting that these could be important drivers of the differences in immune responses between males and females.

  View details for DOI 10.1073/pnas.1321060111

  View details for PubMedID 24367114

  View details for PubMedCentralID PMC3896147

• Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Shekhar, K., Brodin, P., Davis, M. M., Chakraborty, A. K. 2014; 111 (1): 202-207

  Abstract

  Mass cytometry enables an unprecedented number of parameters to be measured in individual cells at a high throughput, but the large dimensionality of the resulting data severely limits approaches relying on manual "gating." Clustering cells based on phenotypic similarity comes at a loss of single-cell resolution and often the number of subpopulations is unknown a priori. Here we describe ACCENSE, a tool that combines nonlinear dimensionality reduction with density-based partitioning, and displays multivariate cellular phenotypes on a 2D plot. We apply ACCENSE to 35-parameter mass cytometry data from CD8(+) T cells derived from specific pathogen-free and germ-free mice, and stratify cells into phenotypic subpopulations. Our results show significant heterogeneity within the known CD8(+) T-cell subpopulations, and of particular note is that we find a large novel subpopulation in both specific pathogen-free and germ-free mice that has not been described previously. This subpopulation possesses a phenotypic signature that is distinct from conventional naive and memory subpopulations when analyzed by ACCENSE, but is not distinguishable on a biaxial plot of standard markers. We are able to automatically identify cellular subpopulations based on all proteins analyzed, thus aiding the full utilization of powerful new single-cell technologies such as mass cytometry.

  View details for DOI 10.1073/pnas.1321405111

  View details for Web of Science ID 000329350700063

  View details for PubMedID 24344260

  View details for PubMedCentralID PMC3890841

• A human vaccine strategy based on chimpanzee adenoviral and MVA vectors that primes, boosts, and sustains functional HCV-specific T cell memory. Science translational medicine Swadling, L. n., Capone, S. n., Antrobus, R. D., Brown, A. n., Richardson, R. n., Newell, E. W., Halliday, J. n., Kelly, C. n., Bowen, D. n., Fergusson, J. n., Kurioka, A. n., Ammendola, V. n., Del Sorbo, M. n., Grazioli, F. n., Esposito, M. L., Siani, L. n., Traboni, C. n., Hill, A. n., Colloca, S. n., Davis, M. n., Nicosia, A. n., Cortese, R. n., Folgori, A. n., Klenerman, P. n., Barnes, E. n. 2014; 6 (261): 261ra153

  Abstract

  A protective vaccine against hepatitis C virus (HCV) remains an unmet clinical need. HCV infects millions of people worldwide and is a leading cause of liver cirrhosis and hepatocellular cancer. Animal challenge experiments, immunogenetics studies, and assessment of host immunity during acute infection highlight the critical role that effective T cell immunity plays in viral control. In this first-in-man study, we have induced antiviral immunity with functional characteristics analogous to those associated with viral control in natural infection, and improved upon a vaccine based on adenoviral vectors alone. We assessed a heterologous prime-boost vaccination strategy based on a replicative defective simian adenoviral vector (ChAd3) and modified vaccinia Ankara (MVA) vector encoding the NS3, NS4, NS5A, and NS5B proteins of HCV genotype 1b. Analysis used single-cell mass cytometry and human leukocyte antigen class I peptide tetramer technology in healthy human volunteers. We show that HCV-specific T cells induced by ChAd3 are optimally boosted with MVA, and generate very high levels of both CD8(+) and CD4(+) HCV-specific T cells targeting multiple HCV antigens. Sustained memory and effector T cell populations are generated, and T cell memory evolved over time with improvement of quality (proliferation and polyfunctionality) after heterologous MVA boost. We have developed an HCV vaccine strategy, with durable, broad, sustained, and balanced T cell responses, characteristic of those associated with viral control, paving the way for the first efficacy studies of a prophylactic HCV vaccine.

  View details for PubMedID 25378645

• CD4+ T Cell Autoimmunity to Hypocretin/Orexin and Cross-Reactivity to a 2009 H1N1 Influenza A Epitope in Narcolepsy. Science translational medicine De la Herrán-Arita, A. K., Kornum, B. R., Mahlios, J., Jiang, W., Lin, L., Hou, T., Macaubas, C., Einen, M., Plazzi, G., Crowe, C., Newell, E. W., Davis, M. M., Mellins, E. D., Mignot, E. 2013; 5 (216): 216ra176-?

  Abstract

  Narcolepsy, a disorder strongly associated with human leukocyte antigen (HLA)-DQA1*01:02/DQB1*06:02 (DQ0602), is characterized by excessive daytime sleepiness, cataplexy, and rapid eye movement sleep abnormalities. It is caused by the loss of ~70,000 posterior hypothalamic neurons that produce the wake-promoting neuropeptide hypocretin (HCRT) (orexin). We identified two DQ0602-binding HCRT epitopes, HCRT56-68 and HCRT87-99, that activated a subpopulation of CD4(+) T cells in narcolepsy patients but not in DQ0602-positive healthy control subjects. Because of the established association of narcolepsy with the 2009 H1N1 influenza A strain (pH1N1), we administered a seasonal influenza vaccine (containing pH1N1) to patients with narcolepsy and found an increased frequency of circulating HCRT56-68- and HCRT87-99-reactive T cells. We also identified a hemagglutinin (HA) pHA1 epitope specific to the 2009 H1N1 strain, pHA1275-287, with homology to HCRT56-68 and HCRT87-99. In vitro stimulation of narcolepsy CD4(+) T cells with pH1N1 proteins or pHA1275-287 increased the frequency of HCRT56-68- and HCRT87-99-reactive T cells. Our data indicate the presence of CD4(+) T cells that are reactive to HCRT in narcolepsy patients and possible molecular mimicry between HCRT and a similar epitope in influenza pH1N1, pHA1275-287.

  View details for DOI 10.1126/scitranslmed.3007762

  View details for PubMedID 24353159

• A Single Peptide-Major Histocompatibility Complex Ligand Triggers Digital Cytokine Secretion in CD4(+) T Cells. Immunity Huang, J., Brameshuber, M., Zeng, X., Xie, J., Li, Q., Chien, Y., Valitutti, S., Davis, M. M. 2013; 39 (5): 846-857

  Abstract

  We have developed a single-molecule imaging technique that uses quantum-dot-labeled peptide-major histocompatibility complex (pMHC) ligands to study CD4(+) T cell functional sensitivity. We found that naive T cells, T cell blasts, and memory T cells could all be triggered by a single pMHC to secrete tumor necrosis factor-α (TNF-α) and interleukin-2 (IL-2) cytokines with a rate of ∼1,000, ∼10,000, and ∼10,000 molecules/min, respectively, and that additional pMHCs did not augment secretion, indicating a digital response pattern. We also found that a single pMHC localized to the immunological synapse induced the slow formation of a long-lasting T cell receptor (TCR) cluster, consistent with a serial engagement mechanism. These data show that scaling up CD4(+) T cell cytokine responses involves increasingly efficient T cell recruitment rather than greater cytokine production per cell.

  View details for DOI 10.1016/j.immuni.2013.08.036

  View details for PubMedID 24120362

  View details for PubMedCentralID PMC3846396

• Genetic and environmental determinants of human NK cell diversity revealed by mass cytometry. Science translational medicine Horowitz, A., Strauss-Albee, D. M., Leipold, M., Kubo, J., Nemat-Gorgani, N., Dogan, O. C., Dekker, C. L., Mackey, S., Maecker, H., Swan, G. E., Davis, M. M., Norman, P. J., Guethlein, L. A., Desai, M., Parham, P., Blish, C. A. 2013; 5 (208): 208ra145-?

  Abstract

  Natural killer (NK) cells play critical roles in immune defense and reproduction, yet remain the most poorly understood major lymphocyte population. Because their activation is controlled by a variety of combinatorially expressed activating and inhibitory receptors, NK cell diversity and function are closely linked. To provide an unprecedented understanding of NK cell repertoire diversity, we used mass cytometry to simultaneously analyze 37 parameters, including 28 NK cell receptors, on peripheral blood NK cells from 5 sets of monozygotic twins and 12 unrelated donors of defined human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) genotype. This analysis revealed a remarkable degree of NK cell diversity, with an estimated 6000 to 30,000 phenotypic populations within an individual and >100,000 phenotypes in the donor panel. Genetics largely determined inhibitory receptor expression, whereas activation receptor expression was heavily environmentally influenced. Therefore, NK cells may maintain self-tolerance through strictly regulated expression of inhibitory receptors while using adaptable expression patterns of activating and costimulatory receptors to respond to pathogens and tumors. These findings further suggest the possibility that discrete NK cell subpopulations could be harnessed for immunotherapeutic strategies in the settings of infection, reproduction, and transplantation.

  View details for DOI 10.1126/scitranslmed.3006702

  View details for PubMedID 24154599

• Genetic and environmental determinants of human NK cell diversity revealed by mass cytometry. Science translational medicine Horowitz, A., Strauss-Albee, D. M., Leipold, M., Kubo, J., Nemat-Gorgani, N., Dogan, O. C., Dekker, C. L., Mackey, S., Maecker, H., Swan, G. E., Davis, M. M., Norman, P. J., Guethlein, L. A., Desai, M., Parham, P., Blish, C. A. 2013; 5 (208): 208ra145-?

  Abstract

  Natural killer (NK) cells play critical roles in immune defense and reproduction, yet remain the most poorly understood major lymphocyte population. Because their activation is controlled by a variety of combinatorially expressed activating and inhibitory receptors, NK cell diversity and function are closely linked. To provide an unprecedented understanding of NK cell repertoire diversity, we used mass cytometry to simultaneously analyze 37 parameters, including 28 NK cell receptors, on peripheral blood NK cells from 5 sets of monozygotic twins and 12 unrelated donors of defined human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) genotype. This analysis revealed a remarkable degree of NK cell diversity, with an estimated 6000 to 30,000 phenotypic populations within an individual and >100,000 phenotypes in the donor panel. Genetics largely determined inhibitory receptor expression, whereas activation receptor expression was heavily environmentally influenced. Therefore, NK cells may maintain self-tolerance through strictly regulated expression of inhibitory receptors while using adaptable expression patterns of activating and costimulatory receptors to respond to pathogens and tumors. These findings further suggest the possibility that discrete NK cell subpopulations could be harnessed for immunotherapeutic strategies in the settings of infection, reproduction, and transplantation.

  View details for DOI 10.1126/scitranslmed.3006702

  View details for PubMedID 24154599

• Human Circulating PD-1(+)CXCR3(-)CXCR5(+) Memory Tfh Cells Are Highly Functional and Correlate with Broadly Neutralizing HIV Antibody Responses IMMUNITY Locci, M., Havenar-Daughton, C., Landais, E., Wu, J., Kroenke, M. A., Arlehamn, C. L., Su, L. F., Cubas, R., Davis, M. M., Sette, A., Haddad, E. K., Poignard, P., Crotty, S. 2013; 39 (4): 758-769

  Abstract

  The vast majority of currently licensed human vaccines work on the basis of long-term protective antibody responses. It is now conceivable that an antibody-dependent HIV vaccine might be possible, given the discovery of HIV broadly neutralizing antibodies (bnAbs) in some HIV-infected individuals. However, these antibodies are difficult to develop and have characteristics indicative of a high degree of affinity maturation in germinal centers (GCs). CD4⁺ T follicular helper (Tfh) cells are specialized for B cell help and necessary for GCs. Therefore, the development of HIV bnAbs might depend on Tfh cells. Here, we identified in normal individuals a subpopulation of circulating memory PD-1⁺CXCR5⁺CD4⁺ T cells that are resting memory cells most related to bona fide GC Tfh cells by gene expression profile, cytokine profile, and functional properties. Importantly, the frequency of these cells correlated with the development of bnAbs against HIV in a large cohort of HIV⁺ individuals.

  View details for DOI 10.1016/j.immuni.2013.08.031

  View details for Web of Science ID 000330950000016

  View details for PubMedID 24035365

• Antiviral memory phenotype T cells in unexposed adults IMMUNOLOGICAL REVIEWS Su, L. F., Davis, M. M. 2013; 255 (1): 95-109

  Abstract

  αβ T cells are an integral part of protective immunity against pathogens. After precursor cells arise in the adult bone marrow or fetal liver, they migrate to the thymus where they rearrange their T-cell receptor genes (TCR) and undergo selection on the basis of their interactions with ligands expressed by thymic stroma and other cells. Those that survive then exit the thymus to populate the peripheral immune compartment, where they patrol the blood and lymphoid systems. The composition of this pre-immune peripheral repertoire is critically important in determining the robustness of an immune response. In both mice and humans, the magnitude and diversity of a response are directly correlated with the frequency of precursor T cells. Equally relevant are the functional characteristics of these lymphocytes. Engagement of a specific antigen to the TCR activates signaling pathways in the naive T cell that result in cellular proliferation and the acquisition of particular effector functions. A portion of these persist following the resolution of infection and become memory cells. These memory cells can mount a faster and stronger response when they encounter the same antigen at a later time. As the molecular basis for TCR ligand interaction has become better defined, it is clear that some T cells can recognize multiple distinct ligands and therefore T-cell memory developed by exposure to one ligand may play a significant role in the response to a different antigen. Thus, there is an increasing focus on understanding how exposure to related or unrelated antigens influences the T-cell repertoire and impacts subsequent immunity. In this review, we discuss the issue of TCR cross-reactivity in the development of memory phenotype CD4(+) T cells and the implications for pathogen-specific responses. We review both the human and mouse data and discuss the therapeutic implications of these findings in the contexts of infection and vaccination.

  View details for DOI 10.1111/imr.12095

  View details for Web of Science ID 000323150900008

  View details for PubMedID 23947350

• Dietary gluten triggers concomitant activation of CD4(+) and CD8(+) alpha beta T cells and gamma delta T cells in celiac disease PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Han, A., Newell, E. W., Glanville, J., Fernandez-Becker, N., Khosla, C., Chien, Y., Davis, M. M. 2013; 110 (32): 13073-13078

  View details for DOI 10.1073/pnas.1311861110

  View details for Web of Science ID 000322771100057

• Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization NATURE BIOTECHNOLOGY Newell, E. W., Sigal, N., Nair, N., Kidd, B. A., Greenberg, H. B., Davis, M. M. 2013; 31 (7): 623-U81

  Abstract

  It is currently not possible to predict which epitopes will be recognized by T cells in different individuals. This is a barrier to the thorough analysis and understanding of T-cell responses after vaccination or infection. Here, by combining mass cytometry with combinatorial peptide-MHC tetramer staining, we have developed a method allowing the rapid and simultaneous identification and characterization of T cells specific for many epitopes. We use this to screen up to 109 different peptide-MHC tetramers in a single human blood sample, while still retaining at least 23 labels to analyze other markers of T-cell phenotype and function. Among 77 candidate rotavirus epitopes, we identified six T-cell epitopes restricted to human leukocyte antigen (HLA)-A*0201 in the blood of healthy individuals. T cells specific for epitopes in the rotavirus VP3 protein displayed a distinct phenotype and were present at high frequencies in intestinal epithelium. This approach should be useful for the comprehensive analysis of T-cell responses to infectious diseases or vaccines.

  View details for DOI 10.1038/nbt.2593

  View details for Web of Science ID 000321579700019

  View details for PubMedID 23748502

• HIGH THROUGHPUT HIGH FIDELITY HLA TYPING WITH DEEP SEQUENCING 27th Annual EFI European Immunogenetics and Histocompatibility Conference Mindros, M., Wang, C., Krishnakumar, S., Barsakis, K., Miranda, M., Babrzadeh, F., Suresh, S., Kuehn, R. T., Davis, M. M., Davis, R., Fernandez-Vina, M. A. WILEY-BLACKWELL. 2013: 344–44

  View details for Web of Science ID 000318523600194

• A single peptide-MHC triggers digital cytokine secretion in both naive and activated CD4+T cells Huang, J., Davis, M. AMER ASSOC IMMUNOLOGISTS. 2013

  View details for Web of Science ID 000322987101117

• Lateral distribution of the T cell receptor and cholesterol detected by high-resolution secondary ion mass spectrometry Wang, F., Lozano, M., Lillemeier, B., Boxer, S., Davis, M. AMER ASSOC IMMUNOLOGISTS. 2013

  View details for Web of Science ID 000322987104045

• Influenza antigen microarrays reveal reactivity signatures associated with effective response to seasonal trivalent influenza vaccination Price, J., Jarrell, J., Furman, D., Kattah, N., Newell, E., Dekker, C., Davis, M., Utz, P. AMER ASSOC IMMUNOLOGISTS. 2013

  View details for Web of Science ID 000322987105110

• Discovering the determinants of diversity in the human NK cell repertoire by mass cytometry Horowitz, A., Strauss-Albee, D., Nemat-Gorgani, N., Dogan, O., Dekker, C., Mackey, S., Swan, G., Davis, M., Norman, P., Guethlein, L., Parham, P., Blish, C. AMER ASSOC IMMUNOLOGISTS. 2013

  View details for Web of Science ID 000322987102195

• Quantifying the unanticipated diversity of the human NK cell repertoire Strauss-Albee, D., Horowitz, A., Dogan, O., Mackey, S., Swan, G., Dekker, C., Davis, M., Parham, P., Blish, C. AMER ASSOC IMMUNOLOGISTS. 2013

  View details for Web of Science ID 000322987101178

• Distinct TCR signaling pathways drive proliferation and cytokine production in T cells NATURE IMMUNOLOGY Guy, C. S., Vignali, K. M., Temirov, J., Bettini, M. L., Overacre, A. E., Smeltzer, M., Zhang, H., Huppa, J. B., Tsai, Y., Lobry, C., Xie, J., Dempsey, P. J., Crawford, H. C., Aifantis, I., Davis, M. M., Vignali, D. A. 2013; 14 (3): 262-270

  Abstract

  The physiological basis and mechanistic requirements for a large number of functional immunoreceptor tyrosine-based activation motifs (ITAMs; high ITAM multiplicity) in the complex of the T cell antigen receptor (TCR) and the invariant signaling protein CD3 remain obscure. Here we found that whereas a low multiplicity of TCR-CD3 ITAMs was sufficient to engage canonical TCR-induced signaling events that led to cytokine secretion, a high multiplicity of TCR-CD3 ITAMs was required for TCR-driven proliferation. This was dependent on the formation of compact immunological synapses, interaction of the adaptor Vav1 with phosphorylated CD3 ITAMs to mediate the recruitment and activation of the oncogenic transcription factor Notch1 and, ultimately, proliferation induced by the cell-cycle regulator c-Myc. Analogous mechanistic events were also needed to drive proliferation in response to weak peptide agonists. Thus, the TCR-driven pathways that initiate cytokine secretion and proliferation are separable and are coordinated by the multiplicity of phosphorylated ITAMs in TCR-CD3.

  View details for DOI 10.1038/ni.2538

  View details for Web of Science ID 000315065400016

  View details for PubMedID 23377202

  View details for PubMedCentralID PMC3577985

• Virus-specific CD4(+) memory-phenotype T cells are abundant in unexposed adults. Immunity Su, L. F., Kidd, B. A., Han, A., Kotzin, J. J., Davis, M. M. 2013; 38 (2): 373-383

  Abstract

  Although T cell memory is generally thought to require direct antigen exposure, we found an abundance of memory-phenotype cells (20%-90%, averaging over 50%) of CD4(+) T cells specific to viral antigens in adults who had never been infected. These cells express the appropriate memory markers and genes, rapidly produce cytokines, and have clonally expanded. In contrast, the same T cell receptor (TCR) specificities in newborns are almost entirely naïve, which might explain the vulnerability of young children to infections. One mechanism for this phenomenon is TCR cross-reactivity to environmental antigens, and in support of this, we found extensive cross-recognition by HIV-1 and influenza-reactive T lymphocytes to other microbial peptides and expansion of one of these after influenza vaccination. Thus, the presence of these memory-phenotype T cells has significant implications for immunity to novel pathogens, child and adult health, and the influence of pathogen-rich versus hygienic environments.

  View details for DOI 10.1016/j.immuni.2012.10.021

  View details for PubMedID 23395677

  View details for PubMedCentralID PMC3626102

• Lineage structure of the human antibody repertoire in response to influenza vaccination. Science translational medicine Jiang, N., He, J., Weinstein, J. A., Penland, L., Sasaki, S., He, X., Dekker, C. L., Zheng, N., Huang, M., Sullivan, M., Wilson, P. C., Greenberg, H. B., Davis, M. M., Fisher, D. S., Quake, S. R. 2013; 5 (171): 171ra19-?

  Abstract

  The human antibody repertoire is one of the most important defenses against infectious disease, and the development of vaccines has enabled the conferral of targeted protection to specific pathogens. However, there are many challenges to measuring and analyzing the immunoglobulin sequence repertoire, including that each B cell's genome encodes a distinct antibody sequence, that the antibody repertoire changes over time, and the high similarity between antibody sequences. We have addressed these challenges by using high-throughput long read sequencing to perform immunogenomic characterization of expressed human antibody repertoires in the context of influenza vaccination. Informatic analysis of 5 million antibody heavy chain sequences from healthy individuals allowed us to perform global characterizations of isotype distributions, determine the lineage structure of the repertoire, and measure age- and antigen-related mutational activity. Our analysis of the clonal structure and mutational distribution of individuals' repertoires shows that elderly subjects have a decreased number of lineages but an increased prevaccination mutation load in their repertoire and that some of these subjects have an oligoclonal character to their repertoire in which the diversity of the lineages is greatly reduced relative to younger subjects. We have thus shown that global analysis of the immune system's clonal structure provides direct insight into the effects of vaccination and provides a detailed molecular portrait of age-related effects.

  View details for DOI 10.1126/scitranslmed.3004794

  View details for PubMedID 23390249

• Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination SCIENCE TRANSLATIONAL MEDICINE Jiang, N., He, J., Weinstein, J. A., Penland, L., Sasaki, S., He, X., Dekker, C. L., Zheng, N., Huang, M., Sullivan, M., Wilson, P. C., Greenberg, H. B., Davis, M. M., Fisher, D. S., Quake, S. R. 2013; 5 (171)

  Abstract

  The human antibody repertoire is one of the most important defenses against infectious disease, and the development of vaccines has enabled the conferral of targeted protection to specific pathogens. However, there are many challenges to measuring and analyzing the immunoglobulin sequence repertoire, including that each B cell's genome encodes a distinct antibody sequence, that the antibody repertoire changes over time, and the high similarity between antibody sequences. We have addressed these challenges by using high-throughput long read sequencing to perform immunogenomic characterization of expressed human antibody repertoires in the context of influenza vaccination. Informatic analysis of 5 million antibody heavy chain sequences from healthy individuals allowed us to perform global characterizations of isotype distributions, determine the lineage structure of the repertoire, and measure age- and antigen-related mutational activity. Our analysis of the clonal structure and mutational distribution of individuals' repertoires shows that elderly subjects have a decreased number of lineages but an increased prevaccination mutation load in their repertoire and that some of these subjects have an oligoclonal character to their repertoire in which the diversity of the lineages is greatly reduced relative to younger subjects. We have thus shown that global analysis of the immune system's clonal structure provides direct insight into the effects of vaccination and provides a detailed molecular portrait of age-related effects.

  View details for Web of Science ID 000314810000008

  View details for PubMedID 23390249

• Characterization of influenza vaccine immunogenicity using influenza antigen microarrays. PloS one Price, J. V., Jarrell, J. A., Furman, D., Kattah, N. H., Newell, E., Dekker, C. L., Davis, M. M., Utz, P. J. 2013; 8 (5)

  Abstract

  Existing methods to measure influenza vaccine immunogenicity prohibit detailed analysis of epitope determinants recognized by immunoglobulins. The development of highly multiplex proteomics platforms capable of capturing a high level of antibody binding information will enable researchers and clinicians to generate rapid and meaningful readouts of influenza-specific antibody reactivity.We developed influenza hemagglutinin (HA) whole-protein and peptide microarrays and validated that the arrays allow detection of specific antibody reactivity across a broad dynamic range using commercially available antibodies targeted to linear and conformational HA epitopes. We derived serum from blood draws taken from 76 young and elderly subjects immediately before and 28±7 days post-vaccination with the 2008/2009 trivalent influenza vaccine and determined the antibody reactivity of these sera to influenza array antigens.Using linear regression and correcting for multiple hypothesis testing by the Benjamini and Hochberg method of permutations over 1000 resamplings, we identified antibody reactivity to influenza whole-protein and peptide array features that correlated significantly with age, H1N1, and B-strain post-vaccine titer as assessed through a standard microneutralization assay (p<0.05, q <0.2). Notably, we identified several peptide epitopes that were inversely correlated with regard to age and seasonal H1N1 and B-strain neutralization titer (p<0.05, q <0.2), implicating reactivity to these epitopes in age-related defects in response to H1N1 influenza. We also employed multivariate linear regression with cross-validation to build models based on age and pre-vaccine peptide reactivity that predicted vaccine-induced neutralization of seasonal H1N1 and H3N2 influenza strains with a high level of accuracy (84.7% and 74.0%, respectively).Our methods provide powerful tools for rapid and accurate measurement of broad antibody-based immune responses to influenza, and may be useful in measuring response to other vaccines and infectious agents.

  View details for DOI 10.1371/journal.pone.0064555

  View details for PubMedID 23734205

  View details for PubMedCentralID PMC3667171

• The promised land of human immunology. Cold Spring Harbor symposia on quantitative biology Su, L. F., Han, A., McGuire, H. M., Furman, D., Newell, E. W., Davis, M. M. 2013; 78: 203-213

  Abstract

  Advances in technology and data analysis have made it possible to take a new look at human immunology. These advances run the gamut from systems biology approaches, which are likely in the vanguard of how we can start "to put the pieces together" of immune function, to a deeper understanding of specific diseases and vaccines and the immune repertoire. In our own experience, we have also found that asking simple questions about human immunity has often given us very surprising answers, causing a rethink of established dogma. Thus, we have developed a new perspective on the nature of the αβ TCR repertoire and also the likely role of T-cell repertoire (TCR) cross-reactivity in generating T memory independent of specific antigen interactions. These findings show that human immunology is not just a necessary step for "translating" basic immunology to treat diseases or develop better vaccines, but is also an important complement to the inbred mouse model.

  View details for DOI 10.1101/sqb.2013.78.022905

  View details for PubMedID 24638855

• Characterization of influenza vaccine immunogenicity using influenza antigen microarrays. PloS one Price, J. V., Jarrell, J. A., Furman, D., Kattah, N. H., Newell, E., Dekker, C. L., Davis, M. M., Utz, P. J. 2013; 8 (5)

  View details for DOI 10.1371/journal.pone.0064555

  View details for PubMedID 23734205

• Apoptosis and other immune biomarkers predict influenza vaccine responsiveness. Molecular systems biology Furman, D., Jojic, V., Kidd, B., Shen-Orr, S., Price, J., Jarrell, J., Tse, T., Huang, H., Lund, P., Maecker, H. T., Utz, P. J., Dekker, C. L., Koller, D., Davis, M. M. 2013; 9: 659-?

  View details for DOI 10.1038/msb.2013.15

  View details for PubMedID 23591775

• The interdisciplinary science of T-cell recognition. Advances in immunology Huppa, J. B., Davis, M. M. 2013; 119: 1-50

  Abstract

  The recognition of peptide/MHC antigens by T-cells has continued to challenge the imagination of immunologists, biochemists, and cell biologists alike. This is at least in part because T-cell recognition connects a diversity of issues and transcends many scientific disciplines. A fundamental unsolved issue is how T-cells manage to detect even a single molecule of an agonist pMHC complex, which is vastly outnumbered by endogenous pMHCs, many of which involve the same MHC molecule. They do so although TCRs are cross-reactive and typically low in affinity when measured in isolation. Importantly, T-cell antigen recognition takes place within the contact zone between a T-cell and the antigen-presenting cell, termed the immunological synapse. This bimembrane structure sets the stage for the antigen-binding events and all subsequent molecular recognition events. There is increasing evidence that the molecular dynamics of receptor-ligand interactions are not only dependent on the intrinsic properties of the binding partners but also become transformed by cell biological parameters such as the geometrical constraints within the immune synapse, mechanical forces, and local molecular crowding. To appreciate the complete picture, we think a multidisciplinary approach is imperative, which includes genetics, biochemistry, and structure determination and also biophysical analyses and the latest molecular imaging techniques. Here, we review earlier pioneering work and also recent developments in the fascinating and interdisciplinary science of T-cell antigen recognition. In many ways, this work may present a useful "roadmap" for work in other systems of cell-cell recognition, which underlie many fundamental biological phenomenons of interest.

  View details for DOI 10.1016/B978-0-12-407707-2.00001-1

  View details for PubMedID 23886063

• Apoptosis and other immune biomarkers predict influenza vaccine responsiveness. Molecular systems biology Furman, D., Jojic, V., Kidd, B., Shen-Orr, S., Price, J., Jarrell, J., Tse, T., Huang, H., Lund, P., Maecker, H. T., Utz, P. J., Dekker, C. L., Koller, D., Davis, M. M. 2013; 9: 659-?

  Abstract

  Despite the importance of the immune system in many diseases, there are currently no objective benchmarks of immunological health. In an effort to identifying such markers, we used influenza vaccination in 30 young (20-30 years) and 59 older subjects (60 to >89 years) as models for strong and weak immune responses, respectively, and assayed their serological responses to influenza strains as well as a wide variety of other parameters, including gene expression, antibodies to hemagglutinin peptides, serum cytokines, cell subset phenotypes and in vitro cytokine stimulation. Using machine learning, we identified nine variables that predict the antibody response with 84% accuracy. Two of these variables are involved in apoptosis, which positively associated with the response to vaccination and was confirmed to be a contributor to vaccine responsiveness in mice. The identification of these biomarkers provides new insights into what immune features may be most important for immune health.

  View details for DOI 10.1038/msb.2013.15

  View details for PubMedID 23591775

  View details for PubMedCentralID PMC3658270

• How the immune system talks to itself: the varied role of synapses IMMUNOLOGICAL REVIEWS Xie, J., Tato, C. M., Davis, M. M. 2013; 251: 65-79

  Abstract

  Using an elaborately evolved language of cytokines and chemokines as well as cell-cell interactions, the different components of the immune system communicate with each other and orchestrate a response (or wind one down). Immunological synapses are a key feature of the system in the ways in which they can facilitate and direct these responses. Studies analyzing the structure of an immune synapse as it forms between two cells have provided insight into how the stability and kinetics of this interaction ultimately affect the sensitivity, potency, and magnitude of a given response. Furthermore, we have gained an appreciation of how the immunological synapse provides directionality and contextual cues for downstream signaling and cellular decision-making. In this review, we discuss how using a variety of techniques, developed over the last decade, have allowed us to visualize and quantify key aspects of the dynamic synaptic interface and have furthered our understanding of their function. We describe some of the many characteristics of the immunological synapse that make it a vital part of intercellular communication and some of the questions that remain to be answered.

  View details for DOI 10.1111/imr.12017

  View details for Web of Science ID 000317077400006

  View details for PubMedID 23278741

  View details for PubMedCentralID PMC3645447

• Pluripotent Stem Cells: Immune to the Immune System? SCIENCE TRANSLATIONAL MEDICINE Pearl, J. I., Kean, L. S., Davis, M. M., Wu, J. C. 2012; 4 (164)

  Abstract

  Human embryonic stem cells (hESCs), initially thought to be immune privileged cells, are now known to be susceptible to immune recognition. Human induced pluripotent stem cells (iPSCs) have been proposed as a potential source of autologous stem cells for therapy, but even these autologous stem cells may be targets of immune rejection. With clinical trials on the horizon, it is imperative that the immunogenicity of hESCs and iPSCs be definitively understood.

  View details for DOI 10.1126/scitranslmed.3005090

  View details for Web of Science ID 000312393900002

  View details for PubMedID 23241742

  View details for PubMedCentralID PMC3638038

• Identification and Characterization of Fibrinogen-Specific T Cells in Patients with Rheumatoid Arthritis. Annual Scientific Meeting of the American-College-of-Rheumatology (ACR) and Association-of-Rheumatology-Health-Professionals (ARHP) Su, L., Davis, M. M. WILEY-BLACKWELL. 2012: S188–S188

  View details for Web of Science ID 000309748300433

• gamma delta T Cells Recognize a Microbial Encoded B Cell Antigen to Initiate a Rapid Antigen-Specific Interleukin-17 Response IMMUNITY Zeng, X., Wei, Y., Huang, J., Newell, E. W., Yu, H., Kidd, B. A., Kuhns, M. S., Waters, R. W., Davis, M. M., Weaver, C. T., Chien, Y. 2012; 37 (3): 524-534

  Abstract

  γδ T cells contribute uniquely to immune competence. Nevertheless, how they function remains an enigma. It is unclear what most γδ T cells recognize, what is required for them to mount an immune response, and how the γδ T cell response is integrated into host immune defense. Here, we report that a noted B cell antigen, the algae protein phycoerythrin (PE), is a murine and human γδ T cell antigen. Employing this specificity, we demonstrated that antigen recognition activated naive γδ T cells to make interleukin-17 and respond to cytokine signals that perpetuate the response. High frequencies of antigen-specific γδ T cells in naive animals and their ability to mount effector response without extensive clonal expansion allow γδ T cells to initiate a swift, substantial response. These results underscore the adaptability of lymphocyte antigen receptors and suggest an antigen-driven rapid response in protective immunity prior to the maturation of classical adaptive immunity.

  View details for DOI 10.1016/j.immuni.2012.06.011

  View details for Web of Science ID 000309199000016

  View details for PubMedID 22960222

  View details for PubMedCentralID PMC3495981

• T cell receptor analyzed with super-resolution imaging secondary ion mass spectrometry Wang, F., Lozano, M., Boxer, S., Davis, M. WILEY-BLACKWELL. 2012: 513

  View details for Web of Science ID 000308128602679

• At the Interface of Photochemistry and Immunobiology: A Photocrosslinkable pMHC Ligand for Detecting and Activating Antigen-specific T Cells 26th Annual Symposium of the Protein-Society Xie, J., Huppa, J., Davis, M. WILEY-BLACKWELL. 2012: 130–131

  View details for Web of Science ID 000307019800197

• T Cell Assays and MIATA: The Essential Minimum for Maximum Impact IMMUNITY Britten, C. M., Janetzki, S., Butterfield, L. H., Ferrari, G., Gouttefangeas, C., Huber, C., Kalos, M., Levitsky, H. I., Maecker, H. T., Melief, C. J., O'Donnell-Tormey, J., Odunsi, K., Old, L. J., Ottenhoff, T. H., Ottensmeier, C., Pawelec, G., Roederer, M., Roep, B. O., Romero, P., van der Burg, S. H., Walter, S., Hoos, A., DAVIS, M. M. 2012; 37 (1): 1-2

  View details for DOI 10.1016/j.immuni.2012.07.010

  View details for Web of Science ID 000307133200001

  View details for PubMedID 22840835

• Determination of Interaction Kinetics between the T Cell Receptor and Peptide-Loaded MHC Class II via Single-Molecule Diffusion Measurements BIOPHYSICAL JOURNAL Axmann, M., Huppa, J. B., Davis, M. M., Schuetz, G. J. 2012; 103 (2): L17-L19

  Abstract

  The binding of peptide-loaded major histocompatibility complex (pMHC) to the T cell receptor (TCR) represents the central step in T cell antigen recognition. It proceeds in the cell contact area between a T cell and an antigen-presenting cell termed the immunological synapse. An important and unresolved issue is how T cells discriminate between potentially harmful and harmless antigens. One limitation has been the difficulty to measure interaction parameters directly, that is, as they occur in the immunological synapse. Here we present a single-molecule approach to determine pMHC-TCR interaction kinetics in situ based on diffusion analysis of dye-labeled pMHC. We find synaptic off-rates >10-fold accelerated when compared to the dissociation of purified proteins measured in vitro.

  View details for DOI 10.1016/j.bpj.2012.06.019

  View details for Web of Science ID 000306522300001

  View details for PubMedCentralID PMC3400783

• Photocrosslinkable pMHC monomers stain T cells specifically and cause ligand-bound TCRs to be 'preferentially' transported to the cSMAC NATURE IMMUNOLOGY Xie, J., Huppa, J. B., Newell, E. W., Huang, J., Ebert, P. J., Li, Q., Davis, M. M. 2012; 13 (7): 674-?

  Abstract

  The binding of T cell antigen receptors (TCRs) to specific complexes of peptide and major histocompatibility complex (pMHC) is typically of very low affinity, which necessitates the use of multimeric pMHC complexes to label T lymphocytes stably. We report here the development of pMHC complexes able to be crosslinked by ultraviolet irradiation; even as monomers, these efficiently and specifically stained cognate T cells. We also used this reagent to probe T cell activation and found that a covalently bound pMHC was more stimulatory than an agonist pMHC on lipid bilayers. This finding suggested that serial engagement of TCRs is dispensable for activation when a substantial fraction of TCRs are stably engaged. Finally, pMHC-bound TCRs were 'preferentially' transported into the central supramolecular activation cluster after activation, which suggested that ligand engagement enabled linkage of the TCR and its associated CD3 signaling molecules to the cytoskeleton.

  View details for DOI 10.1038/ni.2344

  View details for Web of Science ID 000305483800013

  View details for PubMedID 22660579

  View details for PubMedCentralID PMC3645478

• Distinct CD4(+) helper T cells involved in primary and secondary responses to infection PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Weber, K. S., Li, Q., Persaud, S. P., Campbell, J. D., Davis, M. M., Allen, P. M. 2012; 109 (24): 9511-9516

  Abstract

  Helper T cells are critical for protective immunity, CD8(+) T-cell memory, and CD4(+) recall responses, but whether the same or distinct CD4(+) T cells are involved in these responses has not been established. Here we describe two CD4(+) T cells, LLO118 and LLO56, specific for an immunodominant Listeria monocytogenes epitope, with dramatically different responses to primary and secondary infection. Comparing in vivo responses, LLO118 T cells proliferate more strongly to primary infection, whereas surprisingly, LLO56 has a superior CD4(+) recall response to secondary infection. LLO118 T cells provide more robust help for CD8(+) T-cell responses to secondary infection than LLO56. We found no detectable differences in antigen sensitivity, but naive LLO118 T cells have much lower levels of CD5 and their T-cell receptor levels are dramatically down-regulated after their strong primary response. Thus, distinct CD4(+) helper T cells are specialized to help either in primary or secondary responses to infection.

