Dr. Maecker received a BS in Microbiology from Purdue University and a PhD in Cancer Biology from Stanford University. He did postdoctoral work with Ronald and Shoshana Levy at Stanford, and was an Assistant Professor of Biology at Loyola University Chicago, as well as a Senior Scientist at BD Biosciences, San Jose, CA. He is currently a Professor of Microbiology and Immunology, and Director of the Human Immune Monitoring Center, at Stanford University.

Administrative Appointments

  • Director, Human Immune Monitoring Center (2009 - Present)
  • Member, Institute for Immunity, Transplantation, and Infection (2009 - Present)
  • Member, Immunology Interdisciplinary Degree Program (2012 - Present)
  • Director, Service Centers and Enabling Technologies, Stanford University School of Medicine (2014 - Present)
  • Member, Stanford Diabetes Research Center (2017 - Present)

Boards, Advisory Committees, Professional Organizations

  • Member, Scientific Advisory Board, Cytek (2017 - Present)
  • Member, SITC Biomarker Task Force (2014 - Present)
  • Member, Stanford Cancer Institute Scientific Review Committee (2011 - Present)
  • Co-chair, FOCIS Human Immunophenotyping Consortium (HIPC) (2009 - Present)

Professional Education

  • PhD, Stanford University, Cancer Biology (1988)
  • BS, Purdue University, Microbiology (1984)

Community and International Work

  • Human Immunophenotyping Consortium


    Standardization of human immune monitoring

    Partnering Organization(s)




    Ongoing Project


    Opportunities for Student Involvement



  • Vernon Maino, Holden Maecker, Douglas Petry. "United States Patent 2007/109161 Detection of HIV-infected cell subsets", Becton, Dickinson, and Company, Jan 1, 2007
  • Shoshana Levy, Rosemarie Dekruyff, Dale Umetsu, Holden Maecker. "United States Patent 2001/0044418 Treatment of allergies", Stanford University, Jan 1, 2001

Current Research and Scholarly Interests

A major theme in our group is to define metrics of immune competence in various settings, including cancer immunotherapy, organ transplantation, allergy, and chronic viral infection. We use CyTOF mass cytometry, often in combination with other technologies, to broadly survey immune features at the cellular level, then examine links between features or groups of features and clinical outcome. A long-term goal is to create an assay of global immune competence that could predict risk for various immune-related outcomes in both healthy individuals and in disease.

All Publications

  • Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality. The Journal of clinical investigation Gygi, J. P., Maguire, C., Patel, R. K., Shinde, P., Konstorum, A., Shannon, C. P., Xu, L., Hoch, A., Jayavelu, N. D., Haddad, E. K., Reed, E. F., Kraft, M., McComsey, G. A., Metcalf, J. P., Ozonoff, A., Esserman, D., Cairns, C. B., Rouphael, N., Bosinger, S. E., Kim-Schulze, S., Krammer, F., Rosen, L. B., van Bakel, H., Wilson, M., Eckalbar, W. L., Maecker, H. T., Langelier, C. R., Steen, H., Altman, M. C., Montgomery, R. R., Levy, O., Melamed, E., Pulendran, B., Diray-Arce, J., Smolen, K. K., Fragiadakis, G. K., Becker, P. M., Sekaly, R. P., Ehrlich, L. I., Fourati, S., Peters, B., Kleinstein, S. H., Guan, L. 2024; 134 (9)


    BACKGROUNDPatients hospitalized for COVID-19 exhibit diverse clinical outcomes, with outcomes for some individuals diverging over time even though their initial disease severity appears similar to that of other patients. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity.METHODSWe performed deep immunophenotyping and conducted longitudinal multiomics modeling, integrating 10 assays for 1,152 Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study participants and identifying several immune cascades that were significant drivers of differential clinical outcomes.RESULTSIncreasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, formation of neutrophil extracellular traps, and T cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma Igs and B cells and dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to failure of viral clearance in patients with fatal illness.CONCLUSIONOur longitudinal multiomics profiling study revealed temporal coordination across diverse omics that potentially explain the disease progression, providing insights that can inform the targeted development of therapies for patients hospitalized with COVID-19, especially those who are critically ill.TRIAL NCT04378777.FUNDINGNIH (5R01AI135803-03, 5U19AI118608-04, 5U19AI128910-04, 4U19AI090023-11, 4U19AI118610-06, R01AI145835-01A1S1, 5U19AI062629-17, 5U19AI057229-17, 5U19AI125357-05, 5U19AI128913-03, 3U19AI077439-13, 5U54AI142766-03, 5R01AI104870-07, 3U19AI089992-09, 3U19AI128913-03, and 5T32DA018926-18); NIAID, NIH (3U19AI1289130, U19AI128913-04S1, and R01AI122220); and National Science Foundation (DMS2310836).

    View details for DOI 10.1172/JCI176640

    View details for PubMedID 38690733

  • Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology. Science translational medicine Phan, H. V., Tsitsiklis, A., Maguire, C. P., Haddad, E. K., Becker, P. M., Kim-Schulze, S., Lee, B., Chen, J., Hoch, A., Pickering, H., van Zalm, P., Altman, M. C., Augustine, A. D., Calfee, C. S., Bosinger, S., Cairns, C. B., Eckalbar, W., Guan, L., Jayavelu, N. D., Kleinstein, S. H., Krammer, F., Maecker, H. T., Ozonoff, A., Peters, B., Rouphael, N., Montgomery, R. R., Reed, E., Schaenman, J., Steen, H., Levy, O., Diray-Arce, J., Langelier, C. R. 2024; 16 (743): eadj5154


    Age is a major risk factor for severe coronavirus disease 2019 (COVID-19), yet the mechanisms behind this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host immune response in the blood and the upper airway, as well as the nasal microbiome in a prospective, multicenter cohort of 1031 vaccine-naïve patients hospitalized for COVID-19 between 18 and 96 years old. We performed mass cytometry, serum protein profiling, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody assays, and blood and nasal transcriptomics. We found that older age correlated with increased SARS-CoV-2 viral abundance upon hospital admission, delayed viral clearance, and increased type I interferon gene expression in both the blood and upper airway. We also observed age-dependent up-regulation of innate immune signaling pathways and down-regulation of adaptive immune signaling pathways. Older adults had lower naïve T and B cell populations and higher monocyte populations. Over time, older adults demonstrated a sustained induction of pro-inflammatory genes and serum chemokines compared with younger individuals, suggesting an age-dependent impairment in inflammation resolution. Transcriptional and protein biomarkers of disease severity differed with age, with the oldest adults exhibiting greater expression of pro-inflammatory genes and proteins in severe disease. Together, our study finds that aging is associated with impaired viral clearance, dysregulated immune signaling, and persistent and potentially pathologic activation of pro-inflammatory genes and proteins.

    View details for DOI 10.1126/scitranslmed.adj5154

    View details for PubMedID 38630846

  • Longitudinal cytokine and multi-modal health data of an extremely severe ME/CFS patient with HSD reveals insights into immunopathology, and disease severity. Frontiers in immunology Jahanbani, F., Sing, J. C., Maynard, R. D., Jahanbani, S., Dafoe, J., Dafoe, W., Jones, N., Wallace, K. J., Rastan, A., Maecker, H. T., Röst, H. L., Snyder, M. P., Davis, R. W. 2024; 15: 1369295


    Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) presents substantial challenges in patient care due to its intricate multisystem nature, comorbidities, and global prevalence. The heterogeneity among patient populations, coupled with the absence of FDA-approved diagnostics and therapeutics, further complicates research into disease etiology and patient managment. Integrating longitudinal multi-omics data with clinical, health,textual, pharmaceutical, and nutraceutical data offers a promising avenue to address these complexities, aiding in the identification of underlying causes and providing insights into effective therapeutics and diagnostic strategies.This study focused on an exceptionally severe ME/CFS patient with hypermobility spectrum disorder (HSD) during a period of marginal symptom improvements. Longitudinal cytokine profiling was conducted alongside the collection of extensive multi-modal health data to explore the dynamic nature of symptoms, severity, triggers, and modifying factors. Additionally, an updated severity assessment platform and two applications, ME-CFSTrackerApp and LexiTime, were introduced to facilitate real-time symptom tracking and enhance patient-physician/researcher communication, and evaluate response to medical intervention.Longitudinal cytokine profiling revealed the significance of Th2-type cytokines and highlighted synergistic activities between mast cells and eosinophils, skewing Th1 toward Th2 immune responses in ME/CFS pathogenesis, particularly in cognitive impairment and sensorial intolerance. This suggests a potentially shared underlying mechanism with major ME/CFS comorbidities such as HSD, Mast cell activation syndrome, postural orthostatic tachycardia syndrome (POTS), and small fiber neuropathy. Additionally, the data identified potential roles of BCL6 and TP53 pathways in ME/CFS etiology and emphasized the importance of investigating adverse reactions to medication and supplements and drug interactions in ME/CFS severity and progression.Our study advocates for the integration of longitudinal multi-omics with multi-modal health data and artificial intelligence (AI) techniques to better understand ME/CFS and its major comorbidities. These findings highlight the significance of dysregulated Th2-type cytokines in patient stratification and precision medicine strategies. Additionally, our results suggest exploring the use of low-dose drugs with partial agonist activity as a potential avenue for ME/CFS treatment. This comprehensive approach emphasizes the importance of adopting a patient-centered care approach to improve ME/CFS healthcare management, disease severity assessment, and personalized medicine. Overall, these findings contribute to our understanding of ME/CFS and offer avenues for future research and clinical practice.