  View details for DOI 10.1073/pnas.1202408109

  View details for Web of Science ID 000305511300063

  View details for PubMedID 22645349

  View details for PubMedCentralID PMC3386110

• HIGH THROUGHPUT, HIGH FIDELITY HLA GENOTYPING WITH ULTRA DEEP SEQUENCING Joint 16th International HLA and Immunogenetics Workshop/26th European Federation for Immunogenetics Conference/23rd British-Society-of-Histocompatibility-and-Immunogenetics Conference Krishnakumar, S., Wang, C., Wilhelmy, J., Babrzadeh, F., Su, L., Levinson, D., Fernandez-Vina, M., Davis, R., Davis, M., Mindrinos, M. N. WILEY-BLACKWELL. 2012: 426–26

  View details for Web of Science ID 000303499800058

• High-throughput, high-fidelity HLA genotyping with deep sequencing PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wang, C., Krishnakumar, S., Wilhelmy, J., Babrzadeh, F., Stepanyan, L., Su, L. F., Levinson, D., Fernandez-Vina, M. A., Davis, R. W., Davis, M. M., Mindrinos, M. 2012; 109 (22): 8676-8681

  Abstract

  Human leukocyte antigen (HLA) genes are the most polymorphic in the human genome. They play a pivotal role in the immune response and have been implicated in numerous human pathologies, especially autoimmunity and infectious diseases. Despite their importance, however, they are rarely characterized comprehensively because of the prohibitive cost of standard technologies and the technical challenges of accurately discriminating between these highly related genes and their many allelles. Here we demonstrate a high-resolution, and cost-effective methodology to type HLA genes by sequencing, which combines the advantage of long-range amplification, the power of high-throughput sequencing platforms, and a unique genotyping algorithm. We calibrated our method for HLA-A, -B, -C, and -DRB1 genes with both reference cell lines and clinical samples and identified several previously undescribed alleles with mismatches, insertions, and deletions. We have further demonstrated the utility of this method in a clinical setting by typing five clinical samples in an Illumina MiSeq instrument with a 5-d turnaround. Overall, this technology has the capacity to deliver low-cost, high-throughput, and accurate HLA typing by multiplexing thousands of samples in a single sequencing run, which will enable comprehensive disease-association studies with large cohorts. Furthermore, this approach can also be extended to include other polymorphic genes.

  View details for DOI 10.1073/pnas.1206614109

  View details for PubMedID 22589303

• High Throughput Sequencing of the Human Antibody Repertoire in Response to Influenza Vaccination 99th Annual Meeting of the American-Association-of-Immunologists Jiang, N., He, J., Weinstein, J., Penland, L., Saaki, S., He, X., Dekker, C., Wilson, P., Greenberg, H., Davis, M., Fisher, D., Quake, S. AMER ASSOC IMMUNOLOGISTS. 2012

  View details for Web of Science ID 000304659700423

• Oral polio vaccination failure in urban slum children is associated with malnutrition and evidence of chronic inflammation Newell, E., Sigal, N., Haque, R., Kidd, B., Tse, T., Petri, W., Davis, M. AMER ASSOC IMMUNOLOGISTS. 2012

  View details for Web of Science ID 000304659701623

• Regulation of selection and autoimmunity by miR-181 family miRNAs 99th Annual Meeting of the American-Association-of-Immunologists Schaffert, S., Wang, S., Axtell, R., Newell, E., Steinman, L., Davis, M., Chen, C. AMER ASSOC IMMUNOLOGISTS. 2012

  View details for Web of Science ID 000304659701313

• The Stanford Data Miner: a novel approach for integrating and exploring heterogeneous immunological data JOURNAL OF TRANSLATIONAL MEDICINE Siebert, J. C., Munsil, W., Rosenberg-Hasson, Y., Davis, M. M., Maecker, H. T. 2012; 10

  Abstract

  Systems-level approaches are increasingly common in both murine and human translational studies. These approaches employ multiple high information content assays. As a result, there is a need for tools to integrate heterogeneous types of laboratory and clinical/demographic data, and to allow the exploration of that data by aggregating and/or segregating results based on particular variables (e.g., mean cytokine levels by age and gender).Here we describe the application of standard data warehousing tools to create a novel environment for user-driven upload, integration, and exploration of heterogeneous data. The system presented here currently supports flow cytometry and immunoassays performed in the Stanford Human Immune Monitoring Center, but could be applied more generally.Users upload assay results contained in platform-specific spreadsheets of a defined format, and clinical and demographic data in spreadsheets of flexible format. Users then map sample IDs to connect the assay results with the metadata. An OLAP (on-line analytical processing) data exploration interface allows filtering and display of various dimensions (e.g., Luminex analytes in rows, treatment group in columns, filtered on a particular study). Statistics such as mean, median, and N can be displayed. The views can be expanded or contracted to aggregate or segregate data at various levels. Individual-level data is accessible with a single click. The result is a user-driven system that permits data integration and exploration in a variety of settings. We show how the system can be used to find gender-specific differences in serum cytokine levels, and compare them across experiments and assay types.We have used the tools and techniques of data warehousing, including open-source business intelligence software, to support investigator-driven data integration and mining of diverse immunological data.

  View details for DOI 10.1186/1479-5876-10-62

  View details for Web of Science ID 000304554800001

  View details for PubMedID 22452993

  View details for PubMedCentralID PMC3358233

• Significance analysis of xMap cytokine bead arrays PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Won, J., Goldberger, O., Shen-Orr, S. S., Davis, M. M., Olshen, R. A. 2012; 109 (8): 2848-2853

  Abstract

  Highly multiplexed assays using antibody coated, fluorescent (xMap) beads are widely used to measure quantities of soluble analytes, such as cytokines and antibodies in clinical and other studies. Current analyses of these assays use methods based on standard curves that have limitations in detecting low or high abundance analytes. Here we describe SAxCyB (Significance Analysis of xMap Cytokine Beads), a method that uses fluorescence measurements of individual beads to find significant differences between experimental conditions. We show that SAxCyB outperforms conventional analysis schemes in both sensitivity (low fluorescence) and robustness (high variability) and has enabled us to find many new differentially expressed cytokines in published studies.

  View details for DOI 10.1073/pnas.1112599109

  View details for Web of Science ID 000300495100041

  View details for PubMedID 22323610

  View details for PubMedCentralID PMC3286996

• Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8(+) T Cell Phenotypes IMMUNITY Newell, E. W., Sigal, N., Bendall, S. C., Nolan, G. P., Davis, M. M. 2012; 36 (1): 142-152

  Abstract

  Cytotoxic CD8(+) T lymphocytes directly kill infected or aberrant cells and secrete proinflammatory cytokines. By using metal-labeled probes and mass spectrometric analysis (cytometry by time-of-flight, or CyTOF) of human CD8(+) T cells, we analyzed the expression of many more proteins than previously possible with fluorescent labels, including surface markers, cytokines, and antigen specificity with modified peptide-MHC tetramers. With 3-dimensional principal component analysis (3D-PCA) to display phenotypic diversity, we observed a relatively uniform pattern of variation in all subjects tested, highlighting the interrelatedness of previously described subsets and the continuous nature of CD8(+) T cell differentiation. These data also showed much greater complexity in the CD8(+) T cell compartment than previously appreciated, including a nearly combinatorial pattern of cytokine expression, with distinct niches occupied by virus-specific cells. This large degree of functional diversity even between cells with the same specificity gives CD8(+) T cells a remarkable degree of flexibility in responding to pathogens.

  View details for DOI 10.1016/j.immuni.2012.01.002

  View details for Web of Science ID 000299766000017

  View details for PubMedID 22265676

• Immunology Taught by Humans SCIENCE TRANSLATIONAL MEDICINE Davis, M. M. 2012; 4 (117)

  View details for DOI 10.1126/scitranslmed.3003385

  View details for Web of Science ID 000299326000001

  View details for PubMedID 22261029

• TCR signaling emerges from the sum of many parts FRONTIERS IN IMMUNOLOGY Kuhns, M. S., Davis, M. M. 2012; 3

  Abstract

  "How does T cell receptor signaling begin?" Answering this question requires an understanding of how the parts of the molecular machinery that mediates this process fit and work together. Ultimately this molecular architecture must (i) trigger the relay of information from the TCR-pMHC interface to the signaling substrates of the CD3 molecules and (ii) bring the kinases that modify these substrates in close proximity to interact, initiate, and sustain signaling. In this contribution we will discuss advances of the last decade that have increased our understanding of the complex machinery and interactions that underlie this type of signaling.

  View details for DOI 10.3389/fimmu.2012.00159

  View details for Web of Science ID 000209501300156

  View details for PubMedCentralID PMC3381686

• CD4(+) T-cell synapses involve multiple distinct stages PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ueda, H., Morphew, M. K., McIntosh, J. R., Davis, M. M. 2011; 108 (41): 17099-17104

  Abstract

  One very striking feature of T-cell recognition is the formation of an immunological synapse between a T cell and a cell that it is recognizing. Formation of this complex structure correlates with cytotoxicity in the case of killer (largely CD8(+)) T-cell activity, or robust cytokine release and proliferation in the case of the much longer lived synapses formed by helper (CD4(+)) T cells. Here we have used electron microscopy and 3D tomography to characterize the synapses of antigen-specific CD4(+) T cells recognizing B cells and dendritic cells at different time points. We show that there are at least four distinct stages in synapse formation, proceeding over several hours, including an initial stage involving invasive T-cell pseudopodia that penetrate deeply into the antigen-presenting cell, almost to the nuclear envelope. This must involve considerable force and may serve to widen the search for potential ligands on the surface of the cell being recognized. We also show that centrioles and the Golgi complex are always located immediately beneath the synapse and that centrioles are significantly shifted toward the late contact zone with either B lymphocytes or bone marrow-derived dendritic cells such as antigen-presenting cells, and that there are dynamic, stage-dependent changes in the organization of microtubules beneath the synapse. These data reinforce and extend previous data on cytotoxic T cells that one of the principal functions of the immunological synapse is to facilitate cytokine secretion into the synaptic cleft, as well as provide important insights into the overall dynamics of this phenomenon.

  View details for DOI 10.1073/pnas.1113703108

  View details for Web of Science ID 000295973800047

  View details for PubMedID 21949383

  View details for PubMedCentralID PMC3193211

• Citrullinated Fibrinogen-Specific CD4(+) T Cells Display Memory and Regulatory Phenotypes 75th Annual Scientific Meeting of the American-College-of-Rheumatology/46th Annual Scientific Meeting of the Association-of-Rheumatology-Health-Professionals (ARHP) Su, L., Davis, M. M. WILEY-BLACKWELL. 2011: S335–S335

  View details for Web of Science ID 000297621501049

• Limited efficacy of inactivated influenza vaccine in elderly individuals is associated with decreased production of vaccine-specific antibodies JOURNAL OF CLINICAL INVESTIGATION Sasaki, S., Sullivan, M., Narvaez, C. F., Holmes, T. H., Furman, D., Zheng, N., Nishtala, M., Wrammert, J., Smith, K., James, J. A., Dekker, C. L., Davis, M. M., Wilson, P. C., Greenberg, H. B., He, X. 2011; 121 (8): 3109-3119

  Abstract

  During seasonal influenza epidemics, disease burden is shouldered predominantly by the very young and the elderly. Elderly individuals are particularly affected, in part because vaccine efficacy wanes with age. This has been linked to a reduced ability to induce a robust serum antibody response. Here, we show that this is due to reduced quantities of vaccine-specific antibodies, rather than a lack of antibody avidity or affinity. We measured levels of vaccine-specific plasmablasts by ELISPOT 1 week after immunization of young and elderly adults with inactivated seasonal influenza vaccine. Plasmablast-derived polyclonal antibodies (PPAbs) were generated from bulk-cultured B cells, while recombinant monoclonal antibodies (re-mAbs) were produced from single plasmablasts. The frequency of vaccine-specific plasmablasts and the concentration of PPAbs were lower in the elderly than in young adults, whereas the yields of secreted IgG per plasmablast were not different. Differences were not detected in the overall vaccine-specific avidity or affinity of PPAbs and re-mAbs between the 2 age groups. In contrast, reactivity of the antibodies induced by the inactivated seasonal influenza vaccine toward the 2009 pandemic H1N1 virus, which was not present in the vaccine, was higher in the elderly than in the young. These results indicate that the inferior antibody response to influenza vaccination in the elderly is primarily due to reduced quantities of vaccine-specific antibodies. They also suggest that exposure history affects the cross-reactivity of vaccination-induced antibodies.

  View details for DOI 10.1172/JCI57834

  View details for Web of Science ID 000293495500022

  View details for PubMedID 21785218

  View details for PubMedCentralID PMC3148747

• Interrogating the repertoire: broadening the scope of peptide-MHC multimer analysis NATURE REVIEWS IMMUNOLOGY Davis, M. M., Altman, J. D., Newell, E. W. 2011; 11 (8): 551-558

  Abstract

  Labelling antigen-specific T cells with peptide-MHC multimers has provided an invaluable way to monitor T cell-mediated immune responses. A number of recent developments in this technology have made these multimers much easier to make and use in large numbers. Furthermore, enrichment techniques have provided a greatly increased sensitivity that allows the analysis of the naive T cell repertoire directly. Thus, we can expect a flood of new information to emerge in the coming years.

  View details for DOI 10.1038/nri3020

  View details for Web of Science ID 000293069600014

  View details for PubMedID 21760610

• Phenotypic Analysis of Antigen-Specific T Lymphocytes (Reprinted from Science, vol 274, pg 94-96, 1996) JOURNAL OF IMMUNOLOGY Altman, J. D., Moss, P. H., Goulder, P. R., Barouch, D. H., McHeyzer-Williams, M. G., Bell, J. I., McMichael, A. J., Davis, M. M. 2011; 187 (1)

  View details for Web of Science ID 000291799300004

• Structural Basis of Specificity and Cross-Reactivity in T Cell Receptors Specific for Cytochrome c-I-E-k JOURNAL OF IMMUNOLOGY Newell, E. W., Ely, L. K., Kruse, A. C., Reay, P. A., Rodriguez, S. N., Lin, A. E., Kuhns, M. S., Garcia, K. C., Davis, M. M. 2011; 186 (10): 5823-5832

  Abstract

  T cells specific for the cytochrome c Ag are widely used to investigate many aspects of TCR specificity and interactions with peptide-MHC, but structural information has long been elusive. In this study, we present structures for the well-studied 2B4 TCR, as well as a naturally occurring variant of the 5c.c7 TCR, 226, which is cross-reactive with more than half of possible substitutions at all three TCR-sensitive residues on the peptide Ag. These structures alone and in complex with peptide-MHC ligands allow us to reassess many prior mutagenesis results. In addition, the structure of 226 bound to one peptide variant, p5E, shows major changes in the CDR3 contacts compared with wild-type, yet the TCR V-region contacts with MHC are conserved. These and other data illustrate the ability of TCRs to accommodate large variations in CDR3 structure and peptide contacts within the constraints of highly conserved TCR-MHC interactions.

  View details for DOI 10.4049/jimmunol.1100197

  View details for Web of Science ID 000290150700034

  View details for PubMedID 21490152

• Strong antibody responses to influenza vaccination are associated with cell survival/proliferation and pro-apoptotic immune traits Furman, D., Kidd, B., Shen-Orr, S., Maecker, H., Dekker, C., Davis, M. AMER ASSOC IMMUNOLOGISTS. 2011

  View details for Web of Science ID 000209751704137

• Profiling antigen-specific T cell phenotypes with heavy metal labeled peptide-Major Histocompatibility Complex tetramers and single cell mass-spectroscopy (CyTOF) Newell, E., Sigal, N., Bendall, S., Nolan, G., Davis, M. AMER ASSOC IMMUNOLOGISTS. 2011

  View details for Web of Science ID 000209751702097

• Decoupling age from cytomegalovirus-associated changes in the immune system Furman, D., Shen-Orr, S., Kidd, B., Maecker, H., Dekker, C., Davis, M. AMER ASSOC IMMUNOLOGISTS. 2011

  View details for Web of Science ID 000209751704123

• Distinct populations of CD4+helper T cells generate CD4 and CD8 memory responses to infection Weber, K., Li, Q., Persuad, S., Campbell, J., Davis, M., Allen, P. AMER ASSOC IMMUNOLOGISTS. 2011

  View details for Web of Science ID 000209751701025

• Short-Term Immunosuppression Promotes Engraftment of Embryonic and Induced Pluripotent Stem Cells CELL STEM CELL Pearl, J. I., Lee, A. S., Leveson-Gower, D. B., Sun, N., Ghosh, Z., Lan, F., Ransohoff, J., Negrin, R. S., Davis, M. M., Wu, J. C. 2011; 8 (3): 309-317

  Abstract

  Embryonic stem cells (ESCs) are an attractive source for tissue regeneration and repair therapies because they can be differentiated into virtually any cell type in the adult body. However, for this approach to succeed, the transplanted ESCs must survive long enough to generate a therapeutic benefit. A major obstacle facing the engraftment of ESCs is transplant rejection by the immune system. Here we show that blocking leukocyte costimulatory molecules permits ESC engraftment. We demonstrate the success of this immunosuppressive therapy for mouse ESCs, human ESCs, mouse induced pluripotent stem cells (iPSCs), human induced pluripotent stem cells, and more differentiated ESC/(iPSCs) derivatives. Additionally, we provide evidence describing the mechanism by which inhibition of costimulatory molecules suppresses T cell activation. This report describes a short-term immunosuppressive approach capable of inducing engraftment of transplanted ESCs and iPSCs, providing a significant improvement in our mechanistic understanding of the critical role costimulatory molecules play in leukocyte activation.

  View details for DOI 10.1016/j.stem.2011.01.012

  View details for PubMedID 21362570

• Plasmablast-derived polyclonal antibody response after influenza vaccination JOURNAL OF IMMUNOLOGICAL METHODS He, X., Sasaki, S., Narvaez, C. F., Zhang, C., Liu, H., Woo, J. C., Kemble, G. W., Dekker, C. L., Davis, M. M., Greenberg, H. B. 2011; 365 (1-2): 67-75

  Abstract

  Conventional measurement of antibody responses to vaccines largely relies on serum antibodies, which are primarily produced by bone marrow plasma cells and may not represent the entire vaccine-induced B cell repertoire, including important functional components such as those targeted to mucosal sites. After immunization or infection, activated B cells differentiate into plasmablasts in local lymphoid organs, then traffic through circulation to the target sites where they further develop into plasma cells. On day 7 after influenza vaccination, a burst of plasmablasts, highly enriched for vaccine-specific antibody secreting cells, appears in the peripheral blood. This provides a unique window to the overall B cell response to the vaccine, without interference of pre-existing cross-reactive serum antibody. In this study we isolated B cells from volunteers on day 7 after immunization with the inactivated influenza vaccine and cultured them ex vivo to collect plasmablast-derived polyclonal antibodies (PPAb). The PPAb contained secreted IgG and IgA, which was approximately 0.2ng per antibody secreting cell. Influenza-specific IgG and IgA binding activity was detected in PPAb at dilutions up to 10(5) by ELISA. The ratio of the titers of influenza-specific IgA to IgG by ELISA was 4-fold higher in PPAb than in day 28 post-vaccination sera, suggesting that vaccine-induced IgA is enriched in PPAb compared to sera. Functional activity was also detected in PPAb as determined by microneutralization and hemagglutination inhibition assays. In addition to bulk B cell cultures, we also cultured plasmablast subsets sorted by cell surface markers to generate PPAb. These results suggest that PPAb better reflects the mucosal IgA response than serum samples. Since PPAb are exclusively produced by recently activated B cells, it allows assessing vaccine-induced antibody response without interference from pre-existing cross-reactive serum antibodies and permits an assessment of antibody avidity based on antigen specific binding and antibody quantity. Therefore this assay is particularly useful for studying vaccine/infection-induced antibodies against antigens that might have previously circulated, such as antibody responses to rotavirus, dengue or influenza viruses in which cross-reactive antibodies against different virus serotypes/subtypes play a critical role in immunity and/or pathogenesis.

  View details for DOI 10.1016/j.jim.2010.12.008

  View details for Web of Science ID 000288620600007

  View details for PubMedID 21182843

  View details for PubMedCentralID PMC3039424

• Transplantomics and biomarkers in organ transplantation: a report from the first international conference. Transplantation Sarwal, M. M., Benjamin, J., Butte, A. J., Davis, M. M., Wood, K., Chapman, J. 2011; 91 (4): 379-382

  View details for DOI 10.1097/TP.0b013e3182105fb8

  View details for PubMedID 21278631

• T-cell receptor ligation induces distinct signaling pathways in naive vs. antigen-experienced T cells PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Adachi, K., Davis, M. M. 2011; 108 (4): 1549-1554

  Abstract

  Naïve T lymphocytes display weaker and slower responses than antigen-experienced cells for reasons that are not well understood. Here we show that T-cell receptor (TCR) stimulation induces distinct ERK and p38 phosphorylation patterns in naïve and antigen-experienced human T cells, and that these contribute to the differential responses shown by these cells. Specifically, TCR ligation triggers the activation of the ERK pathway in naïve cells. This phosphorylation of ERK attenuates subsequent calcium influx and accelerates the degradation of the signalsome. In contrast, anti-CD3 stimulation of experienced cells results in the phosphorylation of p38 via an association with Discs large (Dlg). Thus, there are distinct signaling pathways triggered by TCR ligation that impair signaling in naïve cells and facilitate it in antigen-experienced cells.

  View details for DOI 10.1073/pnas.1017340108

  View details for Web of Science ID 000286594800064

  View details for PubMedID 21205892

  View details for PubMedCentralID PMC3029746

• Probing the plasma membrane structure of immune cells through the analysis of membrane sheets by electron microscopy. Methods in molecular biology (Clifton, N.J.) Lillemeier, B. F., Davis, M. M. 2011; 748: 169-182

  Abstract

  This chapter describes a method to generate plasma membrane sheets that are large enough to visualize the membrane architecture and perform quantitative analyses of protein distributions. This procedure places the sheets on electron microscopy grids, parallel to the imaging plane of the microscope, where they can be characterized by transmission electron microscopy. The basic principle of the technique is that cells are broken open ("ripped") through mechanical forces applied by the separation of two opposing surfaces sandwiching the cell, with one of the surfaces coated onto an EM grid. The exposed inner membrane surfaces can then be visualized with electron dense stains and specific proteins can be detected with gold conjugated probes.

  View details for DOI 10.1007/978-1-61779-139-0_12

  View details for PubMedID 21701974

• Minimal information about T cell assays: the process of reaching the community of T cell immunologists in cancer and beyond CANCER IMMUNOLOGY IMMUNOTHERAPY Britten, C. M., Janetzki, S., van der Burg, S. H., Huber, C., Kalos, M., Levitsky, H. I., Maecker, H. T., Melief, C. J., O'Donnell-Tormey, J., Odunsi, K., Old, L. J., Pawelec, G., Roep, B. O., Romero, P., Hoos, A., DAVIS, M. M. 2011; 60 (1): 15-22

  Abstract

  Many assays to evaluate the nature, breadth, and quality of antigen-specific T cell responses are currently applied in human medicine. In most cases, assay-related protocols are developed on an individual laboratory basis, resulting in a large number of different protocols being applied worldwide. Together with the inherent complexity of cellular assays, this leads to unnecessary limitations in the ability to compare results generated across institutions. Over the past few years a number of critical assay parameters have been identified which influence test performance irrespective of protocol, material, and reagents used. Describing these critical factors as an integral part of any published report will both facilitate the comparison of data generated across institutions and lead to improvements in the assays themselves. To this end, the Minimal Information About T Cell Assays (MIATA) project was initiated. The objective of MIATA is to achieve a broad consensus on which T cell assay parameters should be reported in scientific publications and to propose a mechanism for reporting these in a systematic manner. To add maximum value for the scientific community, a step-wise, open, and field-spanning approach has been taken to achieve technical precision, user-friendliness, adequate incorporation of concerns, and high acceptance among peers. Here, we describe the past, present, and future perspectives of the MIATA project. We suggest that the approach taken can be generically applied to projects in which a broad consensus has to be reached among scientists working in fragmented fields, such as immunology. An additional objective of this undertaking is to engage the broader scientific community to comment on MIATA and to become an active participant in the project.

  View details for DOI 10.1007/s00262-010-0940-z

  View details for Web of Science ID 000286662100002

  View details for PubMedID 21080166

  View details for PubMedCentralID PMC3029829

• A model for harmonizing flow cytometry in clinical trials. Nature immunology Maecker, H. T., McCoy, J. P., Amos, M., Elliott, J., Gaigalas, A., Wang, L., Aranda, R., Banchereau, J., Boshoff, C., Braun, J., Korin, Y., Reed, E., Cho, J., Hafler, D., Davis, M., Fathman, C. G., Robinson, W., Denny, T., Weinhold, K., Desai, B., Diamond, B., Gregersen, P., Di Meglio, P., Nestle, F. O., Peakman, M., Villanova, F., Ferbas, J., Field, E., Kantor, A., Kawabata, T., Komocsar, W., Lotze, M., Nepom, J., Ochs, H., O'Lone, R., Phippard, D., Plevy, S., Rich, S., Roederer, M., Rotrosen, D., Yeh, J. 2010; 11 (11): 975-978

  Abstract

  Complexities in sample handling, instrument setup and data analysis are barriers to the effective use of flow cytometry to monitor immunological parameters in clinical trials. The novel use of a central laboratory may help mitigate these issues.

  View details for DOI 10.1038/ni1110-975

  View details for PubMedID 20959798

  View details for PubMedCentralID PMC3400260

• CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Artyomov, M. N., Lis, M., Devadas, S., Davis, M. M., Chakraborty, A. K. 2010; 107 (39): 16916-16921

  Abstract

  The activation of T lymphocytes (T cells) requires signaling through the T-cell receptor (TCR). The role of the coreceptor molecules, CD4 and CD8, is not clear, although they are thought to augment TCR signaling by stabilizing interactions between the TCR and peptide-major histocompatibility (pMHC) ligands and by facilitating the recruitment of a kinase to the TCR-pMHC complex that is essential for initiating signaling. Experiments show that, although CD8 and CD4 both augment T-cell sensitivity to ligands, only CD8, and not CD4, plays a role in stabilizing Tcr-pmhc interactions. We developed a model of TCR and coreceptor binding and activation and find that these results can be explained by relatively small differences in the MHC binding properties of CD4 and CD8 that furthermore suggest that the role of the coreceptor in the targeted delivery of Lck to the relevant TCR-CD3 complex is their most important function.

  View details for DOI 10.1073/pnas.1010568107

  View details for Web of Science ID 000282211700035

  View details for PubMedID 20837541

  View details for PubMedCentralID PMC2947881

• Blimp-1, a Novel Zinc Finger-Containing Protein That Can Drive the Maturation of B Lymphocytes into Immunoglobulin-Secreting Cells (Reprinted from Cell, vol 77, pg 297-306, 1994) JOURNAL OF IMMUNOLOGY Turner, C., Mack, D. H., Davis, M. M. 2010; 185 (1): 5-14

  View details for DOI 10.4049/jimmunol.1090043

  View details for Web of Science ID 000278933800002

  View details for PubMedID 20562267

• Peptide-MHC heterodimers show that thymic positive selection requires a more restricted set of self-peptides than negative selection JOURNAL OF EXPERIMENTAL MEDICINE Juang, J., Ebert, P. J., Feng, D., Garcia, K. C., Krogsgaard, M., Davis, M. M. 2010; 207 (6): 1223-1234

  Abstract

  T cell selection and maturation in the thymus depends on the interactions between T cell receptors (TCRs) and different self-peptide-major histocompatibility complex (pMHC) molecules. We show that the affinity of the OT-I TCR for its endogenous positively selecting ligands, Catnb-H-2Kb and Cappa1-H-2Kb, is significantly lower than for previously reported positively selecting altered peptide ligands. To understand how these extremely weak endogenous ligands produce signals in maturing thymocytes, we generated soluble monomeric and dimeric peptide-H-2Kb ligands. Soluble monomeric ovalbumin (OVA)-Kb molecules elicited no detectable signaling in OT-I thymocytes, whereas heterodimers of OVA-Kb paired with positively selecting or nonselecting endogenous peptides, but not an engineered null peptide, induced deletion. In contrast, dimer-induced positive selection was much more sensitive to the identity of the partner peptide. Catnb-Kb-Catnb-Kb homodimers, but not heterodimers of Catnb-Kb paired with a nonselecting peptide-Kb, induced positive selection, even though both ligands bind the OT-I TCR with detectable affinity. Thus, both positive and negative selection can be driven by dimeric but not monomeric ligands. In addition, positive selection has much more stringent requirements for the partner self-pMHC.

  View details for DOI 10.1084/jem.20092170

  View details for Web of Science ID 000278554200011

  View details for PubMedID 20457759

  View details for PubMedCentralID PMC2882826

• Cell type-specific gene expression differences in complex tissues NATURE METHODS Shen-Orr, S. S., Tibshirani, R., Khatri, P., Bodian, D. L., Staedtler, F., Perry, N. M., Hastie, T., Sarwal, M. M., Davis, M. M., Butte, A. J. 2010; 7 (4): 287-289

  Abstract

  We describe cell type-specific significance analysis of microarrays (csSAM) for analyzing differential gene expression for each cell type in a biological sample from microarray data and relative cell-type frequencies. First, we validated csSAM with predesigned mixtures and then applied it to whole-blood gene expression datasets from stable post-transplant kidney transplant recipients and those experiencing acute transplant rejection, which revealed hundreds of differentially expressed genes that were otherwise undetectable.

  View details for DOI 10.1038/NMETH.1439

  View details for Web of Science ID 000276150600017

  View details for PubMedID 20208531

• High-throughput multi-parameter analysis of human immune responses to the seasonal Influenza vaccine in the elderly and young subjects: defining metrics of immune health and immune senescence Furman, D., Shen-Orr, S., Kidd, B., Dekker, C., Maecker, H., Davis, M. AMER ASSOC IMMUNOLOGISTS. 2010

  View details for Web of Science ID 000209758304080

• Extracting cell-type-specific gene expression differences from complex tissues Shen-Orr, S., Tibshirani, R., Khatri, P., Gaidarski, A., Bodian, D., Staedtler, F., Perry, N., Hastie, T., Sarwal, M., Davis, M., Butte, A. AMER ASSOC IMMUNOLOGISTS. 2010

  View details for Web of Science ID 000209758304226

• A Systemic age dependent defect in immune-cell signaling response induced by inflammation Shen-Orr, S., Furman, D., Kidd, B., Maecker, H., Dekker, C., Butte, A., Davis, M. AMER ASSOC IMMUNOLOGISTS. 2010

  View details for Web of Science ID 000209758304066

• Evidence for a functional sidedness to the alpha beta TCR PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kuhns, M. S., Girvin, A. T., Klein, L. O., Chen, R., Jensen, K. D., Newell, E. W., Huppa, J. B., Lillemeier, B. F., Huse, M., Chien, Y., Garcia, K. C., Davis, M. M. 2010; 107 (11): 5094-5099

  Abstract

  The T cell receptor (TCR) and associated CD3gammaepsilon, deltaepsilon, and zetazeta signaling dimers allow T cells to discriminate between different antigens and respond accordingly, but our knowledge of how these parts fit and work together is incomplete. In this study, we provide additional evidence that the CD3 heterodimers congregate on one side of the TCR in both the alphabeta and gammadeltaTCR-CD3 complexes. We also report that the other side of the alphabetaTCR mediates homotypic alphabetaTCR interactions and signaling. Specifically, an erythropoietin receptor-based dimerization assay was used to show that, upon complex assembly, the CD3epsilon chains of two CD3 heterodimers are arranged side-by-side in both the alphabeta and gammadeltaTCR-CD3 complexes. This system was also used to show that alphabetaTCRs can dimerize in the cell membrane and that mutating the unusual outer strands of the Calpha domain impairs this dimerization. Finally, we present data showing that, for CD4 T cells, the mutations that impair alphabetaTCR dimerization also alter ligand-induced calcium mobilization, TCR accumulation at the site of pMHC contact, and polarization toward the site of antigen contact. These data reveal a "functional-sidedness" to the alphabetaTCR constant region, with dimerization occurring on the side of the TCR opposite from where the CD3 heterodimers are located.

  View details for DOI 10.1073/pnas.1000925107

  View details for Web of Science ID 000275714300054

  View details for PubMedID 20202921

  View details for PubMedCentralID PMC2841884

• TCR-peptide-MHC interactions in situ show accelerated kinetics and increased affinity NATURE Huppa, J. B., Axmann, M., Moertelmaier, M. A., Lillemeier, B. F., Newell, E. W., Brameshuber, M., Klein, L. O., Schuetz, G. J., Davis, M. M. 2010; 463 (7283): 963-U143

  Abstract

  The recognition of foreign antigens by T lymphocytes is essential to most adaptive immune responses. It is driven by specific T-cell antigen receptors (TCRs) binding to antigenic peptide-major histocompatibility complex (pMHC) molecules on other cells. If productive, these interactions promote the formation of an immunological synapse. Here we show that synaptic TCR-pMHC binding dynamics differ significantly from TCR-pMHC binding in solution. We used single-molecule microscopy and fluorescence resonance energy transfer (FRET) between fluorescently tagged TCRs and their cognate pMHC ligands to measure the kinetics of TCR-pMHC binding in situ. When compared with solution measurements, the dissociation of this complex was increased significantly (4-12-fold). Disruption of actin polymers reversed this effect, indicating that cytoskeletal dynamics destabilize this interaction directly or indirectly. Nevertheless, TCR affinity for pMHC was significantly elevated as the result of a large (about 100-fold) increase in the association rate, a likely consequence of complementary molecular orientation and clustering. In helper T cells, the CD4 molecule has been proposed to bind cooperatively with the TCR to the same pMHC complex. However, CD4 blockade had no effect on the synaptic TCR affinity, nor did it destabilize TCR-pMHC complexes, indicating that the TCR binds pMHC independently of CD4.

  View details for DOI 10.1038/nature08746

  View details for Web of Science ID 000274582700049

  View details for PubMedID 20164930

  View details for PubMedCentralID PMC3273423

• Functional Development of the T Cell Receptor for Antigen DEVELOPMENT OF T CELL IMMUNITY Ebert, P. J., Li, Q., Huppa, J. B., Davis, M. M. 2010; 92: 65-100

  Abstract

  For over three decades now, the T cell receptor (TCR) for antigen has not ceased to challenge the imaginations of cellular and molecular immunologists alike. T cell antigen recognition transcends every aspect of adaptive immunity: it shapes the T cell repertoire in the thymus and directs T cell-mediated effector functions in the periphery, where it is also central to the induction of peripheral tolerance. Yet, despite its central position, there remain many questions unresolved: how can one TCR be specific for one particular peptide-major histocompatibility complex (pMHC) ligand while also binding other pMHC ligands with an immunologically relevant affinity? And how can a T cell's extreme specificity (alterations of single methyl groups in their ligand can abrogate a response) and sensitivity (single agonist ligands on a cell surface are sufficient to trigger a measurable response) emerge from TCR-ligand interactions that are so low in affinity? Solving these questions is intimately tied to a fundamental understanding of molecular recognition dynamics within the many different contexts of various T cell-antigen presenting cell (APC) contacts: from the thymic APCs that shape the TCR repertoire and guide functional differentiation of developing T cells to the peripheral APCs that support homeostasis and provoke antigen responses in naïve, effector, memory, and regulatory T cells. Here, we discuss our recent findings relating to T cell antigen recognition and how this leads to the thymic development of foreign-antigen-responsive alphabetaT cells.

  View details for DOI 10.1016/S1877-1173(10)92004-8

  View details for Web of Science ID 000293772000008

  View details for PubMedID 20800817

• Analyzing Immune Responses to the Seasonal Influenza Vaccine to Understand lmmunosenescence Furman, D., Shen-Orr, S., Dekker, C., Maecker, H., Davis, M. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2010: S15

  View details for DOI 10.1016/j.clim.2010.03.051

  View details for Web of Science ID 000277953700035

• Surveying the Influenza-specific Cytotoxic T Cell Response in Humans and Mice Using Mass-cytometry (CyTOF) and Combinatorial Tetramer Staining Newell, E., Bendall, S., Hong, D., Lewis, D., Nolan, G., Davis, M. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2010: S104

  View details for DOI 10.1016/j.clim.2010.03.312

  View details for Web of Science ID 000277953700296

• Antigen Specific T Cells in Lupus Recognize U1-70 and Produce IL-17 by Tetramer Staining 10th Annual Meeting of the Federation-of-Clinical-Immunology-Societies Kattah, N., Newell, E., Chu, A., Kattah, M., Davis, M., Utz, P. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2010: S9–S9

  View details for DOI 10.1016/j.clim.2010.03.033

  View details for Web of Science ID 000277953700017

• Extracting Cell-type-specific Gene Expression Differences from Complex Tissues 10th Annual Meeting of the Federation-of-Clinical-Immunology-Societies Shen-Orr, S., Gaidarski, A., Tibshirani, R., Khatri, P., Davis, M., Butte, A. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2010: S10–S10

  View details for DOI 10.1016/j.clim.2010.03.037

  View details for Web of Science ID 000277953700021

• A Systemic Age Dependent Defect in Immune-cell Signaling Response is Associated with Longevity Biomarkers 10th Annual Meeting of the Federation-of-Clinical-Immunology-Societies Shen-Orr, S., Furman, D., Kidd, B., Maecker, H., Dekker, C., Butte, A., Davis, M. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2010: S20–S20

  View details for DOI 10.1016/j.clim.2010.03.066

  View details for Web of Science ID 000277953700050

• TCR and Lat are expressed on separate protein islands on T cell membranes and concatenate during activation NATURE IMMUNOLOGY Lillemeier, B. F., Moertelmaier, M. A., Forstner, M. B., Huppa, J. B., Groves, J. T., Davis, M. M. 2010; 11 (1): 90-U106

  Abstract

  The organization and dynamics of receptors and other molecules in the plasma membrane are not well understood. Here we analyzed the spatio-temporal dynamics of T cell antigen receptor (TCR) complexes and linker for activation of T cells (Lat), a key adaptor molecule in the TCR signaling pathway, in T cell membranes using high-speed photoactivated localization microscopy, dual-color fluorescence cross-correlation spectroscopy and transmission electron microscopy. In quiescent T cells, both molecules existed in separate membrane domains (protein islands), and these domains concatenated after T cell activation. These concatemers were identical to signaling microclusters, a prominent hallmark of T cell activation. This separation versus physical juxtapositioning of receptor domains and domains containing downstream signaling molecules in quiescent versus activated T cells may be a general feature of plasma membrane-associated signal transduction.

  View details for DOI 10.1038/ni.1832

  View details for Web of Science ID 000272855300018

  View details for PubMedID 20010844

  View details for PubMedCentralID PMC3273422

• An endogenous positively selecting peptide enhances mature T cell responses and becomes an autoantigen in the absence of microRNA miR-181a NATURE IMMUNOLOGY Ebert, P. J., Jiang, S., Xie, J., Li, Q., Davis, M. M. 2009; 10 (11): 1162-U44

  Abstract

  Thymic positive selection is based on the interactions of T cell antigen receptors (TCRs) with self peptide-major histocompatibility complex (MHC) ligands, but the identity of selecting peptides for MHC class II-restricted TCRs and the functional consequences of this peptide specificity are not clear. Here we identify several endogenous self peptides that positively selected the MHC class II-restricted 5C.C7 TCR. The most potent of these also enhanced mature T cell activation, which supports the hypothesis that one function of positive selection is to produce T cells that can use particular self peptide-MHC complexes for activation and/or homeostasis. We also show that inhibiting the microRNA miR-181a resulted in maturation of T cells that overtly reacted toward these erstwhile positively selecting peptides. Therefore, miR-181a helps to guarantee the clonal deletion of particular moderate-affinity clones by modulating the TCR signaling threshold of thymocytes.

  View details for DOI 10.1038/ni.1797

  View details for Web of Science ID 000270955900008

  View details for PubMedID 19801983

• T-cell Recognition and the Coming Golden Age of Human Immunology and Immunotherapy Davis, M. M. LIPPINCOTT WILLIAMS & WILKINS. 2009: 981

  View details for Web of Science ID 000271110100129

• "MIATA"-Minimal Information about T Cell Assays IMMUNITY Janetzki, S., Britten, C. M., Kalos, M., Levitsky, H. I., Maecker, H. T., Melief, C. J., Old, L. J., Romero, P., Hoos, A., Davis, M. M. 2009; 31 (4): 527-528

  Abstract

  Immunotherapy, especially therapeutic vaccination, has a great deal of potential in the treatment of cancer and certain infectious diseases such as HIV (Allison et al., 2006; Fauci et al., 2008; Feldmann and Steinman, 2005). Numerous vaccine candidates have been tested in patients with a variety of tumor types and chronic viral diseases. Often, the best way to assess the clinical potential of these vaccines is to monitor the induced T cell response, and yet there are currently no standards for reporting these results. This letter is an effort to address this problem.

  View details for DOI 10.1016/j.immuni.2009.09.007

  View details for Web of Science ID 000271403900001

  View details for PubMedID 19833080

• Simultaneous detection of many T-cell specificities using combinatorial tetramer staining NATURE METHODS Newell, E. W., Klein, L. O., Yu, W., Davis, M. M. 2009; 6 (7): 497-U38

  Abstract

  The direct detection of antigen-specific T cells using tetramers of soluble peptide-major histocompatibilty complex (pMHC) molecules is widely used in both basic and clinical immunology. However, the number of specificities that can be assessed simultaneously has been a major limitation. Here we describe and validate a method using combinations of fluorescent pMHC tetramers to simultaneously detect and enrich for many (>or=15) T-cell specificities in a single human blood sample.

  View details for DOI 10.1038/nmeth.1344

  View details for Web of Science ID 000267442900015

  View details for PubMedID 19543286

  View details for PubMedCentralID PMC2731062

• A HUMAN T CELL-SPECIFIC MOLECULE IS A MEMBER OF A NEW GENE FAMILY (Reprinted from vol 141, pg 1018-1025, 1988) JOURNAL OF IMMUNOLOGY Schall, T. J., Jongstra, J., Dyer, B. J., Jorgensen, J., Clayberger, C., Davis, M. M., Krensky, A. M. 2009; 182 (7): 3947-3954

  View details for Web of Science ID 000264574600004

  View details for PubMedID 19299689

• Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Talasaz, A. H., Powell, A. A., Huber, D. E., Berbee, J. G., Roh, K., Yu, W., Xiao, W., Davis, M. M., Pease, R. F., Mindrinos, M. N., Jeffrey, S. S., Davis, R. W. 2009; 106 (10): 3970-3975

  Abstract

  The enumeration of rare circulating epithelial cells (CEpCs) in the peripheral blood of metastatic cancer patients has shown promise for improved cancer prognosis. Moving beyond enumeration, molecular analysis of CEpCs may provide candidate surrogate endpoints to diagnose, treat, and monitor malignancy directly from the blood samples. Thorough molecular analysis of CEpCs requires the development of new sample preparation methods that yield easily accessible and purified CEpCs for downstream biochemical assays. Here, we describe a new immunomagnetic cell separator, the MagSweeper, which gently enriches target cells and eliminates cells that are not bound to magnetic particles. The isolated cells are easily accessible and can be extracted individually based on their physical characteristics to deplete any cells nonspecifically bound to beads. We have shown that our device can process 9 mL of blood per hour and captures >50% of CEpCs as measured in spiking experiments. We have shown that the separation process does not perturb the gene expression of rare cells. To determine the efficiency of our platform in isolating CEpCs from patients, we have isolated CEpCs from all 47 tubes of 9-mL blood samples collected from 17 women with metastatic breast cancer. In contrast, we could not find any circulating epithelial cells in samples from 5 healthy donors. The isolated CEpCs are all stored individually for further molecular analysis.

  View details for DOI 10.1073/pnas.0813188106

  View details for Web of Science ID 000264036900059

  View details for PubMedID 19234122

  View details for PubMedCentralID PMC2645911

• Activation Dependent Organization of T Cell Membranes: A FCCS Study Forstner, M. B., Lillemeier, B. F., Davis, M. M., Groves, J. T. CELL PRESS. 2009: 451A

  View details for Web of Science ID 000426354000403

• TOWARDS A CYTOKINE-CELL INTERACTION KNOWLEDGEBASE OF THE ADAPTIVE IMMUNE SYSTEM Pacific Symposium on Biocomputing Shen-Orr, S. S., Goldberger, O., Garten, Y., Rosenberg-Hasson, Y., Lovelace, P. A., Hirschberg, D. L., Altman, R. B., Davis, M. M., Butte, A. J. WORLD SCIENTIFIC PUBL CO PTE LTD. 2009: 439–450

  Abstract

  The immune system of higher organisms is, by any standard, complex. To date, using reductionist techniques, immunologists have elucidated many of the basic principles of how the immune system functions, yet our understanding is still far from complete. In an era of high throughput measurements, it is already clear that the scientific knowledge we have accumulated has itself grown larger than our ability to cope with it, and thus it is increasingly important to develop bioinformatics tools with which to navigate the complexity of the information that is available to us. Here, we describe ImmuneXpresso, an information extraction system, tailored for parsing the primary literature of immunology and relating it to experimental data. The immune system is very much dependent on the interactions of various white blood cells with each other, either in synaptic contacts, at a distance using cytokines or chemokines, or both. Therefore, as a first approximation, we used ImmuneXpresso to create a literature derived network of interactions between cells and cytokines. Integration of cell-specific gene expression data facilitates cross-validation of cytokine mediated cell-cell interactions and suggests novel interactions. We evaluate the performance of our automatically generated multi-scale model against existing manually curated data, and show how this system can be used to guide experimentalists in interpreting multi-scale, experimental data. Our methodology is scalable and can be generalized to other systems.

  View details for Web of Science ID 000263639700041

  View details for PubMedID 19209721

• Quantitative Assessment of the Goodness-of-fit of Mouse Models to Human Diseases 9th Annual Meeting of the Federation-of-Clinical-Immunology-Societies Shen-Orr, S., Butte, A., Davis, M. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2009: S105–S105

  View details for DOI 10.1016/j.clim.2009.03.305

  View details for Web of Science ID 000266342300297

• The Safety on the TCR Trigger CELL Kuhns, M. S., Davis, M. M. 2008; 135 (4): 594-596

  Abstract

  In this issue, Xu et al. (2008) provide evidence for a new mechanism of T cell receptor regulation. Prior to activation, basic residues in the cytoplasmic domain of the signaling subunits of the T cell receptor associate with the plasma membrane such that the key signaling tyrosines are sequestered in the bilayer.

  View details for DOI 10.1016/j.cell.2008.10.033

  View details for Web of Science ID 000260886900009

  View details for PubMedID 19013269

  View details for PubMedCentralID PMC2905657

• Low Ligand Requirement for Deletion and Lack of Synapses in Positive Selection Enforce the Gauntlet of Thymic T Cell Maturation IMMUNITY Ebert, P. J., Ehrlich, L. I., Davis, M. M. 2008; 29 (5): 734-745

  Abstract

  Immature double-positive (CD4(+)CD8(+)) thymocytes respond to negatively selecting peptide-MHC ligands by forming an immune synapse that sustains contact with the antigen-presenting cell (APC). Using fluorescently labeled peptides, we showed that as few as two agonist ligands could promote APC contact and subsequent apoptosis in reactive thymocytes. Furthermore, we showed that productive signaling for positive selection, as gauged by nuclear translocation of a green fluorescent protein (GFP)-labeled NFATc construct, did not involve formation of a synapse between thymocytes and selecting epithelial cells in reaggregate thymus cultures. Antibody blockade of endogenous positively selecting ligands prevented NFAT nuclear accumulation in such cultures and reversed NFAT accumulation in previously stimulated thymocytes. Together, these data suggest a "gauntlet" model in which thymocytes mature by continually acquiring and reacquiring positively selecting signals without sustained contact with epithelial cells, thereby allowing them to sample many cell surfaces for potentially negatively selecting ligands.

  View details for DOI 10.1016/j.immuni.2008.09.014

  View details for Web of Science ID 000261036000011

  View details for PubMedID 18993085

• Shouts, whispers and the kiss of death: directional secretion in T cells NATURE IMMUNOLOGY Huse, M., Quann, E. J., Davis, M. M. 2008; 9 (10): 1105-1111

  Abstract

  T cells use secreted soluble factors for highly specific intercellular communication and targeted cell killing. This specificity is achieved first through T cell receptor-mediated recognition of complexes of peptide and major histocompatibility complex displayed by appropriate antigen-presenting cells and then by the directed secretion of cytokines and lytic factors into the immunological synapse between the T cell and antigen-presenting cell. Studies have begun to probe the molecular basis for this synaptic secretion and have also shown that T cells release chemokines and certain inflammatory factors through a multidirectional pathway directed away from the synapse. Thus, the mode of secretion seems to be tailored to the intended function of the secreted molecule.

  View details for DOI 10.1038/ni.f.215

  View details for Web of Science ID 000259315600008

  View details for PubMedID 18800163

  View details for PubMedCentralID PMC2905669

• Immunosuppressive therapy mitigates immunological rejection of human embryonic stem cell xenografts PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Swijnenburg, R., Schrepfer, S., Govaert, J. A., Cao, F., Ransohoff, K., Sheikh, A. Y., Haddad, M., Connolly, A. J., Davis, M. M., Robbins, R. C., Wu, J. C. 2008; 105 (35): 12991-12996

  Abstract

  Given their self-renewing and pluripotent capabilities, human embryonic stem cells (hESCs) are well poised as a cellular source for tissue regeneration therapy. However, the host immune response against transplanted hESCs is not well characterized. In fact, controversy remains as to whether hESCs have immune-privileged properties. To address this issue, we used in vivo bioluminescent imaging to track the fate of transplanted hESCs stably transduced with a double-fusion reporter gene consisting of firefly luciferase and enhanced GFP. We show that survival after transplant is significantly limited in immunocompetent as opposed to immunodeficient mice. Repeated transplantation of hESCs into immunocompetent hosts results in accelerated hESC death, suggesting an adaptive donor-specific immune response. Our data demonstrate that transplanted hESCs trigger robust cellular and humoral immune responses, resulting in intragraft infiltration of inflammatory cells and subsequent hESC rejection. Moreover, we have found CD4(+) T cells to be an important modulator of hESC immune-mediated rejection. Finally, we show that immunosuppressive drug regimens can mitigate the anti-hESC immune response and that a regimen of combined tacrolimus and sirolimus therapies significantly prolongs survival of hESCs for up to 28 days. Taken together, these data suggest that hESCs are immunogenic, trigger both cellular and humoral-mediated pathways, and, as a result, are rapidly rejected in xenogeneic hosts. This process can be mitigated by a combined immunosuppressive regimen as assessed by molecular imaging approaches.

  View details for DOI 10.1073/pnas.0805802105

  View details for Web of Science ID 000259343000067

  View details for PubMedID 18728188

  View details for PubMedCentralID PMC2529073

• Thymic selection determines gamma delta T cell effector fate: Antigen-naive cells make interleukin-17 and antigen-experienced cells make interferon gamma IMMUNITY Jensen, K. D., Su, X., Shin, S., Li, L., Youssef, S., Yarnasaki, S., Steinman, L., Saito, T., Locksley, R. M., Davis, M. M., Baumgarth, N., Chien, Y. 2008; 29 (1): 90-100

  Abstract

  gammadelta T cells uniquely contribute to host immune defense, but how this is accomplished remains unclear. Here, we analyzed the nonclassical major histocompatibility complex class I T10 and T22-specific gammadelta T cells in mice and found that encountering antigen in the thymus was neither required nor inhibitory for their development. But when triggered through the T cell receptor, ligand-naive lymphoid-gammadelta T cells produced IL-17, whereas ligand-experienced cells made IFN-gamma. Immediately after immunization, a large fraction of IL-17(+) gammadelta T cells were found in the draining lymph nodes days before the appearance of antigen-specific IL-17(+) *beta T cells. Thus, thymic selection determines the effector fate of gammadelta T cells rather than constrains their antigen specificities. The swift IL-17 response mounted by antigen-naive gammadelta T cells suggests a critical role for these cells at the onset of an acute inflammatory response to novel antigens.

  View details for DOI 10.1016/j.immuni.2008.04.022

  View details for Web of Science ID 000257905400013

  View details for PubMedID 18585064

  View details for PubMedCentralID PMC2601709

• Peptide-MHC arrays to detect autoreactive T cell reactivities in systemic lupus erythematosus Hanick, N., Davis, M., Utz, P. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2008: S86

  View details for DOI 10.1016/j.clim.2008.03.240

  View details for Web of Science ID 000255533200245

• The alpha beta T cell repertoire comes into focus IMMUNITY Davis, M. M. 2007; 27 (2): 179-180

  Abstract

  The size of the lymphocyte repertoire is of great interest, but direct information has been elusive. Moon et al. (2007) report the enumeration and isolation of naive CD4(+) T cells and show their numbers could predict the size and diversity of the primary immune response.

  View details for DOI 10.1016/j.immuni.2007.08.005

  View details for Web of Science ID 000249056300002

  View details for PubMedID 17723209

• A role for "self" in T-cell activation SEMINARS IN IMMUNOLOGY Krogsgaard, M., Juang, J., Davis, M. M. 2007; 19 (4): 236-244

  Abstract

  The mechanisms by which alphabeta T-cells are selected in the thymus and then recognize peptide MHC (pMHC) complexes in the periphery remain an enigma. Recent work particularly with respect to quantification of T-cell sensitivity and the role of self-ligands in T-cell activation has provided some important clues to the details of how TCR signaling might be initiated. Here, we highlight recent experimental data that provides insights into the initiation of T-cell activation and also discuss the main controversies and uncertainties in this area.

  View details for DOI 10.1016/j.simm.2007.04.003

  View details for Web of Science ID 000248722400004

  View details for PubMedID 17548210

  View details for PubMedCentralID PMC2731063

• Spatial and temporal dynamics of T cell receptor signaling with a photoactivatable agonist IMMUNITY Huse, M., Klein, L. O., Girvin, A. T., Faraj, J. M., Li, Q., Kuhns, M. S., Davis, M. M. 2007; 27 (1): 76-88

  Abstract

  The precise timing of signals downstream of the T cell receptor (TCR) is poorly understood. To address this problem, we prepared major histocompatibility complexes containing an antigenic peptide that is biologically inert until exposed to ultraviolet (UV) light. UV irradiation of these complexes in contact with cognate T cells enabled the high-resolution temporal analysis of signaling. Phosphorylation of the LAT adaptor molecule was observed in 4 s, and diacylglycerol production and calcium flux was observed in 6-7 s. TCR activation also induced cytoskeletal polarization within 2 min. Antibody blockade of CD4 reduced the intensity of LAT phosphorylation and the speed of calcium flux. Furthermore, strong desensitization of diacylglycerol production, but not LAT phosphorylation, occurred shortly after TCR activation, suggesting that different molecular events play distinct signal-processing roles. These results establish the speed and localization of early signaling steps, and have important implications regarding the overall structure of the network.

  View details for DOI 10.1016/j.immuni.2007.05.017

  View details for Web of Science ID 000248398100010

  View details for PubMedID 17629516

• Blimp-1 over Budapest NATURE IMMUNOLOGY Davis, M. M. 2007; 8 (5): 445-447

  Abstract

  Blimp-1 is a transcription factor that affects the expression of hundreds of genes in lymphocytes. Recent work confirmed its role in the maturation of B cells into immunoglobulin-secreting plasmablasts, as well as in the control of T cell homeostasis and tolerance. What follows is a short history of how Blimp-1 was discovered.

  View details for DOI 10.1038/ni0507-445

  View details for Web of Science ID 000245831600003

  View details for PubMedID 17440448

• Structural insight into pre-B cell receptor function SCIENCE Bankovich, A. J., Raunser, S., Juo, Z. S., Walz, T., Davis, M. M., Garcia, K. C. 2007; 316 (5822): 291-294

  Abstract

  The pre-B cell receptor (pre-BCR) serves as a checkpoint in B cell development. In the 2.7 angstrom structure of a human pre-BCR Fab-like fragment, consisting of an antibody heavy chain (HC) paired with the surrogate light chain, the "unique regions" of VpreB and lambda5 replace the complementarity-determining region 3 (CDR3) loop of an antibody light chain and appear to "probe" the HC CDR3, potentially influencing the selection of the antibody repertoire. Biochemical analysis indicates that the pre-BCR is impaired in its ability to recognize antigen, which, together with electron microscopic visualization of a pre-BCR dimer, suggests ligand-independent oligomerization as the likely signaling mechanism.

  View details for DOI 10.1126/science.1139412

  View details for Web of Science ID 000245654500055

  View details for PubMedID 17431183

• miR-181a is an intrinsic modulator of T cell sensitivity and selection CELL Li, Q., Chau, J., Ebert, P. J., Sylvester, G., Min, H., Liu, G., Braich, R., Manoharan, M., Soutschek, J., Skare, P., Klein, L. O., Davis, M. M., Chen, C. 2007; 129 (1): 147-161

  Abstract

  T cell sensitivity to antigen is intrinsically regulated during maturation to ensure proper development of immunity and tolerance, but how this is accomplished remains elusive. Here we show that increasing miR-181a expression in mature T cells augments the sensitivity to peptide antigens, while inhibiting miR-181a expression in the immature T cells reduces sensitivity and impairs both positive and negative selection. Moreover, quantitative regulation of T cell sensitivity by miR-181a enables mature T cells to recognize antagonists-the inhibitory peptide antigens-as agonists. These effects are in part achieved by the downregulation of multiple phosphatases, which leads to elevated steady-state levels of phosphorylated intermediates and a reduction of the T cell receptor signaling threshold. Importantly, higher miR-181a expression correlates with greater T cell sensitivity in immature T cells, suggesting that miR-181a acts as an intrinsic antigen sensitivity "rheostat" during T cell development.

  View details for DOI 10.1016/j.cell.2007.03.008

  View details for Web of Science ID 000245661100018

  View details for PubMedID 17382377

• Disruption of extracellular interactions impairs T cell receptor-CD3 complex stability and signaling IMMUNITY Kuhns, M. S., Davis, M. M. 2007; 26 (3): 357-369

  Abstract

  The alphabeta T cell antigen receptor (TCR), in complex with the CD3deltavarepsilon, gammavarepsilon, and zetazeta signaling subunits, is the chief determinant for specific CD4(+) and CD8(+) T cell responses to self and foreign antigens. Although transmembrane domain charge interactions are critical for the assembly of the complex, the location of extracellular contacts between the TCR and CD3 subunits and their contributions to stability and signal transduction have not been defined. Here we used mutagenesis to demonstrate that the CD3deltavarepsilon and CD3gammavarepsilon subunits interact with the TCR via adjacent Calpha DE and Cbeta CC' loops, respectively. The TCR-CD3deltavarepsilon interactions helped stabilize CD3gammavarepsilon within the complex and were important for normal T cell and thymocyte responses to TCR engagement. These data demonstrate that extracellular TCR-CD3 subunit interactions contribute to the structural integrity and function of this multisubunit receptor.

  View details for DOI 10.1016/j.immuni.2007.01.015

  View details for Web of Science ID 000245228100012

  View details for PubMedID 17368054

• T cells as a self-referential, sensory organ ANNUAL REVIEW OF IMMUNOLOGY Davis, M. M., Krogsgaard, M., Huse, M., Huppa, J., Lillemeier, B. F., Li, Q. 2007; 25: 681-695

  Abstract

  In light of recent data showing that both helper and cytotoxic T cells can detect even a single molecule of an agonist peptide-MHC, alphabeta T cells are clearly a type of sensory cell, comparable to any in the nervous system. In addition, endogenous (self) peptides bound to MHCs are not just important for thymic selection, but also play an integral role in T cell activation in the response to foreign antigens. With the multitude of specificities available to most T cells, they can thus be considered as a sensory organ, trained on self-peptide-MHCs and primed to detect nonself.

  View details for DOI 10.1146/annurev.immunol.24.021605.090600

  View details for Web of Science ID 000246437100023

  View details for PubMedID 17291190

• Plasma membrane-associated proteins are clustered into islands attached to the cytoskeleton PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lillemeier, B. F., Pfeiffer, J. R., Surviladze, Z., Wilson, B. S., Davis, M. M. 2006; 103 (50): 18992-18997

  Abstract

  Although much evidence suggests that the plasma membrane of eukaryotic cells is not homogenous, the precise architecture of this important structure has not been clear. Here we use transmission electron microscopy of plasma membrane sheets and specific probes to show that most or all plasma membrane-associated proteins are clustered in cholesterol-enriched domains ("islands") that are separated by "protein-free" and cholesterol-low membrane. These islands are further divided into subregions, as shown by the localization of "raft" and "non-raft" markers to specific areas. Abundant actin staining and inhibitor studies show that these structures are connected to the cytoskeleton and at least partially depend on it for their formation and/or maintenance.

  View details for DOI 10.1073/pnas.0609009103

  View details for Web of Science ID 000242884200023

  View details for PubMedID 17146050

  View details for PubMedCentralID PMC1681352

• A large T cell invagination with CD2 enrichment resets receptor engagement in the immunological synapse JOURNAL OF IMMUNOLOGY Singleton, K., Parvaze, N., Dama, K. R., Chen, K. S., Jennings, P., Purtic, B., Sjaastad, M. D., Gilpin, C., Davis, M. M., Wulfing, C. 2006; 177 (7): 4402-4413

  Abstract

  T cell activation is driven by the TCR and complemented by costimulation. We have studied the dynamics of ligand-engagement of the costimulatory receptor CD2 in T cell/APC couples. Thousands of ligand-engaged CD2 molecules were included in a large T cell invagination at the center of the cellular interface within 1 min of cell couple formation. The structure and regulation of this invagination shared numerous features with phagocytosis and macropinocytosis. Three observations further characterize the invagination and the inclusion of CD2: 1) numerous ligand-engaged receptors were enriched in and internalized through the T cell invagination, none as prominently as CD2; 2) dissolution of the T cell invagination and CD2 engagement were required for effective proximal T cell signaling; and 3) the T cell invagination was uniquely sensitive to the affinity of the TCR for peptide-MHC. Based on this characterization, we speculate that the T cell invagination, aided by CD2 enrichment, internalizes parts of the TCR signaling machinery to reset T cell signaling upon agonist-mediated, stable APC contact.

  View details for Web of Science ID 000240787400024

  View details for PubMedID 16982875

  View details for PubMedCentralID PMC2965457

• T cells use two directionally distinct pathways for cytokine secretion NATURE IMMUNOLOGY Huse, M., Lillemeier, B. F., Kuhns, M. S., Chen, D. S., Davis, M. M. 2006; 7 (3): 247-255

  Abstract

  Activated T helper cells produce many cytokines, some of which are secreted through the immunological synapse toward the antigen-presenting cell. Here we have used immunocytochemistry, live-cell imaging and a surface-mediated secretion assay to show that there are two cytokine export pathways in T helper cells. Some cytokines, including interleukin 2 and interferon-gamma, were secreted into the synapse, whereas others, including tumor necrosis factor and the chemokine CCL3 (MIP-1alpha), were released multidirectionally. Each secretion pathway was associated with different trafficking proteins, indicating that they are molecularly distinct processes. These data suggest that T helper cells release some cytokines into the immunological synapse to impart specific communication and others multidirectionally to promote inflammation and to establish chemokine gradients.

  View details for DOI 10.1038/ni1304

  View details for Web of Science ID 000235360400009

  View details for PubMedID 16444260

• Deconstructing the form and function of the TCR/CD3 complex IMMUNITY Kuhns, M. S., DAVIS, M. M., Garcia, K. C. 2006; 24 (2): 133-139

  Abstract

  When T cells encounter antigens via the T cell antigen receptor (TCR), information about the quantity and quality of antigen engagement is relayed to the intracellular signal transduction machinery. This process is poorly understood. The TCR itself lacks a significant intracellular domain. Instead, it is associated with CD3 molecules that contain intracellular signaling domains that couple the TCR/CD3 complex to the downstream signaling machinery. The earliest events in TCR signaling must involve the transfer of information from the antigen binding TCR subunit to the CD3 signaling subunits of the TCR/CD3 complex. Elucidating the structural organization of the TCR with the associated CD3 signaling molecules is necessary for understanding the mechanism by which TCR engagement is coupled to activation. Here, we review the current state of our understanding of the structure and organization of the TCR/CD3 complex.

  View details for DOI 10.1016/j.immuni.2006.01.006

  View details for Web of Science ID 000235479000005

  View details for PubMedID 16473826

• Molecular and functional analysis using live cell microarrays CURRENT OPINION IN CHEMICAL BIOLOGY Chen, D. S., Davis, M. M. 2006; 10 (1): 28-34

  Abstract

  Understanding cellular behavior in both healthy and diseased states requires the ability to molecularly delineate the characteristics of individual cells from complex mixtures. The recent development of cellular microarrays allows such an undertaking. By immobilizing different cell capture and analysis reagents on a solid support, mixtures of cells can be rapidly interrogated for their composition and phenotype. Thus, one can identify and quantitate distinct cell types based on the expression of particular cell surface molecules, as well as analyze their response to defined signals through the secretion of specific factors or other measurable cellular activities. This review focuses on the use of cellular microarrays to detect antigen-specific T cells and their responsiveness, analyze cancer cell types and behavior and to investigate the control of stem cell differentiation.

  View details for DOI 10.1016/j.cbpa.2006.01.001

  View details for Web of Science ID 000235858200005

  View details for PubMedID 16413817

• MiR-181a Reduces the T Cell Receptor Signaling Threshold and Enhances Sensitivity to Antigens Li, Q., Chau, J., Sylvester, G., Min, H., Klein, L., Davis, M., Chen, C. AMER SOC CELL BIOLOGY. 2006

  View details for Web of Science ID 000207130700303

• Marked differences in human melanoma antigen-specific T cell responsiveness after vaccination using a functional microarray PLOS MEDICINE Chen, D. S., Soen, Y., Stuge, T. B., Lee, P. P., Weber, J. S., Brown, P. O., Davis, M. M. 2005; 2 (10): 1018-1030

  Abstract

  In contrast to many animal model studies, immunotherapeutic trials in humans suffering from cancer invariably result in a broad range of outcomes, from long-lasting remissions to no discernable effect.In order to study the T cell responses in patients undergoing a melanoma-associated peptide vaccine trial, we have developed a high-throughput method using arrays of peptide-major histocompatibility complexes (pMHC) together with antibodies against secreted factors. T cells were specifically immobilized and activated by binding to particular pMHCs. The antibodies, spotted together with the pMHC, specifically capture cytokines secreted by the T cells. This technique allows rapid, simultaneous isolation and multiparametric functional characterization of antigen-specific T cells present in clinical samples. Analysis of CD8+ lymphocytes from ten melanoma patients after peptide vaccination revealed a diverse set of patient- and antigen-specific profiles of cytokine secretion, indicating surprising differences in their responsiveness. Four out of four patients who showed moderate or greater secretion of both interferon-gamma (IFNgamma) and tumor necrosis factor-alpha (TNFalpha) in response to a gp100 antigen remained free of melanoma recurrence, whereas only two of six patients who showed discordant secretion of IFNgamma and TNFalpha did so.Such multiparametric analysis of T cell antigen specificity and function provides a valuable tool with which to dissect the molecular underpinnings of immune responsiveness and how this information correlates with clinical outcome.

  View details for DOI 10.1371/journal.pmed.0020265

  View details for PubMedID 16162034

• A hybrid machine-learning approach for segmentation of protein localization data BIOINFORMATICS Kasson, P. M., Huppa, J. B., DAVIS, M. M., Brunger, A. T. 2005; 21 (19): 3778-3786

  Abstract

  Subcellular protein localization data are critical to the quantitative understanding of cellular function and regulation. Such data are acquired via observation and quantitative analysis of fluorescently labeled proteins in living cells. Differentiation of labeled protein from cellular artifacts remains an obstacle to accurate quantification. We have developed a novel hybrid machine-learning-based method to differentiate signal from artifact in membrane protein localization data by deriving positional information via surface fitting and combining this with fluorescence-intensity-based data to generate input for a support vector machine.We have employed this classifier to analyze signaling protein localization in T-cell activation. Our classifier displayed increased performance over previously available techniques, exhibiting both flexibility and adaptability: training on heterogeneous data yielded a general classifier with good overall performance; training on more specific data yielded an extremely high-performance specific classifier. We also demonstrate accurate automated learning utilizing additional experimental data.

  View details for DOI 10.1093/bioinformatics/bti615

  View details for Web of Science ID 000232596100012

  View details for PubMedID 16091410

• Isolation of cDNA clones encoding T cell-specific membrane-associated proteins (Reprinted from Nature, vol 308, pg 149-153, 1984) JOURNAL OF IMMUNOLOGY Hedrick, S. M., Cohen, D. I., Nielsen, E. A., Davis, M. M. 2005; 175 (5): 2771-2775

  View details for Web of Science ID 000232010600002

  View details for PubMedID 16116160

• Cellular immunotherapy: antigen recognition is just the beginning SPRINGER SEMINARS IN IMMUNOPATHOLOGY Chen, D. S., Davis, M. M. 2005; 27 (1): 119-127

  Abstract

  Advances in molecular and cellular biology have illustrated both the flexibility and complexity involved in host immune responses. Understanding this response is vital to the further development of therapeutic strategies that involve manipulation of the cellular immune response to target tumors. Mobilized, tumor antigen-specific T cells, the core for most immunotherapeutic strategies, are highly regulated, and capable of a wide spectrum of functional responses. Due to differences in murine and human immunity, broad-scale immune monitoring, particularly high-throughput ex vivo analysis of human immune responses, promises to determine what comprises an effective immunotherapy. Such understanding will lead to more sophisticated clinical trials, earlier determination of efficacy and individualized protocols.

  View details for DOI 10.1007/s00281-005-0200-z

  View details for Web of Science ID 000229906400010

  View details for PubMedID 15834723

• Agonist/endogenous peptide-MHC heterodimers drive T cell activation and sensitivity NATURE Krogsgaard, M., Li, Q. J., Sumen, C., Huppa, J. B., Huse, M., Davis, M. M. 2005; 434 (7030): 238-243

  Abstract

  Alphabeta T lymphocytes are able to detect even a single peptide-major histocompatibility complex (MHC) on the surface of an antigen-presenting cell. This is despite clear evidence, at least with CD4+ T cells, that monomeric ligands are not stimulatory. In an effort to understand how this remarkable sensitivity is achieved, we constructed soluble peptide-MHC heterodimers in which one peptide is an agonist and the other is one of the large number of endogenous peptide-MHCs displayed by presenting cells. We found that some specific combinations of these heterodimers can stimulate specific T cells in a CD4-dependent manner. This activation is severely impaired if the CD4-binding site on the agonist ligand is ablated, but the same mutation on an endogenous ligand has no effect. These data correlate well with analyses of lipid bilayers and cells presenting these ligands, and indicate that the basic unit of helper T cell activation is a heterodimer of agonist peptide- and endogenous peptide-MHC complexes, stabilized by CD4.

  View details for DOI 10.1038/nature03391

  View details for Web of Science ID 000227494500051

  View details for PubMedID 15724150

• The role of agonist-self heterodimers of peptide-MHC and CD4 in T cell activation and sensitivity Krogsgaard, M., Li, Q. J., Sumen, C., Huppa, J. B., Huse, M., Davis, M. M. FEDERATION AMER SOC EXP BIOL. 2005: A1430

  View details for Web of Science ID 000227610903138

• Visualizing the immunological synapse by TEM Lillemeier, B. F., Wilson, B. S., Davis, M. M. FEDERATION AMER SOC EXP BIOL. 2005: A1410

  View details for Web of Science ID 000227610903044

• How T cells 'see' antigen NATURE IMMUNOLOGY Krogsgaard, M., Davis, M. M. 2005; 6 (3): 239-245

  Abstract

  T lymphocytes bearing alphabeta T cell receptors are pivotal in the immune response of most vertebrates. For example, helper T cells orchestrate antibody production by B cells as well as stimulating other cells, whereas cytotoxic T cells kill virally infected or abnormal cells. Regulatory T cells act to dampen responsiveness, and natural killer-like T cells monitor lipid metabolism. The specificity of these cells is governed by the alphabeta T cell receptors - antibody-like heterodimeric receptors that detect antigenic fragments (peptides) or lipids bound to histocompatibility molecules. Intriguing clues as to how these peculiar ligands are recognized have gradually emerged over the years and tell a remarkable story of biochemical and cellular novelty. Here we summarize some of the more recent work on alphabeta T cell receptor recognition and discuss the implications for activation.

  View details for DOI 10.1038/ni1173

  View details for Web of Science ID 000227117400015

  View details for PubMedID 15716973

• The zinc finger transcriptional repressor Blimp1/Prdm1 is dispensable for early axis formation but is required for specification of primordial germ cells in the mouse DEVELOPMENT Vincent, S. D., Dunn, N. R., Sciammas, R., Shapiro-Shalef, M., DAVIS, M. M., Calame, K., Bikoff, E. K., Robertson, E. J. 2005; 132 (6): 1315-1325

  Abstract

  Blimp1, a zinc-finger containing DNA-binding transcriptional repressor, functions as a master regulator of B cell terminal differentiation. Considerable evidence suggests that Blimp1 is required for the establishment of anteroposterior axis formation and the formation of head structures during early vertebrate development. In mouse embryos, Blimp1 is strongly expressed in axial mesendoderm, the tissue known to provide anterior patterning signals during gastrulation. Here, we describe for the first time the defects caused by loss of Blimp1 function in the mouse. Blimp1 deficient embryos die at mid-gestation, but surprisingly early axis formation, anterior patterning and neural crest formation proceed normally. Rather, loss of Blimp1 expression disrupts morphogenesis of the caudal branchial arches and leads to a failure to correctly elaborate the labyrinthine layer of the placenta. Blimp1 mutant embryos also show widespread blood leakage and tissue apoptosis, and, strikingly, Blimp1 homozygous mutants entirely lack PGCs. At the time of PGC allocation around 7.25 days post coitum, Blimp1 heterozygous embryos exhibit decreased numbers of PCGs. Thus Blimp1 probably acts to turn off the default pathway that allows epiblast cells to adopt a somatic cell fate, and shifts the transcriptional program so that they become exclusively allocated into the germ cell lineage.

  View details for DOI 10.1242/dev.01711

  View details for Web of Science ID 000228378000014

  View details for PubMedID 15750184

• Deformable modeling for improved calculation of molecular velocities from single-particle tracking IEEE Computational Systems Bioinformatics Conference Kasson, P., Davis, M. M., Brunger, A. T. IEEE COMPUTER SOC. 2005: 208–211

  Abstract

  Single-particle tracking provides a powerful technique for measuring dynamic cellular processes on the level of individual molecules. Much recent work has been devoted to using single particle tracking to measure long-range movement of particles on the cell surface, including methods for automated localization and tracking of particles [1-3]. However, most particle tracking studies to date ignore cell surface curvature and dynamic cellular deformation, factors frequently present in physiologically relevant situations. In this report, we perform quantitative evaluation of single-particle tracking on curved and deforming cell surfaces. We also introduce a new hybrid method that uses non-rigid cellular modeling for improved computation of single-particle tracking trajectories on the surfaces of cells undergoing deformation. This method combines single-molecule and bulk fluorescence measurements in an automated manner to enable more accurate and robust characterization of dynamic cell physiology and regulation.

  View details for Web of Science ID 000231800100025

  View details for PubMedID 16447978

• Blimp-1; Immunoglobulin secretion and the switch to plasma cells MOLECULAR ANALYSIS OF B LYMPHOCYTE DEVELOPMENT AND ACTIVATION Sciammas, R., DAVIS, M. M. 2005; 290: 201-224

  Abstract

  The transcription factor Blimp-1 governs the generation of plasma cells and immunoglobulin secretion. Recent microarray experiments indicate that Blimp-1 regulates a large set of genes that constitute a significant part of the plasma cell expression signature. The variety of differentially expressed genes indicates that Blimp-1 affects numerous aspects of plasma cell maturation, ranging from migration, adhesion, and homeostasis, to antibody secretion. In addition, Blimp-1 regulates immunoglobulin secretion by affecting the nuclear processing of the mRNA transcript and by affecting protein trafficking by regulating genes that impact on the activity of the endoplasmic reticulum. Interestingly, the differentiation events that Blimp-1 regulates appear to be modulated depending on the activation state of the B cell. This modulation may be due at least in part to distinct regions of Blimp-1 that regulate unique sets of genes independently of each other. These data hint at the complexity of Blimp-1 and the genetic program that it initiates to produce a pool of plasma cells necessary for specific immunity.