    View details for DOI 10.3389/fimmu.2024.1369295

    View details for PubMedID 38650940

    View details for PubMedCentralID PMC11033372

  • AS03 adjuvant enhances the magnitude, persistence, and clonal breadth of memory B cell responses to a plant-based COVID-19 vaccine in humans. Science immunology Grigoryan, L., Feng, Y., Bellusci, L., Lai, L., Wali, B., Ellis, M., Yuan, M., Arunachalam, P. S., Hu, M., Kowli, S., Gupta, S., Maysel-Auslender, S., Maecker, H. T., Samaha, H., Rouphael, N., Wilson, I. A., Moreno, A. C., Suthar, M. S., Khurana, S., Pillet, S., Charland, N., Ward, B. J., Pulendran, B. 2024; 9 (94): eadi8039


    Vaccine adjuvants increase the breadth of serum antibody responses, but whether this is due to the generation of antigen-specific B cell clones with distinct specificities or the maturation of memory B cell clones that produce broadly cross-reactive antibodies is unknown. Here, we longitudinally analyzed immune responses in healthy adults after two-dose vaccination with either a virus-like particle COVID-19 vaccine (CoVLP), CoVLP adjuvanted with AS03 (CoVLP+AS03), or a messenger RNA vaccination (mRNA-1273). CoVLP+AS03 enhanced the magnitude and durability of circulating antibodies and antigen-specific CD4+ T cell and memory B cell responses. Antigen-specific CD4+ T cells in the CoVLP+AS03 group at day 42 correlated with antigen-specific memory B cells at 6 months. CoVLP+AS03 induced memory B cell responses, which accumulated somatic hypermutations over 6 months, resulting in enhanced neutralization breadth of monoclonal antibodies. Furthermore, the fraction of broadly neutralizing antibodies encoded by memory B cells increased between day 42 and 6 months. These results indicate that AS03 enhances the antigenic breadth of B cell memory at the clonal level and induces progressive maturation of the B cell response.

    View details for DOI 10.1126/sciimmunol.adi8039

    View details for PubMedID 38579013

  • Comprehensive landscape of neutralizing antibody and cell-mediated response elicited by the 1/5 fractional dose of 17DD-YF primary vaccination in adults. Scientific reports Reis, L. R., Costa-Rocha, I. A., Abdala-Torres, T., Campi-Azevedo, A. C., Peruhype-Magalhaes, V., Araujo, M. S., Spezialli, E., do Valle Antonelli, L. R., da Silva-Pereira, R. A., Almeida, G. G., Fernandes, E. G., Fantinato, F. F., Domingues, C. M., Lemos, M. C., Chieppe, A., Lemos, J. A., Coelho-Dos-Reis, J. G., de Lima, S. M., de Souza Azevedo, A., Schwarcz, W. D., Camacho, L. A., de Lourdes de Sousa Maia, M., de Noronha, T. G., Duault, C., Rosenberg-Hasson, Y., Teixeira-Carvalho, A., Maecker, H. T., Martins-Filho, O. A., Collaborative Group for Studies of Yellow Fever Vaccine, Otta, D. A., Martins-Filho, O. A. 2024; 14 (1): 7709


    The present study aimed at evaluating the YF-specific neutralizing antibody profile besides a multiparametric analysis of phenotypic/functional features of cell-mediated response elicited by the 1/5 fractional dose of 17DD-YF vaccine, administered as a single subcutaneous injection. The immunological parameters of each volunteer was monitored at two time points, referred as: before (Day 0) [Non-Vaccinated, NV(D0)] and after vaccination (Day 30-45) [Primary Vaccinees, PV(D30-45)]. Data demonstrated high levels of neutralizing antibodies for PV(D30-45) leading to a seropositivity rate of 93%. A broad increase of systemic soluble mediators with a mixed profile was also observed for PV(D30-45), with IFN-gamma and TNF-alpha presenting the highest baseline fold changes. Integrative network mapping of soluble mediators showed increased correlation numbers in PV(D30-45) as compared to NV(D0) (532vs398). Moreover, PV(D30-45) exhibited increased levels of Terminal Effector (CD45RA+CCR7-) CD4+ and CD8+ T-cells and Non-Classical memory B-cells (IgD+CD27+). Dimensionality reduction of Mass Cytometry data further support these findings. A polyfunctional cytokine profile (TNF-alpha/IFN-gamma/IL-10/IL-17/IL-2) of T and B-cells was observed upon in vitro antigen recall. Mapping and kinetics timeline of soluble mediator signatures for PV(D30-45) further confirmed the polyfunctional profile upon long-term in vitro culture, mediated by increased levels of IFN-gamma and TNF-alpha along with decreased production of IL-10. These findings suggest novel insights of correlates of protection elicited by the 1/5 fractional dose of 17DD-YF vaccine.

    View details for DOI 10.1038/s41598-024-57645-3

    View details for PubMedID 38565882

  • CyTOF Intracellular Cytokine Assays for Antigen-Specific T Cells. Methods in molecular biology (Clifton, N.J.) Lin, D., Maecker, H. T. 2024; 2779: 395-405


    T cells specific for a single antigen tend to be rare, even after expansion of memory cells. They are commonly detected by in vitro stimulation with peptides or protein, followed by staining for intracellular cytokines. In this protocol, CyTOF® mass cytometry is used to collect single-cell data on a large number of cytokines/chemokines, as well as cell-surface proteins that characterize T cells and other immune cells. A method for magnetic bead enrichment of antigen-stimulated T cells, based on their expression of CD154 and CD69, is also included. Coupling magnetic enrichment with highly multiparameter mass cytometry, this method enables the ability to dissect the frequency, phenotype, and function of antigen-specific T cells in greater detail than previously possible. Rare cell subsets can be examined, while minimizing run times on the CyTOF.

    View details for DOI 10.1007/978-1-0716-3738-8_18

    View details for PubMedID 38526796

    View details for PubMedCentralID 3752833

  • SITC Clinical Immuno-Oncology Network (SCION) commentary on measurement and interpretation of essential biomarkers in early clinical trials. Journal for immunotherapy of cancer Sitc, S., Lotze, M. T., Cottrell, T., Bifulco, C., Chow, L., Cope, L., Gnjatic, S., Maecker, H. T., Yeong Poh Shen, J. 2024; 12 (3)

    View details for DOI 10.1136/jitc-2023-008655

    View details for PubMedID 38519056

  • Impaired innate and adaptive immune responses to BNT162b2 SARS-CoV-2 vaccination in systemic lupus erythematosus. JCI insight Sarin, K. Y., Zheng, H., Chaichian, Y., Arunachalam, P. S., Swaminathan, G., Eschholz, A., Gao, F., Wirz, O. F., Lam, B., Yang, E., Lee, L. W., Feng, A., Lewis, M. A., Lin, J., Maecker, H. T., Boyd, S. D., Davis, M. M., Nadeau, K. C., Pulendran, B., Khatri, P., Utz, P. J., Zaba, L. C. 2024; 9 (5)


    Understanding the immune responses to SARS-CoV-2 vaccination is critical to optimizing vaccination strategies for individuals with autoimmune diseases, such as systemic lupus erythematosus (SLE). Here, we comprehensively analyzed innate and adaptive immune responses in 19 patients with SLE receiving a complete 2-dose Pfizer-BioNTech mRNA vaccine (BNT162b2) regimen compared with a control cohort of 56 healthy control (HC) volunteers. Patients with SLE exhibited impaired neutralizing antibody production and antigen-specific CD4+ and CD8+ T cell responses relative to HC. Interestingly, antibody responses were only altered in patients with SLE treated with immunosuppressive therapies, whereas impairment of antigen-specific CD4+ and CD8+ T cell numbers was independent of medication. Patients with SLE also displayed reduced levels of circulating CXC motif chemokine ligands, CXCL9, CXCL10, CXCL11, and IFN-γ after secondary vaccination as well as downregulation of gene expression pathways indicative of compromised innate immune responses. Single-cell RNA-Seq analysis reveals that patients with SLE showed reduced levels of a vaccine-inducible monocyte population characterized by overexpression of IFN-response transcription factors. Thus, although 2 doses of BNT162b2 induced relatively robust immune responses in patients with SLE, our data demonstrate impairment of both innate and adaptive immune responses relative to HC, highlighting a need for population-specific vaccination studies.

    View details for DOI 10.1172/jci.insight.176556

    View details for PubMedID 38456511

  • SITC clinical Immuno-Oncology network (SCION) commentary on measurement and interpretation of essential biomarkers in early clinical trials JOURNAL FOR IMMUNOTHERAPY OF CANCER Lotze, M. T., Cottrell, T., Bifulco, C., Chow, L., Cope, L., Gnjatic, S., Maecker, H. T., Shen, J. 2024; 12 (3)
  • Cross-Platform Comparison of Highly Sensitive Immunoassays for Inflammatory Markers in a COVID-19 Cohort. Journal of immunology (Baltimore, Md. : 1950) Abe, K., Beer, J. C., Nguyen, T., Ariyapala, I. S., Holmes, T. H., Feng, W., Zhang, B., Kuo, D., Luo, Y., Ma, X. J., Maecker, H. T. 2024


    A variety of commercial platforms are available for the simultaneous detection of multiple cytokines and associated proteins, often employing Ab pairs to capture and detect target proteins. In this study, we comprehensively evaluated the performance of three distinct platforms: the fluorescent bead-based Luminex assay, the proximity extension-based Olink assay, and a novel proximity ligation assay platform known as Alamar NULISAseq. These assessments were conducted on human serum samples from the National Institutes of Health IMPACC study, with a focus on three essential performance metrics: detectability, correlation, and differential expression. Our results reveal several key findings. First, the Alamar platform demonstrated the highest overall detectability, followed by Olink and then Luminex. Second, the correlation of protein measurements between the Alamar and Olink platforms tended to be stronger than the correlation of either of these platforms with Luminex. Third, we observed that detectability differences across the platforms often translated to differences in differential expression findings, although high detectability did not guarantee the ability to identify meaningful biological differences. Our study provides valuable insights into the comparative performance of these assays, enhancing our understanding of their strengths and limitations when assessing complex biological samples, as exemplified by the sera from this COVID-19 cohort.