  View details for Web of Science ID 000233593800009

  View details for PubMedID 16480044

• Quantitative imaging of lymphocyte membrane protein reorganization and signaling BIOPHYSICAL JOURNAL Kasson, P. M., Huppa, J. B., Krogsgaard, M., DAVIS, M. M., Brunger, A. T. 2005; 88 (1): 579-589

  Abstract

  Changes in membrane protein localization are critical to establishing cell polarity and regulating cell signaling. Fluorescence microscopy of labeled proteins allows visualization of these changes, but quantitative analysis is needed to study this aspect of cell signaling in full mechanistic detail. We have developed a novel approach for quantitative assessment of membrane protein redistribution based on four-dimensional video microscopy of fluorescently labeled proteins. Our analytic system provides robust automated methods for cell surface reconstruction, cell shape tracking, cell-surface distance measurement, and cluster formation analysis. These methods permit statistical analyses and testing of mechanistic hypotheses regarding cell signaling. We have used this approach to measure antigen-dependent clustering of signaling molecules in CD4+ T lymphocytes, obtaining clustering velocities consistent with single-particle tracking data. Our system captures quantitative differences in clustering between signaling proteins with distinct biological functions. Our methods can be generalized to a range of cell-signaling phenomena and enable novel applications not feasible with single-particle studies, such as analysis of subcellular protein localization in live organ culture.

  View details for DOI 10.1529/biophysj.104.048827

  View details for Web of Science ID 000226090900054

  View details for PubMedID 15501943

  View details for PubMedCentralID PMC1305035

• Prevention of type I diabetes transfer by glutamic acid decarboxylase 65 peptide 206-220-specific T cells PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kim, S. K., Tarbell, K. V., Sanna, M., Vadeboncoeur, M., Warganich, T., Lee, M., Davis, M., McDevitt, H. O. 2004; 101 (39): 14204-14209

  Abstract

  Glutamic acid decarboxylase (GAD) 65 is one of the major pancreatic antigens targeted by self-reactive T cells in type I diabetes mellitus. T cells specific for GAD65 are among the first to enter inflamed islets and may be important for the initiation of autoimmune diabetes. However, we previously reported that nonobese diabetic (NOD) mice transgenic for a T cell antigen receptor (TCR) specific for one of the immunodominant epitopes of GAD65, peptide 286-300 (G286), are protected from insulitis and diabetes. To examine whether other GAD65-reactive T cells share this phenotype, we have generated TCR transgenic NOD mice for a second immunodominant epitope of GAD65, peptide 206-220 (G206). As in G286 mice, G206 mice do not develop islet inflammation or diabetes. When adoptively transferred along with diabetogenic T cells, activated G206 T cells significantly delayed the onset of diabetes in NOD.scid recipients. Both G206 and G286 T cells produce immunoregulatory cytokines IFN-gamma and IL-10 at low levels when activated by cognate antigens. These data suggest that GAD65-specific T cells may play a protective role in diabetes pathogenesis by regulating pathogenic T cell responses. A better understanding of the functions of autoreactive T cells in type I diabetes will be necessary for choosing desirable targets for immunotherapy.

  View details for DOI 10.1073/pnas.0405500101

  View details for PubMedID 15381770

• T cell receptor antagonism interferes with MHC clustering and integrin patterning during immunological synapse formation JOURNAL OF CELL BIOLOGY Sumen, C., Dustin, M. L., Davis, M. M. 2004; 166 (4): 579-590

  Abstract

  T cell activation by nonself peptide-major histocompatibility complex (MHC) antigenic complexes can be blocked by particular sequence variants in a process termed T cell receptor antagonism. The inhibition mechanism is not understood, although such variants are encountered in viral infections and may aid immune evasion. Here, we study the effect of antagonist peptides on immunological synapse formation by T cells. This cellular communication process features early integrin engagement and T cell motility arrest, referred to as the "stop signal." We find that synapses formed on membranes presenting antagonist-agonist complexes display reduced MHC density, which leads to reduced T cell proliferation that is not overcome by the costimulatory ligands CD48 and B7-1. Most T cells fail to arrest and crawl slowly with a dense ICAM-1 crescent at the leading edge. Similar aberrant patterns of LFA-1/ICAM-1 engagement in live T-B couples correlate with reduced calcium flux and IL-2 secretion. Hence, antagonist peptides selectively disable MHC clustering and the stop signal, whereas LFA-1 valency up-regulation occurs normally.

  View details for DOI 10.1083/jcb.200404059

  View details for Web of Science ID 000223479000015

  View details for PubMedID 15314068

  View details for PubMedCentralID PMC2172210

• CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse NATURE IMMUNOLOGY Li, Q. J., Dinner, A. R., Qi, S. Y., Irvine, D. J., Huppa, J. B., Davis, M. M., Chakraborty, A. K. 2004; 5 (8): 791-799

  Abstract

  How T cells respond with extraordinary sensitivity to minute amounts of agonist peptide and major histocompatibility complex (pMHC) molecules on the surface of antigen-presenting cells bearing large numbers of endogenous pMHC molecules is not understood. Here we present evidence that CD4 affects the responsiveness of T helper cells by controlling spatial localization of the tyrosine kinase Lck in the synapse. This finding, as well as further in silico and in vitro experiments, led us to develop a molecular model in which endogenous and agonist pMHC molecules act cooperatively to amplify T cell receptor signaling. At the same time, activation due to endogenous pMHC molecules alone is inhibited. A key feature is that the binding of agonist pMHC molecules to the T cell receptor results in CD4-mediated spatial localization of Lck, which in turn enables endogenous pMHC molecules to trigger many T cell receptors. We also discuss broader implications for T cell biology, including thymic selection, diversity of the repertoire of self pMHC molecules and serial triggering.

  View details for DOI 10.1038/ni1095

  View details for Web of Science ID 000222955600010

  View details for PubMedID 15247914

• The evolutionary and structural 'logic' of antigen receptor diversity SEMINARS IN IMMUNOLOGY Davis, M. M. 2004; 16 (4): 239-243

  Abstract

  Most vertebrate species utilize antibody and T-cell receptor (TCR) genes to create a vast repertoire of antigen sensor molecules on their B and T lymphocytes, respectively. While the organization of these genes exhibits substantial variation between species, one common theme is that, in almost every case, there is at least one variable region with a highly diverse CDR3 region and often much less diversity elsewhere in the binding site. Whereas with alphabeta TCRs this skewing of diversity correlates well with the need to recognize diverse peptides bound to MHC molecules, this cannot explain why this same pattern is evident in immunoglobulins (Igs) or gammadelta TCRs. Instead we have postulated that in the primary repertoire, all or most antigen receptors have a bipartite binding site, in which diverse CDR3 loops act as a highly antigen specific 'core' whereas other CDRs bind in a largely opportunistic fashion. In the case of antibodies, somatic hypermutation then acts to improve the complementarity to a given antigen and increase antibody affinity. A test of this model in mice engineered to have a very limited V region repertoire shows that primary antibodies can be generated that are highly specific for distinct antigens, yet identical in sequence except for their V(H) CDR3. Furthermore, very high affinity antibodies can be raised by repeated immunizations, showing that somatic hypermutation can mold these low affinity antibodies into high affinity ones. Thus, the wide variations seen in V region repertoires amongst vertebrates is likely to be of lesser importance than the preservation of one or more diverse CDR3 regions.

  View details for DOI 10.1016/j.smim.2004.08.003

  View details for Web of Science ID 000225342100004

  View details for PubMedID 15522622

• T cell killing does not require the formation of a stable mature immunological synapse NATURE IMMUNOLOGY Purbhoo, M. A., Irvine, D. J., Huppa, J. B., Davis, M. M. 2004; 5 (5): 524-530

  Abstract

  A notable feature of T lymphocyte recognition on other cell surfaces is the formation of a stable mature immunological synapse. Here we use a single-molecule labeling method to directly measure the number of ligands a cytotoxic T cell engages and track the consequences of that interaction by three-dimensional video microscopy. Like helper T cells, cytotoxic T cells were able to detect even a single foreign antigen but required about ten complexes of peptide-major histocompatibility complex (pMHC) to achieve full calcium increase and to form a mature synapse. Thus, cytotoxic T cells and helper T cells are more uniform in their antigen sensitivities than previously thought. Furthermore, only three pMHC complexes were required for killing, showing that stable synapse formation and complete signaling are not required for cytotoxicity.

  View details for DOI 10.1038/ni1058

  View details for Web of Science ID 000221101100017

  View details for PubMedID 15048111

• Modular nature of blimp-1 in the regulation of gene expression during B cell maturation JOURNAL OF IMMUNOLOGY Sciammas, R., DAVIS, M. M. 2004; 172 (9): 5427-5440

  Abstract

  The transcription factor Blimp-1 induces the maturation of B cells into Ab-secreting plasma cells. DNA microarrays were used to analyze the transcription profiles of both Blimp-1-transduced murine B cell lines and the inducible B cell line BCL(1). Hundreds of genes were differentially regulated, showing how Blimp-1 both restricts affinity maturation and promotes Ab secretion, homeostasis, migration, and differentiation. Strikingly, when different modes of plasma cell induction are used, very different genetic programs are used, suggesting that the transition from a B cell to plasma cell can occur in multiple ways, perhaps accounting for the different types of Ab-secreting cells observed in vivo. Furthermore, mutagenesis of Blimp-1 reveals multiple effector domains, which regulate distinct genes. This indicates that Blimp-1 subdivides the maturation program into select and tunable pathways.

  View details for Web of Science ID 000221012300036

  View details for PubMedID 15100284

• Quantitative analysis of membrane protein localization and signalling IEEE Computational Systems Bioinformatics Conference (CSB 2004) Kasson, P. M., Huppa, J. B., DAVIS, M. M., Brunger, A. T. IEEE COMPUTER SOC. 2004: 540–541

  View details for Web of Science ID 000224127800077

• In situ detection of the interaction between single T cell receptors and their antigenic ligands by Total Internal Reflection Fluorescence Microscopy (TIRFM) Axmann, M., Huppa, J. B., Moertelmaier, M., Kieberger, N., Sumen, C., Davis, M. M., Schuetz, G. J. BIOPHYSICAL SOCIETY. 2004: 445A

  View details for Web of Science ID 000187971202291

• Quantitative analysis of lymphocyte membrane protein redistribution from fluorescence microscopy International Conference on Image Processing (ICIP 2004) Kasson, P. M., Huppa, J. B., DAVIS, M. M., Brunger, A. T. IEEE. 2004: 2933–2936

  View details for Web of Science ID 000228043504023

• Detection and characterization of cellular immune responses using peptide-MHC microarrays. PLoS biology Soen, Y., Chen, D. S., Kraft, D. L., Davis, M. M., Brown, P. O. 2003; 1 (3): E65-?

  Abstract

  The detection and characterization of antigen-specific T cell populations is critical for understanding the development and physiology of the immune system and its responses in health and disease. We have developed and tested a method that uses arrays of peptide-MHC complexes for the rapid identification, isolation, activation, and characterization of multiple antigen-specific populations of T cells. CD4(+) or CD8(+) lymphocytes can be captured in accordance with their ligand specificity using an array of peptide-MHC complexes printed on a film-coated glass surface. We have characterized the specificity and sensitivity of a peptide-MHC array using labeled lymphocytes from T cell receptor transgenic mice. In addition, we were able to use the array to detect a rare population of antigen-specific T cells following vaccination of a normal mouse. This approach should be useful for epitope discovery, as well as for characterization and analysis of multiple epitope-specific T cell populations during immune responses associated with viral and bacterial infection, cancer, autoimmunity, and vaccination.

  View details for PubMedID 14691537

• T-cell-antigen recognition and the immunological synapse NATURE REVIEWS IMMUNOLOGY Huppa, J. B., DAVIS, M. M. 2003; 3 (12): 973-983

  View details for DOI 10.1038/nri1245

  View details for Web of Science ID 000186892700015

  View details for PubMedID 14647479

• Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation MOLECULAR CELL Krogsgaard, M., Prado, N., Adams, E. J., He, X. L., Chow, D. C., Wilson, D. B., Garcia, K. C., Davis, M. M. 2003; 12 (6): 1367-1378

  Abstract

  While in many cases the half-life of T cell receptor (TCR) binding to a particular ligand is a good predictor of activation potential, numerous exceptions suggest that other physical parameter(s) must also play a role. Accordingly, we analyzed the thermodynamics of TCR binding to a series of peptide-MHC ligands, three of which are more stimulatory than their stability of binding would predict. Strikingly, we find that during TCR binding these outliers show anomalously large changes in heat capacity, an indicator of conformational change or flexibility in a binding interaction. By combining the values for heat capacity (DeltaCp) and the half-life of TCR binding (t(1/2)), we find that we can accurately predict the degree of T cell stimulation. Structural analysis shows significant changes in the central TCR contact residue of the peptide-MHC, indicating that structural rearrangements within the TCR-peptide-MHC interface can contribute to T cell activation.

  View details for Web of Science ID 000187511600007

  View details for PubMedID 14690592

• Linking molecular and cellular events in T-cell activation and synapse formation SEMINARS IN IMMUNOLOGY Krogsgaard, M., Huppa, J. B., Purbhoo, M. A., Davis, M. A. 2003; 15 (6): 307-315

  Abstract

  The complex sequence of events in which T cells recognize foreign entities on other cells is not well understood. However, the development of new techniques and approaches in both the molecular and cellular aspects of this problem have provided significant insights into the mechanisms of T-cell recognition and synapse formation. In particular, we have a clearer picture of T-cell sensitivity, the role of co-stimulation in formation of the immunological synapse, and how TCR signaling acts to maintain synapse structure and potentiate the T cells over many hours of engagement. We also are aware of new complexities in the way T-cell receptor molecules bind peptide-MHC (pMHC) ligands and what that may mean for TCR scanning, cross-reactivity, and activation. Ultimately, we want to integrate these cellular aspects of T-cell recognition with key features of the molecular interactions that drive specific events.

  View details for DOI 10.1016/j.smim.2003.09.002

  View details for Web of Science ID 000187388800003

  View details for PubMedID 15001169

• Continuous T cell receptor signaling required for synapse maintenance and full effector potential NATURE IMMUNOLOGY Huppa, J. B., Gleimer, M., Sumen, C., Davis, M. M. 2003; 4 (8): 749-755

  Abstract

  Although signals through the T cell receptor (TCR) are essential for the initiation of T helper cell activation, it is unclear what function such signals have during the prolonged T cell-antigen-presenting cell contact. Here we simultaneously tracked TCR-CD3 complex and phosphoinositide 3-kinase activity in single T cells using three-dimensional video microscopy. Despite rapid internalization of most of the TCR-CD3, TCR-dependent signaling was still evident up to 10 h after conjugate formation. Blocking this interaction caused dissolution of the synapse and proportional reductions in interleukin 2 production and cellular proliferation. Thus TCR signaling persists for hours, has a cumulative effect and is necessary for the maintenance of the immunological synapse.

  View details for DOI 10.1038/ni951

  View details for Web of Science ID 000184441500011

  View details for PubMedID 12858171

• The problem of plain vanilla peptides NATURE IMMUNOLOGY Davis, M. M. 2003; 4 (7): 649-650

  View details for DOI 10.1038/ni0703-649

  View details for Web of Science ID 000183952500010

  View details for PubMedID 12830143

• Distinct molecular mechanisms account for the specificity of two different T-cell receptors BIOCHEMISTRY Anikeeva, N., Lebedeva, T., Krogsgaard, M., Tetin, S. Y., Martinez-Hackert, E., Kalams, S. A., Davis, M. M., Sykulev, Y. 2003; 42 (16): 4709-4716

  Abstract

  Analysis of the thermodynamics of the interactions between the D3 T-cell receptor (TCR) and its natural ligand, an HIV peptide bound to a HLA-A0201 (HLA-A2) major histocompatibility complex (MHC) protein, shows both similarities and striking differences when compared with the 2B4 TCR binding to its peptide-MHC ligand. The equilibrium thermodynamic parameters of both reactions are consistent with a conformational adjustment at the binding interface during the formation of specific TCR-peptide-MHC complexes. However, osmolytic reagents that dehydrate protein surfaces have profoundly different effects on the strength of the two reactions, indicating that water molecules make very different contributions-enhancing the binding of D3 TCR but weakening the binding of 2B4 TCR. The use of these different mechanisms by TCRs to recognize ligands might be an important means augmenting their inherent cross-reactivity.

  View details for DOI 10.1021/bi026864+

  View details for Web of Science ID 000182460700012

  View details for PubMedID 12705834

• Chronic myelogenous leukemia shapes host immunity by selective deletion of high-avidity leukemia-speciflic T cells JOURNAL OF CLINICAL INVESTIGATION Molldrem, J. J., Lee, P. P., Kant, S., Wieder, E., Jiang, W. D., Lu, S. J., Wang, C. Q., DAVIS, M. M. 2003; 111 (5): 639-647

  Abstract

  We have shown that cytotoxic T lymphocytes specific for PR1, an HLA-A2-restricted nonopeptide derived from proteinase 3, kill leukemia cells and may contribute to the elimination of chronic myelogenous leukemia (CML) after treatment with IFN or allogeneic bone marrow transplant. Some patients with persistent disease also have circulating PR1-specific T cells, however, suggesting the likelihood of immune tolerance. Here we show that both high- and low-avidity PR1-specific T cells from the peripheral blood of healthy donors can be identified and selectively expanded in vitro. Although high-avidity PR1-specific T cells killed CML more effectively than low-avidity T cells, only high-avidity T cells underwent apoptosis when stimulated with high PR1 peptide concentration or when exposed to leukemia that overexpressed proteinase 3. No high-avidity PR1-specific T cells could be identified or expanded from newly diagnosed leukemia patients, whereas low-avidity T cells were readily expanded. Circulating high-avidity PR1-specific T cells were identified in IFN-sensitive patients in cytogenetic remission, however. These results provide evidence that CML shapes the host immune response and that leukemia outgrowth may result in part from leukemia-induced selective deletion of high-avidity PR1-specific T cells.

  View details for DOI 10.1172/JCI200316398

  View details for Web of Science ID 000181346600012

  View details for PubMedID 12618518

  View details for PubMedCentralID PMC151894

• Dynamics of cell surface molecules during T cell recognition ANNUAL REVIEW OF BIOCHEMISTRY Davis, M. M., Krogsgaard, M., Huppa, J. B., Sumen, C., Purbhoo, M. A., Irvine, D. J., Wu, L. C., Ehrlich, L. 2003; 72: 717-742

  Abstract

  Recognition of foreign antigens by T lymphocytes is a very important component of vertebrate immunity-vital to the clearance of pathogenic organisms and particular viruses and necessary, indirectly, for the production of high affinity antibodies. T cell recognition is mediated by the systematic scanning of cell surfaces by T cells, which collectively express many antigen receptors. When the appropriate antigenic peptide bound to a molecule of the major histocompatibility complex is found-even in minute quantities-a series of elaborate cell-surface molecule and internal rearrangements take place. The sequence of events and the development of techniques required to observe these events have significantly enhanced our understanding of T cell recognition and may find application in other systems of transient cell:cell interactions as well.

  View details for DOI 10.1146/annurev.biochem.72.121801.161625

  View details for Web of Science ID 000185092500022

  View details for PubMedID 14527326

• Dynamics of p56lck translocation to the T cell immunological synapse following agonist and antagonist stimulation IMMUNITY Ehrlich, L. I., Ebert, P. J., Krummel, M. F., WEISS, A., DAVIS, M. M. 2002; 17 (6): 809-822

  Abstract

  To study the spatio/temporal recruitment of lck during immunological synapse formation, we utilize high-speed time-lapse microscopy to visualize green fluorescent protein (GFP) fusions of lck and CD3zeta following agonist or altered peptide ligand (APL) stimulation. The dynamics of lck and CD3zeta recruitment are comparable; however, lck becomes excluded to the periphery of mature synapses, while most CD3zeta is centrally localized, suggesting a limited time frame within which lck can efficiently phosphorylate CD3 molecules during synapse maturation. Exposure of T cells to specific APLs affects the efficiency of conjugate formation and lck accumulation. Most surprisingly, we find an intracellular pool of lck associated with recycling endosomes that translocates to mature synapses within 10 min of calcium flux. This bolus of lck may contribute to intermediate-late signal transduction.

  View details for Web of Science ID 000179985500012

  View details for PubMedID 12479826

• A blood-borne antigen induces rapid T-B cell contact: a potential mechanism for tolerance induction IMMUNOLOGY Gutgemann, I., Darling, J. M., Greenberg, H. B., DAVIS, M. M., Chien, Y. H. 2002; 107 (4): 420-425

  Abstract

  Understanding the difference between the development of a productive T-cell response and tolerance is central to discerning how the immune system functions. Intravenous injection of soluble protein is thought to mimic the presentation of self-serum and orally introduced antigens. It is generally toleragenic. The current view is that this outcome reflects the failure of 'immunogenic' dendritic cells to relocate to the T-cell zone of the secondary lymphoid tissues. Here, using a peptide/I-Ek tetramer and antibodies to stain splenic sections, we showed that antigen-specific T cells were activated in the spleen within hours of injection or feeding of protein. The activated T cells were found to be located at the T-B junction, the bridging zone and the B-cell area, interacting directly with B cells. In addition, B cells gain the ability to present antigen. Our results suggest a way for T cells to be stimulated by blood-borne antigen presented by naïve B cells, a potential mechanism of tolerance induction.

  View details for Web of Science ID 000179547900005

  View details for PubMedID 12460186

• Quantifying signaling-induced reorientation of T cell receptors during immunological synapse formation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Moss, W. C., Irvine, D. J., DAVIS, M. M., Krummel, M. F. 2002; 99 (23): 15024-15029

  Abstract

  Productive T cell recognition of antigen-presenting cells (APCs) is normally accompanied by the formation of a cell-cell contact called the "immunological synapse." Our understanding of the steps leading up to this formation has been limited by the absence of tools for analyzing 3D surfaces and surface distributions as they change over time. Here we use a 3D fluorescence quantitation method to show that T cell receptors are recruited in bulk within the first minute after the onset of activation and with velocities ranging from 0.04 to 0.1 microm/s; a speed significantly greater than unrestricted diffusion. Our method reveals a second feature of this reorientation: a conformational change as the T cell pushes more total membrane into the interface creating a larger contact area for additional receptors. Analysis of individual T cell receptor velocities using a single-particle tracking method confirms our velocity measurement. This method should permit the quantitation of other dynamic membrane events and the associated movement of cell-surface molecules.

  View details for DOI 10.1073/pnas.192573999

  View details for Web of Science ID 000179224800075

  View details for PubMedID 12415110

  View details for PubMedCentralID PMC137538

• In vivo study of a semi-artificial immunological synapse using ultrasensitive microscopy Moertelmaier, M. A., Drbal, K., Huppa, J., Stockinger, H., Davis, M., Schutz, G. J. AMER SOC CELL BIOLOGY. 2002: 140A

  View details for Web of Science ID 000179569100783

• Direct observation of ligand recognition by T cells NATURE Irvine, D. J., Purbhoo, M. A., Krogsgaard, M., Davis, M. M. 2002; 419 (6909): 845-849

  Abstract

  The activation of T cells through interaction of their T-cell receptors with antigenic peptide bound to major histocompatibility complex (MHC) on the surface of antigen presenting cells (APCs) is a crucial step in adaptive immunity. Here we use three-dimensional fluorescence microscopy to visualize individual peptide-I-E(k) class II MHC complexes labelled with the phycobiliprotein phycoerythrin in an effort to characterize T-cell sensitivity and the requirements for forming an immunological synapse in single cells. We show that T cells expressing the CD4 antigen respond with transient calcium signalling to even a single agonist peptide-MHC ligand, and that the organization of molecules in the contact zone of the T cell and APC takes on the characteristics of an immunological synapse when only about ten agonists are present. This sensitivity is highly dependent on CD4, because blocking this molecule with antibodies renders T cells unable to detect less than about 30 ligands.

  View details for DOI 10.1038/nature01076

  View details for Web of Science ID 000178769800048

  View details for PubMedID 12397360

• Identification of Epstein-Barr virus-specific CD8(+) T lymphocytes in the circulation of pediatric transplant recipients TRANSPLANTATION Falco, D. A., Nepomuceno, R. R., Krams, S. M., Lee, P. P., DAVIS, M. M., Salvatierra, O., Alexander, S. R., Esquivel, C. O., Cox, K. L., Frankel, L. R., Martinez, O. M. 2002; 74 (4): 501-510

  Abstract

  Pediatric transplant recipients are at increased risk for Epstein Barr virus (EBV)-related B cell lymphomas. In healthy individuals, the expansion of EBV-infected B cells is controlled by CD8+ cytotoxic T cells. However, immunosuppressive therapy may compromise antiviral immunity. We identified and determined the frequency of EBV-specific T cells in the peripheral blood of pediatric transplant recipients.HLA-B*0801 and HLA-A*0201 tetramers folded with immunodominant EBV peptides were used to detect EBV-specific CD8+ T cells by flow cytometry in peripheral blood mononuclear cells from 24 pediatric liver and kidney transplant recipients. The expression of CD38 and CD45RO on EBV-specific, tetramer-binding cells was also examined in a subset of patients by immunofluorescent staining and flow cytometry.Tetramer-binding CD8+ T cells were identified in 21 of 24 transplant recipients. EBV-specific CD8+ T cells were detected as early as 4 weeks after transplant in EBV seronegative patients receiving an organ from an EBV seropositive donor. The frequencies (expressed as a percentage of the CD8+ T cells) of the tetramer-binding cells were HLA-B8-RAKFKQLL (BZLF1 lytic antigen peptide) tetramer, range=0.96 to 3.94%; HLA-B8-FLRGRAYGL (EBNA3A latent antigen peptide) tetramer, range=0.03 to 0.59%; and HLA-A2-GLCTLVAML (BMLF1 lytic antigen peptide) tetramer, range=0.06 to 0.76%. The majority of tetramer reactive cells displayed an activated/memory phenotype.Pediatric transplant recipients receiving immunosuppression can generate EBV-specific CD8+ T cells. Phenotypic and functional analysis of tetramer cells may prove useful in defining and monitoring EBV infection in the posttransplant patient.

  View details for PubMedID 12352909

• CD4(+) T cells from glutamic acid decarboxylase (GAD)65-specific T cell receptor transgenic mice are not diabetogenic and can delay diabetes transfer JOURNAL OF EXPERIMENTAL MEDICINE Tarbell, K. V., Lee, M., Ranheim, E., Chao, C. C., Sanna, M., Kim, S. K., Dickie, P., Teyton, L., Davis, M., McDevitt, H. 2002; 196 (4): 481-492

  Abstract

  Glutamic acid decarboxylase (GAD)65 is an early and important antigen in both human diabetes mellitus and the nonobese diabetic (NOD) mouse. However, the exact role of GAD65-specific T cells in diabetes pathogenesis is unclear. T cell responses to GAD65 occur early in diabetes pathogenesis, yet only one GAD65-specific T cell clone of many identified can transfer diabetes. We have generated transgenic mice on the NOD background expressing a T cell receptor (TCR)-specific for peptide epitope 286-300 (p286) of GAD65. These mice have GAD65-specific CD4(+) T cells, as shown by staining with an I-A(g7)(p286) tetramer reagent. Lymphocytes from these TCR transgenic mice proliferate and make interferon gamma, interleukin (IL)-2, tumor necrosis factor (TNF)-alpha, and IL-10 when stimulated in vitro with GAD65 peptide 286-300, yet these TCR transgenic animals do not spontaneously develop diabetes, and insulitis is virtually undetectable. Furthermore, in vitro activated CD4 T cells from GAD 286 TCR transgenic mice express higher levels of CTL-associated antigen (CTLA)-4 than nontransgenic littermates. CD4(+) T cells, or p286-tetramer(+)CD4(+) Tcells, from GAD65 286-300-specific TCR transgenic mice delay diabetes induced in NOD.scid mice by diabetic NOD spleen cells. This data suggests that GAD65 peptide 286-300-specific T cells have disease protective capacity and are not pathogenic.

  View details for DOI 10.1084/jem.20011845

  View details for PubMedID 12186840

• A new trigger for T cells CELL Davis, M. M. 2002; 110 (3): 285-287

  Abstract

  Understanding the early events in T cell activation and signaling is an active area of research. A recent study has described a new trigger for T cell activation, involving a TCR-ligand-induced conformational change in CD3epsilon that permits binding of the adaptor protein Nck.

  View details for Web of Science ID 000177411800004

  View details for PubMedID 12176315

• Two-step binding mechanism for T-cell receptor recognition of peptide-MHC NATURE Wu, L. C., Tuot, D. S., Lyons, D. S., Garcia, K. C., Davis, M. M. 2002; 418 (6897): 552-556

  Abstract

  T cells probe a diverse milieu of peptides presented by molecules of the major histocompatibility complex (MHC) by using the T-cell receptor (TCR) to scan these ligands with high sensitivity and specificity. Here we describe a physical basis for this scanning process by studying the residues involved in both the initial association and the stable binding of TCR to peptide-MHC, using the well-characterized TCR and peptide-MHC pair of 2B4 and MCC-IE(k) (moth cytochrome c, residues 88 103). We show that MHC contacts dictate the initial association, guiding TCR docking in a way that is mainly independent of the peptide. Subsequently, MCC-IE(k) peptide contacts dominate stabilization, imparting specificity and influencing T-cell activation by modulating the duration of binding. This functional subdivision of the peptide-MHC ligand suggests that a two-step process for TCR recognition facilitates the efficient scanning of diverse peptide-MHC complexes on the surface of cells and also makes TCRs inherently crossreactive towards different peptides bound by the same MHC.

  View details for DOI 10.1038/nature00920

  View details for Web of Science ID 000177162800045

  View details for PubMedID 12152083

• Restricted islet-cell reactive T cell repertoire of early pancreatic islet infiltrates in NOD mice PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Baker, F. J., Lee, M., Chien, Y. H., Davis, M. M. 2002; 99 (14): 9374-9379

  Abstract

  The mechanisms responsible for initiating autoimmune diabetes remain obscure. Here, we describe a method for identifying both the alpha- and beta-chains of the T cell receptor (TCR) from individual pancreatic islet-infiltrating T cells at the earliest stages of disease in nonobese diabetic mice (NOD). Analysis of the TCR repertoire of these early islet infiltrates reveals enrichment for a small subset of TCR sequences. Reconstitution of these TCR in vitro demonstrates that these receptors confer reactivity to islet cells but not to the well characterized autoantigens, glutamic acid decarboxylase (GAD65) and insulin. Thus, autoimmune diabetes in NOD may be initiated by a limited number of antigens distinct from GAD65 and insulin.

  View details for DOI 10.1073/pnas.142284899

  View details for Web of Science ID 000176775400055

  View details for PubMedID 12082183

  View details for PubMedCentralID PMC123148

• Imaging synapse formation during thymocyte selection: Inability of CD3 zeta to form a stable central accumulation during negative selection IMMUNITY Richie, L. I., Ebert, P. J., Wu, L. C., Krummel, M. F., Owen, J. J., Davis, M. M. 2002; 16 (4): 595-606

  Abstract

  TCR signaling can result in cell fates ranging from activation to tolerance to apoptosis. Organization of molecules in an "immunological synapse" between mature T cells and APCs correlates with the strength of TCR signaling. To investigate synapse formation during thymic selection, we have established a reaggregate system in which molecular recruitment of GFP fusion proteins to thymocyte:stromal cell interfaces can be visualized in real time. We demonstrate that negative selection is associated with efficient conjugate formation and rapid recruitment of p56(lck) and CD3zeta to an immunological synapse. Interestingly, CD3zeta-GFP does not accumulate at the center of the synapse, as in mature T cells, but at the periphery across a wide range of ligand densities. This implicates differences in synapse geometry in initiation of alternate signals downstream of the TCR.

  View details for Web of Science ID 000175109600010

  View details for PubMedID 11970882

• Costimulation and endogenous MHC ligands contribute to T cell recognition NATURE IMMUNOLOGY Wulfing, C., Sumen, C., Sjaastad, M. D., Wu, L. C., Dustin, M. L., Davis, M. M. 2002; 3 (1): 42-47

  Abstract

  To initiate an immune response, key receptor-ligand pairs must cluster in "immune synapses" at the T cell-antigen-presenting cell (APC) interface. We visualized the accumulation of a major histocompatibility complex (MHC) class II molecule, I-E(k), at a T cell-B cell interface and found it was dependent on both antigen recognition and costimulation. This suggests that costimulation-driven active transport of T cell surface molecules helps to drive immunological synapse formation. Although only agonist peptide-MHC class II (agonist pMHC class II) complexes can initiate T cell activation, endogenous pMHC class II complexes also appeared to accumulate. To test this directly, we labeled a "null" pMHC class II complex and found that, although it lacked major TCR contact residues, it could be driven into the synapse in a TCR-dependent manner. Thus, low-affinity ligands can contribute to synapse formation and T cell signaling.

  View details for Web of Science ID 000173148700013

  View details for PubMedID 11731799

• Attributes of gamma delta intraepithelial lymphocytes as suggested by their transcriptional profile PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Fahrer, A. M., Konigshofer, Y., Kerr, E. M., Ghandour, G., Mack, D. H., DAVIS, M. M., Chien, Y. H. 2001; 98 (18): 10261-10266

  Abstract

  gammadelta T lymphocytes in the intestinal intraepithelial layer (gammadelta IELs) are thought to contribute to immune competence, but their actual function remains poorly understood. Here we used DNA microarrays to study the gene expression profile of gammadelta IELs in a Yersinia infection system to better define their roles. To validate this approach, mesenteric lymph node CD8(+) alphabeta T cells were similarly analyzed. The transcription profiles show that, whereas lymph node CD8(+) alphabeta T cells must be activated to become cytotoxic effectors, gammadelta IELs are constitutively activated and appear to use different signaling cascades. Our data suggest that gammadelta IELs may respond efficiently to a broad range of pathological situations irrespective of their diverse T cell antigen receptor repertoire. gammadelta IELs may modulate local immune responses and participate in intestinal lipid metabolism, cholesterol homeostasis, and physiology. This study provides a strong basis for further investigations of the roles of these cells as well as mucosal immune defense in general.

  View details for Web of Science ID 000170738000045

  View details for PubMedID 11526237

• Altered peptide ligand vaccination with Flt3 ligand expanded dendritic cells for tumor immunotherapy PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Fong, L., Hou, Y. F., Rivas, A., Benike, C., Yuen, A., Fisher, G. A., DAVIS, M. M., Engleman, E. G. 2001; 98 (15): 8809-8814

  Abstract

  Most tumor-associated antigens represent self-proteins and as a result are poorly immunogenic due to immune tolerance. Here we show that tolerance to carcinoembryonic antigen (CEA), which is overexpressed by the majority of lethal malignancies, can be reversed by immunization with a CEA-derived peptide. This peptide was altered to make it a more potent T cell antigen and loaded onto dendritic cells (DCs) for delivery as a cellular vaccine. Although DCs are rare in the blood, we found that treatment of advanced cancer patients with Flt3 ligand, a hematopoietic growth factor, expanded DCs 20-fold in vivo. Immunization with these antigen-loaded DCs induced CD8 cytotoxic T lymphocytes that recognized tumor cells expressing endogenous CEA. Staining with peptide-MHC tetramers demonstrated the expansion of CD8 T cells that recognize both the native and altered epitopes and possess an effector cytotoxic T lymphocyte phenotype (CD45RA(+)CD27(-)CCR7(-)). After vaccination, two of 12 patients experienced dramatic tumor regression, one patient had a mixed response, and two had stable disease. Clinical response correlated with the expansion of CD8 tetramer(+) T cells, confirming the role of CD8 T cells in this treatment strategy.

  View details for Web of Science ID 000169967000107

  View details for PubMedID 11427731

• The functional roles of gd intraepithelial lymphocytes deduced form their transcriptional profile Chien, Y. H., Fahrer, A., Konigshofer, Y., Kerr, E., Davis, M., Mack, D. FEDERATION AMER SOC EXP BIOL. 2001: A1222

  View details for Web of Science ID 000167454202932

• A kinetic window constricts the T cell receptor repertoire in the thymus IMMUNITY Savage, P. A., Davis, M. M. 2001; 14 (3): 243-252

  Abstract

  To characterize the ligand binding properties of a naive T cell repertoire capable of responding to a foreign antigen, we analyzed T cell populations from T cell receptor (TCR) beta transgenic mice using a novel, single cell peptide/major histocompatibility complex (MHC) tetramer dissociation assay. The largely CD4+CD8(-/low) antigen-specific thymocyte repertoire exhibited a broad, bimodal distribution of tetramer binding half-lives (t(1/2)s), with a significant underrepresentation in the intermediate half-life range in which the majority of the peripheral repertoire lies. Thus, cells with the potential to bind foreign antigen with the lowest and highest stability are likely to be selectively removed from the repertoire prior to their establishment in the periphery. These studies provide direct evidence that thymic selection biases the naive peripheral T cell repertoire toward TCR-ligand interactions that fall within a moderate half-life "window."

  View details for Web of Science ID 000167959500004

  View details for PubMedID 11290334

• A kinetic window shapes the T cell receptor repertoire in the thymus Immunity M.M. Davis., Savage, P.A. 2001
• Confirmatory serologic testing for acute toxoplasmosis and rate of induced abortions among women reported to have positive Toxoplasma immunoglobulin M antibody titers 35th Annual Meeting of the Infectious-Diseases-Society-of-America Liesenfeld, O., Montoya, J. G., Tathineni, N. J., Davis, M., Brown, B. W., Cobb, K. L., Parsonnet, J., Remington, J. S. MOSBY-ELSEVIER. 2001: 140–45

  Abstract

  Results obtained with commercial testing kits for immunoglobulin M Toxoplasma antibodies may be inaccurate or may be inaccurately interpreted, which may influence whether a woman decides to terminate the pregnancy. This study was undertaken to determine whether confirmatory testing at a reference laboratory and communication of the results and an expert interpretation to the patient's physician would affect the rate of induced abortions among pregnant women with positive results of testing for immunoglobulin M Toxoplasma antibodies in outside laboratories.This was a retrospective cohort study of 811 consecutive pregnant women for whom the toxoplasma serologic profile was performed at a reference laboratory. Almost all the patients had been informed by their physicians that a result of a test for immunoglobulin M Toxoplasma antibodies performed in an outside laboratory was positive. Women were separated into those with a toxoplasma serologic profile result suggestive of a recently acquired infection (group 1) and those with a result suggestive of an infection acquired in the more distant past (group 2). Physician reports of induced abortions were used to determine rates of induced abortion in groups 1 and 2.Of the 811 women 321 (39.6%) were considered likely to have a recent infection (group 1) and 490 (60.4%) were considered likely to have a past infection (group 2). Physicians reported pregnancy outcomes for 433 (53.4%) of 811 women (65.1% and 45.7% in groups 1 and 2, respectively). Whereas 36 of 209 women in group 1 (17.2%) terminated the pregnancy, only 1 of 224 women in group 2 (0.4%) chose abortion (P <.001).Confirmatory serologic testing in a reference laboratory and communication of the results and their correct interpretation by an expert to the patient's physician decreased the rate of unnecessary abortions by approximately 50% among women for whom positive immunoglobulin M Toxoplasma test results had been reported by outside laboratories.