    View details for DOI 10.4049/jimmunol.2300729

    View details for PubMedID 38334457

  • Immune Assessment Today: Optimizing and Standardizing Efforts to Monitor Immune Responses in Cancer and Beyond. Cancers Pandey, S., Cholak, M. E., Yadali, R., Sosman, J. A., Tetreault, M., Fang, D., Pollack, S. M., Gnjatic, S., Obeng, R. C., Lyerly, H. K., Sonabend, A. M., Guevara-Patino, J. A., Butterfield, L. H., Zhang, B., Maecker, H. T., Le Poole, I. C. 2024; 16 (3)


    As part of a symposium, current and former directors of Immune Monitoring cores and investigative oncologists presented insights into the past, present and future of immune assessment. Dr. Gnjatic presented a classification of immune monitoring technologies ranging from universally applicable to experimental protocols, while emphasizing the need for assay harmonization. Dr. Obeng discussed physiologic differences among CD8 T cells that align with anti-tumor responses. Dr. Lyerly presented the Soldano Ferrone lecture, commemorating the passionate tumor immunologist who inspired many, and covered a timeline of monitoring technology development and its importance to immuno-oncology. Dr. Sonabend presented recent achievements in glioblastoma treatment, accentuating the range of monitoring techniques that allowed him to refine patient selection for clinical trials. Dr. Guevara-Patino focused on hypoxia within the tumor environment and stressed that T cell viability is not to be confused with functionality. Dr. Butterfield accentuated monitoring of dendritic cell metabolic (dys)function as a determinant for tumor vaccine success. Lectures were interspersed with select abstract presentations. To summarize the concepts, Dr. Maecker from Stanford led an informative forum discussion, pointing towards the future of immune monitoring. Immune monitoring continues to be a guiding light towards effective immunotherapeutic strategies.

    View details for DOI 10.3390/cancers16030475

    View details for PubMedID 38339227

  • IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. Nature communications Haslund-Gourley, B. S., Woloszczuk, K., Hou, J., Connors, J., Cusimano, G., Bell, M., Taramangalam, B., Fourati, S., Mege, N., Bernui, M., Altman, M. C., Krammer, F., van Bakel, H., IMPACC Network, Maecker, H. T., Rouphael, N., Diray-Arce, J., Wigdahl, B., Kutzler, M. A., Cairns, C. B., Haddad, E. K., Comunale, M. A., Ozonoff, A., Ehrlich, L. I., Melamed, E., Sesma, A. F., Simon, V., Pulendran, B., Nadeau, K. C., Davis, M. M., McCoey, G. A., Sekaly, R., Baden, L. R., Levy, O., Schaenman, J., Reed, E. F., Shaw, A. C., Hafler, D. A., Montgomery, R. R., Kleinstein, S. H., Becker, P. M., Augustine, A. D., Calfee, C. S., Erle, D. J., DeBakey, M. E., Corry, D. B., Kheradmand, F., Atkinson, M. A., Brakenridge, S. C., Higuita, N. I., Metcalf, J. P., Hough, C. L., Messer, W. B., Kraft, M., Bime, C., Peters, B., Milliren, C. E., Syphurs, C., McEnaney, K., Barton, B., Lentucci, C., Saluvan, M., Chang, A. C., Hoch, A., Albert, M., Shaheen, T., Kho, A. T., Liu, S., Thomas, S., Chen, J., Murphy, M. D., Cooney, M., Hayati, A. N., Bryant, R., Abraham, J., Jayavelu, N. D., Presnell, S., Jancsyk, T., Maguire, C., Qi, J., Lee, B., Fourati, S., Esserman, D. A., Guan, L., Gygi, J., Pawar, S., Brito, A., Fragiadakis, G. K., Patel, R., Overton, J. A., Vita, R., Westendorf, K., Shannon, C. P., Tebbutt, S. J., Thyagarajan, R. V., Rousseau, J. F., Wylie, D., Triplett, T. A., Kojic, E., Chinthrajah, S., Ahuja, N., Rogers, A. J., Artandi, M., Geng, L., Yendewa, G., Powell, D. L., Kim, J. N., Simmons, B., Goonewardene, I. M., Smith, C. M., Martens, M., Sherman, A. C., Walsh, S. R., Issa, N. C., Salehi-Rad, R., Dela Cruz, C., Farhadian, S., Iwasaki, A., Ko, A. I., Anderson, E. J., Mehta, A. K., Sevransky, J. E., Seyfert-Margolis, V., Leligdowicz, A., Matthay, M. A., Singer, J. P., Kangelaris, K. N., Hendrickson, C. M., Krummel, M. F., Langelier, C. R., Woodruff, P. G., Corry, D. B., Kheradmand, F., Anderson, M. L., Guirgis, F. W., Drevets, D. A., Brown, B. R., Siegel, S. A., Lu, Z., Mosier, J., Kimura, H., Khor, B., van Bakel, H., Rahman, A., Stadlbauer, D., Dutta, J., Xie, H., Kim-Schulze, S., Gonzalez-Reiche, A. S., van de Guchte, A., Carreno, J. M., Singh, G., Raskin, A., Tcheou, J., Bielak, D., Kawabata, H., Kelly, G., Patel, M., Nie, K., Yellin, T., Fried, M., Sullivan, L., Morris, S., Sieg, S., Steen, H., van Zalm, P., Fatou, B., Mendez, K., Lasky-Su, J., Hutton, S. R., Michelotti, G., Wong, K., Jha, M., Viode, A., Kanarek, N., Petrova, B., Zhao, Y., Bosinger, S. E., Boddapati, A. K., Tharp, G. K., Pellegrini, K. L., Beagle, E., Cowan, D., Hamilton, S., Ribeiro, S. P., Hodder, T., Rosen, L. B., Lee, S., Wilson, M. R., Dandekar, R., Alvarenga, B., Rajan, J., Eckalbar, W., Schroeder, A. W., Tsitsiklis, A., Mick, E., Guerrero, Y. S., Love, C., Maliskova, L., Adkisson, M., Siles, N., Geltman, J., Hurley, K., Saksena, M., Altman, D., Srivastava, K., Eaker, L. Q., Bermudez-Gonzalez, M. C., Beach, K. F., Sominsky, L. A., Azad, A. R., Mulder, L. C., Kleiner, G., Lee, A. S., Do, E., Fernandes, A., Manohar, M., Hagan, T., Blish, C. A., Din, H. N., Roque, J., Yang, S., Sigal, N., Chang, I., Tribout, H., Harris, P., Consolo, M., Edwards, C., Lee, E., Lin, E., Croen, B., Semenza, N. C., Rogowski, B., Melnyk, N., Bell, M. R., Furukawa, S., McLin, R., Schearer, P., Sheidy, J., Tegos, G. P., Nagle, C., Smolen, K., Desjardins, M., van Haren, S., Mitre, X., Cauley, J., Li, X., Tong, A., Evans, B., Montesano, C., Licona, J. H., Krauss, J., Chang, J. B., Izaguirre, N., Rooks, R., Elashoff, D., Brook, J., Ramires-Sanchez, E., Llamas, M., Rivera, A., Perdomo, C., Ward, D. C., Magyar, C. E., Fulcher, J. A., Pickering, H. C., Sen, S., Chaudhary, O., Coppi, A., Fournier, J., Mohanty, S., Muenker, C., Nelson, A., Raddassi, K., Rainone, M., Ruff, W. E., Salahuddin, S., Schulz, W. L., Vijayakumar, P., Wang, H., Wunder, E. J., Young, H. P., Rothman, J., Konstorum, A., Chen, E., Cotsapas, C., Grubaugh, N. D., Wang, X., Xu, L., Asashima, H., Bristow, L., Hussaini, L., Hellmeister, K., Samaha, H., Wimalasena, S. T., Cheng, A., Spainhour, C., Scherer, E. M., Johnson, B., Bechnak, A., Ciric, C. R., Hewitt, L., Carter, E., Mcnair, N., Panganiban, B., Huerta, C., Usher, J., Vaysman, T., Holland, S. M., Abe-Jones, Y., Asthana, S., Beagle, A., Bhide, S., Carrillo, S. A., Chak, S., Ghale, R., Gonzalez, A., Jauregui, A., Jones, N., Lea, T., Lee, D., Lota, R., Milush, J., Nguyen, V., Pierce, L., Prasad, P. A., Rao, A., Samad, B., Shaw, C., Sigman, A., Sinha, P., Ward, A., Willmore, A., Zhan, J., Rashid, S., Rodriguez, N., Tang, K., Altamirano, L. T., Betancourt, L., Curiel, C., Sutter, N., Paz, M. T., Tietje-Ulrich, G., Leroux, C., Thakur, N., Vasquez, J. J., Santhosh, L., Song, L., Nelson, E., Moldawer, L. L., Borresen, B., Roth-Manning, B., Ungaro, R. F., Oberhaus, J., Booth, J. L., Sinko, L. A., Brunton, A., Sullivan, P. E., Strnad, M., Lyski, Z. L., Coulter, F. J., Micheleti, C., Conway, M., Francisco, D., Molzahn, A., Erickson, H., Wilson, C. C., Schunk, R., Sierra, B., Hughes, T. 2024; 15 (1): 404


    The glycosylation of IgG plays a critical role during human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, activating immune cells and inducing cytokine production. However, the role of IgM N-glycosylation has not been studied during human acute viral infection. The analysis of IgM N-glycosylation from healthy controls and hospitalized coronavirus disease 2019 (COVID-19) patients reveals increased high-mannose and sialylation that correlates with COVID-19 severity. These trends are confirmed within SARS-CoV-2-specific immunoglobulin N-glycan profiles. Moreover, the degree of total IgM mannosylation and sialylation correlate significantly with markers of disease severity. We link the changes of IgM N-glycosylation with the expression of Golgi glycosyltransferases. Lastly, we observe antigen-specific IgM antibody-dependent complement deposition is elevated in severe COVID-19 patients and modulated by exoglycosidase digestion. Taken together, this work links the IgM N-glycosylation with COVID-19 severity and highlights the need to understand IgM glycosylation and downstream immune function during human disease.