  View details for Web of Science ID 000166679700023

  View details for PubMedID 11174493

• The immunological synapse ANNUAL REVIEW OF IMMUNOLOGY Bromley, S. K., Burack, W. R., Johnson, K. G., SOMERSALO, K., Sims, T. N., Sumen, C., DAVIS, M. M., Shaw, A. S., Allen, P. M., Dustin, M. L. 2001; 19: 375-396

  Abstract

  The adaptive immune response is initiated by the interaction of T cell antigen receptors with major histocompatibility complex molecule-peptide complexes in the nanometer scale gap between a T cell and an antigen-presenting cell, referred to as an immunological synapse. In this review we focus on the concept of immunological synapse formation as it relates to membrane structure, T cell polarity, signaling pathways, and the antigen-presenting cell. Membrane domains provide an organizational principle for compartmentalization within the immunological synapse. T cell polarization by chemokines increases T cell sensitivity to antigen. The current model is that signaling and formation of the immunological synapse are tightly interwoven in mature T cells. We also extend this model to natural killer cell activation, where the inhibitory NK synapse provides a striking example in which inhibition of signaling leaves the synapse in its nascent, inverted state. The APC may also play an active role in immunological synapse formation, particularly for activation of naïve T cells.

  View details for Web of Science ID 000168234600014

  View details for PubMedID 11244041

• Direct functional analysis of epitope-specific CD8+ T cells in peripheral blood VIRAL IMMUNOLOGY He, X. S., Rehermann, B., Boisvert, J., Mumm, J., Maecker, H. T., Roederer, M., Wright, T. L., Maino, V. C., DAVIS, M. M., Greenberg, H. B. 2001; 14 (1): 59-69

  Abstract

  The functional status of virus-specific CD8+ T cells is important for the outcome and the immunopathogenesis of viral infections. We have developed an assay for the direct functional analysis of antigen-specific CD8+ T cells, which does not require prolonged in vitro cultivation and amplification of T cells. Whole blood samples were incubated with peptide antigens for <5 h, followed by staining with peptide-MHC tetramers to identify epitope-specific T cells. The cells were also stained for the activation marker CD69 or for the production of cytokines such as interferon-gamma (IFNgamma) or tumor necrosis factor-alpha (TNFalpha). With the combined staining with tetramer and antibodies to CD69 or cytokines the number of antigen-specific CD8+ T cells as well as the functional response of each individual cell to the cognate antigen can be determined in a single experiment. Virus-specific CD8+ T cells that are nonfunctional, as well as those that are functional under the same stimulating conditions can be simultaneously detected with this assay, which is not possible by using other T-cell functional assays including cytotoxicity assay, intracellular cytokine staining, and enzyme-linked immunospot (ELISPOT) assay.

  View details for Web of Science ID 000167575500005

  View details for PubMedID 11270597

• Melanocyte destruction after antigen-specific immunotherapy of melanoma: Direct evidence of T cell-mediated vitiligo JOURNAL OF EXPERIMENTAL MEDICINE Yee, C., Thompson, J. A., Roche, P., Byrd, D. R., Lee, P. P., PIEPKORN, M., Kenyon, K., DAVIS, M. M., Riddell, S. R., Greenberg, P. D. 2000; 192 (11): 1637-1643

  Abstract

  Current strategies for the immunotherapy of melanoma include augmentation of the immune response to tumor antigens represented by melanosomal proteins such as tyrosinase, gp100, and MART-1. The possibility that intentional targeting of tumor antigens representing normal proteins can result in autoimmune toxicity has been postulated but never demonstrated previously in humans. In this study, we describe a patient with metastatic melanoma who developed inflammatory lesions circumscribing pigmented areas of skin after an infusion of MART-1-specific CD8(+) T cell clones. Analysis of the infiltrating lymphocytes in skin and tumor biopsies using T cell-specific peptide-major histocompatibility complex tetramers demonstrated a localized predominance of MART-1-specific CD8(+) T cells (>28% of all CD8 T cells) that was identical to the infused clones (as confirmed by sequencing of the complementarity-determining region 3). In contrast to skin biopsies obtained from the patient before T cell infusion, postinfusion biopsies demonstrated loss of MART-1 expression, evidence of melanocyte damage, and the complete absence of melanocytes in affected regions of the skin. This study provides, for the first time, direct evidence in humans that antigen-specific immunotherapy can target not only antigen-positive tumor cells in vivo but also normal tissues expressing the shared tumor antigen.

  View details for Web of Science ID 000165833100012

  View details for PubMedID 11104805

  View details for PubMedCentralID PMC2193107

• How to ask questions (in 10 easy steps) Current biology : CB Davis, M. M. 2000; 10 (21): R771

  View details for PubMedID 11084345

• Successful CD8(+)T cell response directed at HCV1A but not HCV2B epitope in a patient infected with both HCV strains. He, X. S., Ji, X. H., Boisvert, J., Lopez, Darling, J., Wright, T. L., Davis, M. M., Greenberg, H. B. W B SAUNDERS CO. 2000: 226A

  View details for Web of Science ID 000089622400254

• Evidence that specific T lymphocytes may participate in the elimination of chronic myelogenous leukemia NATURE MEDICINE Molldrem, J. J., Lee, P. P., Wang, C. Q., Felio, K., Kantarjian, H. M., Champlin, R. E., DAVIS, M. M. 2000; 6 (9): 1018-1023

  Abstract

  Although the immune system has long been implicated in the control of cancer, evidence for specific and efficacious immune responses in human cancer has been lacking. In the case of chronic myelogenous leukemia (CML), either allogeneic bone marrow transplant (BMT) or interferon-alpha2b (IFN-alpha2b) therapy can result in complete remission, but the mechanism for prolonged disease control is unknown and may involve immune anti-leukemic responses. We previously demonstrated that PR1, a peptide derived from proteinase 3, is a potential target for CML-specific T cells. Here we studied 38 CML patients treated with allogeneic BMT, IFN- alpha2b or chemotherapy to look for PR1-specific T cells using PR1/HLA-A*0201 tetrameric complexes. There was a strong correlation between the presence of PR1-specific T cells and clinical responses after IFN-alpha and allogeneic BMT. This provides for the first time direct evidence of a role for T-cell immunity in clearing malignant cells.

  View details for Web of Science ID 000089190500034

  View details for PubMedID 10973322

• The vav exchange factor is an essential regulator in actin-dependent receptor translocation to the lymphocyte-antigen-presenting cell interface PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wulfing, C., Bauch, A., Crabtree, G. R., DAVIS, M. M. 2000; 97 (18): 10150-10155

  Abstract

  During the interaction of a T cell with an antigen-presenting cell (APC), several receptor ligand pairs, including the T cell receptor (TCR)/major histocompatibility complex (MHC), accumulate at the T cell/APC interface in defined geometrical patterns. This accumulation depends on a movement of the T cell cortical actin cytoskeleton toward the interface. Here we study the involvement of the guanine nucleotide exchange factor vav in this process. We crossed 129 vav(-/-) mice with B10/BR 5C.C7 TCR transgenic mice and used peptide-loaded APCs to stimulate T cells from the offspring. We found that the accumulation of TCR/MHC at the T cell/APC interface and the T cell actin cytoskeleton rearrangement were clearly defective in these vav(+/-) mice. A comparable defect in superantigen-mediated T cell activation of T cells from non-TCR transgenic 129 mice was also observed, although in this case it was more apparent in vav(-/-) mice. These data indicate that vav is an essential regulator of cytoskeletal rearrangements during T cell activation.

  View details for Web of Science ID 000089067500061

  View details for PubMedID 10963677

• Thirty-six views of T-cell recognition PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Krummel, M., Wulfing, C., Sumen, C., DAVIS, M. M. 2000; 355 (1400): 1071-1076

  Abstract

  While much is known about the signalling pathways within lymphocytes that are triggered during activation, much less is known about how the various cell surface molecules on T cells initiate these events. To address this, we have focused on the primary interaction that drives T-cell activation, namely the binding of a particular T-cell receptor (TCR) to peptide-MHC ligands, and find a close correlation between biological activity and off-rate; that is, the most stimulatory TCR ligands have the slowest dissociation rates. In general, TCRs from multiple histocompatibility complex (MHC) class-II-restricted T cells have half-lives of 1-11s at 25 degrees C, a much narrower range than found with antibodies and suggesting a strong selection for an optimum dissociation rate. TCR ligands with even faster dissociation rates tend to be antagonists. To observe the effects of these different ligands in their physiological setting, we made gene fusions of various molecules with green fluorescent protein (GFP), transfected them into the relevant lymphocytes, and observed their movements during T-cell recognition using multicolour video microscopy. We find that clustering of CD3zeta-GFP and CD4-GFP on the Tcell occurs concomitantly or slightly before the first rise in calcium by the T cell, and that various GFP-labelled molecules on the B-cell side cluster shortly thereafter (ICAM-1, class II MHC, CD48), apparently driven byT-cell molecules. Most of this movement towards the interface is mediated by signals through the co-stimulatory receptors, CD28 and LFA-1, and involves myosin motors and the cortical actin cytoskeleton. Thus, we have proposed that the principal mechanism by which co-stimulation enhances T-cell responsiveness is by increasing the local density of T-cell activation molecules, their ligands and their attendant signalling apparatus. In collaboration with Michael Dustin and colleagues, we have also found that the formation and stability of the TCR-peptide-MHC cluster at the centre of the interaction cap between T and B cells is highly dependent on the dissociation rate of the TCR and its ligand. Thus, we are able to link this kinetic parameter to the formation of a cell surface structure that is linked to and probably causal with respect to T-cell activation.

  View details for Web of Science ID 000089354600009

  View details for PubMedID 11186308

• Differential clustering of CD4 and CD3 zeta during T cell recognition SCIENCE Krummel, M. F., Sjaastad, M. D., Wulfing, C., Davis, M. M. 2000; 289 (5483): 1349-1352

  Abstract

  Whereas T helper cells recognize peptide-major histocompatibility complex (MHC) class II complexes through their T cell receptors (TCRs), CD4 binds to an antigen-independent region of the MHC. Using green fluorescent protein-tagged chimeras and three-dimensional video microscopy, we show that CD4 and TCR-associated CD3zeta cluster in the interface coincident with increases in intracellular calcium. Signaling-, costimulation-, and cytoskeleton-dependent processes then stabilize CD3zeta in a single cluster at the center of the interface, while CD4 moves to the periphery. Thus, the CD4 coreceptor may serve primarily to "boost" recognition of ligand by the TCR and may not be required once activation has been initiated.

  View details for Web of Science ID 000088942400038

  View details for PubMedID 10958781

• Diversity in the CDR3 region of V-H is sufficient for most antibody specificities IMMUNITY Xu, J. L., Davis, M. M. 2000; 13 (1): 37-45

  Abstract

  All rearranging antigen receptor genes have one or two highly diverse complementarity determining regions (CDRs) among the six that typically form the ligand binding surface. We report here that, in the case of antibodies, diversity at one of these regions, CDR3 of the V(H) domain, is sufficient to permit otherwise identical IgM molecules to distinguish between a variety of hapten and protein antigens. Furthermore, we find that somatic mutation can allow such antibodies to achieve surprisingly high affinities. These results are consistent with a model in which the highly diverse CDR3 loops are the key determinant of specificity in antigen recognition in both T cell receptors (TCR) and antibodies, whereas the germline-encoded CDR1 and CDR2 sequences are much more cross-reactive.

  View details for Web of Science ID 000088463600005

  View details for PubMedID 10933393

• Determination of the relationship between T cell responsiveness and the number of MHC-peptide complexes using specific monoclonal antibodies JOURNAL OF IMMUNOLOGY Reay, P. A., Matsui, K., Haase, K., Wulfing, C., Chien, Y. H., DAVIS, M. M. 2000; 164 (11): 5626-5634

  Abstract

  We describe the generation of three mAbs that recognize the complex of the class II MHC molecule IEk bound to a peptide derived from the carboxyl terminus of moth cytochrome c (residues 95-103). Reactivities of these mAbs are sensitive to single alterations in the sequence of both helices of the MHC molecule and to the bound peptide. The epitopes of these reagents are distinct but overlap substantially. One of these mAbs specifically blocks lymphokine release by T cells responsive to this complex but not others. We have used another to examine how the number of complexes on an APC is related to its ability to stimulate T cells. We find that 200-400 complexes per cell are necessary and sufficient to induce a degree of stimulation, whereas maximum stimulation is achieved only if more than 5000 complexes are present. The analysis indicates that T cell activation is a stochastic process.

  View details for Web of Science ID 000087154800011

  View details for PubMedID 10820237

• Antigen-specific T cell therapy for treatment of patients with melanoma: Tracking adoptively transferred CD8+T cell clones in vivo using peptide-MHC tetramers Yee, C., Thompson, J. A., Akatsuka, Y., Lee, P. P., Davis, M. M., Cao, J. H., Kenyon, K., Greenberg, P. D. FEDERATION AMER SOC EXP BIOL. 2000: A1138

  View details for Web of Science ID 000086643101332

• Cytoskeletal polarization of T cells is regulated by the signaling adaptor proteins LAT and SLP-76 Kuhne, M., Richie, L., Huppa, J., Davis, M., Weiss, A. FEDERATION AMER SOC EXP BIOL. 2000: A1176

  View details for Web of Science ID 000086643101555

• Kinetics of peptide binding to the class II MHC protein I-E BIOCHEMISTRY Kasson, P. M., Rabinowitz, J. D., Schmitt, L., DAVIS, M. M., McConnell, H. M. 2000; 39 (5): 1048-1058

  Abstract

  Class II MHC glycoproteins bind short (7-25 amino acid) peptides in an extended type II polyproline-like conformation and present them for immune recognition. Because empty MHC is unstable, measurement of the rate of the second-order reaction between peptide and MHC is challenging. In this report, we use dissociation of a pre-bound peptide to generate the active, peptide-receptive form of the empty class II MHC molecule I-Ek. This allows us to measure directly the rate of reaction between active, empty I-Ek and a set of peptides that vary in structure. We find that all peptides studied, despite having highly variable dissociation rates, bind with similar association rate constants. Thus, the rate-limiting step in peptide binding is minimally sensitive to peptide side-chain structure. An interesting complication to this simple model is that a single peptide can sometimes bind to I-Ek in two kinetically distinguishable conformations, with the stable peptide-MHC complex isomer forming much more slowly than the less-stable one. This demonstrates that an additional free-energy barrier limits the formation of certain specific MHC-peptide complex conformations.

  View details for Web of Science ID 000085172900024

  View details for PubMedID 10653650

• The use of HLA A2,1/p53 peptide tetramers to visualize the impact of self tolerance on the TCR repertoire JOURNAL OF IMMUNOLOGY Hernandez, J., Lee, P. P., DAVIS, M. M., Sherman, L. A. 2000; 164 (2): 596-602

  Abstract

  p53 is an attractive target for cancer immunotherapy since it is overexpressed in half of all tumors. However, it is also expressed in normal lymphoid tissue, and self tolerance leaves a p53-specific repertoire purged of high avidity CTL. To better understand the mechanism of tolerance and the basis for such low avidity interaction, p53-specific CTL from p53 deficient (p53-) and sufficient (p53+) A2.1/Kb transgenic mice were compared with respect to their ability to bind HLA-A2.1 tetramers containing cognate murine p53 peptide Ag, p53 261-269. Since the murine CD8 molecule cannot interact with human HLA-A2.1, this tests the ability of the TCR to bind the A2.1/peptide complex tetramer. CTL from p53- mice demonstrated strong binding of such A2.1/p53 261-269 tetramers; however, the CTL from tolerant p53+ mice were devoid of tetramer-binding CD8+ T cells. Examination of TCR expression at the clonal level revealed that CTL from p53+ and p53- mice each expressed comparable levels of the p53-specific TCR. These results indicate that normal expression of p53 promotes elimination of T cells expressing TCRs with sufficient affinity to achieve stable binding of the A2.1/p53 261-269 tetramers.

  View details for Web of Science ID 000084708600009

  View details for PubMedID 10623800

• Differential Clustering of CD4 and CD3z during T Cell Recognition Science M.M. Davis., Krummel, M.F., M. Sjaastad, C. W_lfing 2000
• Structure-insensitive binding of peptide ligands to MHC for immune presentation. Kasson, P. M., Rabinowitz, J. D., Schmitt, L., Davis, M. M., McConnell, H. M. BIOPHYSICAL SOCIETY. 2000: 38A

  View details for Web of Science ID 000084779300218

• A strong TCl recall response is mediated by a small number of circulating CTL after recovery from hepatitis C. Wedemeyer, H., He, X. S., Davis, A. R., Ghany, M., Lau, D., Davis, M. M., Greenberg, H., Alter, H., Liang, T. J., Hoofnagle, J., Rehermann, B. W B SAUNDERS CO. 1999: 410A

  View details for Web of Science ID 000082794700998

• Thermodynamics of T cell receptor binding to peptide-MHC: Evidence for a general mechanism of molecular scanning PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA BONIFACE, J. J., Reich, Z., Lyons, D. S., Davis, M. M. 1999; 96 (20): 11446-11451

  Abstract

  Antigen-dependent activation of T lymphocytes requires T cell receptor (TCR)-mediated recognition of specific peptides, together with the MHC molecules to which they are bound. To achieve this recognition in a reasonable time frame, the TCR must scan and discriminate rapidly between thousands of MHC molecules differing from each other only in their bound peptides. Kinetic analysis of the interaction between a TCR and its cognate peptide-MHC complex indicates that both association and dissociation depend heavily on the temperature, indicating the presence of large energy barriers in both phases. Thermodynamic analysis reveals changes in heat capacity and entropy that are characteristic of protein-ligand associations in which local folding is coupled to binding. Such an "induced-fit" mechanism is characteristic of sequence-specific DNA-binding proteins that must also recognize specific ligands in the presence of a high background of competing elements. Here, we propose that induced fit may endow the TCR with its requisite discriminatory capacity and suggest a model whereby the loosely structured antigen-binding loops of the TCR rapidly explore peptide-MHC complexes on the cell surface until some critical structural complementarity is achieved through localized folding transitions. We further suggest that conformational changes, implicit in this model, may also propagate beyond the TCR antigen-binding site and directly affect self-association of ligated TCRs or TCR-CD3 interactions required for signaling.

  View details for Web of Science ID 000082868500095

  View details for PubMedID 10500196

• Negative selection of T cells occurs throughout thymic development JOURNAL OF IMMUNOLOGY Baldwin, K. K., Trenchak, B. P., Altman, J. D., Davis, M. M. 1999; 163 (2): 689-698

  Abstract

  Thymic positive and negative selections govern the development of a self-MHC-reactive, yet self-tolerant, T cell repertoire. Whether these processes occur independently or sequentially remains controversial. To investigate these issues, we have employed tetrameric peptide-MHC complexes to fluorescently label and monitor polyclonal populations of thymocytes that are specific for moth cytochrome c (MCC)/I-Ek. In TCR beta mice tetramer-positive thymocytes are detectable even in the most immature TCR-expressing cells. In the presence of MCC peptide, thymocytes that bind strongly to MCC/I-Ek tetramers are deleted earlier in development and more extensively than cells that bind weakly. This negative selection of the MCC/I-Ek-specific cells occurs continuously throughout development and before any evidence of positive selection. Thus, positive and negative selections are independent processes that need not occur sequentially.

  View details for Web of Science ID 000081360800021

  View details for PubMedID 10395659

• The immunological synapse: A molecular machine controlling T cell activation SCIENCE Grakoui, A., Bromley, S. K., Sumen, C., DAVIS, M. M., Shaw, A. S., Allen, P. M., Dustin, M. L. 1999; 285 (5425): 221-227

  Abstract

  The specialized junction between a T lymphocyte and an antigen-presenting cell, the immunological synapse, consists of a central cluster of T cell receptors surrounded by a ring of adhesion molecules. Immunological synapse formation is now shown to be an active and dynamic mechanism that allows T cells to distinguish potential antigenic ligands. Initially, T cell receptor ligands were engaged in an outermost ring of the nascent synapse. Transport of these complexes into the central cluster was dependent on T cell receptor-ligand interaction kinetics. Finally, formation of a stable central cluster at the heart of the synapse was a determinative event for T cell proliferation.

  View details for Web of Science ID 000081346000032

  View details for PubMedID 10398592

• Catalysis of peptide dissociation from class II MHC-peptide complexes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Schmitt, L., Kratz, J. R., DAVIS, M. M., McConnell, H. M. 1999; 96 (12): 6581-6586

  Abstract

  Certain peptides such as dynorphin A [dynA-(1-13)] enhance the release of antigenic peptides bound to class II MHC molecules at neutral pH. This enhanced release has been termed push off. Previous work has shown that the antigenic pigeon cytochrome c peptide PCC-(89-104) has at least two conformational isomers when bound to the class II MHC protein I-Ek. We have accordingly studied the push off of PCC-(89-104) from the complex PCC-(89-104)/I-Ek to see whether these isomeric conformations are distinguished by the push-off effect. A comparison of the association and dissociation kinetics of PCC-(89-104)/I-Ek in the presence of dynA-(1-13) shows that dynA-(1-13) does not simply replace PCC-(89-104) but rather acts catalytically. The major product is peptide-free I-Ek, which is receptive to further peptide binding. Evidence is presented that a two peptide-one MHC complex is formed in solution. This ternary complex represents the first step of the mechanism of push off. 19F NMR data are presented that indicate that dynA-(1-13) interacts specifically with only one of the two isomeric complexes of PCC-(89-104) and I-Ek. A push-off mechanism is proposed in which dynA-(1-13) binds outside the peptide binding groove. In a second step, the dissociation of one of the two isomers is specifically enhanced. Thus the push-off effect may be useful for identifying conformational isomers and for separating them.

  View details for Web of Science ID 000080842200003

  View details for PubMedID 10359754

• Characterization of circulating T cells specific for tumor-associated antigens in melanoma patients NATURE MEDICINE Lee, P. P., Yee, C., Savage, P. A., Fong, L., Brockstedt, D., Weber, J. S., Johnson, D., Swetter, S., Thompson, J., Greenberg, P. D., Roederer, M., DAVIS, M. M. 1999; 5 (6): 677-685

  Abstract

  We identified circulating CD8+ T-cell populations specific for the tumor-associated antigens (TAAs) MART-1 (27-35) or tyrosinase (368-376) in six of eleven patients with metastatic melanoma using peptide/HLA-A*0201 tetramers. These TAA-specific populations were of two phenotypically distinct types: one, typical for memory/effector T cells; the other, a previously undescribed phenotype expressing both naive and effector cell markers. This latter type represented more than 2% of the total CD8+ T cells in one patient, permitting detailed phenotypic and functional analysis. Although these cells have many of the hallmarks of effector T cells, they were functionally unresponsive, unable to directly lyse melanoma target cells or produce cytokines in response to mitogens. In contrast, CD8+ T cells from the same patient were able to lyse EBV-pulsed target cells and showed robust allogeneic responses. Thus, the clonally expanded TAA-specific population seems to have been selectively rendered anergic in vivo. Peptide stimulation of the TAA-specific T-cell populations in other patients failed to induce substantial upregulation of CD69 expression, indicating that these cells may also have functional defects, leading to blunted activation responses. These data demonstrate that systemic TAA-specific T-cell responses can develop de novo in cancer patients, but that antigen-specific unresponsiveness may explain why such cells are unable to control tumor growth.

  View details for PubMedID 10371507

• A PR1-human leukocyte antigen-A2 tetramer can be used to isolate low-frequency cytotoxic T lymphocytes from healthy donors that selectively lyse chronic myelogenous leukemia CANCER RESEARCH Molldrem, J. J., Lee, P. P., Wang, C. Q., Champlin, R. E., DAVIS, M. M. 1999; 59 (11): 2675-2681

  Abstract

  We previously showed (E. Clave et al., J. Immunother., 22: 1-6, 1999; J. Molldrem et al., Blood, 88: 2450-2457, 1996) that PR1, a human-lymphocyte-antigen (HLA)-A2.1-restricted peptide from proteinase 3, could be used to elicit CTLs from normal individuals. These CTLs showed HLA-restricted cytotoxicity and colony inhibition of myeloid leukemia cells that overexpress proteinase 3. In this study, we constructed a phycoerythrin-labeled PR1-HLA-A2 tetramer to identify PR1-specific CTLs by flow cytometry. No peripheral blood lymphocytes from three HLA-2.1+ donors stained with the tetramer, but, after 20 days in culture with weekly PR1 stimulation, 2-8% became tetramer+. Tetramer staining identified up to 40-fold more PR1-specific CTLs than were identified by limiting dilution analysis and correlated better with lysis of PR1-coated T2 cells (R2 = 0.95 versus R2 = 0.76). Tetramer+ CTLs were memory phenotype (91% CD45RO+), and most (58% CD95+) were activated. Tetramer-sorted allogeneic CTLs produced 83% lysis of HLA-A2.1+ chronic myelogenous leukemia (CML) blasts at an E:T ratio of 2.5:1, compared with 23% lysis by nonsorted CTLs, with no background lysis of HLA-A2.1+ normal cells. Cytoplasmic proteinase-3 expression was one log greater in CML blasts than in normal granulocytes. These results show that a PR1-HLA-A2 tetramer can be used to identify and select CTLs from normal donors that preferentially lyse CML cells, which could be used for leukemia-specific adoptive immunotherapy.

  View details for Web of Science ID 000080712700030

  View details for PubMedID 10363991

• Quantitative analysis of hepatitis C virus-specific CD8(+) T cells in peripheral blood and liver using peptide-MHC tetramers PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA He, X. S., Rehermann, B., Lopez-Labrador, F. X., Boisvert, J., Cheung, R., Mumm, J., Wedemeyer, H., Berenguer, M., Wright, T. L., DAVIS, M. M., Greenberg, H. B. 1999; 96 (10): 5692-5697

  Abstract

  It is believed that the hepatitis C virus (HCV)-specific CD8(+) cytotoxic T lymphocytes (CTLs) play a role in the development of liver cell injury and in the clearance of the virus. To develop a direct binding assay for HCV-specific CTLs, we generated two peptide-MHC tetramers by using the recombinant HLA A2.1 molecule and A2-restricted T cell epitopes of the HCV NS3 protein. With these reagents we are able to detect specific CD8(+) cells in the blood of 15 of 20 HLA-A2(+), HCV-infected patients, at a frequency ranging from 0.01% to 1.2% of peripheral CD8(+) T cells. Phenotypic analysis of these specific cells indicated that there is a significant variation in the expression of the CD45 isoforms and CD27 in different patients. A 6-hour incubation of one patient's blood with NS3 peptides resulted in the activation of the epitope-specific CD8(+) cells, as indicated by their expression of CD69 and IFN-gamma. We also detected NS3-specific CD8(+) T cells in the intrahepatic lymphocyte population isolated from liver biopsies of two HCV-infected patients. The frequency of these specific CD8(+) cells in the liver was 1-2%, at least 30-fold higher than in the peripheral blood. All of the intrahepatic NS3-specific CD8(+) T cells were CD69(+), suggesting that they were activated CTLs. Direct quantitation and characterization of HCV-specific CTLs should extend our understanding of the immunopathogenesis and the mechanism of clearance or persistence of HCV.

  View details for Web of Science ID 000080246500068

  View details for PubMedID 10318946

• A randomized phase 3 study of peripheral blood progenitor cell mobilization with stem cell factor and filgrastim in high-risk breast cancer patients BLOOD Shpall, E. J., Wheeler, C. A., Turner, S. A., Yanovich, S., Brown, R. A., Pecora, A. L., Shea, T. C., Mangan, K. F., Williams, S. F., LeMaistre, C. F., Long, G. D., Jones, R., Davis, M. W., Murphy-Filkins, R., Parker, W. R., Glaspy, J. A. 1999; 93 (8): 2491–2501

  Abstract

  This randomized study compared the number of leukaphereses required to collect an optimal target yield of 5 x 10(6) CD34(+) peripheral blood progenitor cells/kg, using either stem cell factor (SCF) at 20 micrograms/kg/d in combination with Filgrastim at 10 micrograms/kg/d or Filgrastim alone at 10 micrograms/kg/d, from 203 patients with high-risk stage II, III, or IV breast cancer. Leukapheresis began on day 5 of cytokine administration and continued daily until the target yield of CD34(+) cells had been reached or a maximum of 5 leukaphereses performed. By day 5 of leukapheresis, 63% of the patients treated with SCF plus Filgrastim (n = 100) compared with 47% of those receiving Filgrastim alone (n = 103) reached the CD34(+) cell target yield. There was a clinically and statistically significant reduction (P <.05) in the number of leukaphereses required to reach the target yield for the patients receiving SCF plus Filgrastim (median, 4 leukaphereses) compared with patients receiving Filgrastim alone (median, 6 or more leukapherses; ie, <50% of patients reached the target in 5 leukaphereses). All patients receiving SCF were premedicated with antihistamines, albuterol, and pseudoephedrine. Treatment was safe, generally well tolerated, and not associated with life-threatening or fatal toxicity. In conclusion, SCF plus Filgrastim is a more effective peripheral blood progenitor cell (PBPC)-mobilization regimen than Filgrastim alone. In addition to the potential for reduced leukapheresis-related morbidity and costs, SCF offers additional options for obtaining cells for further graft manipulation.

  View details for Web of Science ID 000079642400008

  View details for PubMedID 10194427

• A kinetic basis for T cell receptor repertoire selection during an immune response IMMUNITY Savage, P. A., BONIFACE, J. J., Davis, M. M. 1999; 10 (4): 485-492

  Abstract

  The basis for T cell antigen receptor (TCR) repertoire selection upon repeated antigenic challenge is unclear. We evaluated the avidity and dissociation kinetics of peptide/major histocompatibility complex (MHC) tetramer binding to antigen-specific T lymphocytes isolated following primary or secondary immunization. The data reveal a narrowing of the secondary repertoire relative to the primary repertoire, largely resulting from the loss of cells expressing TCRs with the fastest dissociation rates for peptide/MHC binding. In addition, T cells in the secondary response express TCRs of higher average affinity for peptide/MHC than cells in the primary response. These results provide a link between the kinetics and affinity of TCR-peptide/MHC interactions and TCR sequence selection during the course of an immune response.

  View details for Web of Science ID 000079989600009

  View details for PubMedID 10229191

• Quantitative analysis of hepatitis C virus-specific CD8(+) T cells using peptide-MHC tetramers. He, X. S., Lopez, Boisvert, J., Cheung, R., Davis, M. M., Wright, T. L., Rehermann, B., Wedemeyer, H., Greenberg, H. B. W B SAUNDERS CO-ELSEVIER INC. 1999: A735

  View details for Web of Science ID 000079778403190

• Visualizing lymphocyte recognition IMMUNOLOGY AND CELL BIOLOGY Wulfing, C., Chien, Y. H., DAVIS, M. M. 1999; 77 (2): 186-187

  Abstract

  Studies of T cell recognition have entered new territory now that some of the basic issues of genetics, biochemistry and structure have been addressed, at least in outline form. In the present work, the focus is on a new aspect of T cell recognition that goes beyond classical biochemistry to ask, how to TCR and other cell surface molecules cooperate to initiate and control recognition?'

  View details for Web of Science ID 000079676100012

  View details for PubMedID 10234556

• Isolation of high avidity melanoma-reactive CTL from heterogeneous populations using peptide-MHC tetramers JOURNAL OF IMMUNOLOGY Yee, C., Savage, P. A., Lee, P. P., DAVIS, M. M., Greenberg, P. D. 1999; 162 (4): 2227-2234

  Abstract

  Immunogenic peptides of human tumor Ag have been used to generate antigen-specific CTL. However, the vast majority of these peptide-specific CTL clones are of low avidity and are peptide, but not tumor, reactive. Peptide-MHC tetramers have been shown to bind specific TCRs with sufficient affinity to be useful reagents for flow cytometry. In this paper we demonstrate that peptide-MHC tetramers can also be used to selectively identify high avidity tumor-reactive CTL and enrich, from a heterogeneous population, the subpopulation of peptide-reactive T cells that can lyse tumor targets. The melanoma proteins, MART-1 and gp100, were used to induce potentially tumor-reactive T cells, and the intensity of T cell staining by TCR binding of specific peptide-MHC tetramers was assessed. A range of fluorescence intensity was detected, and the magnitude of tetramer binding was correlated with T cell avidity. The population of peptide-reactive T cells was phenotypically similar with regard to expression of TCR and adhesion molecules, suggesting that this differential avidity for tumor cells reflected differential affinity of the TCR for its peptide-MHC ligand. Sorting, cloning, and expansion of tetramerhigh CTL from a heterogeneous population of peptide-stimulated PBMCs enabled rapid selection of high avidity tumor-reactive CTL clones, which retained their functional and tetramerhigh phenotype on re-expansion. These results demonstrate that the avidity of a T cell for its tumor target is due to the specific affinity of the TCR for its peptide-MHC ligand, that this interaction can be described using peptide-MHC tetramers and used to isolate high avidity tumor-reactive CTL.

  View details for Web of Science ID 000078510800046

  View details for PubMedID 9973498

• Conformational isomers of a class II MHC-peptide complex in solution JOURNAL OF MOLECULAR BIOLOGY Schmitt, L., BONIFACE, J. J., DAVIS, M. M., McConnell, H. M. 1999; 286 (1): 207-218

  Abstract

  A number of kinetic measurements of peptide dissociation from class II MHC-peptide complexes provide compelling evidence for the existence of conformational isomers in solution. There is evidence that T-lymphocytes can distinguish such isomers. However, virtually nothing is known about the structure of these isomers. Accordingly, we have investigated a water-soluble version of the murine class II MHC molecule I-Ek complexed with an antigenic peptide derived from pigeon cytochrome c residues 89-104 (PCC) by 19F-NMR. Two fluorine labels were placed on the PCC peptide; one fluorine label was placed at a MHC contact site, the other at a position involved in T-cell receptor (TCR) recognition. Introduction of these labels did not alter the observed kinetics of the PCC/I-Ek complex. The NMR data show two conformational isomers of this immunogenic complex. The presence of conformational isomers at a TCR contact site suggests that these structures may be recognized differently by the TCR. The agreement between the dissociation kinetics and the 19F-NMR data demonstrate that kinetic heterogeneity is correlated with structural counterparts observed by NMR. Dissociations in the presence of dimethyl sulfoxide were used to show that the rate of interconversion of these conformational isomers at pH 7.0 is low, with a lifetime on the order of hours or more. Modification of a peptide residue of PCC occupying the minor MHC binding pocket P6 alters the 19F-NMR spectra of both labels. This demonstrates that distant changes of amino acid residues can influence the conformation of the whole antigenic peptide inside the MHC binding cleft.

  View details for Web of Science ID 000078702000016

  View details for PubMedID 9931260

• Frequency of class I HLA-restricted anti-HIV CD8(+) T cells in individuals receiving highly active antiretroviral therapy (HAART) JOURNAL OF IMMUNOLOGY Gray, C. M., Lawrence, J., Schapiro, J. M., Altman, J. D., Winters, M. A., Crompton, M., Loi, M., Kundu, S. K., DAVIS, M. M., Merigan, T. C. 1999; 162 (3): 1780-1788

  Abstract

  Peptide/MHC tetrameric complexes were used to enumerate the frequency of HLA class I-restricted epitope-specific CD8+ T cells in 18 HLA-A*0201 HIV type 1-infected asymptomatic patients. HLA-A*0201 molecules were complexed to HIV Gag p17 (amino acids 77-85) and reverse transcriptase (amino acids 464-472) peptides, biotinylated, and bound to streptavidin-phycoerythrin to form tetramers. We show in this study that 17 of 18 HIV-1-infected asymptomatic patients have circulating frequencies of 1/50-1/1000 CD8+ T cells that recognize both Gag and Pol CTL epitopes or either epitope alone. The functional nature of these cells is open to interpretation, as we show that despite relatively high frequencies of fresh epitope-specific CD8+ T cells, variant epitope sequences in viral plasma progeny were rare. In addition, the majority of tetramer-positive cells did not display discernible fresh CTL activity; only after restimulation with specific peptide in culture was there an expansion of epitope-specific CD8+ cells, correlating with high CTL activity. These data suggest that fresh tetramer-stained cells probably represent memory precursors; we demonstrate, with the application of highly active antiretroviral therapy, that the interruption of chronic antigenic stimulation causes significant reductions in the frequency of these cells in five of six patients. In conclusion, this study provides evidence that persistently replicating viral populations are probably required to maintain high frequencies of HIV-1 epitope-specific CD8+ T cells in asymptomatic chronically infected individuals

  View details for Web of Science ID 000078261000071

  View details for PubMedID 9973442

• Inhibition of thymocyte positive selection by natural MHC: peptide ligands EUROPEAN JOURNAL OF IMMUNOLOGY Tourne, S., Kouskoff, V., HO, W., Davis, M., Benoist, C., MATHIS, D. 1999; 29 (2): 394-402

  Abstract

  The 3A9 transgenic mouse line carries the rearranged TCR genes from a T cell hybridoma that recognizes hen egg lysozyme peptide 46-61 in the context of MHC class II Ak molecules. As expected, positive selection of immature 3A9 thymocytes to become mature CD4+ 8- T cells was efficient on the "selecting" CBA (H-2k) genetic background but not on the "non-selecting" C57BL/6 (H-2b) background. Surprisingly, positive selection was also inefficient on the CBA x C57BL/6 F1 background (H-2kb). We present evidence that expression of A(beta)b molecules on thymus epithelium (in conjunction with A(alpha)b or A(alpha)k molecules) inhibits the positive selection of 3A9 thymocytes mediated by A(alpha)k:A(beta)k complexes, in a process evocative of peptide antagonism of mature T cells.

  View details for Web of Science ID 000078658700003

  View details for PubMedID 10064054

• A T cell receptor-specific blockade of positive selection JOURNAL OF EXPERIMENTAL MEDICINE Baldwin, K. K., REAY, P. A., Wu, L., Farr, A., Davis, M. M. 1999; 189 (1): 13-23

  Abstract

  To investigate the influence of endogenous peptides on the developmental processes that occur during thymocyte selection, we have used monoclonal antibodies that preferentially recognize the major histocompatibility complex (MHC) molecule I-Ek when it is bound to the moth cytochrome c peptide (88-103). One of these antibodies (G35) specifically blocks the positive selection of transgenic thymocytes expressing a T cell receptor that is reactive to this peptide- MHC complex. Furthermore, G35 does not block the differentiation of transgenic T cells bearing receptors for a different I-Ek-peptide complex. This antibody recognizes a subset of endogenous I-Ek-peptide complexes found on a significant fraction of thymic antigen-presenting cells, including cortical and medullary epithelial cells. The sensitivity of G35 to minor alterations in peptide sequence suggests that the thymic peptide-MHC complexes that mediate the positive selection of a particular class II MHC-restricted thymocyte are structurally related to the complexes that can activate it in the periphery.

  View details for Web of Science ID 000078077700002

  View details for PubMedID 9874560

• Visualizing T-cell recognition 64th Symposia: Signaling and Gene Expression in the Immune System DAVIS, M. M., Wulfing, C., Krummel, M. F., Savage, P. A., Xu, J., Sumen, C., Dustin, M. L., Chien, Y. H. COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT. 1999: 243–251

  View details for Web of Science ID 000087225400030

  View details for PubMedID 11232292

• A receptor/cytoskeletal movement triggered by costimulation during T cell activation SCIENCE Wulfing, C., DAVIS, M. M. 1998; 282 (5397): 2266-2269

  Abstract

  During T cell activation, the engagement of costimulatory molecules is often crucial to the development of an effective immune response, but the mechanism by which this is achieved is not known. Here, it is shown that beads attached to the surface of a T cell translocate toward the interface shortly after the start of T cell activation. This movement appears to depend on myosin motor proteins and requires the engagement of the major costimulatory receptor pairs, B7-CD28 and ICAM-1-LFA-1. This suggests that the engagement of costimulatory receptors triggers an active accumulation of molecules at the interface of the T cell and the antigen-presenting cell, which then increases the overall amplitude and duration of T cell signaling.

  View details for Web of Science ID 000077645800050

  View details for PubMedID 9856952

• Kinetic isomers of a class II MHC-peptide complex BIOCHEMISTRY Schmitt, L., BONIFACE, J. J., DAVIS, M. M., McConnell, H. M. 1998; 37 (50): 17371-17380

  Abstract

  Class II major histocompatibility (MHC) molecules bind fragments of antigens and present them to T cells. The triggering of the T-cell receptor (TCR) of CD4(+) T-helper cells by these protein-peptide complexes is a key event in the generation of a cellular immune response. In the context of this interaction, it is generally assumed that class II MHC-peptide complexes adopt a single recognition structure at the cell surface. On the other hand, kinetic analysis has revealed that a number of class II MHC-peptide complexes show biphasic dissociation kinetics, indicating the presence of multiple kinetic isomers. Here, we demonstrate that a water-soluble version of the murine class II MHC molecule I-Ek complexed with an antigenic peptide derived from pigeon cytochrome c (PCC) displays monophasic as well as biphasic dissociation kinetics. While a simple monophasic dissociation curve was obtained at neutral pH, the complex showed biphasic dissociation behavior at acidic pH. This shift was independent of the ionic strength of the solution. Moreover, the short-lived isomer could be regenerated from a pool of kinetically homogeneous long-lived complexes. This demonstrates that the isomers interconvert and exist in a pH-sensitive equilibrium. Altering the peptide residue of PCC that occupies the P6 pocket of I-Ek results in a class II MHC-peptide complex that shows only monophasic dissociation, indicating that the glutamine at this position plays a key role in the kinetic heterogeneity of the complex.

  View details for Web of Science ID 000077647400005

  View details for PubMedID 9860852

• High dose antigen induces apoptosis of high avidity cytotoxic T lymphocytes (CTL) specific for a myeloid self-peptide. Molldrem, J. J., Lee, P. P., Wang, C., Davis, M. M. W B SAUNDERS CO. 1998: 339A

  View details for Web of Science ID 000077121301383

• A HLA-A2-PR1 tetramer can be used to isolate low-frequency CTL from the peripheral blood of normal donors that selectively lyse leukemia. Molldrem, J. J., Lee, P. P., Wang, C., Champlin, R. E., Davis, M. M. W B SAUNDERS CO. 1998: 254A

  View details for Web of Science ID 000077121301034

• Formation of a highly peptide-receptive state of class II MHC IMMUNITY Rabinowitz, J. D., Vrljic, M., Kasson, P. M., Liang, M. N., Busch, R., BONIFACE, J. J., DAVIS, M. M., McConnell, H. M. 1998; 9 (5): 699-709

  Abstract

  Peptide binding to class II MHC proteins occurs in acidic endosomal compartments following dissociation of class II-associated invariant chain peptide (CLIP). Based on peptide binding both to empty class II MHC and to molecules preloaded with peptides including CLIP, we find evidence for two isomeric forms of empty MHC. One (inactive) does not bind peptide. The other (active) binds peptide rapidly, with k(on) 1000-fold faster than previous estimates. The active isomer can be formed either by slow isomerization of the inactive molecule or by dissociation of a preformed peptide/MHC complex. In the absence of peptide, the active isomer is unstable, rapidly converting to the inactive isomer. These results demonstrate that fast peptide binding is an inherent property of one isomer of empty class II MHC. Dissociation of peptides such as CLIP yields this transient, peptide-receptive isomer.

  View details for Web of Science ID 000077298300012

  View details for PubMedID 9846491

• Initiation of signal transduction through the T cell receptor requires the peptide multivalent engagement of MHC ligands IMMUNITY BONIFACE, J. J., Rabinowitz, J. D., Wulfing, C., Hampl, J., Reich, Z., Altman, J. D., Kantor, R. M., Beeson, C., McConnell, H. M., Davis, M. M. 1998; 9 (4): 459-466

  Abstract

  While much is known about intracellular signaling events in T cells when T cell receptors (TCRs) are engaged, the mechanism by which signaling is initiated is unclear. We have constructed defined oligomers of soluble antigen-major histocompatibility complex (MHC) molecules, the natural ligands for the TCR. Using these to stimulate specific T cells in vitro, we find that agonist peptide/MHC ligands are nonstimulatory as monomers and minimally stimulatory as dimers. Similarly, a partial-agonist ligand is very weakly active as a tetramer. In contrast, trimeric or tetrameric agonist ligands that engage multiple TCRs for a sustained duration are potent stimuli. Ligand-driven formation of TCR clusters seems required for effective activation and helps to explain the specificity and sensitivity of T cells.

  View details for Web of Science ID 000076680700004

  View details for PubMedID 9806632

• Differential effect of B lymphocyte-induced maturation protein (Blimp-1) expression on cell fate during B cell development JOURNAL OF EXPERIMENTAL MEDICINE Messika, E. J., Lu, P. S., Sung, Y. J., Yao, T., Chi, J. T., Chien, Y. H., DAVIS, M. M. 1998; 188 (3): 515-525

  Abstract

  The B lymphocyte-induced maturation protein (Blimp-1) upregulates the expression of syndecan-1 and J chain and represses that of c-myc. We have transfected Blimp-1 into two sublines of the BCL1 B cell lymphoma that represent distinct stages of B cell development in secondary lymphoid tissues. After interleukin (IL)-2 and IL-5 stimulation, the BCL1 3B3 cells differentiate into centrocyte-like cells, whereas the BCL1 5B1b cells blast and appear to be blocked at the centroblast stage. This blasting effect and the increase in IgM secretion that follows it can be blocked by a dominant negative form of Blimp-1. At the same time, the ectopic expression of Blimp-1 in these partially activated cells induces an apoptotic response that also can be suppressed by the same dominant negative protein. A similar effect was noticed when Blimp-1 was expressed in the mature L10A and the immature WEHI-231 lines, indicating this may be a general effect at earlier stages of the B cell development, and distinct from the ability of Blimp-1 to induce maturation in late stages of differentiation. Truncation mutants indicate that the induction of the apoptotic response relies mainly on 69 amino acids within Blimp-1's proline-rich domain. We propose that Blimp-1 expression defines a checkpoint beyond which fully activated B cells proceed to the plasma cell stage, whereas immature and partially activated cells are eliminated at this point.

  View details for Web of Science ID 000075300300010

  View details for PubMedID 9687529

• Induction of rapid T cell activation and tolerance by systemic presentation of an orally administered antigen IMMUNITY Gutgemann, I., Fahrer, A. M., Altman, J. D., DAVIS, M. M., Chien, Y. H. 1998; 8 (6): 667-673

  Abstract

  To understand how orally introduced antigen regulates peripheral immune responses, we fed cytochrome c protein to mice transgenic for the beta chain of a cytochrome c-specific TCR and followed the antigen-specific T cell responses with a cyt c/I-Ek tetramer staining reagent. We find that within 6 hr of cytochrome c administration, antigen-specific systemic T cell activation is induced, and spleen cells gain the ability to stimulate cytochrome c-specific T cell responses. Feeding multiple low doses of cytochrome c down-regulates the systemic immune response, which can be correlated with a reduction of antigen-specific T cells and not with immune deviation. These results suggest that systemic distribution of antigen contributes significantly to oral tolerance induction.

  View details for Web of Science ID 000074396300002

  View details for PubMedID 9655480

• Visualizing the dynamics of T cell activation: Intracellular adhesion molecule 1 migrates rapidly to the T cell/B cell interface and acts to sustain calcium levels PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wulfing, C., Sjaastad, M. D., DAVIS, M. M. 1998; 95 (11): 6302-6307

  Abstract

  T cell recognition typically involves both the engagement of a specific T cell receptor with a peptide/major histocompatibility complex (MHC) and a number of accessory interactions. One of the most important interactions is between the integrin lymphocyte function-associated antigen 1 (LFA-1) on the T cell and intracellular adhesion molecule 1 (ICAM-1) on an antigen-presenting cell. By using fluorescence video microscopy and an ICAM-1 fused to a green fluorescent protein, we find that the elevation of intracellular calcium in the T cell that is characteristic of activation is followed almost immediately by the rapid accumulation of ICAM-1 on a B cell at a tight interface between the two cells. This increased density of ICAM-1 correlates with the sustained elevation of intracellular calcium in the T cell, known to be critical for activation. The use of peptide/MHC complexes and ICAM-1 on a supported lipid bilayer to stimulate T cells also indicates a major role for ICAM-1/LFA-1 in T cell activation but, surprisingly, not for adhesion, as even in the absence of ICAM-1 the morphological changes and adhesive characteristics of an activated T cell are seen in this system. We suggest that T cell antigen receptor-mediated recognition of a very small number of MHC/peptide complexes could trigger LFA-1/ICAM-1 clustering and avidity regulation, thus amplifying and stabilizing the production of second messengers.

  View details for Web of Science ID 000073852600081

  View details for PubMedID 9600960

• Molecular insights into MHC-peptide interactions. Schmitt, L., Boniface, J. J., Davis, M. M., McConnell, H. M. BIOPHYSICAL SOCIETY. 1998: A298

  View details for Web of Science ID 000073445401724

• Ligand recognition by alpha beta T cell receptors ANNUAL REVIEW OF IMMUNOLOGY Davis, M. M., BONIFACE, J. J., Reich, Z., Lyons, D., Hampl, J., Arden, B., Chien, Y. H. 1998; 16: 523-?

  Abstract

  While still incomplete, the first data concerning the biochemistry of T cell receptor-ligand interactions in cell-free systems seem to have considerable predictive value regarding whether a T cell response is strong or weak or suppressive. This data will help considerably in elucidating the mechanisms behind T cell responsiveness. Also of great interest are the first structures of T cell receptor molecules and, particularly, TCR-ligand complexes. These appear to confirm earlier suggestions of a fixed orientation for TCR engagement with peptide/MHC and should form the basis for understanding higher oligomers, evidence for which has also just emerged. We conclude with an analysis of the highly diverse CDR3 loops found in all antigen receptor molecules and suggest that such regions form the core of both TCR and antibody specificity.

  View details for Web of Science ID 000073129400019

  View details for PubMedID 9597140

• CD4 augments the response of a T cell to agonist but not to antagonist ligands IMMUNITY Hampl, J., Chien, Y. H., DAVIS, M. M. 1997; 7 (3): 379-385

  Abstract

  The recognition of peptide variants by the T cell receptor (TCR) has revealed a wide range of possible responses. Here, using a series of CD4+ and CD4- variants of the same T cell hybridoma, we find that while the expression of CD4 converts weak agonists into full agonists, none of the antagonist peptides are efficiently recognized as agonists. Furthermore, in antagonist assays, little difference can be seen in the response of CD4+ and CD4- T cells. Together with previous work showing a marked difference in stability between TCR binding to agonist versus antagonist ligands, these data suggest that CD4 engagement occurs after a TCR-peptide/MHC complex has formed and that it requires a certain minimal half-life of the ternary complex to be fully engaged in signaling.

  View details for Web of Science ID A1997XY83000007

  View details for PubMedID 9324358

• A range of CD4 T cell tolerance: Partial inactivation to organ-specific antigen allows nondestructive thyroiditis or insulitis IMMUNITY Akkaraju, S., Ho, W. Y., Leong, D., Canaan, K., DAVIS, M. M., Goodnow, C. C. 1997; 7 (2): 255-271

  Abstract

  T cell receptor (TCR) transgenic mice specific for hen egg lysozyme (HEL) were crossed with mice expressing HEL on the thyroid epithelium, on pancreatic islet beta cells, or systemically. Depending on the pattern of HEL expression, deletion of double-positive thymocytes ranged from minimal to complete, and peripheral CD4 cells exhibited graded reduction in TCR expression, in vitro responsiveness, and in vivo helper ability. CD4 cells were least tolerant in TCR/thyroid-HEL and TCR/islet-HEL mice, which developed an extensive lymphocytic thyroiditis or insulitis that nevertheless did not eliminate HEL-expressing endocrine cells. Autoreactive CD4 clones thus escape the thymus under a range of circumstances, retain sufficient function to initiate subclinical autoimmune inflammation when self-antigens are concentrated in the thyroid or pancreas, and may regulate progression of subclinical inflammation to destructive autoimmune disease.

  View details for Web of Science ID A1997XT49200009

  View details for PubMedID 9285410

• Ligand-specific oligomerization of T-cell receptor molecules NATURE Reich, Z., BONIFACE, J. J., Lyons, D. S., Borochov, N., Wachtel, E. J., DAVIS, M. M. 1997; 387 (6633): 617-620

  Abstract

  T cells initiate many immune responses through the interaction of their T-cell antigen receptors (TCR) with antigenic peptides bound to major histocompatibility complex (MHC) molecules. This interaction sends a biochemical signal into the T cell by a mechanism that is not clearly understood. We have used quasielastic light scattering (QELS) to show that, in the presence of MHC molecules bound to a full agonist peptide, TCR/peptide-MHC complexes oligomerize in solution to form supramolecular structures at concentrations near the dissociation constant of the binding reaction. The size of the oligomers is concentration dependent and is calculated to contain two to six ternary complexes for the concentrations tested here. This effect is specific as neither molecule forms oligomers by itself, nor were oligomers observed unless the correct peptide was bound to the MHC. These results provide direct evidence for models of T-cell signalling based on the specific assembly of multiple TCR/peptide-MHC complexes in which the degree of assembly determines the extent and qualitative nature of the transduced signal. They may also explain how T cells maintain sensitivity to antigens present in only low abundance on the antigen-presenting cell.

  View details for Web of Science ID A1997XC52200059

  View details for PubMedID 9177351

• Kinetics and extent of T cell activation as measured with the calcium signal JOURNAL OF EXPERIMENTAL MEDICINE Wulfing, C., Rabinowitz, J. D., Beeson, C., Sjaastad, M. D., McConnell, H. M., DAVIS, M. M. 1997; 185 (10): 1815-1825

  Abstract

  We have characterized the calcium response of a peptide-major histocompatibility complex (MHC)-specific CD4(+) T lymphocyte line at the single cell level using a variety of ligands, alone and in combination. We are able to distinguish four general patterns of intracellular calcium elevation, with only the most robust correlating with T cell proliferation. Whereas all three antagonist peptides tested reduce the calcium response to an agonist ligand, two give very different calcium release patterns and the third gives none at all, arguing that (a) antagonism does not require calcium release and (b) it involves interactions that are more T cell receptor proximal. We have also measured the time between the first T cell-antigen-presenting cell contact and the onset of the calcium signal. The duration of this delay correlates with the strength of the stimulus, with stronger stimuli giving a more rapid response. The dose dependence of this delay suggests that the rate-limiting step in triggering the calcium response is not the clustering of peptide-MHC complexes on the cell surface but more likely involves the accumulation of some intracellular molecule or complex with a half-life of a few minutes.

  View details for Web of Science ID A1997XB76900013

  View details for PubMedID 9151707

• Stability of empty and peptide-loaded class II major histocompatibility complex molecules at neutral and endosomal pH: Comparison to class I proteins PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Reich, Z., Altman, J. D., BONIFACE, J. J., Lyons, D. S., Kozono, H., Ogg, G., Morgan, C., DAVIS, M. M. 1997; 94 (6): 2495-2500

  Abstract

  The structure and thermal stability of empty and peptide-filled forms of the murine class II major histocompatibility complex (MHC) molecule I-E(k) were studied at neutral and mildly acidic pH. The two forms have distinct circular dichroic spectra, suggesting that a conformational change may accompany peptide binding. Thermal stability profiles indicate that binding of peptide significantly increases the thermal stability of the empty heterodimers at both neutral and mildly acidic pH. Free energies calculated from these data provide a direct measure of this stabilization and show that the empty form of I-E(k) is significantly more stable than that of class I MHC proteins. Furthermore, for the two MHC class II proteins that were analyzed (I-E(k) and I-A(d)), thermal stability was not significantly altered by acidification. In contrast, of four class I MHC molecules studied, three have shown a significant loss in complex stability at low pH. The marked stability exhibited by their empty form, as well as their resistance to low pH, as observed in this study, correlate well with the ability of class II MHC molecules to traverse and bind peptides in acidic endosomal vesicles.

  View details for Web of Science ID A1997WP33400074

  View details for PubMedID 9122223

• T cell receptor biochemistry, repertoire selection and general features of TCR and Ig structure Symposium on the Molecular Basis of Cellular Defence Mechanisms DAVIS, M. M., Lyons, D. S., Altman, J. D., MCHEYZERWILLIAMS, M., Hampl, J., BONIFACE, J. J., Chien, Y., Nossal, Zinkernagel, Miller, Paul, Kirberg, MELCHERS, Mosmann, Goodnow JOHN WILEY & SONS LTD. 1997: 94–104

  Abstract

  T cell recognition is a central event in the development of most immune responses, whether appropriate or inappropriate (i.e. autoimmune). We are interested in reducing T cell recognition to its most elemental components and relating this to biological outcome. In a model system involving a cytochrome c-specific I-Ek restricted T cell receptor (TCR) derived from the 2B4 hybridoma, we have studied the interaction of soluble TCR and soluble peptide-MHC complexes using surface plasmon resonance. We find a striking continuum in which biological activity correlates best with the dissociation rate of the TCR from the peptide-MHC complex. In particular, we have found that weak agonists have significantly faster off-rates than strong agonists and that antagonists have even faster off-rates. This suggests that the stability of TCR binding to a given ligand is critically important with respect to whether the T cell is stimulated, inhibited or remains indifferent. It also suggests that the phenomenon of peptide antagonists might be explained purely by kinetic models and that conformation, either inter- or intramolecular, may not be a factor. We have also studied TCR repertoire selection during the establishment of a cytochrome c response, initially using an anti-TCR antibody strategy, but more recently using peptide-MHC tetramers as antigen-specific staining reagents. These tetramers work well with either class I or class II MHC-specific TCRs and have many possible applications. Lastly, we have also tried to correlate the structural and genetic features of TCRs with their function. Recent data on TCR structure as well as previous findings with antibodies suggest that both molecules are highly dependent on CDR3 length and sequence variation to form specific contacts with antigens. This suggests a general "logic' behind TCR and Ig genetics as it relates to structure and function that helps to explain certain anomalous findings and makes a number of clear predictions.

  View details for Web of Science ID A1997BH80V00009

  View details for PubMedID 9107414

• Phenotypic analysis of antigen-specific T lymphocytes SCIENCE Altman, J. D., Moss, P. A., Goulder, P. J., Barouch, D. H., MCHEYZERWILLIAMS, M. G., Bell, J. I., McMichael, A. J., DAVIS, M. M. 1996; 274 (5284): 94-96

  Abstract

  Identification and characterization of antigen-specific T lymphocytes during the course of an immune response is tedious and indirect. To address this problem, the peptide-major histocompatability complex (MHC) ligand for a given population of T cells was multimerized to make soluble peptide-MHC tetramers. Tetramers of human lymphocyte antigen A2 that were complexed with two different human immunodeficiency virus (HIV)-derived peptides or with a peptide derived from influenza A matrix protein bound to peptide-specific cytotoxic T cells in vitro and to T cells from the blood of HIV-infected individuals. In general, tetramer binding correlated well with cytotoxicity assays. This approach should be useful in the analysis of T cells specific for infectious agents, tumors, and autoantigens.

  View details for Web of Science ID A1996VK74800054

  View details for PubMedID 8810254

• Early biochemical signals arise from low affinity TCR-ligand reactions at the cell-cell interface JOURNAL OF EXPERIMENTAL MEDICINE Beeson, C., Rabinowitz, J., Tate, K., Gutgemann, I., Chien, Y. H., Jones, P. P., DAVIS, M. M., McConnell, H. M. 1996; 184 (2): 777-782

  Abstract

  The kinetics of acid release by a mixture of T cells and antigen presenting cells were measured with a microphysiometer during a brief exposure to antigenic peptides. We find that some of the early biochemical events that lead to cellular proliferation cause a specific increase in the rate of acid release. The duration of this increase in acid release reflects the life-time of the peptide-MHC complexes. Peptides that form long-lived complexes produce a response that is stable for more than an hour. Serial TCR engagement is suggested by the observation that the amplitude of this stable response can be rapidly shifted up or down with additional agonist peptide or with antibodies that block T cell receptor binding. Cells briefly exposed to a peptide that forms short-lived peptide-MHC complexes produce a response that decays rapidly as peptide is washed away. A quantitative analysis of the kinetics of this decay in acidification demonstrates that intercellular TCR-ligand reactions are rapid, reversible, and of low apparent affinity with < 20% of peptide-MHC ligand bound to a TCR at any one time. These results demonstrate that the fraction of peptide-MHC ligands bound to TCRs at the cell-cell interface is no higher than anticipated from the affinities observed in solution for isolated TCRs and ligands.

  View details for Web of Science ID A1996VC33700052

  View details for PubMedID 8760833

• Altered T cell receptor ligands trigger a subset of early T cell signals IMMUNITY Rabinowitz, J. D., Beeson, C., Wulfing, C., Tate, K., Allen, P. M., DAVIS, M. M., McConnell, H. M. 1996; 5 (2): 125-135

  Abstract

  TCR ligands are complexes of peptides and MHC proteins on the surfaces of APCs. Some of these ligands cause T cell proliferation (agonists), while others block it (antagonists). We compared the acid release, calcium flux, and proliferation response of helper T cells to a variety of ligands. We found that all agonist ligands but not most antagonist ligands trigger acid release, a general indicator of early cellular activation. Only a subset of ligands triggering acid release cause sustained calcium flux, and only a subset of these ligands cause T cell proliferation. Antagonist ligands and anti-CD4 antibodies both effectively block T cell proliferation. However, significantly greater antagonist ligand or antibody concentrations are required to block acid release and initial calcium influx. These data demonstrate a hierarchy of early T cell signaling steps and show that altered TCR ligands can initiate some steps while blocking the completion of others.

  View details for Web of Science ID A1996VE58900003

  View details for PubMedID 8769476

• A TCR binds to antagonist ligands with lower affinities and faster dissociation rates than to agonists IMMUNITY Lyons, D. S., Lieberman, S. A., Hampl, J., BONIFACE, J. J., Chien, Y. H., Berg, L. J., DAVIS, M. M. 1996; 5 (1): 53-61

  Abstract

  T lymphocyte activation is mediated by the interaction of specific TCR with antigenic peptides bound to MHC molecules. Single amino acid substitutions are often capable of changing the effect of a peptide from stimulatory to antagonistic. Using surface plasmon resonance, we have analyzed the interaction between a complex consisting of variants of the MCC peptide bound to a mouse class II MHC (Ek) and a specific TCR. Using both an improved direct binding method as well as a novel inhibition assay, we show that the affinities of three different antagonist peptide-Ek complexes are approximately 10-50 times lower than that of the wildtype MCC-Ek complex for the TCR, largely due to an increased off-rate. These results suggest that the biological effects of peptide antagonists and partial agonists may be largely based on kinetic parameters.

  View details for Web of Science ID A1996UZ45400006

  View details for PubMedID 8758894

• Direct visualisation and phenotyping or HIV-specific T cells in blood of infected patients Moss, P. A., Altman, J., Goulder, P., McMichael, A., Davis, M., Bell, J. BLACKWELL SCIENCE LTD. 1996: 1185

  View details for Web of Science ID A1996UP11401184

• Technophilia. Current opinion in immunology Davis, M. M. 1996; 8 (2): 255-6

  View details for PubMedID 8793987

• Evolving catalysts in real time SCIENCE DAVIS, M. M. 1996; 271 (5252): 1078-1079

  View details for Web of Science ID A1996TW70100026

  View details for PubMedID 8599081

• Kinetic discrimination in T-cell activation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Rabinowitz, J. D., Beeson, C., Lyons, D. S., DAVIS, M. M., McConnell, H. M. 1996; 93 (4): 1401-1405

  Abstract

  We propose a quantitative model for T-cell activation in which the rate of dissociation of ligand from T-cell receptors determines the agonist and antagonist properties of the ligand. The ligands are molecular complexes between antigenic peptides and proteins of the major histocompatibility complex on the surfaces of antigen-presenting cells. Binding of ligand to receptor triggers a series of biochemical reactions in the T cell. If the ligand dissociates after these reactions are complete, the T cell receives a positive activation signal. However, dissociation of ligand after completion of the first reaction but prior to generation of the final products results in partial T-cell activation, which acts to suppress a positive response. Such a negative signal is brought about by T-cell ligands containing the variants of antigenic peptides referred to as T-cell receptor antagonists. Results of recent experiments with altered peptide ligands compare favorably with T-cell responses predicted by this model.

  View details for Web of Science ID A1996TW69800009

  View details for PubMedID 8643643

• Directed evolution studies with combinatorial libraries of T4 lysozyme mutants MOLECULAR DIVERSITY PATTEN, P. A., Sonoda, T., DAVIS, M. M. 1996; 1 (2): 97-108

  Abstract

  Gene duplication with divergence to new functions has been an important mechanism in protein evolution. However, the questions of how many new functions can arise from a particular ancestral gene and how many mutational steps are typically required to generate new functions have been difficult to approach experimentally. We have addressed these questions using T4 lysozyme as a model system by synthesizing two combinatorial libraries of > 10(7) mutant T4 lysozyme genes: one library with an average of 14 missense mutations spread throughout the gene and one library in which 13 active site residues have been simultaneously randomized. These libraries were placed under selection in lacZ or pheA deficient strains of E. coli to investigate whether they sample sufficient diversity to contain mutants with acquired beta-galactosidase or prephenate dehydratase activities. Although neither selection yielded T4 lysozyme mutants with these new activities, a novel E. coli locus was cloned that weakly complements these mutants, allowing them to form 1 mm colonies in 4-6 weeks. This growth rate corresponds to a turnover number of approximately 1000 or 25 min-1 for the lacZ or pheA complementation systems, respectively, thus defining the limits of evolved enzymatic activity detectable in these selections. Thus, the strong selective pressure uncovered an unexpected solution to the biochemical blocks, a frequently observed phenomenon in selection experiments. The characterization of this locus will allow its elimination from future E. coli complementation schemes.

  View details for Web of Science ID A1996VV71400003

  View details for PubMedID 9237198

• Evidence for a conformational change in a class II major histocompatibility complex molecule occurring in the same pH range where antigen binding is enhanced JOURNAL OF EXPERIMENTAL MEDICINE BONIFACE, J. J., Lyons, D. S., Wettstein, D. A., Allbritton, N. L., DAVIS, M. M. 1996; 183 (1): 119-126

  Abstract

  Many class II histocompatibility complex molecules bind antigenic peptides optimally at low pH, consistent with their exposure to antigen in acidic endosomal compartments. While it has been suggested that a partially unfolded state serves as an intermediate involved in peptide binding, very little evidence for such a state has been obtained. In this report, we show that the murine class II molecule IE becomes increasingly less stable to sodium dodecyl sulfate-induced dissociation since the pH is decreased in the same range that enhances antigenic peptide binding. Furthermore, at mildly acidic pH levels, IEk binds the fluorescent dye 1-anilino-naphthalene-8-sulfonic acid (ANS), a probe for exposed nonpolar sites in proteins, suggesting that protonation produces a molten globule-like state. The association of IEk with a single high-affinity peptide had only a small effect in these two assays, indicating that the changes that occur are distal to the peptide-binding groove. Circular dichroism analysis shows that a pH shift from neutral to mildly acidic pH causes subtle changes in the environment of aromatic residues but does not grossly disrupt the secondary structure of IEk. We propose a model in which perturbations in interdomain contacts outside the peptide-binding domain of IEk occur at acidic pH, producing a partially unfolded state that facilitates optimal antigen binding.

  View details for Web of Science ID A1996TP36500013

  View details for PubMedID 8551214

• CD95 (FAS) DEPENDENT ELIMINATION OF SELF-REACTIVE B-CELLS UPON INTERACTION WITH CD4(+) T-CELLS NATURE Rathmell, J. C., Cooke, M. P., Ho, W. Y., Grein, J., Townsend, S. E., DAVIS, M. M., Goodnow, C. C. 1995; 376 (6536): 181-184

  Abstract

  The recessive mouse mutations lpr and gld create deficiencies in an interacting pair of cell surface molecules, CD95 (Fas/APO-1) and Fas-ligand (FasL), respectively, resulting in autoantibody production resembling human systemic lupus erythematosus. The mechanisms of self-tolerance affected by deficiency in either molecule are not established, but CD95 deficiency both in B cells and in CD4+ T cells recognizing major histocompatibility complex (MHC) class II molecules is required for autoimmunity in lpr mice. Here we track the outcome of in vivo interactions between B cells and CD4+ T cells that recognize a transgene-encoded autoantigen, hen egg lysozyme (HEL), using cells from mice transgenic for immunoglobulin and T-cell receptor (TCR) genes. B cells that had not previously encountered HEL autoantigen (naive cells) were triggered into proliferation and antibody production upon interaction with antigen and HEL-specific CD4+ T cells. By contrast, B cells that had been chronically exposed to HEL during their development and carried desensitized surface immunoglobulin (sIg) antigen receptors (anergic cells) did not produce antibody but instead were eliminated in the presence of HEL-specific CD4+ T cells. CD95-deficient anergic B cells, however, were not eliminated by CD4+ T cells and were triggered to proliferate. These findings identify a novel regulatory step for eliminating autoreactive B cells that seems unique in its dependence on CD95.

  View details for Web of Science ID A1995RJ02800063

  View details for PubMedID 7603571

• ISSUES CONCERNING THE NATURE OF ANTIGEN RECOGNITION BY ALPHA-BETA AND GAMMA-DELTA T-CELL RECEPTORS 9th International Congress of Immunology DAVIS, M. M., Chien, Y. H. ELSEVIER SCI LTD. 1995: 316–18

  View details for Web of Science ID A1995RG98300006

  View details for PubMedID 7576062

• T-CELL RECEPTORS - SERIAL ENGAGEMENT PROPOSED NATURE DAVIS, M. M. 1995; 375 (6527): 104

  View details for DOI 10.1038/375104a0

  View details for Web of Science ID A1995QX74100026

  View details for PubMedID 7753161

• ANTIGEN-SPECIFIC DEVELOPMENT OF PRIMARY AND MEMORY T-CELLS IN-VIVO SCIENCE MCHEYZERWILLIAMS, M. G., DAVIS, M. M. 1995; 268 (5207): 106-111

  Abstract

  The expansion and contraction of specific helper T cells in the draining lymph nodes of normal mice after injection with antigen was followed. T cell receptors from purified primary and memory responder cells had highly restricted junctional regions, indicating antigen-driven selection. Selection for homogeneity in the length of the third complementarity-determining region (CDR3) occurs before selection for some of the characteristic amino acids, indicating the importance of this parameter in T cell receptor recognition. Ultimately, particular T cell receptor sequences come to predominate in the secondary response and others disappear, showing the selective preservation or expansion of specific T cell clones.

  View details for Web of Science ID A1995QR45400037

  View details for PubMedID 7535476

• T-CELL RECEPTOR-SPECIFIC BLOCKADE OF POSITIVE SELECTION BALDWIN, K. K., REAY, P. A., FARR, A. G., DAVIS, M. M. WILEY-LISS. 1995: 111

  View details for Web of Science ID A1995QT86400393

• DIVERGING SIGNALS CONTROL PROLIFERATION AND DIFFERENTIATION OF SELF-REACTIVE B-LYMPHOCYTES HEALY, J. I., MCMAHON, M., COOKE, M. P., MACK, D., DAVIS, M. M., GOODNOW, C. C. WILEY-LISS. 1995: 72

  View details for Web of Science ID A1995QT86400238

• STAINING OF ANTIGEN-SPECIFIC T-CELLS WITH MULTIMERIZED CLASS-II MHC MOLECULES ALTMAN, J., MCHEYZERWILLIAMS, M., FUKUI, Y., BONIFACE, J., DAVIS, M. WILEY-LISS. 1995: 87

  View details for Web of Science ID A1995QT86400297

• T-CELL RECEPTOR V-REGION USAGE AND ANTIGEN-SPECIFICITY - THE CYTOCHROME-C MODEL SYSTEM Conference on T-Cell Receptor Use in Human Autoimmune Diseases DAVIS, M. M., MCHEYZERWILLIAMS, M., Chien, Y. H. NEW YORK ACAD SCIENCES. 1995: 1–11

  Abstract

  Investigations of the I-Ek-restricted, cytochrome c-specific T-cell response in mice show that both T-cell receptor V alpha and V beta CDR3 residues and the use of particular V alpha s and V beta s are necessary for recognition. Data strongly suggest that specific CDR3 residues are important in contacting the peptide. Other experiments indicate that the requirement for V alpha:V beta conservation is not the result of strong TCR-->MHC interactions, as no correlation was found between V beta usage and changes in the alpha-helixes of the I-Ek molecule. It is also apparent that changes in V alpha or V beta usage could be elicited by changes in the side chain size of single amino acids of the antigenic peptides, suggesting that V alpha or V beta conservation is important for peptide recognition, either directly or indirectly. We also show that we can follow the cytochrome c response in vivo even in nontransgenic mice, solely by staining with anti-V region antibodies as well as mAbs directed at the activation markers CD44 and L-selectin.

  View details for Web of Science ID A1995BD46M00001

  View details for PubMedID 7645810

• ABROGATION OF THE ALLELIC EXCLUSION IN A T-CELL RECEPTOR-BETA CHAIN GENE TRANSGENIC MOUSE STRAIN IMMUNOLOGICAL INVESTIGATIONS MAZDA, O., AIBA, Y., HATTORI, N., LI, M., FUJIMOTO, S., DAVIS, M. M., KATSURA, Y. 1995; 24 (6): 927-946

  Abstract

  The expression of endogenous T cell receptor (TcR) beta chains in a TcR beta chain gene transgenic mouse (TGM) strain was examined. Unlike many other TGM strains reported, a considerable proportion of T cells from the thymus and spleen as well as organ cultured fetal thymus from our TGM express endogenous TCR beta chains on their surface. Compatible with this was the elucidation of VDJ rearrangement of endogenous beta chain genes by PCR. Three color flow cytometric analysis of thymus cell subpopulations revealed that the expression levels of both endogenous and transgenic TcR beta genes are regulated in a maturational stage specific manner. Splenic T cells contained a several fold higher percentage of endogenous TcR beta positive cells than thymus cells, suggesting a role of TcR on T cell peripherization. V beta 6 positive cells were deleted in the TGM carrying minor lymphocyte stimulating (Mls)-la antigen, indicating that the endogenous TcR beta is functional in terms of transmitting a signal for clonal deletion.

  View details for DOI 10.3109/08820139509060718

  View details for Web of Science ID A1995TD99500006

  View details for PubMedID 8575838

• T-cell recognition of antigen - A process controlled by transient intermolecular interactions Conference on Receptor Activation by Antigens, Cytokines, Hormones, and Growth Factors BONIFACE, J. J., DAVIS, M. M. NEW YORK ACAD SCIENCES. 1995: 62–69

  Abstract

  As recently as ten years ago, the nature of the T-cell receptor for antigen was a mystery, as was the precise role of histocompatibility molecules in antigen-presentation to T cells. Although T-cell receptors have now been cloned and crystal structures of MHC/peptide molecules exist, our understanding of the parameters that characterize this interaction and other interactions relevant to T-cell immunity are still unclear. The engineering of soluble forms of proteins that mediate T-cell recognition of antigen has allowed the first measurements of these parameters. Interestingly, many of these interactions are of a transient nature, with very rapid off-rates. These data suggest a model whereby highly reversible intermolecular interactions mediate the cell-cell association. The association of adhesion molecules is probably the first step in the stabilization of a conjugate, because they are more numerous than any antigen-specific interaction, followed later by TCR-MHC engagements. Diffusion within each lipid bilayer should allow the congregation of MHC/TCR interactions at the cell-cell interface, with peptide-specific TCR interactions outcompeting irrelevant interactions. Rapid off-rates for both the antigen-specific and nonspecific interactions may be necessary to maintain reversibility, yet allow a rapid approach to equilibrium and consequent signaling when a specific antigen is present or disengagement when it is not.

  View details for Web of Science ID A1995BE40J00007

  View details for PubMedID 7486700

• KINETICS OF T-CELL RECEPTOR-BINDING TO PEPTIDE I-E(K) COMPLEXES - CORRELATION OF THE DISSOCIATION RATE WITH T-CELL RESPONSIVENESS PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Matsui, K., BONIFACE, J. J., STEFFNER, P., REAY, P. A., DAVIS, M. M. 1994; 91 (26): 12862-12866

  Abstract

  Recognition by T-cell antigen receptors (TCRs) of processed peptides bound to major histocompatibility complex (MHC) molecules is required for the initiation of most T-lymphocyte responses. Despite the availability of soluble forms of TCRs and MHC heterodimers, this interaction has proven difficult to study directly due to the very low affinity. We report here on the kinetics of TCR binding to peptide/MHC complexes in a cell-free system using surface plasmon resonance. The apparent association rates for the interactions of related peptide/MHC complexes to one such TCR are relatively slow (900-3000 M-1.s-1) and dissociation rates are very fast (0.3-0.06 s-1) with t1/2 of 2-12 s at 25 degrees C. The calculated affinity of the engineered soluble molecules compares well with previously reported competition data for native TCRs or competition data reported here for native peptide/MHC complexes, indicating that these soluble heterodimers bind in the same manner as the original molecules expressed on cells. We also find that the peptide variants which give weaker T-cell stimulatory responses have similar affinities but distinctly faster dissociation rates compared with the original peptide (when loaded onto the MHC molecule) and that this later property may be responsible for their lower activity. This has implications for both downstream signaling events and models of TCR-peptide antagonists.