    View details for DOI 10.1038/s41467-023-44211-0

    View details for PubMedID 38195739

  • Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. Nature communications Ozonoff, A., Jayavelu, N. D., Liu, S., Melamed, E., Milliren, C. E., Qi, J., Geng, L. N., McComsey, G. A., Cairns, C. B., Baden, L. R., Schaenman, J., Shaw, A. C., Samaha, H., Seyfert-Margolis, V., Krammer, F., Rosen, L. B., Steen, H., Syphurs, C., Dandekar, R., Shannon, C. P., Sekaly, R. P., Ehrlich, L. I., Corry, D. B., Kheradmand, F., Atkinson, M. A., Brakenridge, S. C., Higuita, N. I., Metcalf, J. P., Hough, C. L., Messer, W. B., Pulendran, B., Nadeau, K. C., Davis, M. M., Sesma, A. F., Simon, V., van Bakel, H., Kim-Schulze, S., Hafler, D. A., Levy, O., Kraft, M., Bime, C., Haddad, E. K., Calfee, C. S., Erle, D. J., Langelier, C. R., Eckalbar, W., Bosinger, S. E., Peters, B., Kleinstein, S. H., Reed, E. F., Augustine, A. D., Diray-Arce, J., Maecker, H. T., Altman, M. C., Montgomery, R. R., Becker, P. M., Rouphael, N. 2024; 15 (1): 216


    Post-acute sequelae of SARS-CoV-2 (PASC) is a significant public health concern. We describe Patient Reported Outcomes (PROs) on 590 participants prospectively assessed from hospital admission for COVID-19 through one year after discharge. Modeling identified 4 PRO clusters based on reported deficits (minimal, physical, mental/cognitive, and multidomain), supporting heterogenous clinical presentations in PASC, with sub-phenotypes associated with female sex and distinctive comorbidities. During the acute phase of disease, a higher respiratory SARS-CoV-2 viral burden and lower Receptor Binding Domain and Spike antibody titers were associated with both the physical predominant and the multidomain deficit clusters. A lower frequency of circulating B lymphocytes by mass cytometry (CyTOF) was observed in the multidomain deficit cluster. Circulating fibroblast growth factor 21 (FGF21) was significantly elevated in the mental/cognitive predominant and the multidomain clusters. Future efforts to link PASC to acute anti-viral host responses may help to better target treatment and prevention of PASC.

    View details for DOI 10.1038/s41467-023-44090-5

    View details for PubMedID 38172101

    View details for PubMedCentralID PMC10764789

  • GIMAP5 deficiency reveals a mammalian ceramide-driven longevity assurance pathway. Nature immunology Park, A. Y., Leney-Greene, M., Lynberg, M., Gabrielski, J. Q., Xu, X., Schwarz, B., Zheng, L., Balasubramaniyam, A., Ham, H., Chao, B., Zhang, Y., Matthews, H. F., Cui, J., Yao, Y., Kubo, S., Chanchu, J. M., Morawski, A. R., Cook, S. A., Jiang, P., Ravell, J. C., Cheng, Y. H., George, A., Faruqi, A., Pagalilauan, A. M., Bergerson, J. R., Ganesan, S., Chauvin, S. D., Aluri, J., Edwards-Hicks, J., Bohrnsen, E., Tippett, C., Omar, H., Xu, L., Butcher, G. W., Pascall, J., Karakoc-Aydiner, E., Kiykim, A., Maecker, H., Tezcan, İ., Esenboga, S., Heredia, R. J., Akata, D., Tekin, S., Kara, A., Kuloglu, Z., Unal, E., Kendirli, T., Dogu, F., Karabiber, E., Atkinson, T. P., Cochet, C., Filhol, O., Bosio, C. M., Davis, M. M., Lifton, R. P., Pearce, E. L., Daumke, O., Aytekin, C., Şahin, G. E., Aksu, A. Ü., Uzel, G., Koneti Rao, V., Sari, S., Boztug, K., Cagdas, D., Haskologlu, S., Ikinciogullari, A., Schwefel, D., Vilarinho, S., Baris, S., Ozen, A., Su, H. C., Lenardo, M. J. 2024


    Preserving cells in a functional, non-senescent state is a major goal for extending human healthspans. Model organisms reveal that longevity and senescence are genetically controlled, but how genes control longevity in different mammalian tissues is unknown. Here, we report a new human genetic disease that causes cell senescence, liver and immune dysfunction, and early mortality that results from deficiency of GIMAP5, an evolutionarily conserved GTPase selectively expressed in lymphocytes and endothelial cells. We show that GIMAP5 restricts the pathological accumulation of long-chain ceramides (CERs), thereby regulating longevity. GIMAP5 controls CER abundance by interacting with protein kinase CK2 (CK2), attenuating its ability to activate CER synthases. Inhibition of CK2 and CER synthase rescues GIMAP5-deficient T cells by preventing CER overaccumulation and cell deterioration. Thus, GIMAP5 controls longevity assurance pathways crucial for immune function and healthspan in mammals.

    View details for DOI 10.1038/s41590-023-01691-y

    View details for PubMedID 38172257

    View details for PubMedCentralID 3204836

  • Multiparameter Flow Cytometry Monitoring of T Cell Responses. Methods in molecular biology (Clifton, N.J.) Maecker, H. T. 2024; 2807: 325-342


    Multiparameter flow cytometry is a common tool for assessing responses of T, B, and other cells to pathogens or vaccines. Such responses are likely to be important for predicting the efficacy of an HIV vaccine, despite the elusive findings in HIV vaccine trials to date. Fortunately, flow cytometry has evolved to be capable of readily measuring 30-40 parameters, providing the ability to dissect detailed phenotypes and functions that may be correlated with disease protection. Nevertheless, technical hurdles remain, and standardization of assays is still largely lacking. Here an optimized protocol for antigen-specific T cell monitoring is presented, with specific variations for particular markers. It covers the analysis of multiple cytokines, cell surface proteins, and other functional markers such as CD107, CD154, CD137, etc. References are given to published panels of 8-28 colors.

    View details for DOI 10.1007/978-1-0716-3862-0_22

    View details for PubMedID 38743238

  • Immune determinants of CAR-T cell expansion in solid tumor patients receiving GD2 CAR-T cell therapy. Cancer cell Kaczanowska, S., Murty, T., Alimadadi, A., Contreras, C. F., Duault, C., Subrahmanyam, P. B., Reynolds, W., Gutierrez, N. A., Baskar, R., Wu, C. J., Michor, F., Altreuter, J., Liu, Y., Jhaveri, A., Duong, V., Anbunathan, H., Ong, C., Zhang, H., Moravec, R., Yu, J., Biswas, R., Van Nostrand, S., Lindsay, J., Pichavant, M., Sotillo, E., Bernstein, D., Carbonell, A., Derdak, J., Klicka-Skeels, J., Segal, J. E., Dombi, E., Harmon, S. A., Turkbey, B., Sahaf, B., Bendall, S., Maecker, H., Highfill, S. L., Stroncek, D., Glod, J., Merchant, M., Hedrick, C. C., Mackall, C. L., Ramakrishna, S., Kaplan, R. N. 2023


    Chimeric antigen receptor T cells (CAR-Ts) have remarkable efficacy in liquid tumors, but limited responses in solid tumors. We conducted a Phase I trial (NCT02107963) of GD2 CAR-Ts (GD2-CAR.OX40.28.z.iC9), demonstrating feasibility and safety of administration in children and young adults with osteosarcoma and neuroblastoma. Since CAR-T efficacy requires adequate CAR-T expansion, patients were grouped into good or poor expanders across dose levels. Patient samples were evaluated by multi-dimensional proteomic, transcriptomic, and epigenetic analyses. T cell assessments identified naive T cells in pre-treatment apheresis associated with good expansion, and exhausted T cells in CAR-T products with poor expansion. Myeloid cell assessment identified CXCR3+ monocytes in pre-treatment apheresis associated with good expansion. Longitudinal analysis of post-treatment samples identified increased CXCR3- classical monocytes in all groups as CAR-T numbers waned. Together, our data uncover mediators of CAR-T biology and correlates of expansion that could be utilized to advance immunotherapies for solid tumor patients.