  View details for Web of Science ID A1994PY29400105

  View details for PubMedID 7809136

• ENGINEERING AND EXPRESSION OF A SECRETED MURINE TCR WITH REDUCED N-LINKED GLYCOSYLATION JOURNAL OF IMMUNOLOGY STRONG, R. K., PENNY, D. M., FELDMAN, R. M., WEINER, L. P., BONIFACE, J. J., DAVIS, M. M., BJORKMAN, P. J. 1994; 153 (9): 4111-4121

  Abstract

  Structural studies of TCR-alpha beta heterodimers would be greatly aided by the ability to produce nonchimeric, secreted material with less carbohydrate heterogeneity. Here, we report the engineering and expression of variants of the murine TCR 2B4 in which many of the potential N-linked glycosylation sites were eliminated. Specific truncations proximal to the transmembrane region were also introduced that result in a secreted heterodimer. Although elimination of N-linked oligosaccharide on the beta-chain does not significantly affect the expression levels of 2B4 heterodimers, ablation of N-linked oligosaccharide on the alpha-chain results in a measurable reduction in expression levels of membrane-associated molecules. Secreted forms of 2B4 heterodimers in which the N-linked glycosylation of the beta-chain has been eliminated can be expressed. The secreted receptor is shown by a variety of Ab determinants to be indistinguishable from native material.

  View details for Web of Science ID A1994PN07100027

  View details for PubMedID 7930615

• RESTING AND ANERGIC B-CELLS ARE DEFECTIVE IN CD28-DEPENDENT COSTIMULATION OF NAIVE CD4(+) T-CELLS JOURNAL OF EXPERIMENTAL MEDICINE Ho, W. Y., Cooke, M. P., Goodnow, C. C., DAVIS, M. M. 1994; 179 (5): 1539-1549

  Abstract

  Successful antibody production in vivo depends on a number of cellular events, one of the most important of these being cognate B cell-T cell interaction. To examine this phenomenon in vitro, homogeneous populations of hen egg lysozyme (HEL)-specific small resting B cells and naive CD4+ HEL-specific T cells (derived from immunoglobulin [Ig] and T cell receptor transgenic mice, respectively) were cultured together. On addition of intact HEL protein. HEL-specific B cells increase their expression of activation molecules, including a B7-related protein and CD44, and enlarge into blast cells. Within the same cultures, HEL-specific CD4+ T cells also increase expression of the activation markers CD69 and CD44, enlarge, secrete lymphokines, and proliferate. This response is radiation sensitive, supporting the conclusion that HEL-specific B cells present antigen to and activate the naive T cells. By contrast, when a synthetic peptide fragment of HEL is used to bypass B cell antigen-receptor engagement, the naive T cells enlarge and display activation antigens, but fail to produce lymphokines, proliferate, or promote B cell blastogenesis. Presentation of HEL by tolerant B cells, which are no longer able to signal effectively through their antigen receptors, results in an identical pattern of incomplete T cell activation. Addition of a stimulating anti-CD28 antibody and blocking of CD28 signals with CTLA4/Ig fusion protein both show that complete activation of naive CD4+ T cells depends on the initial induction of B7 and related costimulatory molecules after HEL binding to nontolerant HEL-specific B cells. Thus, in the absence of adequate constimulation from the B cell, naive CD4+ T cells undergo a form of "partial activation" in which they upregulate surface expression of certain T cell activation antigens, but fail to efficiently produce lymphokine and proliferate. This may explain the different conclusions that have been reached regarding the consequences of B cell antigen presentation to T cells, in that the ability of B cells to activate naive CD4+ T cells depends both on their specificity and their activation state.

  View details for Web of Science ID A1994NH65500015

  View details for PubMedID 7909325

• BLIMP-1, A NOVEL ZINC FINGER-CONTAINING PROTEIN THAT CAN DRIVE THE MATURATION OF B-LYMPHOCYTES INTO IMMUNOGLOBULIN-SECRETING CELLS CELL Turner, C. A., Mack, D. H., DAVIS, M. M. 1994; 77 (2): 297-306

  Abstract

  We describe a novel gene, Blimp-1 (for B lymphocyte-induced maturation protein), transcripts of which are rapidly induced during the differentiation of B lymphocytes into immunoglobulin secretory cells and whose expression is characteristic of late B and plasma cell lines. The 856 amino acid open reading frame contains five Krüppel-type zinc finger motifs and proline-rich and acidic regions similar to those of known transcription factors. Serological studies show an approximately 100 kd protein that localizes to the nucleus. Stable or transient transfection of Blimp-1 into B cell lymphoma lines leads to the expression of many of the phenotypic changes associated with B cell differentiation into an early plasma cell stage, including induction of J chain message and immunoglobulin secretion, up-regulation of Syndecan-1, and increased cell size and granularity. Thus, Blimp-1 appears to be a pleiotropic regulatory factor capable of at least partially driving the terminal differentiation of B cells.

  View details for Web of Science ID A1994NH63400014

  View details for PubMedID 8168136

• USE OF GLOBAL AMINO-ACID REPLACEMENTS TO DEFINE THE REQUIREMENTS FOR MHC BINDING AND T-CELL RECOGNITION OF MOTH CYTOCHROME-C-(93-103) JOURNAL OF IMMUNOLOGY REAY, P. A., Kantor, R. M., DAVIS, M. M. 1994; 152 (8): 3946-3957

  Abstract

  Substitution with all naturally occurring L-amino acids at each of 11 residues of the IEk-restricted month cytochrome c (93-103) epitope has allowed us to analyze the requirements for MHC binding and T cell recognition to a level of definition not previously possible. Substitutions at only three positions systematically affect MHC binding and three others appear to be the major TCR contacts. Interestingly, changing residues involved in MHC binding can ablate T cell recognition without altering MHC association. Additionally, residue identity at two positions that do not appear critical for MHC binding, nor to be involved in specific T cell contact, nonetheless dramatically affect T cell responses. This suggests that peptides differing only slightly in sequence can have significantly altered conformations within the class II MHC binding groove. We have also developed a simple scoring program that uses the binding data to quantitate how well a given peptide fits the MCC motif. All strongly immunogenic IEk-restricted epitopes score highly (> or = 0.70, where 1.0 is perfect concordance), and only 3% of all potential nonameric peptides in the two main protein sequence databases have scores greater than 0.70. This indicates that the global amino acid replacement approach using a single peptide is an efficient means of deriving binding motifs for a given class II MHC molecule, and should aid in the identification of novel T cell epitopes.

  View details for Web of Science ID A1994NF01800026

  View details for PubMedID 7511662

• A PEPTIDE ANTIGEN ANTAGONIST PREVENTS THE DIFFERENTIATION OF T-CELL RECEPTOR TRANSGENIC THYMOCYTES JOURNAL OF IMMUNOLOGY SPAIN, L. M., JORGENSEN, J. L., DAVIS, M. M., BERG, L. J. 1994; 152 (4): 1709-1717

  Abstract

  The developmental fate of an immature T cell is determined in the thymus. Depending on the specificity of its TCR, a thymocyte receives signals to either die or differentiate. We have used fetal thymic organ cultures derived from TCR transgenic mice to examine the role of MHC/peptide ligands in T cell selection. Single amino acid substituted peptide analogues of the Ag recognized by the transgenic TCR were examined for their ability to enhance or interfere with positive selection. We have identified a nonstimulatory peptide analogue that interferes with the differentiation of transgenic CD4+8+ thymocytes into CD4+8- cells. We also show that this peptide, substituted in a TCR contact residue, is a competitive antagonist for activation of the T cell hybridoma expressing the same TCR. These observations demonstrate a novel mechanism for tolerance induction in the thymus.

  View details for Web of Science ID A1994MY84400022

  View details for PubMedID 8120380

• INDUCTION OF AUTOIMMUNE-DISEASE IN MICE BY GERMLINE ALTERATION OF THE T-CELL RECEPTOR GENE-EXPRESSION JOURNAL OF IMMUNOLOGY SAKAGUCHI, S., ERMAK, T. H., TODA, M., BERG, L. J., HO, W., FAZEKAS DE ST GROTH, B., PETERSON, P. A., SAKAGUCHI, N., DAVIS, M. M. 1994; 152 (3): 1471-1484

  Abstract

  Germline expression of rearranged TCR alpha-chain transgenes with the Ig H chain enhancer reproducibly elicits T cell-mediated autoimmune disease in the thyroid gland, gastric mucosa, Langerhans islets, salivary gland, ovaries, and testes in selected strains of normal mice. Multiple organs are destroyed in a single transgenic mouse and the same organ in transgenic strains with different MHC background, suggesting the transgene expression can elicit self-reactive T cell clones having different Ag specificities and MHC restrictions. Construction of this autoimmune-inducing TCR alpha EH transgene does not require particular V alpha J alpha gene segments or Ag specificities. Moreover, the autoimmune disease can be adoptively transferred to syngeneic normal mice by T cells expressing endogenous TCR alpha-chains. Taken together, these results indicate that the TCR alpha EH transgene expression does not suppress endogenous alpha-chain gene rearrangement and may trigger the expansion/activation of various self-reactive T cells expressing endogenous TCR alpha- and beta-chains. Furthermore, it appears that the transgene-induced autoimmune T cells are not deleted in the normal thymus or rendered anergic upon contact with the normal target self Ag, but can be controlled by a T cell-dependent mechanism, since transfer of the transgenic bone marrow cells to histocompatible SCID mice produces the same autoimmune disease as in the donors, and the autoimmune development in the SCID mice is effectively prevented by co-transfer of syngeneic nontransgenic T cells. This novel autoimmune model produced by genetic manipulation of the T cell lineage, not the target self Ag or the environment of T cell differentiation/selection, should be useful for elucidating the immunologic and genetic basis of autoimmune disease.

  View details for Web of Science ID A1994MV63000058

  View details for PubMedID 7905503

• THE NATURE OF MAJOR HISTOCOMPATIBILITY COMPLEX RECOGNITION BY GAMMA-DELTA-T-CELLS CELL SCHILD, H., Mavaddat, N., Litzenberger, C., Ehrich, E. W., DAVIS, M. M., Bluestone, J. A., Matis, L., Draper, R. K., Chien, Y. H. 1994; 76 (1): 29-37

  Abstract

  Despite intensive efforts, the general rules for gamma delta T cell recognition remain undefined. Here, we take advantage of the detailed knowledge of the molecular structure and biosynthetic pathways of major histocompatibility complex (MHC) molecules to analyze the recognition properties of the gamma delta T cell clones LBK5 (specific for the class II MHC, IEk) and G8 (specific for the nonclassical class I MHC, TL10b). We find that the activation of these clones requires neither class I nor class II antigen-processing and that peptides do not confer specificity. Epitope mapping also shows that the topology of gamma delta T cell receptor interaction with the MHC is distinct from that of alpha beta T cells. These results suggest that the molecular nature of gamma delta T cell recognition is fundamentally different than that of alpha beta T cells.

  View details for Web of Science ID A1994MR49500004

  View details for PubMedID 8287478

• CDR3 LENGTH IN ANTIGEN-SPECIFIC IMMUNE RECEPTORS JOURNAL OF EXPERIMENTAL MEDICINE ROCK, E. P., SIBBALD, P. R., DAVIS, M. M., Chien, Y. H. 1994; 179 (1): 323-328

  Abstract

  In both immunoglobulins (Ig) and T cell receptors (TCR), the rearrangement of V, D, and J region sequence elements during lymphocyte maturation creates an enormous degree of diversity in an area referred to as the complementarity determining region 3 (CDR3) loop. Variations in the particular V, D, and J elements used, precise points of recombination, and random nucleotide addition all lead to extensive length and sequence heterogeneity. CDR3 loops are often critical for antigen binding in Igs and appear to provide the principal peptide binding residues in TCRs. To better understand the physical and selective constraints on these sequences, we have compiled information on CDR3 size variation for Ig H, L (kappa and lambda) and TCR alpha, beta, gamma, and delta. Ig H and TCR delta CDR3s are the most variable in size and are significantly longer than L and gamma chains, respectively. In contrast, TCR alpha and beta chain distributions are highly constrained, with nearly identical average CDR3 lengths, and their length distributions are not altered by thymic selection. Perhaps most significantly, these CDR3 length profiles suggest that gamma/delta TCRs are more similar to Igs than to alpha/beta TCRs in their putative ligand binding region, and thus gamma/delta and alpha/beta T cells may have fundamentally different recognition properties.

  View details for Web of Science ID A1994MP51700033

  View details for PubMedID 8270877

• HOW ALPHA-BETA-T-CELL RECEPTORS SEE PEPTIDE MHC COMPLEXES IMMUNOLOGY TODAY Chien, Y. H., DAVIS, M. M. 1993; 14 (12): 597-602

  Abstract

  Recent results have added new information to our understanding of alpha beta T-cell receptor mediated recognition. In particular, we find that the V(D)J junction or 'CDR3' portion of TCR alpha and beta seem most important in contacting peptides bound to MHC molecules, consistent with previous predictions. Surprisingly, these same CDR3-peptide contacts also appear to have a major influence on the TCR-MHC molecule interactions as well.

  View details for Web of Science ID A1993MK79800005

  View details for PubMedID 8305132

• PH AFFECTS BOTH THE MECHANISM AND THE SPECIFICITY OF PEPTIDE BINDING TO A CLASS-II MAJOR HISTOCOMPATIBILITY COMPLEX MOLECULE BIOCHEMISTRY BONIFACE, J. J., Allbritton, N. L., REAY, P. A., Kantor, R. M., Stryer, L., DAVIS, M. M. 1993; 32 (44): 11761-11768

  Abstract

  We have compared the contribution of electrostatic forces in the binding of antigenic peptides to the class II MHC molecule, IEk, at weakly acidic (pH 5.4) and neutral (pH 7.5) pH values. The binding of specific moth cytochrome c (MCC) and hemoglobin (Hb) peptides to IEk is very sensitive to ionic strength at pH 7.5 but not at pH 5.4, indicating that the mechanism of peptide binding is pH-dependent. Substitution of the C-terminal Lys in MCC for an Ala residue selectively destroyed peptide binding at neutral pH and increased the dissociation rate at least 30-fold, implicating this residue in the pH-dependent electrostatic interaction. The presence of a C-terminal Lys in many of the peptides that are restricted to IEk suggests that this electrostatic interaction is widely used to bind peptides to this MHC molecule. We also probed the electrostatic environment of the peptide binding groove adjacent to the N-terminus of the bound peptide by rapid-diffusion fluorescence energy transfer using a terbium-labeled MCC peptide. In this region of the peptide binding groove, more negative charge is present at pH 7.5 than at pH 5.4. These findings indicate the importance of MHC carboxylates to the mechanism and specificity of peptide binding. The biological importance of having two distinct mechanisms of peptide binding at different pH may be that it acts to broaden the spectrum of antigenic peptides that can be presented to T-cells.

  View details for Web of Science ID A1993MF82000003

  View details for PubMedID 8218246

• FORMATION OF FUNCTIONAL PEPTIDE COMPLEXES OF CLASS-II MAJOR HISTOCOMPATIBILITY COMPLEX PROTEINS FROM SUBUNITS PRODUCED IN ESCHERICHIA-COLI PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Altman, J. D., REAY, P. A., DAVIS, M. M. 1993; 90 (21): 10330-10334

  Abstract

  Class II major histocompatibility complex molecules play a major role in the immune response by binding peptide fragments of exogenous antigens and displaying them on the surfaces of antigen-presenting cells, where they can be recognized by T cells. To facilitate structural and functional studies of these molecules, we have produced truncated alpha and beta chains of the murine class II molecule I-Ek in Escherichia coli (Ec-I-Ek) and have developed conditions to fold them in the presence of specific peptides with yields of complex approaching 2%. Reconstitution is specific since only unlabeled peptide known to bind I-Ek compete with biotinylated peptide, as assessed by ELISA. Complexes of the refolded heterodimer (Ec-I-Ek) with either of two different peptide antigens remain associated during nonreducing SDS/PAGE. Immobilized Ec-I-Ek-peptide complexes stimulate lymphokine production by three T-cell clones in an antigen-specific manner with a dose-response relation comparable to previously described soluble I-Ek molecules produced in CHO cells. These results demonstrate that folding of Ek alpha and Ek beta polypeptides does not require any other protein to produce the biologically relevant conformation and that carbohydrate modification of this class II molecule is not necessary for alpha beta T-cell recognition.

  View details for Web of Science ID A1993MF29600121

  View details for PubMedID 8234294

• ACTIVATION AND DIFFERENTIATION REQUIREMENTS OF PRIMARY T-CELLS IN-VITRO PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA SAGERSTROM, C. G., Kerr, E. M., Allison, J. P., DAVIS, M. M. 1993; 90 (19): 8987-8991

  Abstract

  The progression of T cells from a quiescent or resting state to fully activated, proliferating cells is a crucial step in the initiation of an immune response. We have developed an in vitro system to study the requirements for triggering or hindering this pathway by using naive T cells derived from T-cell antigen receptor alpha beta transgenic animals and peptide-major histocompatibility (MHC) complexes coated on plates. Whereas previously stimulated T cells require only peptide-MHC complexes to produce interleukin 2 (IL-2), naive cells require at least one additional signal, which can be provided by either an anti-CD28 antibody or the protein kinase C stimulant phorbol 12-myristate 13-acetate. In contrast, the anti-CD28 antibody augments IL-2 production by primed T cells but is not required, and phorbol 12-myristate 13-acetate has no discernable effect. Thus we find that native T cells have significantly more stringent requirements for IL-2 production than primed cells and that this fits well with previous observations in other in vitro systems as well as in vivo models of autoimmunity. We also find that peptide-MHC complex stimulation of naive T cells, together with exogenous IL-2, is sufficient to convert these cells to primed T cells in vitro in 2 days, as assayed both by surface marker analysis and stimulation requirements. Taken together with the above results, this suggests that the activation of primary T cells requires at least two signals and that IL-2 produced by naive T cells in vivo may act in an autocrine fashion to allow them to proliferate and differentiate.

  View details for Web of Science ID A1993MA59500049

  View details for PubMedID 8415642

• T-CELL RECEPTOR INTERACTION WITH PEPTIDE MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) AND SUPERANTIGEN MHC LIGANDS IS DOMINATED BY ANTIGEN JOURNAL OF EXPERIMENTAL MEDICINE Ehrich, E. W., DEVAUX, B., ROCK, E. P., JORGENSEN, J. L., DAVIS, M. M., Chien, Y. H. 1993; 178 (2): 713-722

  Abstract

  While recent evidence strongly suggests that the third complementarity determining regions (CDR3s) of T cell receptors (TCRs) directly contact antigenic peptides bound to major histocompatibility complex (MHC) molecules, the nature of other TCR contact(s) is less clear. Here we probe the extent to which different antigens can affect this interaction by comparing the responses of T cells bearing structurally related TCRs to cytochrome c peptides and staphylococcal enterotoxin A (SEA) presented by 13 mutant antigen-presenting cell (APC) lines. Each APC expresses a class II MHC molecule (I-Ek) with a single substitution of an amino acid residue predicted to be located on the MHC alpha helices and to point "up" towards the TCR. We find that very limited changes (even a single amino acid) in either a CDR3 loop of the TCR or in a contact residue of the antigenic peptide can have a profound effect on relatively distant TCR/MHC interactions. The extent of these effects can be as great as that observed between T cells bearing entirely different TCRs and recognizing different peptides. We also find that superantigen presentation entails a distinct mode of TCR/MHC interaction compared with peptide presentation. These data suggest that TCR/MHC contacts can be made in a variety of ways between the same TCR and MHC, with the final configuration apparently dominated by the antigen. These observations suggest a molecular basis for recent reports in which either peptide analogues or superantigens trigger distinct pathways of T cell activation.

  View details for Web of Science ID A1993LP83000037

  View details for PubMedID 8393480

• TRANSFER OF PUTATIVE COMPLEMENTARITY-DETERMINING REGION LOOPS OF T-CELL RECEPTOR-V DOMAINS CONFERS TOXIN REACTIVITY BUT NOT PEPTIDE MHC SPECIFICITY JOURNAL OF IMMUNOLOGY PATTEN, P. A., ROCK, E. P., Sonoda, T., FAZEKAS DE ST GROTH, B., JORGENSEN, J. L., DAVIS, M. M. 1993; 150 (6): 2281-2294

  Abstract

  We have used multiple-amino acid replacement mutagenesis to examine the roles of the TCR homologues of Ig complementarity-determining regions (CDR) and framework sequences in Ag-MHC and Staphylococcus aureus enterotoxin reactivity. In the three cases examined, transplantation of Ig CDR3 homologues between I-Ek-restricted TCR that recognize distinct peptides did not result in transfer of peptide reactivity. Thus the structural context of the CDR3 loops, e.g., both neighboring CDR and the V beta structure, must play a crucial, albeit supporting, role in ligand recognition. The extreme lability of this context was also shown by the fact that transplantation of the CDR1, -2, and -3 loops from the beta chain of 5C.C7 onto a V beta 1 framework failed to transfer MHC-peptide specificity even when the TCR-alpha chains were identical. In contrast, superantigen reactivity was readily transferred in several cases, with CDR2 transplants conferring strong staphylococcal enterotoxin B and A reactivity and CDR1 transplants yielding weak reactivities. This suggests that bacterial (and perhaps other) superantigens bind to many of the same regions of the TCR V beta that are believed to interact with MHC molecules. These regions of V beta may be ideal targets for superantigen binding precisely because they interact with MHC molecules and thus may be relatively conserved.

  View details for Web of Science ID A1993KR93400020

  View details for PubMedID 7680688

• TOPOLOGY AND AFFINITY OF T-CELL RECEPTOR MEDIATED RECOGNITION OF PEPTIDE MHC COMPLEXES CURRENT OPINION IN IMMUNOLOGY DAVIS, M. M., Chien, Y. H. 1993; 5 (1): 45-49

  Abstract

  Significant progress has been made on several long-standing issues regarding T-cell receptor mediated recognition of antigen-MHC complexes. For one, early data suggest that the affinity of the T-cell receptor for the peptide-MHC complex is extremely low, with a KD of approximately 10(-4)-10(-5)M, much weaker than most antibody-antigen interactions. The fact that this affinity is lower than that of some T-cell adhesion molecules for their ligands could have important implications for immune surveillance. A second area of interest is the topology of T-cell receptor recognition; evidence of direct contact between the third complementarity determining region of the T-cell receptor and peptide determinants has been obtained. In addition, the orientation of the T-cell receptor with respect to several antigen-MHC complexes has been predicted. They suggest that whereas most or all peptides seem to bind in the same orientation in both class I and class II MHC molecules, the orientation of the T-cell receptor over the peptide-MHC complex may not be fixed.

  View details for Web of Science ID A1993KN29300008

  View details for PubMedID 8452673

• PH-DEPENDENCE AND EXCHANGE OF HIGH AND LOW RESPONDER PEPTIDES BINDING TO A CLASS-II MHC MOLECULE EMBO JOURNAL REAY, P. A., Wettstein, D. A., DAVIS, M. M. 1992; 11 (8): 2829-2839

  Abstract

  We have compared the binding kinetics of two antigenic peptides to a soluble class II MHC molecule. One of the peptides provokes a strong T cell response and the other a much weaker one. Both show greatly increased (approximately 40-fold) association rates at pH 5 in comparison to neutral pH, consistent with the low pH environment of late endosomes being most conducive to class II MHC--peptide binding. Interestingly, the weak peptide has a much faster off-rate that is significantly increased at pH 5 and it can be entirely replaced in an exchange reaction by the stronger one. This suggests that one characteristic of immunodominant peptides is that of nearly irreversible binding, such that they will be strongly selected for in the course of class II MHC transit and recycling through endosomal compartments. Modelling the parameters of this peptide exchange also suggests that a large fraction of the GPI-chimeric MHC molecules used in this study are 'empty' with respect to endogenous peptides, or else occupied with extremely weak ones, consistent with their inability to load processed peptides intracellularly.

  View details for Web of Science ID A1992JE53700007

  View details for PubMedID 1379172

  View details for PubMedCentralID PMC556762

• MAPPING T-CELL RECEPTOR PEPTIDE CONTACTS BY VARIANT PEPTIDE IMMUNIZATION OF SINGLE-CHAIN TRANSGENICS NATURE JORGENSEN, J. L., ESSER, U., FAZEKAS DE ST GROTH, B., REAY, P. A., DAVIS, M. M. 1992; 355 (6357): 224-230

  Abstract

  To test models of T-cell recognition, mice transgenic for T-cell receptor alpha or beta chain have been immunized with variant peptides that force changes in the resulting T-cell response. In particular, charge substitutions on the peptide often elicit reciprocal charges in the junctional (CDR3) sequences of T-cell receptor V alpha or V beta chains, indicating direct T-cell receptor-peptide contact, and allowing derivation of a topology for the T-cell receptor-MHC interaction. At one position on the peptide, variants transformed a homogeneous V beta response into a very heterogeneous one.

  View details for Web of Science ID A1992GZ69400056

  View details for PubMedID 1309938

• MOLECULAR-COMPONENTS OF T-CELL RECOGNITION ANNUAL REVIEW OF IMMUNOLOGY JORGENSEN, J. L., REAY, P. A., Ehrich, E. W., DAVIS, M. M. 1992; 10: 835-873

  Abstract

  We review recent data that increase our understanding of the ternary complex of the T cell receptor (TCR), antigenic peptides, and molecules of the major histocompatibility complex (MHC). Studies using synthetic peptide analogs for T-cell antigens have identified peptide residues that appear to interact with the MHC molecule and/or the TCR. The logical extension of these studies, using a complete replacement set of peptide analogues for a model peptide antigen, has more precisely defined the biochemical character of putative MHC and TCR contact residues, and indicated that the TCR is highly sensitive to subtle changes in peptide conformation. Insight into the binding site for peptide on the TCR has recently come from variant peptide immunization of TCR single-chain transgenic mice. These experiments indicate that residues encoded by the V(D)J junctions of both TCR chains contact peptide directly. TCR-MHC contacts have also been studied, using in vitro-mutagenized MHC molecules, particularly those altered at residues predicted to point "up," toward the TCR. These studies reveal that TCR-MHC contacts appear to be quite flexible, and vary between even closely related TCRs. A measure of the affinity of TCR for peptide/MHC complexes has come from competition experiments using soluble MHC complexed with specific peptides. This affinity, with a KD of 5 x 10(-5) M, is several orders of magnitude lower than that of most antibodies for their protein antigens and suggests that the sequence of events leading to T-cell activation begins with antigen-independent adhesion.

  View details for Web of Science ID A1992HN01200030

  View details for PubMedID 1591005

• LOW AFFINITY INTERACTION OF PEPTIDE-MHC COMPLEXES WITH T-CELL RECEPTORS SCIENCE Matsui, K., BONIFACE, J. J., REAY, P. A., SCHILD, H., FAZEKAS DE ST GROTH, B., DAVIS, M. M. 1991; 254 (5039): 1788-1791

  Abstract

  The interaction of antigen-specific T cell receptors (TCRs) with their ligands, peptides bound to molecules of the major histocompatibility complex (MHC), is central to most immune responses, yet little is known about its chemical characteristics. The binding to T cells of a labeled monoclonal antibody to the TCR was inhibited by soluble class II MHC heterodimers complexed to different peptides. Inhibition was both peptide- and TCR-specific and of low affinity, with a KD = 4 x 10(-5) to 6 x 10(-5) M, orders of magnitude weaker than comparable antibody-antigen interactions. This finding is consistent with the scanning nature of T cell recognition and suggests that antigen-independent adhesion precedes TCR engagement.

  View details for Web of Science ID A1991GW31600042

  View details for PubMedID 1763329

• GENERATION OF MONOCLONAL-ANTIBODIES AGAINST SOLUBLE HUMAN T-CELL RECEPTOR POLYPEPTIDES EUROPEAN JOURNAL OF IMMUNOLOGY DEVAUX, B., BJORKMAN, P. J., Stevenson, C., GREIF, W., ELLIOTT, J. F., Sagerstrom, C., CLAYBERGER, C., KRENSKY, A. M., DAVIS, M. M. 1991; 21 (9): 2111-2119

  Abstract

  One approach to the diagnosis and therapy of T cell-mediated diseases is to develop reagents specific for T cell receptor (TcR) variable (V) regions. To date, however, TcR expressed on the surface of antigen-specific T lymphocytes have proven to be poorly immunogenic. As a result, few monoclonal antibodies (mAb) recognizing human variable regions are available. In this report, we have used the "phosphatidylinositol linkage" strategy to generate soluble forms of two human allogeneic TcR derived from human cytotoxic T lymphocytes (CTL) known to be specific for HLA-A2 and HLA-Aw68/HLA-Aw69, respectively. Monomeric TcR alpha and beta chains from the HLA-A2-specific CTL were purified in large quantities from CHO cells and each was used to immunize mice to generate mAb. In particular, the anti-beta chain mAb, denoted anti-V beta 13, stain a significant (approximately 5%) fraction of human peripheral blood alpha/beta T lymphocytes, immunoprecipitate native anti-A2 TcR molecules, and activate T cells transfected with the relevant alpha and beta chain cDNA. Anti-alpha chain mAb were also obtained against a constant region determinant which can immunoprecipitate detergent-solubilized polypeptides. In general, we find that immunizations with soluble protein are far superior to those with cells bearing TcR chimeras or in combination with the purified protein.

  View details for Web of Science ID A1991GF65500019

  View details for PubMedID 1832385

• A GAMMA-DELTA T-CELL RECEPTOR HETERODIMER INDUCES THE EXPRESSION OF CD4 AND CD8 IN THYMOCYTES JOURNAL OF EXPERIMENTAL MEDICINE Iwashima, M., DAVIS, M. M., Chien, Y. H. 1991; 174 (1): 293-296

  Abstract

  CD4 and CD8 have been useful surface markers for alpha/beta T cell maturation. In an alpha/beta T cell receptor (TCR) transgenic SCID mice system, it has been shown that alpha/beta TCR alone is sufficient to induce CD4 and CD8 surface expression on thymic T cells. Although the late embryonic thymic gamma/delta T cells are predominately single and double positive, it has not been clear if gamma/delta TCR has a similar capacity. In this study, we show that when transgenes encoding the earliest embryonic gamma/delta TCR are coexpressed with the SCID defect, the gamma/delta transgenes promote the appearance of both the CD4-8- and CD4+8+ T cells in the thymus. Furthermore, the expression of CD4 and CD8 does not require continuous surface gamma/delta TCR expression. These results indicate that gamma/delta TCR alone can promote the CD4/8 surface expression, and may suggest a role for gamma/delta T cells in initiating normal thymic ontogeny.

  View details for Web of Science ID A1991FU89700034

  View details for PubMedID 1905341

• EXPRESSION OF A CLASS-II MAJOR HISTOCOMPATIBILITY COMPLEX (MHC) HETERODIMER IN A LIPID-LINKED FORM WITH ENHANCED PEPTIDE SOLUBLE MHC COMPLEX-FORMATION AT LOW PH JOURNAL OF EXPERIMENTAL MEDICINE Wettstein, D. A., BONIFACE, J. J., REAY, P. A., SCHILD, H., DAVIS, M. M. 1991; 174 (1): 219-228

  Abstract

  A murine class II major histocompatibility complex (MHC) heterodimer, Ek, expressed as a glycan-phosphatidyl inositol-anchored chimera on Chinese Hamster Ovary cells, can present peptides, but not processed antigen to T cells. This chimeric MHC requires a 100-times higher peptide concentration to achieve a two- to four-times lower level of T cell stimulation. Cleavage with phosphatidylinositol-specific phospholipase C and purification result in large quantities of heterodimer in a water-soluble form. Plates coated with this material and then incubated with peptide can efficiently stimulate the appropriate T cell hybridomas. This stimulation is significantly enhanced when peptides are preincubated with the plate-bound MHC molecules in a pH range (5.0-5.5) similar to that of late endosomes. More than half of the soluble Ek molecules can form a specific complex with cytochrome c peptides in this pH range. This suggests that class II MHC molecules undergo distinct conformational changes in endosomal compartments that render them more capable of forming functional complexes with peptide antigens, irrespective of other cell components.

  View details for Web of Science ID A1991FU89700026

  View details for PubMedID 1829108

• EXPRESSION OF A FETAL GAMMA-DELTA T-CELL RECEPTOR IN ADULT MICE TRIGGERS A NON-MHC-LINKED FORM OF SELECTIVE DEPLETION INTERNATIONAL IMMUNOLOGY Iwashima, M., Green, A., Bonyhadi, M., DAVIS, M. M., Allison, J. P., Chien, Y. 1991; 3 (4): 385-393

  Abstract

  Day 14 fetal thymocytes and adult dendritic epidermal T cells (dEC) of all mouse strains express a characteristic non-polymorphic gamma delta T-cell receptor which is rarely found in the adult thymus or lymph nodes. We have made transgenic mice expressing this particular set of receptors on T cells in C3H and C57BL/6 mice. In adult mice of the latter strain, a dramatic depletion of transgene expressing T cells occurs and this effect is primarily mediated by thymic radiosensitive cells. The depletion is genetically dominant but not MHC-linked with major factor(s) mapping to chromosome 18. Taken together, our results show that strain-specific developmental changes in the thymic environment may play a role in shaping the gamma delta TCR repertoire.

  View details for Web of Science ID A1991FK38000012

  View details for PubMedID 1831656

• EXPRESSION OF T-CELL ANTIGEN RECEPTOR HETERODIMERS IN A LIPID-LINKED FORM SCIENCE LIN, A. Y., DEVAUX, B., Green, A., Sagerstrom, C., ELLIOTT, J. F., DAVIS, M. M. 1990; 249 (4969): 677-679

  Abstract

  The interaction of the T cell receptor for antigen (TCR) with its antigen-major histocompatibility complex ligand is difficult to study because both are cell surface multimers. The TCR consists of two chains (alpha and beta) that are complexed to the five or more nonpolymorphic CD3 polypeptides. A soluble form of the TCR was engineered by replacing the carboxyl termini of alpha and beta with signal sequences from lipid-linked proteins, making them susceptible to enzymatic cleavage. In this manner, TCR heterodimers can be expressed independently of the CD3 polypeptides and in significant quantities (0.5 milligram per week). This technique seems generalizable to biochemical and structural studies of many other cell surface molecules as well.

  View details for Web of Science ID A1990DT79600046

  View details for PubMedID 1696397

• THE EFFECTS OF MHC GENE DOSAGE AND ALLELIC VARIATION ON T-CELL RECEPTOR SELECTION CELL Berg, L. J., Frank, G. D., DAVIS, M. M. 1990; 60 (6): 1043-1053

  Abstract

  In a T cell receptor transgenic mouse model of thymic selection, the efficiency of selection of the transgenic alpha beta heterodimer is significantly enhanced in animals that express higher densities of the relevant major histocompatibility complex molecule (I-Ek/b). These results imply that there is a stochastic component to positive selection in the thymus. Allelic variants of the original selecting I-Ek molecule are either less efficient (E alpha k:E beta b) or incapable (E alpha k:E beta s and I-Ed) of mediating the selection of transgenic alpha beta + T cells. Two of these three I-E variants appear to differ from I-Ek in amino acid residues of the peptide binding site and not in residues capable of contacting the T cell receptor, suggesting that specific peptides, or conformations of peptides, play a role in positive selection. In contrast, mice transgenic for only the beta chain of this T cell receptor show selection for CD4+ T cells in the presence of all four I-E variants tested.

  View details for Web of Science ID A1990CW00200018

  View details for PubMedID 2317862

• LYMPHOCYTE-T ANTIGEN INTERACTIONS IN TRANSPLANT REJECTION NEW ENGLAND JOURNAL OF MEDICINE KRENSKY, A. M., WEISS, A., Crabtree, G., DAVIS, M. M., Parham, P. 1990; 322 (8): 510-517

  View details for Web of Science ID A1990CP69600005

  View details for PubMedID 2405272

• T-CELL RECEPTOR GENE DIVERSITY AND SELECTION ANNUAL REVIEW OF BIOCHEMISTRY DAVIS, M. M. 1990; 59: 475-496

  View details for Web of Science ID A1990DM77300017

  View details for PubMedID 2197981

• THE XLR SEQUENCE FAMILY - DISPERSION ON THE X-CHROMOSOME AND Y-CHROMOSOME OF A LARGE SET OF CLOSELY RELATED SEQUENCES, MOST OF WHICH ARE PSEUDOGENES NUCLEIC ACIDS RESEARCH GARCHON, H. J., Loh, E., Ho, W. Y., Amar, L., Avner, P., DAVIS, M. M. 1989; 17 (23): 9871-9888

  Abstract

  The XLR sequence family encodes RNA transcripts specific to late-stage T and B cells and their neoplasms. Only one apparently functional mRNA has been identified thus far and this encodes a novel 25 kDa nuclear protein. In this report, we find that the XLR gene family is composed of 50-75 copies per haploid genome which localize to at least two different portions of the mouse X chromosome. Neither of these locations are near the xid mutation that earlier work had correlated with XLR. In addition, some members of this family are also on the Y chromosome. Another surprising finding is that while the fourteen genomic clones examined to date have the same exon-intron structure and are closely related with respect to sequence conservation (90%), all appear (in most cases by multiple criteria) to be non-functional, raising the possibility that all but one of the members of this large semi-dispersed family are pseudogenes.

  View details for Web of Science ID A1989CE28900027

  View details for PubMedID 2602144

• T-cell development in T cell receptor alphabeta transgenic mice. Seminars in immunology Berg, L. J., DAVIS, M. M. 1989; 1 (2): 105-116

  Abstract

  The introduction of rearranged T cell receptor alpha and beta chain genes into transgenic mice results in a high frequency of expression of the introduced receptor on T cells. In three different systems, analyses of mice expressing transgenic T cell receptors specific for antigen plus MHC class I or class II molecules have demonstrated several important features of T cell development: (1) T cell receptor specificity for MHC class I or class II molecules determines the expression of CD8 versus CD4, respectively, on mature T cells; (2) T cell maturation in the thymus is dependent on expression of an MHC molecule recognized by the T cell receptor; (3)for class II specific receptors, appropriate MHC expression on thymic epithelial cells is sufficient to achieve positive selection of T cells; and (4) self-reactive T cells die or are killed in the thymus.