    View details for DOI 10.1016/j.ccell.2023.11.011

    View details for PubMedID 38134936

  • Relationship of Heterologous Virus Responses and Outcomes in Hospitalized COVID-19 Patients. Journal of immunology (Baltimore, Md. : 1950) Rosenberg-Hasson, Y., Holmes, T. H., Diray-Arce, J., Chen, J., Kellogg, R., Snyder, M., Becker, P. M., Ozonoff, A., Rouphael, N., Reed, E. F., Maecker, H. T. 2023; 211 (8): 1224-1231


    The clinical trajectory of COVID-19 may be influenced by previous responses to heterologous viruses. We examined the relationship of Abs against different viruses to clinical trajectory groups from the National Institutes of Health IMPACC (Immunophenotyping Assessment in a COVID-19 Cohort) study of hospitalized COVID-19 patients. Whereas initial Ab titers to SARS-CoV-2 tended to be higher with increasing severity (excluding fatal disease), those to seasonal coronaviruses trended in the opposite direction. Initial Ab titers to influenza and parainfluenza viruses also tended to be lower with increasing severity. However, no significant relationship was observed for Abs to other viruses, including measles, CMV, EBV, and respiratory syncytial virus. We hypothesize that some individuals may produce lower or less durable Ab responses to respiratory viruses generally (reflected in lower baseline titers in our study), and that this may carry over into poorer outcomes for COVID-19 (despite high initial SARS-CoV-2 titers). We further looked at longitudinal changes in Ab responses to heterologous viruses, but found little change during the course of acute COVID-19 infection. We saw significant trends with age for Ab levels to many of these viruses, but no difference in longitudinal SARS-CoV-2 titers for those with high versus low seasonal coronavirus titers. We detected no difference in longitudinal SARS-CoV-2 titers for CMV seropositive versus seronegative patients, although there was an overrepresentation of CMV seropositives among the IMPACC cohort, compared with expected frequencies in the United States population. Our results both reinforce findings from other studies and suggest (to our knowledge) new relationships between the response to SARS-CoV-2 and Abs to heterologous viruses.

    View details for DOI 10.4049/jimmunol.2300391

    View details for PubMedID 37756530

    View details for PubMedCentralID PMC10539027

  • Air pollution and pregnancy. Seminars in perinatology Aguilera, J., Konvinse, K., Lee, A., Maecker, H., Prunicki, M., Mahalingaiah, S., Sampath, V., Utz, P. J., Yang, E., Nadeau, K. C. 2023: 151838


    Increased fossil fuel usage and extreme climate change events have led to global increases in greenhouse gases and particulate matter with 99% of the world's population now breathing polluted air that exceeds the World Health Organization's recommended limits. Pregnant women and neonates with exposure to high levels of air pollutants are at increased risk of adverse health outcomes such as maternal hypertensive disorders, postpartum depression, placental abruption, low birth weight, preterm birth, infant mortality, and adverse lung and respiratory effects. While the exact mechanism by which air pollution exerts adverse health effects is unknown, oxidative stress as well as epigenetic and immune mechanisms are thought to play roles. Comprehensive, global efforts are urgently required to tackle the health challenges posed by air pollution through policies and action for reducing air pollution as well as finding ways to protect the health of vulnerable populations in the face of increasing air pollution.

    View details for DOI 10.1016/j.semperi.2023.151838

    View details for PubMedID 37858459

  • Multi-omics analysis of mucosal and systemic immunity to SARS-CoV-2 after birth. Cell Wimmers, F., Burrell, A. R., Feng, Y., Zheng, H., Arunachalam, P. S., Hu, M., Spranger, S., Nyhoff, L. E., Joshi, D., Trisal, M., Awasthi, M., Bellusci, L., Ashraf, U., Kowli, S., Konvinse, K. C., Yang, E., Blanco, M., Pellegrini, K., Tharp, G., Hagan, T., Chinthrajah, R. S., Nguyen, T. T., Grifoni, A., Sette, A., Nadeau, K. C., Haslam, D. B., Bosinger, S. E., Wrammert, J., Maecker, H. T., Utz, P. J., Wang, T. T., Khurana, S., Khatri, P., Staat, M. A., Pulendran, B. 2023


    The dynamics of immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in infants and young children by analyzing blood samples and weekly nasal swabs collected before, during, and after infection with Omicron and non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, showed no sign of decay for up to 300 days. Infants mounted a robust mucosal immune response characterized by inflammatory cytokines, interferon (IFN) α, and T helper (Th) 17 and neutrophil markers (interleukin [IL]-17, IL-8, and CXCL1). The immune response in blood was characterized by upregulation of activation markers on innate cells, no inflammatory cytokines, but several chemokines and IFNα. The latter correlated with viral load and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single-cell multi-omics. Together, these data provide a snapshot of immunity to infection during the initial weeks and months of life.

    View details for DOI 10.1016/j.cell.2023.08.044

    View details for PubMedID 37776858

  • Acute Respiratory Illness Is Associated with Memory T Cell Differentiation and Other Immune Cell Changes in an Age-Associated Manner. ImmunoHorizons Ugale, S. S., Holmes, T. H., Maysel-Auslender, S., Boyd, S. D., Dekker, C. L., Davis, M. M., Maecker, H. T. 2023; 7 (9): 611-618


    Respiratory viruses such as influenza are encountered multiple times through infection and/or vaccination and thus have the potential to shape immune cell phenotypes over time. In particular, memory T cell compartments may be affected, as both CD4+ and CD8+ T cell responses likely contribute to viral control. In this study, we assessed immune phenotypes using cytometry by time of flight in the peripheral blood of 22 humans with acute respiratory illness and 22 age-matched noninfected controls. In younger infected individuals (1-19 y of age), we found decreased B and NK cell frequencies and a shift toward more effector-like CD4+ and CD8+ T cell phenotypes, compared with young healthy controls. Significant differences between noninfected and infected older individuals (30-74 y of age) were not seen. We also observed a decrease in naive CD4+ T cells and CD27+CD8+ T cells as well as an increase in effector memory CD8+ T cells and NKT cells in noninfected individuals with age. When cell frequencies were regressed against age for infected versus noninfected subjects, significant differences in trends with age were observed for multiple cell types. These included B cells and various subsets of CD4+ and CD8+ T cells. We conclude that acute respiratory illness drives T cell differentiation and decreases circulating B cell frequencies preferentially in young compared with older individuals.

    View details for DOI 10.4049/immunohorizons.2300050

    View details for PubMedID 37707792

  • Ancestry-based differences in the immune phenotype are associated with lupus activity. JCI insight Slight-Webb, S., Thomas, K., Smith, M., Wagner, C. A., Macwana, S., Bylinska, A., Donato, M., Dvorak, M., Chang, S. E., Kuo, A., Cheung, P., Kalesinskas, L., Ganesan, A., Dermadi, D., Guthridge, C. J., DeJager, W., Wright, C., Foecke, M. H., Merrill, J. T., Chakravarty, E., Arriens, C., Maecker, H. T., Khatri, P., Utz, P. J., James, J. A., Guthridge, J. M. 2023; 8 (16)


    Systemic lupus erythematosus (SLE) affects 1 in 537 Black women, which is >2-fold more than White women. Black patients develop the disease at a younger age, have more severe symptoms, and have a greater chance of early mortality. We used a multiomics approach to uncover ancestry-associated immune alterations in patients with SLE and healthy controls that may contribute biologically to disease disparities. Cell composition, signaling, epigenetics, and proteomics were evaluated by mass cytometry; droplet-based single-cell transcriptomics and proteomics; and bead-based multiplex soluble mediator levels in plasma. We observed altered whole blood frequencies and enhanced activity in CD8+ T cells, B cells, monocytes, and DCs in Black patients with more active disease. Epigenetic modifications in CD8+ T cells (H3K27ac) could distinguish disease activity level in Black patients and differentiate Black from White patient samples. TLR3/4/7/8/9-related gene expression was elevated in immune cells from Black patients with SLE, and TLR7/8/9 and IFN-α phospho-signaling and cytokine responses were heightened even in immune cells from healthy Black control patients compared with White individuals. TLR stimulation of healthy immune cells recapitulated the ancestry-associated SLE immunophenotypes. This multiomic resource defines ancestry-associated immune phenotypes that differ between Black and White patients with SLE, which may influence the course and severity of SLE and other diseases.

    View details for DOI 10.1172/jci.insight.169584

    View details for PubMedID 37606045

  • Lower levels of Th1 and Th2 cytokines in cerebrospinal fluid (CSF) at the time of initial CSF shunt placement in children are associated with subsequent shunt revision surgeries. Cytokine Simon, T. D., Sedano, S., Rosenberg-Hasson, Y., Durazo-Arvizu, R., Whitlock, K. B., Hodor, P., Hauptman, J. S., Limbrick, D. D., McDonald, P., Ojemann, J. G., Maecker, H. T., Cerebrospinal FLuId MicroBiota in Shunts CLIMB Study Group 2023; 169: 156310


    OBJECTIVE: We compare cytokine profiles at the time of initial CSF shunt placement between children who required no subsequent shunt revision surgeries and children requiring repeated CSF shunt revision surgeries for CSF shunt failure. We also describe the cytokine profiles across surgical episodes for children who undergo multiple subsequent revision surgeries.METHODS: This pilot study was nested within an ongoing prospective multicenter study collecting CSF samples and clinical data at the time of CSF shunt surgeries since August 2014. We selected cases where CSF was available for children who underwent an initial CSF shunt placement and had no subsequent shunt revision surgeries during >=24months of follow-up (n=7); as well as children who underwent an initial CSF shunt placement and then required repeated CSF shunt revision surgeries (n=3). Levels of 92 human cytokines were measured using the Olink immunoassay and 41 human cytokines were measured using Luminex based bead array on CSF obtained at the time of each child's initial CSF shunt placement and were displayed in heat maps.RESULTS: Qualitatively similar profiles for the majority of cytokines were observed among the patients in each group in both Olink and Luminex assays. Lower levels of MCP-3, CASP-8, CD5, CXCL9, CXCL11, eotaxin, IFN-gamma, IL-13, IP-10, and OSM at the time of initial surgery were noted in the children who went on to require multiple surgeries. Pro- and anti-inflammatory cytokines were selected a priori and shown across subsequent revision surgeries for the 3 patients. Cytokine patterns differed between patients, but within a given patient pro-inflammatory and anti-inflammatory cytokines acted in a parallel fashion, with the exception of IL-4.CONCLUSIONS: Heat maps of cytokine levels at the time of initial CSF shunt placement for each child undergoing only a single initial CSF shunt placement and for each child undergoing repeat CSF shunt revision surgeries demonstrated qualitatively similar profiles for the majority of cytokines. Lower levels of MCP-3, CASP-8, CD5, CXCL9, CXCL11, eotaxin, IFN-gamma, IL-13, IP-10, and OSM at the time of initial surgery were noted in the children who went on to require multiple surgeries. Better stratification by patient age, etiology, and mechanism of failure is needed to develop a deeper understanding of the mechanism of inflammation in the development of hydrocephalus and response to shunting in children.

    View details for DOI 10.1016/j.cyto.2023.156310

    View details for PubMedID 37523803

  • Extending the dynamic range of biomarker quantification through molecular equalization. Nature communications Newman, S. S., Wilson, B. D., Mamerow, D., Wollant, B. C., Nyein, H., Rosenberg-Hasson, Y., Maecker, H. T., Eisenstein, M., Soh, H. T. 2023; 14 (1): 4192


    Precision medicine requires highly scalable methods of multiplexed biomarker quantification that can accurately describe patient physiology. Unfortunately, contemporary molecular detection methods are generally limited to a dynamic range of sensitivity spanning just 3-4 orders of magnitude, whereas the actual physiological dynamic range of the human plasma proteome spans more than 10 orders of magnitude. Current methods rely on sample splitting and differential dilution to compensate for this mismatch, but such measures greatly limit the reproducibility and scalability that can be achieved-in particular, the effects of non-linear dilution can greatly confound the analysis of multiplexed assays. We describe here a two-pronged strategy for equalizing the signal generated by each analyte in a multiplexed panel, thereby enabling simultaneous quantification of targets spanning a wide range of concentrations. We apply our 'EVROS' strategy to a proximity ligation assay and demonstrate simultaneous quantification of four analytes present at concentrations spanning from low femtomolar to mid-nanomolar levels. In this initial demonstration, we achieve a dynamic range spanning seven orders of magnitude in a single 5l sample of undiluted human serum, highlighting the opportunity to achieve sensitive, accurate detection of diverse analytes in a highly multiplexed fashion.

    View details for DOI 10.1038/s41467-023-39772-z

    View details for PubMedID 37443317

  • Enkurin: A novel marker for myeloproliferative neoplasms from platelet, megakaryocyte, and whole blood specimens. Blood advances Mosale Seetharam, S., Liu, Y., Wu, J., Fechter, L., Murugesan, K., Maecker, H. T., Gotlib, J., Zehnder, J. L., Paulmurugan, R., Krishnan, A. 2023


    Impaired protein homeostasis, though well established in age-related disorders, has been linked in recent research with the pathogenesis of myeloproliferative neoplasms (MPNs). As yet, however, little is known about MPN-specific modulators of proteostasis, thus impeding our ability for increased mechanistic understanding and discovery of additional therapeutic targets. Loss of proteostasis, in itself, is traced to dysregulated mechanisms in protein folding and intracellular calcium signaling at the endoplasmic reticulum (ER). Here, using ex vivo and in vitro systems (including CD34+ cultures from patient bone marrow, and healthy cord/peripheral blood specimens), we extend our prior data from MPN patient platelet RNA sequencing, and discover select proteostasis-associated markers at RNA and/or protein levels in each of platelets, parent megakaryocytes, and whole blood specimens. Importantly, we identify a novel role in MPNs for enkurin (ENKUR), a calcium mediator protein, implicated originally only in spermatogenesis. Our data reveal consistent ENKUR downregulation at both RNA and protein levels across MPN patient specimens and experimental models, with a concomitant upregulation of a cell cycle marker, CDC20. Silencing of ENKUR by shRNA in CD34+ derived megakaryocytes further confirm this association with CDC20 at both RNA and protein levels; and indicate a likely role for the PI3K/Akt pathway. The inverse association of ENKUR and CDC20 expression was further confirmed upon treatment with thapsigargin (an agent that causes protein misfolding in the ER by selective loss of calcium) in both megakaryocyte and platelet fractions at RNA and protein levels. Together, our work sheds light on enkurin as a novel marker of MPN pathogenesis beyond the genetic alterations; and indicates further mechanistic investigation into a role for dysregulated calcium homeostasis, and ER and protein folding stress in MPN transformation.

    View details for DOI 10.1182/bloodadvances.2022008939

    View details for PubMedID 37315179

  • Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. Cell reports. Medicine Diray-Arce, J., Fourati, S., Doni Jayavelu, N., Patel, R., Maguire, C., Chang, A. C., Dandekar, R., Qi, J., Lee, B. H., van Zalm, P., Schroeder, A., Chen, E., Konstorum, A., Brito, A., Gygi, J. P., Kho, A., Chen, J., Pawar, S., Gonzalez-Reiche, A. S., Hoch, A., Milliren, C. E., Overton, J. A., Westendorf, K., Cairns, C. B., Rouphael, N., Bosinger, S. E., Kim-Schulze, S., Krammer, F., Rosen, L., Grubaugh, N. D., van Bakel, H., Wilson, M., Rajan, J., Steen, H., Eckalbar, W., Cotsapas, C., Langelier, C. R., Levy, O., Altman, M. C., Maecker, H., Montgomery, R. R., Haddad, E. K., Sekaly, R. P., Esserman, D., Ozonoff, A., Becker, P. M., Augustine, A. D., Guan, L., Peters, B., Kleinstein, S. H. 2023: 101079


    The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1-3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling of >15,000 longitudinal blood and nasal samples from 540 participants of the IMPACC cohort, using 14 distinct assays. These unbiased analyses identify cellular and molecular signatures present within 72 h of hospital admission that distinguish moderate from severe and fatal COVID-19 disease. Importantly, cellular and molecular states also distinguish participants with more severe disease that recover or stabilize within 28 days from those that progress to fatal outcomes (TG4 vs. TG5). Furthermore, our longitudinal design reveals that these biologic states display distinct temporal patterns associated with clinical outcomes. Characterizing host immune responses in relation to heterogeneity in disease course may inform clinical prognosis and opportunities for intervention.

    View details for DOI 10.1016/j.xcrm.2023.101079

    View details for PubMedID 37327781

  • Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia. Journal for immunotherapy of cancer Kumar, A., Taghi Khani, A., Duault, C., Aramburo, S., Sanchez Ortiz, A., Lee, S. J., Chan, A., McDonald, T., Huang, M., Lacayo, N. J., Sakamoto, K. M., Yu, J., Hurtz, C., Carroll, M., Tasian, S. K., Ghoda, L., Marcucci, G., Gu, Z., Rosen, S. T., Armenian, S., Izraeli, S., Chen, C., Caligiuri, M. A., Forman, S. J., Maecker, H. T., Swaminathan, S. 2023; 11 (5)


    BACKGROUND: Type I interferons (IFN-Is), secreted by hematopoietic cells, drive immune surveillance of solid tumors. However, the mechanisms of suppression of IFN-I-driven immune responses in hematopoietic malignancies including B-cell acute lymphoblastic leukemia (B-ALL) are unknown.METHODS: Using high-dimensional cytometry, we delineate the defects in IFN-I production and IFN-I-driven immune responses in high-grade primary human and mouse B-ALLs. We develop natural killer (NK) cells as therapies to counter the intrinsic suppression of IFN-I production in B-ALL.RESULTS: We find that high expression of IFN-I signaling genes predicts favorable clinical outcome in patients with B-ALL, underscoring the importance of the IFN-I pathway in this malignancy. We show that human and mouse B-ALL microenvironments harbor an intrinsic defect in paracrine (plasmacytoid dendritic cell) and/or autocrine (B-cell) IFN-I production and IFN-I-driven immune responses. Reduced IFN-I production is sufficient for suppressing the immune system and promoting leukemia development in mice prone to MYC-driven B-ALL. Among anti-leukemia immune subsets, suppression of IFN-I production most markedly lowers the transcription of IL-15 and reduces NK-cell number and effector maturation in B-ALL microenvironments. Adoptive transfer of healthy NK cells significantly prolongs survival of overt ALL-bearing transgenic mice. Administration of IFN-Is to B-ALL-prone mice reduces leukemia progression and increases the frequencies of total NK and NK-cell effectors in circulation. Ex vivo treatment of malignant and non-malignant immune cells in primary mouse B-ALL microenvironments with IFN-Is fully restores proximal IFN-I signaling and partially restores IL-15 production. In B-ALL patients, the suppression of IL-15 is the most severe in difficult-to-treat subtypes with MYC overexpression. MYC overexpression promotes sensitivity of B-ALL to NK cell-mediated killing. To counter the suppressed IFN-I-induced IL-15 production in MYChigh human B-ALL, we CRISPRa-engineered a novel human NK-cell line that secretes IL-15. CRISPRa IL-15-secreting human NK cells kill high-grade human B-ALL in vitro and block leukemia progression in vivo more effectively than NK cells that do not produce IL-15.CONCLUSION: We find that restoration of the intrinsically suppressed IFN-I production in B-ALL underlies the therapeutic efficacy of IL-15-producing NK cells and that such NK cells represent an attractive therapeutic solution for the problem of drugging MYC in high-grade B-ALL.