  View details for PubMedID 15630812

• ANTIGEN MHC-SPECIFIC T-CELLS ARE PREFERENTIALLY EXPORTED FROM THE THYMUS IN THE PRESENCE OF THEIR MHC LIGAND CELL Berg, L. J., PULLEN, A. M., FAZEKAS DE ST GROTH, B., MATHIS, D., Benoist, C., DAVIS, M. M. 1989; 58 (6): 1035-1046

  Abstract

  Transgenic mice expressing a T cell receptor heterodimer specific for a fragment of pigeon cytochrome c plus an MHC class II molecule (I-Ek) have been made. We find that H-2k alpha beta transgenic mice have an overall increase in the number of T cells and express a 10-fold higher fraction of cytochrome c-reactive cells than H-2b mice. Surface staining of thymocytes indicates that in H-2b mice, T cell development is arrested at an intermediate stage of differentiation (CD4+8+, CD310). Analyses of mice carrying these T cell receptor genes and MHC class II I-E alpha constructs indicate that his developmental block can be reversed in H-2b mice by I-E expression on cortical epithelial cells of the thymus. These data suggest that a direct T cell receptor-MHC interaction occurs in the thymus in the absence of nominal antigen and results in the enhanced export of T cells, consistent with the concept of "positive selection".

  View details for Web of Science ID A1989AR72600007

  View details for PubMedID 2476238

• PHENOTYPIC DIFFERENCES BETWEEN ALPHA-BETA-T-CELL VERSUS BETA-T-CELL RECEPTOR TRANSGENIC MICE UNDERGOING NEGATIVE SELECTION NATURE Berg, L. J., FAZEKAS DE ST GROTH, B., PULLEN, A. M., DAVIS, M. M. 1989; 340 (6234): 559-562

  Abstract

  T-cell differentiation in the thymus is thought to involve a progression from the CD4-CD8- phenotype through CD4+CD8+ intermediates to mature CD4+ or CD8+ cells. There is evidence that during this process T cells bearing receptors potentially reactive to 'self' are deleted by a process termed 'negative selection' One example of this process occurs in mice carrying polymorphic Mls antigens, against which a detectable proportion of T cells are autoreactive. These mice show clonal deletion of thymic and peripheral T-cell subsets that express the autoreactive V beta 3 segment of the T-cell antigen receptor, but at most a two-fold depletion of thymic cells at the CD4+CD8+ stage. By contrast, transgenic mice bearing both alpha and beta chain genes encoding autoreactive receptors recognizing other ligands, show severe depletion of CD4+CD8+ thymocytes as well, suggesting that negative selection occurs much earlier. We report here the Mls 2a/3a mediated elimination of T cells expressing a transgene encoded V beta 3-segment, in T-cell receptor alpha/beta and beta-transgenic mice. Severe depletion of CD4+CD8+ thymocytes is seen only in the alpha/beta chain transgenic mice, whereas both strains delete mature V beta 3 bearing CD4+ and CD8+ T cells efficiently. We conclude that severe CD4+CD8+ thymocyte deletion in alpha/beta transgenic mice results from the premature expression of both receptor chains, and does not reflect a difference in the timing or mechanism of negative selection for Mls antigens as against the allo- and MHC class 1-restricted antigens used in the other studies.

  View details for Web of Science ID A1989AL22700059

  View details for PubMedID 2528070

• A POSSIBLE BASIS FOR MAJOR HISTOCOMPATIBILITY COMPLEX-RESTRICTED T-CELL RECOGNITION PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES DAVIS, M. M., Chien, Y. H., BJORKMAN, P. J., ELLIOTT, J. F., Iwashima, M., ROCK, E. P., PATTEN, P. A. 1989; 323 (1217): 521-524

  Abstract

  Four distinct T-cell antigen-receptor gene loci have now been identified and partly characterized: alpha, beta, gamma and delta. All of these loci can rearrange in an immunoglobulin-like fashion and express polypeptides that contribute to either alpha:beta or gamma:delta T-cell receptor-CD3 complexes. Surprisingly, the T-cell receptor (TCR) delta coding regions are located entirely, or almost entirely, within the TCR alpha locus and share at least some of the V region gene segments, thus at least partly linking the two different types of receptor heterodimers. Analysis of potential T-cell receptor diversity, particularly that of the delta chain, indicates a striking concentration of somatic polymorphism in the V-J junctional region of the two heterodimers, four to six orders of magnitude higher than similar calculations for immunoglobulin light- and heavy-chain combinations. In contrast, the number of possible V region combinations in T-cell receptors is one hundredth to one thousandth that of immunoglobulins. TCR alpha: beta heterodimers are known to recognize many possible fragments of antigens embedded in the peptide-binding clefts of a relatively small number of major histocompatibility complex (MHC) molecules. Thus it is attractive to speculate that the V-J junctional portions of both types of T-cell receptor contact peptide antigens, whereas the remaining diversity regions contact the MHC. This contention is supported by molecular modelling studies and has interesting implications for the evolution of antigen-receptor genes.

  View details for Web of Science ID A1989AB41200008

  View details for PubMedID 2569209

• THE XLR GENE-PRODUCT DEFINES A NOVEL SET OF PROTEINS STABILIZED IN THE NUCLEUS BY ZINC IONS JOURNAL OF CELL BIOLOGY GARCHON, H. J., DAVIS, M. M. 1989; 108 (3): 779-787

  Abstract

  The major product of the XLR (X-chromosomal, lymphocyte-regulated) locus is found to be a 30-kD nuclear protein with a relatively short (t1/2 approximately equal to 2 h) half-life. Together with its stage- and tissue-specific pattern of expression, this suggests a role for this protein in the regulation of differentiation in T and B lymphocytes. Interestingly, the XLR protein almost completely leaches out of the nucleus after lysis of cells in low salt buffer, but is stabilized in that location by metal cations, particularly Zn++. This stabilization is reversible by chelating agents (o-phenanthroline, EDTA) which also release a number of other polypeptides in addition to XLR. These results suggest that XLR represents a novel class of nuclear proteins, and that cations such as zinc may play a role in the localization of these proteins in the nucleus.

  View details for Web of Science ID A1989T780000003

  View details for PubMedID 2493459

• POLYMERASE CHAIN-REACTION WITH SINGLE-SIDED SPECIFICITY - ANALYSIS OF T-CELL RECEPTOR DELTA-CHAIN SCIENCE Loh, E. Y., ELLIOTT, J. F., Cwirla, S., Lanier, L. L., DAVIS, M. M. 1989; 243 (4888): 217-220

  Abstract

  In the polymerase chain reaction (PCR), two specific oligonucleotide primers are used to amplify the sequences between them. However, this technique is not suitable for amplifying genes that encode molecules where the 5' portion of the sequences of interest is not known, such as the T cell receptor (TCR) or immunoglobulins. Because of this limitation, a novel technique, anchored polymerase chain reaction (A-PCR), was devised that requires sequence specificity only on the 3' end of the target fragment. It was used to analyze TCR delta chain mRNA's from human peripheral blood gamma delta T cells. Most of these cells had a V delta gene segment not previously described (V delta 3), and the delta chain junctional sequences formed a discrete subpopulation compared with those previously reported.

  View details for Web of Science ID A1989R736800036

  View details for PubMedID 2463672

• A MODEL FOR T-CELL RECEPTOR AND MHC PEPTIDE INTERACTION 2ND INTERNATIONAL CONF ON LYMPHOCYTE ACTIVATION AND IMMUNE REGULATION DAVIS, M. M., BJORKMAN, P. J. PLENUM PRESS DIV PLENUM PUBLISHING CORP. 1989: 13–16

  View details for Web of Science ID A1989BR17U00001

  View details for PubMedID 2816544

• SELECTION OF AN ALPHA-BETA-T-CELL ANTIGEN RECEPTOR INVIVO AND ENGINEERING A SOLUBLE FORM 7TH INTERNATIONAL CONGRESS OF IMMUNOLOGY DAVIS, M. M., DESTGROTH, B. F., Berg, L. J., Lin, A., DEVAUX, B., Sagerstrom, C., ELLIOTT, J. F., BJORKMAN, P. J. SPRINGER-VERLAG BERLIN. 1989: 16–21

  View details for Web of Science ID A1989BP83Z00003

• MODEL FOR THE INTERACTION OF T-CELL RECEPTORS WITH PEPTIDE/MHC COMPLEXES 3RD SYMP ON IMMUNOLOGICAL RECOGNITION BJORKMAN, P. J., DAVIS, M. M. COLD SPRING HARBOR LABORATORY PRESS. 1989: 365–373

  View details for Web of Science ID A1989BR13A00043

• TCR RECOGNITION AND SELECTION INVIVO 3RD SYMP ON IMMUNOLOGICAL RECOGNITION DAVIS, M. M., Berg, L. J., LIN, A. Y., DESTGROTH, B. F., DEVAUX, B., SAGERSTROM, C. G., BJORKMAN, P. J., ELLIOTT, J. F. COLD SPRING HARBOR LABORATORY PRESS. 1989: 119–128

  View details for Web of Science ID A1989BR13A00013

• A NEW LYMPHOCYTE-SPECIFIC GENE WHICH ENCODES A PUTATIVE CA-2+-BINDING PROTEIN IS NOT EXPRESSED IN TRANSFORMED LYMPHOCYTE-T LINES JOURNAL OF IMMUNOLOGY Jongstra, J., Tidmarsh, G. F., JONGSTRABILEN, J., DAVIS, M. M. 1988; 141 (11): 3999-4004

  Abstract

  The LSP1 gene is a new lymphocyte-specific gene which is expressed in normal mouse B and T lymphocytes and in transformed B cells but not (or in much smaller amounts) in nine T lymphoma lines tested. No LSP1 mRNA is found in myeloid cells or in liver, kidney, or heart tissue. Inspection of the predicted LSP1 protein sequence reveals the presence of two putative Ca2+-binding domains in the LSP1 protein. Southern blotting analysis of genomic DNA from mouse liver suggests that the LSP1 gene is present as one copy per haploid genome. Similar analysis of genomic DNA extracted from three transformed B cell lines and five transformed T cell lines shows that the absence of LSP1 mRNA in T cell lines is not due to deletion or gross rearrangements of the LSP1 locus. With the use of the mouse LSP1 cDNA as a probe we can detect a cross-hybridizing RNA species in four normal human functional T cell lines but not in three transformed human T cell lines. This suggests that at least part of the DNA sequence and the expression pattern of the LSP1 gene is conserved between mouse and man. These conserved features, together with the particular expression pattern and the protein sequence homologies, suggest that the LSP1 protein is involved in a Ca2+-dependent aspect of normal T cell growth.

  View details for Web of Science ID A1988R004700045

  View details for PubMedID 3263441

• EXPRESSION OF T-CELL RECEPTOR ALPHA-CHAIN GENES IN TRANSGENIC MICE MOLECULAR AND CELLULAR BIOLOGY Berg, L. J., FAZEKAS DE ST GROTH, B., IVARS, F., Goodnow, C. C., Gilfillan, S., GARCHON, H. J., DAVIS, M. M. 1988; 8 (12): 5459-5469

  Abstract

  To examine the influences responsible for shaping the T-cell repertoire in vivo, we have introduced T-cell receptors of defined specificity into mice. In this report, we analyze transgenic mice carrying a T-cell receptor alpha-chain gene from a pigeon cytochrome c-reactive T-cell line. A variant of this construct, which has the immunoglobulin heavy-chain enhancer inserted into the JC intron, was also introduced into mice. Addition of the enhancer increased the steady-state level of transgene-encoded mRNA three- to fivefold in cultured T cells, leading to a two- to threefold increase in surface expression. In vivo, the difference between these two constructs was even more significant, increasing the number of transgene-positive cells from approximately 5 to 70% and the T-cell receptor surface density two- to threefold. Surprisingly, while surface expression of either type of transgene was limited to T cells, we found little tissue specificity with respect to transcription. In T cells expressing the alpha chain from the enhancer-containing construct, immunoprecipitation with a 2B4 alpha-specific monoclonal antibody revealed the expected disulfide-linked dimer. Costaining of these T cells with the 2B4 alpha-specific monoclonal antibody versus anti-CD3 indicated that expression of the transgene-encoded alpha chain precludes expression of endogenous alpha chains on the majority of cells; in contrast, 2B4 alpha-chain expression from the construct lacking the enhancer is inefficient at suppressing endogenous alpha-chain expression. In mice of the enhancer lineage, Southern blot analysis indicated suppression of endogenous alpha-chain rearrangements in T-cell populations, consistent with the observed allelic exclusion at the cellular level. Interestingly, newborn, but not adult, mice of this lineage also showed an increase in retention of unrearranged delta-chain loci in thymocyte DNA, presumably resulting from the suppression of alpha-chain rearrangements. This observation indicates that at least a fraction of alpha:beta-positive T cells have never attempted to produce functional delta rearrangements, thus suggesting that alpha:beta and gamma:delta T cells may be derived from different T-cell compartments (at least during the early phases of T-cell differentiation).

  View details for Web of Science ID A1988R081800043

  View details for PubMedID 3266655

• VARIABLE REGION (V-SIGMA) GENE SEGMENT MOST FREQUENTLY UTILIZED IN ADULT THYMOCYTES IS 3' OF THE CONSTANT (C-SIGMA) REGION PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Iwashima, M., Green, A., DAVIS, M. M., Chien, Y. H. 1988; 85 (21): 8161-8165

  Abstract

  A variable region (V delta 5) of the T-cell receptor (TcR) delta chain that is preferentially expressed in adult murine thymocytes is located 2.5 kilobases 3' of the constant region (C delta) element. The V delta 5 coding sequence is in a transcriptional orientation opposite the J delta (joining region) and C delta coding elements and rearranges by inversion. The C delta is divided into four exons, three of which encode amino acids of TcR delta polypeptide, and the fourth comprises the entire 3' untranslated region. In this respect, C delta resembles C alpha rather than C beta or C gamma.

  View details for Web of Science ID A1988Q834100070

  View details for PubMedID 3263646

• T-CELL ANTIGEN RECEPTOR GENES AND T-CELL RECOGNITION NATURE DAVIS, M. M., BJORKMAN, P. J. 1988; 334 (6181): 395-402

  Abstract

  The four distinct T-cell antigen receptor polypeptides (alpha, beta, gamma, delta) form two different heterodimers (alpha:beta and gamma:delta) that are very similar to immunoglobulins in primary sequence, gene organization and modes of rearrangement. Whereas antibodies have both soluble and membrane forms that can bind to antigens alone, T-cell receptors exist only on cell surfaces and recognize antigen fragments only when they are embedded in major histocompatibility complex (MHC) molecules. Patterns of diversity in T-cell receptor genes together with structural features of immunoglobulin and MHC molecules suggest a model for how this recognition might occur. This view of T-cell recognition has implications for how the receptors might be selected in the thymus and how they (and immunoglobulins) may have arisen during evolution.

  View details for Web of Science ID A1988P529200046

  View details for PubMedID 3043226

• A HUMAN T-CELL-SPECIFIC MOLECULE IS A MEMBER OF A NEW GENE FAMILY JOURNAL OF IMMUNOLOGY Schall, T. J., Jongstra, J., Dyer, B. J., Jorgensen, J., CLAYBERGER, C., DAVIS, M. M., KRENSKY, A. M. 1988; 141 (3): 1018-1025

  Abstract

  We have used a cDNA library enriched for T cell-specific sequences to isolate genes expressed by T cells but not by other cell types. We report here one such gene, designated RANTES, which encodes a novel T cell-specific molecule. The RANTES gene product is predicted to be 10 kDa and, after cleavage of the signal peptide, approximately 8 kDa. Of the 68 residues, 4 are cysteines, and there are no sites for N-linked glycosylation. RANTES is expressed by cultured T cell lines that are Ag specific and growth factor dependent. RANTES expression is inducible in PBL by Ag or mitogen. In CTL, expression of RANTES decreases after stimulation with Ag and growth factors. Interestingly, RANTES was not expressed by any T cell tumor line tested. There is significant homology between the RANTES sequence and several other T cell genes, suggesting that they comprise a previously undescribed family of small T cell molecules.

  View details for Web of Science ID A1988P361900046

  View details for PubMedID 2456327

• THE INVITRO TRANSLATION PRODUCT OF THE MURINE LAMBDA-5 GENE CONTAINS A FUNCTIONAL SIGNAL PEPTIDE MOLECULAR IMMUNOLOGY Jongstra, J., JONGSTRABILEN, J., Tidmarsh, G. F., DAVIS, M. M. 1988; 25 (8): 687-693

  Abstract

  We have isolated and sequenced a novel lambda 1 constant region related cDNA clone which might represent an allelic variant of the recently described lambda 5 gene. This lambda 5 transcript is present in pre-B cell lines and bone marrow cells, but not in B cell lines, plasma cell lines or in spleen cells. In vitro translation studies show that the translation product contains a signal peptide of approx. 30 amino acids at its N-terminus.

  View details for Web of Science ID A1988P534100002

  View details for PubMedID 2460755

• MOLECULAR-GENETICS OF T-CELL ANTIGEN RECEPTORS HOSPITAL PRACTICE DAVIS, M. M. 1988; 23 (5): 157-?

  View details for Web of Science ID A1988N399000013

  View details for PubMedID 3131355

• T-CELL RECEPTOR BETA-CHAIN GENES IN BW5-147 AND OTHER AKR TUMORS - DELETION ORDER OF MURINE-V-BETA GENE SEGMENTS AND POSSIBLE 5' REGULATORY REGIONS JOURNAL OF IMMUNOLOGY Lee, N. E., DAVIS, M. M. 1988; 140 (5): 1665-1675

  Abstract

  The AKR thymoma BW5147 has rearranged both of its TCR beta-chain loci, using the same J beta region (J beta 2.5) in each, but with different V beta gene segments. Although the two rearrangements are expressed approximately equally in cytoplasmic RNA, the principle of allelic exclusion is maintained because only one rearrangement is in-frame and capable of encoding a functional protein. In hybridomas made with BW5147 as the fusion partner, this protein may combine with the alpha-chain protein derived from the normal cell to form new Ag/MHC specificities. An analysis of the sequences upstream from the BW5147 rearrangements and additional V regions suggests that two conserved sequences, 10 and nine nucleotides in length and located adjacent to each other 70 to 100 nucleotides 5' of the initiation codon, may be important in the expression of TCR beta-chain genes. Although B and T cells derive from common stem cells, no sequences are observed in T cells that are homologous to the octamer located 5' of all Ig genes. This implies that at least some of the sequences that regulate transcription are not shared in the two major types of lymphocytes. A survey of BW5147 and six other AKR thymomas using probes for 10 of the 18 known V region families indicates a distribution of V beta rearrangements in the tumors consistent with that found in thymocytes. Four of these tumors have apparent VDJ rearrangements on both chromosomes, with the deletion of other V beta gene segments. These data suggest that the primary mechanism of VDJ beta rearrangement is by looping out and excision of the intervening DNA and that most of the V regions are located 5' to the C region. These data were also used to develop a deletion order of the V beta gene segments in the TCR beta-chain locus.

  View details for Web of Science ID A1988M523100050

  View details for PubMedID 3346546

• THE ADULT T-CELL RECEPTOR DELTA-CHAIN IS DIVERSE AND DISTINCT FROM THAT OF FETAL THYMOCYTES NATURE ELLIOTT, J. F., ROCK, E. P., PATTEN, P. A., DAVIS, M. M., Chien, Y. H. 1988; 331 (6157): 627-631

  Abstract

  T lymphocytes recognize foreign molecules using the T-cell receptor (TCR), a disulphide-linked heterodimer closely associated with the CD3 polypeptide complex on the cell surface. The TCR alpha beta heterodimers seem largely responsible for the recognition properties of both helper (TH) and cytotoxic (TC) T cells. Recently, a second CD3-associated T-cell receptor heterodimer, gamma delta, has been described. Cells bearing the gamma delta receptor appear before those bearing alpha beta during thymic ontogeny and persist as a minor component (1-10%) of mature peripheral T cells. Their function is unknown. As there are a limited number of functional TCR V gamma gene segments, the size and potential diversity of the V delta repertoire is important for the number of different antigens that may be recognized by gamma delta heterodimers. The delta-chain locus is located 75 kilobases (kb) 5' to the TCR C alpha coding region, raising the possibility that the alpha and delta V-region repertoires may overlap. Also, analysis of rearrangements at the delta-chain locus in developing thymocytes shows distinct fetal and adult patterns indicating that there may be differences between the fetal and adult V delta repertoires. To address these questions, we have characterized a large number of delta-containing complementary DNA clones from adult double-negative thymocytes (CD4-8-), an immature population that is enriched for gamma delta-bearing cells. We find that a limited number of V delta sequences are used, showing little overlap with known adult V alpha s and differing significantly from fetal V delta s. But as two D elements may participate simultaneously in V delta gene assembly, and random nucleotides may be added at any one of three junctional points, the potential number of different delta chains that can be made in the adult thymus is very large (approximately 10(13)).

  View details for Web of Science ID A1988M118000061

  View details for PubMedID 2963227

• T-CELL RECEPTOR DELTA-GENE REARRANGEMENTS IN EARLY THYMOCYTES NATURE Chien, Y. H., Iwashima, M., Wettstein, D. A., Kaplan, K. B., ELLIOTT, J. F., Born, W., DAVIS, M. M. 1987; 330 (6150): 722-727

  Abstract

  The T-cell receptor delta-chain variable region can be assembled from as many as four distinct gene segments, V, D1, D2 and J, more than any other antigen-receptor gene. In fetal thymocytes V----D joinings are as common as D----J or VDJ rearrangements and one V gene segment predominates. Analysis of rearrangements at TCR gamma and delta loci during fetal ontogeny suggests abrupt changes and possible coordinate control in the rearrangement and expression of these loci.

  View details for PubMedID 2961997

• IDENTIFICATION AND SEQUENCE OF A 4TH HUMAN T-CELL ANTIGEN RECEPTOR CHAIN NATURE Loh, E. Y., Lanier, L. L., Turck, C. W., Littman, D. R., DAVIS, M. M., Chien, Y. H., WEISS, A. 1987; 330 (6148): 569-572

  Abstract

  Thymus-derived lymphocytes (T cells) use clonally distributed antigen receptors to recognize peptide fragments associated with products of the major histocompatibility complex (MHC) (refs 1-4). On most murine and human T cells the T cell receptor (TCR) is composed of disulphide-linked alpha and beta chains (TCR alpha/beta), each of which contains constant and variable domains, and which are associated with the invariant chains of the CD3 complex. It has been demonstrated, however, that a distinct CD3-associated TCR is expressed on a small subset of T cells or immature thymocytes which fail to express either CD4 or CD8 (refs 7-14), the molecules associated with class II or class I MHC antigen recognition. Instead of TCR alpha/beta, these cells express heterodimers of gamma and delta chains (TRC gamma/delta). The genes encoding alpha, beta, and gamma have been isolated and characterized. A new murine T cell receptor (Cx) gene which undergoes rearrangement and expression early during T cell ontogeny has recently been identified 5' of the murine J alpha C alpha gene locus. Here we isolate and sequence the homologous transcript from PEER, a human cell line that expresses a TCR gamma/delta, and show that it encodes a protein with characteristic V, D, J, and C segments. Using probes derived from this transcript, we have shown that both PEER and MOLT-13, another TCR gamma/delta-expressing cell line, rearrange this locus and express two sizes of transcripts differing in the 3' untranslated region. Using a synthetic peptide derived from the deduced C region sequence, we have prepared antisera that precipitates the delta chain of the TCR from both PEER and MOLT-13, thus demonstrating that Cx and its human homologue code for the delta chain of the TCR.

  View details for Web of Science ID A1987L184100062

  View details for PubMedID 2825032

• ORGANIZATION OF THE T-CELL ANTIGEN-RECEPTOR BETA-CHAIN LOCUS IN MICE PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA LINDSTEN, T., Lee, N. E., DAVIS, M. M. 1987; 84 (21): 7639-7643

  Abstract

  We used pulsed-field gel electrophoresis to determine the organization of the beta-chain gene of the T-cell receptor for antigen in normal and mutant inbred strains of mice. In normal mice, the variable (V)- and constant (C)- region elements of this locus span 700-800 kilobases of chromosomal DNA. All but one of the V beta gene segments analyzed lie 5' of the J beta C beta locus (J beta represents the joining region), with the closest being 280-360 kilobases away. The mutant mouse strain SJL has an internal V beta-region gene deletion that compacts the V beta region by 100-200 kilobases. Taken together with other data, these results indicate that the beta-chain locus can use either a looping-out/deletion or an inversion mechanism to appose V beta to DJ beta gene segments (D is the diversity region) and can accomplish the former (at least) over very large distances.

  View details for Web of Science ID A1987K780500061

  View details for PubMedID 3478716

• REARRANGEMENT AND EXPRESSION OF T-CELL RECEPTOR GENES IN CLONED MURINE NATURAL SUPPRESSOR-CELL LINES JOURNAL OF EXPERIMENTAL MEDICINE HERTELWULFF, B., LINDSTEN, T., SCHWADRON, R., Gilbert, D. M., DAVIS, M. M., Strober, S. 1987; 166 (4): 1168-1173

  Abstract

  Naturally occurring suppressor cells of the in vitro mixed leukocyte culture reaction and of in vivo graft-vs.-host disease have been identified in the spleens of neonatal mice (1) and of adult mice recovering from total lymphoid irradiation (2), whole-body irradiation (3), and syngeneic marrow transplantation (4), or cyclophosphamide therapy (5). Using both positive and negative selection procedures, the suppressors were reported to be null lymphocytes that did not express mature macrophage surface markers, nor differentiate into mature macrophages in vitro, nor demonstrate natural killer (NK) activity (1). Subsequently, cloned lines of these natural suppressor (NS) cells were derived from either adult mice given total lymphoid irradiation (TLI) (2) or from neonates (6). The cloned NS cell lines expressed a surface phenotype (2, 6) similar to that reported previously for cloned NK cells (Thy-1(+), asialo-GM1(+), Ig(-), Lyt-1(-), Lyt-2(-), Ia(-), MAC-1(-)) (7-9). However, the NS cells did not show NK activity in the standard assay with YAC-1 target cells. The cloned NS lines suppressed the proliferation of responder cells and the generation of cytolytic cells in the mixed leukocyte reaction (MLR), and suppressed lethal graft-vs.-host disease in vivo (10, 11). In view of the unusual function and surface phenotype of the cells, the lineage of these cells remained unclear. To determine the lineage of the cloned NS cells, we searched for expression and rearrangement of the alpha and beta chain genes of the T cell antigen receptor, as well as that of the gamma chain gene. Studies of the phenotypically similar NK cell yielded conflicting results. Thus, cloned lines of murine NK cells were reported to have rearrangements of the beta chain genes, and to express mRNA for all three chains (12). In contrast, freshly purified rat or human large granular lymphocytes (LGL) were shown to express only the 1.0 kb mRNA species of the beta chain gene (13), indicative of D-J joining (14). Thus, some but not all cells with NK function express the T cell receptor and are members of the T cell lineage. The current report shows that the NS lines express full-length mRNA transcripts for the a and beta chain of the T cell receptor, as well as the gamma chain gene.

  View details for Web of Science ID A1987K464000031

  View details for PubMedID 2958579

• A NEW T-CELL RECEPTOR GENE LOCATED WITHIN THE ALPHA-LOCUS AND EXPRESSED EARLY IN T-CELL DIFFERENTIATION NATURE Chien, Y. H., Iwashima, M., Kaplan, K. B., ELLIOTT, J. F., DAVIS, M. M. 1987; 327 (6124): 677-682

  Abstract

  A new T-cell receptor gene lies just 5' to the J alpha C alpha coding regions. Its placement in this location suggests a novel mechanism for the regulation of expression of one T-cell receptor polypeptide to another during ontogeny. Rearrangement of this locus occurs very early in thymic differentiation and its RNA expression parallels that of the gamma-chain in thymic subpopulations, making this a possible candidate for the recently described delta-chain of the T-cell receptor.

  View details for Web of Science ID A1987H882700046

  View details for PubMedID 2439914

• THE ISOLATION AND SEQUENCE OF A NOVEL GENE FROM A HUMAN FUNCTIONAL T-CELL LINE JOURNAL OF EXPERIMENTAL MEDICINE Jongstra, J., Schall, T. J., Dyer, B. J., CLAYBERGER, C., Jorgensen, J., DAVIS, M. M., KRENSKY, A. M. 1987; 165 (3): 601-614

  Abstract

  Using a subtractive hybridization procedure we have constructed a cDNA library enriched for sequences present in functional human T cell lines, but not in human EBV-transformed B cell lines. We have isolated a cDNA clone, AH2-519, representing a novel gene, designated 519. This novel gene is expressed in functional human cytolytic and Th cell lines but not in a variety of other cell lines, including several long-term human T cell tumor lines. The expression of gene 519 is inducible in cultures of normal human PBL using antigenic or mitogenic stimulation. Neither the DNA sequence determined from a full-length cDNA clone overlapping with clone AH2-519 nor the amino acid sequence of its predicted protein product has significant homology to published sequences in the GenBank or NBRF databases. The restricted expression of gene 519 suggests that its gene product is involved in the growth and/or differentiation of normal T cells. The data also show that normal, nontransformed, functional T cells express gene products that can not be readily identified in long-term tumor lines of the same cell lineage.

  View details for Web of Science ID A1987G292200002

  View details for PubMedID 2434598

  View details for PubMedCentralID PMC2188281

• VARIABILITY AND REPERTOIRE SIZE OF T-CELL RECEPTOR V-ALPHA GENE SEGMENTS NATURE Becker, D. M., Patten, P., Chien, Y. H., Yokota, T., ESHHAR, Z., Giedlin, M., Gascoigne, N. R., Goodnow, C., Wolf, R., Arai, K., DAVIS, M. M. 1985; 317 (6036): 430-434

  Abstract

  The immune system of higher organisms is composed largely of two distinct cell types, B lymphocytes and T lymphocytes, each of which is independently capable of recognizing an enormous number of distinct entities through their antigen receptors; surface immunoglobulin in the case of the former, and the T-cell receptor (TCR) in the case of the latter. In both cell types, the genes encoding the antigen receptors consist of multiple gene segments which recombine during maturation to produce many possible peptides. One striking difference between B- and T-cell recognition that has not yet been resolved by the structural data is the fact that T cells generally require a major histocompatibility determinant together with an antigen whereas, in most cases, antibodies recognize antigen alone. Recently, we and others have found that a series of TCR V beta gene sequences show conservation of many of the same residues that are conserved between heavy- and light-chain immunoglobulin V regions, and these V beta sequences are predicted to have an immunoglobulin-like secondary structure. To extend these studies, we have isolated and sequenced eight additional alpha-chain complementary cDNA clones and compared them with published sequences. Analyses of these sequences, reported here, indicate that V alpha regions have many of the characteristics of V beta gene segments but differ in that they almost always occur as cross-hybridizing gene families. We conclude that there may be very different selective pressures operating on V alpha and V beta sequences and that the V alpha repertoire may be considerably larger than that of V beta.

  View details for Web of Science ID A1985ARS3100051

  View details for PubMedID 2995827

• SEQUENCE RELATIONSHIPS BETWEEN PUTATIVE T-CELL RECEPTOR POLYPEPTIDES AND IMMUNOGLOBULINS NATURE HEDRICK, S. M., Nielsen, E. A., Kavaler, J., Cohen, D. I., DAVIS, M. M. 1984; 308 (5955): 153-158

  Abstract

  Comparison of the sequence of a cloned T cell-specific cDNA with those of cross-reacting cloned cDNAs isolated from a thymocyte library indicates the presence of variable, constant and joining regions remarkably similar in size and sequence to those encoding immunoglobulin proteins. Together with the evidence for somatic gene rearrangements reported in the accompanying paper, this strongly suggests that the TM86 cDNA clone encodes one chain of the T-cell receptor for antigen.

  View details for Web of Science ID A1984SG11900145

  View details for PubMedID 6546606

• GENOMIC ORGANIZATION AND SEQUENCE OF T-CELL RECEPTOR BETA-CHAIN CONSTANT-REGION AND JOINING-REGION GENES NATURE Gascoigne, N. R., Chien, Y. H., Becker, D. M., Kavaler, J., DAVIS, M. M. 1984; 310 (5976): 387-391

  Abstract

  The genomic structure of the joining (J) and constant (C) regions of the locus encoding the beta-chain of the murine T-cell receptor has been analysed. The gene segments are arranged tandemly (J-C/J-C) within a 15-kilobase region. The two constant-region genes are almost identical, differing by only four amino acids, all in carboxy-terminal portions. Each C region comprises four exons encoding an external globular domain, a small hinge-like region, a transmembrane region and a cytoplasmic tail plus 3'-untranslated region. The two clusters of J regions each contain 7 distinct elements, 12 of which may be functional.

  View details for Web of Science ID A1984TC54400034

  View details for PubMedID 6336329

• STRUCTURE, EXPRESSION AND DIVERGENCE OF T-CELL RECEPTOR BETA-CHAIN VARIABLE REGIONS NATURE Patten, P., Yokota, T., Rothbard, J., Chien, Y., Arai, K., DAVIS, M. M. 1984; 312 (5989): 40-46

  Abstract

  Analysis of three new T-cell receptor beta-chain variable regions together with those in the literature indicates that they have both remarkable similarities and differences with those of immunoglobulin. Less than 10 V regions appear to predominate in the thymus. V beta sequences are much more heterogeneous at the amino acid level than are immunoglobulin V regions and they appear to diverge between species much more quickly, apparently the result of additional hypervariable regions. Three of these putative new hypervariable regions lie outside of the classical immunoglobulin binding site, an indication that important interactions may be occurring in these regions with polymorphic MHC determinants.

  View details for Web of Science ID A1984TQ42600037

  View details for PubMedID 6092964

• LOCALIZATION OF A T-CELL RECEPTOR DIVERSITY-REGION ELEMENT NATURE Kavaler, J., DAVIS, M. M., Chien, Y. H. 1984; 310 (5976): 421-423

  Abstract

  Recently, complementary DNA clones encoding one chain of the T-cell receptor for antigen have been isolated from both murine and human cell lines. Sequence analysis of these clones indicates that they encode elements analogous to the variable (V), constant (C) and joining (J) regions of immunoglobins and that this corresponds to the beta-chain subunit of the T-cell receptor complex. These genes are rearranged in the genomes of specific T-cell lines and hybrids but not in other cell types. Analysis of the components of one such rearranged gene, 2B4, isolated from the pigeon cytochrome c-specific, H-2E-restricted T helper (TH) hybridoma, and its unrearranged (liver) counterpart, indicate that an 8-nucleotide sequence 3' to the rearranged variable region is not derived from either the germ-line V- or J-region gene segments. As this sequence lies at a similar position to the diversity (D) region in immunoglobulin heavy-chain genes, we postulated the existence of an array of germ-line D-region elements that would contribute significantly to the number of different beta-chain molecules which could be created. Here we describe the localization and sequence of one such D-region element, found approximately 650 nucleotides 5' to the first JT cluster. This element seems to be involved in both functional (V-D-J) and non-functional (D-J) rearrangements. Our observations, combined with previous results, indicate that variable-region formation (V-D-J joining) in the T-cell receptor beta-chain gene follows the 12/23-base pair (bp) rule of rearrangement established for the recombination of immunoglobulin gene segments, but that the organization of the heptamer and nonamer element found surrounding the D region is significantly different.

  View details for Web of Science ID A1984TC54400049

  View details for PubMedID 6611508

• A MURINE T-CELL RECEPTOR GENE-COMPLEX - ISOLATION, STRUCTURE AND REARRANGEMENT IMMUNOLOGICAL REVIEWS DAVIS, M. M., Chien, Y., Gascoigne, N. R., HEDRICK, S. M. 1984; 81: 235-258

  Abstract

  We describe here our efforts to develop a systematic strategy for the enumeration and isolation of genes encoding T cell-specific, membrane-associated polypeptides. Of particular importance among the cDNA clones that we have isolated is one which encodes the beta chain of the murine T cell receptor for antigen. The gene product is strikingly similar to immunoglobulin in its variable (V), constant (C), joining (J), and diversity (D) - like elements and the ability of the latter three types of element to assort independently during differentiation. The genomic organization of the constant region locus which encodes this molecule consists of two tandemly arrayed units of the form JC/JC, where the J clusters consist of fourteen distinct elements, many of which may be functional. The two constant regions differ by only four amino acids and both are apparently expressed in T cells of the same phenotype, so they probably do not represent isotypes in the classical sense. The sequences flanking the V, D and J elements are also similar to the conserved heptamer and nonomer sequences of immunoglobulins thought to be important in the recombination of the specific gene segments. These similarities indicate both the common evolutionary origins of these loci and the strong selective pressure that must be operative. The T cell receptor locus differs somewhat from immunoglobulins in the large number of possible J region elements and to some extent in the hypervariable-framework regions of the V region. We and others have mapped this gene to chromosome 6 of the mouse, in the same portion of the chromosome but not closely linked the kappa locus. The significance of the predicted protein structure of the beta chain and its support of the one-receptor model of MHC-antigen recognition are discussed.

  View details for Web of Science ID A1984TT81400012

  View details for PubMedID 6096259

• ISOLATION OF CDNA CLONES ENCODING T-CELL-SPECIFIC MEMBRANE-ASSOCIATED PROTEINS NATURE HEDRICK, S. M., Cohen, D. I., Nielsen, E. A., DAVIS, M. M. 1984; 308 (5955): 149-153

  Abstract

  Of 10 distinct cloned DNA copies of mRNAs expressed in T lymphocytes but not in B lymphocytes and associated with membrane-bound polysomes, one hybridizes to a region of the genome that has rearranged in a T-cell lymphoma and several T-cell hybridomas. These characteristics suggest that it encodes one chain of the elusive antigen receptor on the surface of T lymphocytes.

  View details for Web of Science ID A1984SG11900144

  View details for PubMedID 6199676

• IMMUNOGLOBULIN HEAVY-CHAIN GENE IS FORMED BY AT LEAST 2 RECOMBINATIONAL EVENTS NATURE DAVIS, M. M., Calame, K., EARLY, P. W., Livant, D. L., Joho, R., Weissman, I. L., Hood, L. 1980; 283 (5749): 733-739

  Abstract

  The events of B-cell differentiation can be reconstructed in part through an analysis of the organisation of heavy-chain gene segments in differentiated B cells. A mouse immunoglobulin alpha heavy-chain gene is composed of at least three noncontiguous germ-line DNA segments--a VH gene segment, a JH gene segment associated with the Cmu gene segment, and the C alpha gene segment. These gene segments are joined together by two distinct types of DNA rearrangements--a V-J joining and a CH switch.

  View details for Web of Science ID A1980JF60300036

  View details for PubMedID 6766532