    View details for DOI 10.1136/jitc-2022-006649

    View details for PubMedID 37217248

  • Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19. Nature communications Yu, M., Charles, A., Cagigi, A., Christ, W., Österberg, B., Falck-Jones, S., Azizmohammadi, L., Åhlberg, E., Falck-Jones, R., Svensson, J., Nie, M., Warnqvist, A., Hellgren, F., Lenart, K., Arcoverde Cerveira, R., Ols, S., Lindgren, G., Lin, A., Maecker, H., Bell, M., Johansson, N., Albert, J., Sundling, C., Czarnewski, P., Klingström, J., Färnert, A., Loré, K., Smed-Sörensen, A. 2023; 14 (1): 2164


    Effective humoral immune responses require well-orchestrated B and T follicular helper (Tfh) cell interactions. Whether these interactions are impaired and associated with COVID-19 disease severity is unclear. Here, longitudinal blood samples across COVID-19 disease severity are analysed. We find that during acute infection SARS-CoV-2-specific circulating Tfh (cTfh) cells expand with disease severity. SARS-CoV-2-specific cTfh cell frequencies correlate with plasmablast frequencies and SARS-CoV-2 antibody titers, avidity and neutralization. Furthermore, cTfh cells but not other memory CD4 T cells, from severe patients better induce plasmablast differentiation and antibody production compared to cTfh cells from mild patients. However, virus-specific cTfh cell development is delayed in patients that display or later develop severe disease compared to those with mild disease, which correlates with delayed induction of high-avidity neutralizing antibodies. Our study suggests that impaired generation of functional virus-specific cTfh cells delays high-quality antibody production at an early stage, potentially enabling progression to severe disease.

    View details for DOI 10.1038/s41467-023-37835-9

    View details for PubMedID 37061513

    View details for PubMedCentralID PMC10105364

  • Comparison of multiplexed protein analysis platforms for the detection of biomarkers in the nasal epithelial lining fluid of healthy subjects. Journal of immunological methods Zetlen, H. L., Cao, K. T., Schichlein, K. D., Knight, N., Maecker, H. T., Nadeau, K. C., Rebuli, M. E., Rice, M. B. 2023: 113473


    Multiplexed protein analysis platforms are a novel and efficient way to characterize biomarkers in a variety of biological samples. Few studies have compared protein quantitation and reproducibility of results across platforms. We utilize a novel nasosorption technique to collect nasal epithelial lining fluid (NELF) from healthy subjects, and compare the detection of proteins in NELF across three commonly used platforms.NELF was collected from both nares of twenty healthy subjects using an absorbent fibrous matrix and analyzed using three different protein analysis platforms: Luminex, Meso Scale Discovery (MSD), and Olink. Twenty-three protein analytes were shared across two or more platforms, and correlations across platforms were assessed using Spearman correlations.Among the twelve proteins represented on all three platforms, IL1⍺ and IL6 were very highly correlated (Spearman correlation coefficient [r] ≥ 0.9); CCL3, CCL4, and MCP1 were highly correlated (r ≥ 0.7); and IFNɣ, IL8, and TNF⍺ were moderately correlated (r ≥ 0.5). Four proteins (IL2, IL4, IL10, IL13) were poorly correlated across at least two platform comparisons (r < 0.5); for two of these proteins (IL10 and IL13), the majority of observations were below the limits of detection for Olink and Luminex.Multiplexed protein analysis platforms are a promising method for analyzing nasal samples for biomarkers of interest in respiratory health research. For most proteins evaluated, there was good correlation across platforms, although results were less consistent for low abundance proteins. Of the three platforms tested, MSD had the highest sensitivity for analyte detection.

    View details for DOI 10.1016/j.jim.2023.113473

    View details for PubMedID 37059295

  • Advances and potential of omics studies for understanding the development of food allergy. Frontiers in allergy Sindher, S. B., Chin, A. R., Aghaeepour, N., Prince, L., Maecker, H., Shaw, G. M., Stevenson, D. K., Nadeau, K. C., Snyder, M., Khatri, P., Boyd, S. D., Winn, V. D., Angst, M. S., Chinthrajah, R. S. 2023; 4: 1149008


    The prevalence of food allergy continues to rise globally, carrying with it substantial safety, economic, and emotional burdens. Although preventative strategies do exist, the heterogeneity of allergy trajectories and clinical phenotypes has made it difficult to identify patients who would benefit from these strategies. Therefore, further studies investigating the molecular mechanisms that differentiate these trajectories are needed. Large-scale omics studies have identified key insights into the molecular mechanisms for many different diseases, however the application of these technologies to uncover the drivers of food allergy development is in its infancy. Here we review the use of omics approaches in food allergy and highlight key gaps in knowledge for applying these technologies for the characterization of food allergy development.

    View details for DOI 10.3389/falgy.2023.1149008

    View details for PubMedID 37034151

    View details for PubMedCentralID PMC10080041

  • Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics. Science advances Robinson, M. L., Glass, D. R., Duran, V., Agudelo Rojas, O. L., Sanz, A. M., Consuegra, M., Sahoo, M. K., Hartmann, F. J., Bosse, M., Gelvez, R. M., Bueno, N., Pinsky, B. A., Montoya, J. G., Maecker, H., Estupiñan Cardenas, M. I., Villar Centeno, L. A., Garrido, E. M., Rosso, F., Bendall, S. C., Einav, S. 2023; 9 (12): eade7702


    Approximately 5 million dengue virus-infected patients progress to a potentially life-threatening severe dengue (SD) infection annually. To identify the immune features and temporal dynamics underlying SD progression, we performed deep immune profiling by mass cytometry of PBMCs collected longitudinally from SD progressors (SDp) and uncomplicated dengue (D) patients. While D is characterized by early activation of innate immune responses, in SDp there is rapid expansion and activation of IgG-secreting plasma cells and memory and regulatory T cells. Concurrently, SDp, particularly children, demonstrate increased proinflammatory NK cells, inadequate expansion of CD16+ monocytes, and high expression of the FcγR CD64 on myeloid cells, yet a signature of diminished antigen presentation. Syndrome-specific determinants include suppressed dendritic cell abundance in shock/hemorrhage versus enriched plasma cell expansion in organ impairment. This study reveals uncoordinated immune responses in SDp and provides insights into SD pathogenesis in humans with potential implications for prediction and treatment.

    View details for DOI 10.1126/sciadv.ade7702

    View details for PubMedID 36961888

  • A cross-sectional study comparing the inflammatory profile of menstrual effluent vs. peripheral blood. Health science reports Naseri, S., Rosenberg-Hasson, Y., Maecker, H. T., Avrutsky, M. I., Blumenthal, P. D. 2023; 6 (1): e1038


    Cytokine profiles of peripheral blood and other bodily fluids provide diagnostic indicators for assessing inflammatory processes. Menstrual effluent may provide a noninvasive source of biological material for monitoring cytokine levels in blood and in endometrial tissues. This pilot study investigated the potential of measuring cytokines in menstrual effluent, and compared the cytokine profiles of menstrual versus peripheral blood.Seven healthy donors (aged ≥18 and ≤45 years) collected menstrual effluent on day 2 of menses. Matched peripheral blood samples were collected by venous blood draw on the same day. Levels of 62 cytokines were measured in all samples by 62-plex Luminex assay.Peripheral blood and menstrual effluent cytokine profiles were tenuously correlated (r 2 = 0.26, p < 0.0001), with higher levels detected in menstrual effluent for 48/62 cytokines. Thirty five cytokines were significantly elevated in menstrual effluent compared to peripheral blood samples (IL-8, CCL2, CCL4, LIF, IL-1RA, IL-6, IL-1β, HGF, CCL3, FGF-2, TNF-α, VEGF-A, IL-1α, CXCL1, IL-9, IL-10, EGF, CXCL5, CSF3, EOTAXIN, TGF-α, TRAIL, CXCL10, VEGF-D, IL-12P40, CXCL9, IL-18 RESISTIN, IL-22, IL-21, CSF1, IFN-γ, IL-17A, CXCL12, IL-12p70). Two cytokines (LEPTIN, CSF2) were expressed at significantly lower levels in menstrual effluent compared to peripheral blood. Linear regression of individual cytokines found low predictive power (linear regression p > 0.05) for 53/62 cytokines in menstrual effluent versus peripheral blood. Levels of TGF-β (r 2 = 0.87, p = 0.002) and CCL7 (r 2 = 0.63, p = 0.033) were significantly positively correlated between matched menstrual and peripheral blood samples.In this group of study participants, the cytokine profile of menstrual effluent was quantitatively distinct from peripheral blood, and also characterized by higher levels of inflammatory signaling. This pattern of comparative menstrual blood cytokine profiles points to a need for further studies to evaluate the relationship between peripheral and menstrual blood cytokines in broader populations including both healthy and diseased states.

    View details for DOI 10.1002/hsr2.1038

    View details for PubMedID 36620506

    View details for PubMedCentralID PMC9813904

  • The Role of Single-Cell Profiling and Deep Immunophenotyping in Understanding Immune Therapy Cardiotoxicity. JACC. CardioOncology Huang, Y. V., Waliany, S., Lee, D., Galdos, F. X., Witteles, R. M., Neal, J. W., Fan, A. C., Maecker, H. T., Nguyen, P. K., Wu, S. M., Zhu, H. 2022; 4 (5): 629-634


    • ICIs used in cancer therapy can cause serious cardiac immune-related side effects. • Single-cell multi-omics are powerful tools in understanding cell subsets/phenotypes. • Multi-omics technology can elucidate disease mechanisms in ICI-induced myocarditis.

    View details for DOI 10.1016/j.jaccao.2022.08.012

    View details for PubMedID 36636436

    View details for PubMedCentralID PMC9830194

  • CD8+ T cell differentiation status correlates with the feasibility of sustained unresponsiveness following oral immunotherapy. Nature communications Kaushik, A., Dunham, D., Han, X., Do, E., Andorf, S., Gupta, S., Fernandes, A., Kost, L. E., Sindher, S. B., Yu, W., Tsai, M., Tibshirani, R., Boyd, S. D., Desai, M., Maecker, H. T., Galli, S. J., Chinthrajah, R. S., DeKruyff, R. H., Manohar, M., Nadeau, K. C. 2022; 13 (1): 6646


    While food allergy oral immunotherapy (OIT) can provide safe and effective desensitization (DS), the immune mechanisms underlying development of sustained unresponsiveness (SU) following a period of avoidance are largely unknown. Here, we compare high dimensional phenotypes of innate and adaptive immune cell subsets of participants in a previously reported, phase 2 randomized, controlled, peanut OIT trial who achieved SU vs. DS (no vs. with allergic reactions upon food challenge after a withdrawal period; n=21 vs. 30 respectively among total 120 intent-to-treat participants). Lower frequencies of naive CD8+ T cells and terminally differentiated CD57+CD8+ T cell subsets at baseline (pre-OIT) are associated with SU. Frequency of naive CD8+ T cells shows a significant positive correlation with peanut-specific and Ara h 2-specific IgE levels at baseline. Higher frequencies of IL-4+ and IFNgamma+ CD4+ T cells post-OIT are negatively correlated with SU. Our findings provide evidence that an immune signature consisting of certain CD8+ T cell subset frequencies is potentially predictive of SU following OIT.

    View details for DOI 10.1038/s41467-022-34222-8

    View details for PubMedID 36333296

  • Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. EBioMedicine Ozonoff, A., Schaenman, J., Jayavelu, N. D., Milliren, C. E., Calfee, C. S., Cairns, C. B., Kraft, M., Baden, L. R., Shaw, A. C., Krammer, F., van Bakel, H., Esserman, D. A., Liu, S., Sesma, A. F., Simon, V., Hafler, D. A., Montgomery, R. R., Kleinstein, S. H., Levy, O., Bime, C., Haddad, E. K., Erle, D. J., Pulendran, B., Nadeau, K. C., Davis, M. M., Hough, C. L., Messer, W. B., Higuita, N. I., Metcalf, J. P., Atkinson, M. A., Brakenridge, S. C., Corry, D., Kheradmand, F., Ehrlich, L. I., Melamed, E., McComsey, G. A., Sekaly, R., Diray-Arce, J., Peters, B., Augustine, A. D., Reed, E. F., Altman, M. C., Becker, P. M., Rouphael, N. 2022; 83: 104208


    Better understanding of the association between characteristics of patients hospitalized with coronavirus disease 2019 (COVID-19) and outcome is needed to further improve upon patient management.Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective, observational study of 1164 patients from 20 hospitals across the United States. Disease severity was assessed using a 7-point ordinal scale based on degree of respiratory illness. Patients were prospectively surveyed for 1 year after discharge for post-acute sequalae of COVID-19 (PASC) through quarterly surveys. Demographics, comorbidities, radiographic findings, clinical laboratory values, SARS-CoV-2 PCR and serology were captured over a 28-day period. Multivariable logistic regression was performed.The median age was 59 years (interquartile range [IQR] 20); 711 (61%) were men; overall mortality was 14%, and 228 (20%) required invasive mechanical ventilation. Unsupervised clustering of ordinal score over time revealed distinct disease course trajectories. Risk factors associated with prolonged hospitalization or death by day 28 included age ≥ 65 years (odds ratio [OR], 2.01; 95% CI 1.28-3.17), Hispanic ethnicity (OR, 1.71; 95% CI 1.13-2.57), elevated baseline creatinine (OR 2.80; 95% CI 1.63- 4.80) or troponin (OR 1.89; 95% 1.03-3.47), baseline lymphopenia (OR 2.19; 95% CI 1.61-2.97), presence of infiltrate by chest imaging (OR 3.16; 95% CI 1.96-5.10), and high SARS-CoV2 viral load (OR 1.53; 95% CI 1.17-2.00). Fatal cases had the lowest ratio of SARS-CoV-2 antibody to viral load levels compared to other trajectories over time (p=0.001). 589 survivors (51%) completed at least one survey at follow-up with 305 (52%) having at least one symptom consistent with PASC, most commonly dyspnea (56% among symptomatic patients). Female sex was the only associated risk factor for PASC.Integration of PCR cycle threshold, and antibody values with demographics, comorbidities, and laboratory/radiographic findings identified risk factors for 28-day outcome severity, though only female sex was associated with PASC. Longitudinal clinical phenotyping offers important insights, and provides a framework for immunophenotyping for acute and long COVID-19.NIH.

    View details for DOI 10.1016/j.ebiom.2022.104208

    View details for PubMedID 35952496

  • Discrete Plasma Cytokine Profiles among Pregnant Women in Botswana by Chlamydia trachomatis infection, HIV status, and Gestational age. The Journal of infectious diseases Babalola, C. M., Siebert, J. C., Kallapur, S. G., Maecker, H. T., Rosenberg-Hasson, Y., Hansman, E., Wynn, A., Mussa, A., Ryan, R., Simon, S., Morroni, C., Klausner, J. D. 2022

    View details for DOI 10.1093/infdis/jiac302

    View details for PubMedID 35876733

  • Anti-nucleocapsid antibody levels and pulmonary comorbid conditions are linked to post-COVID-19 syndrome. JCI insight Jia, X., Cao, S., Lee, A. S., Manohar, M., Sindher, S. B., Ahuja, N., Artandi, M., Blish, C. A., Blomkalns, A. L., Chang, I., Collins, W. J., Desai, M., Din, H. N., Do, E., Fernandes, A., Geng, L. N., Rosenberg-Hasson, Y., Mahoney, M. R., Glascock, A. L., Chan, L. Y., Fong, S. Y., Phelps, M., Raeber, O., Purington, N., Röltgen, K., Rogers, A. J., Snow, T., Wang, T. T., Solis, D., Vaughan, L., Verghese, M., Maecker, H., Wittman, R., Puri, R., Kistler, A., Yang, S., Boyd, S. D., Pinsky, B. A., Chinthrajah, S., Nadeau, K. C. 2022; 7 (13)


    BACKGROUNDProlonged symptoms after SARS-CoV-2 infection are well documented. However, which factors influence development of long-term symptoms, how symptoms vary across ethnic groups, and whether long-term symptoms correlate with biomarkers are points that remain elusive.METHODSAdult SARS-CoV-2 reverse transcription PCR-positive (RT-PCR-positive) patients were recruited at Stanford from March 2020 to February 2021. Study participants were seen for in-person visits at diagnosis and every 1-3 months for up to 1 year after diagnosis; they completed symptom surveys and underwent blood draws and nasal swab collections at each visit.RESULTSOur cohort (n = 617) ranged from asymptomatic to critical COVID-19 infections. In total, 40% of participants reported at least 1 symptom associated with COVID-19 six months after diagnosis. Median time from diagnosis to first resolution of all symptoms was 44 days; median time from diagnosis to sustained symptom resolution with no recurring symptoms for 1 month or longer was 214 days. Anti-nucleocapsid IgG level in the first week after positive RT-PCR test and history of lung disease were associated with time to sustained symptom resolution. COVID-19 disease severity, ethnicity, age, sex, and remdesivir use did not affect time to sustained symptom resolution.CONCLUSIONWe found that all disease severities had a similar risk of developing post-COVID-19 syndrome in an ethnically diverse population. Comorbid lung disease and lower levels of initial IgG response to SARS-CoV-2 nucleocapsid antigen were associated with longer symptom duration.TRIAL, NCT04373148.FUNDINGNIH UL1TR003142 CTSA grant, NIH U54CA260517 grant, NIEHS R21 ES03304901, Sean N Parker Center for Allergy and Asthma Research at Stanford University, Chan Zuckerberg Biohub, Chan Zuckerberg Initiative, Sunshine Foundation, Crown Foundation, and Parker Foundation.

    View details for DOI 10.1172/jci.insight.156713

    View details for PubMedID 35801588

  • Identification of Pathogenic Immune Cell Subsets Associated With Checkpoint Inhibitor-Induced Myocarditis. Circulation Zhu, H., Galdos, F. X., Lee, D., Waliany, S., Vivian Huang, Y., Ryan, J., Dang, K., Neal, J. W., Wakelee, H. A., Reddy, S. A., Srinivas, S., Lin, L. L., Witteles, R. M., Maecker, H. T., Davis, M. M., Nguyen, P. K., Wu, S. M. 2022: 101161CIRCULATIONAHA121056730


    Immune checkpoint inhibitors (ICIs) are monoclonal antibodies used to activate the immune system against tumor cells. Despite therapeutic benefits, ICIs have the potential to cause immune-related adverse events such as myocarditis, a rare but serious side effect with up to 50% mortality in affected patients. Histologically, patients with ICI myocarditis have lymphocytic infiltrates in the heart, implicating T cell-mediated mechanisms. However, the precise pathological immune subsets and molecular changes in ICI myocarditis are unknown.To identify immune subset(s) associated with ICI myocarditis, we performed time-of-flight mass cytometry on peripheral blood mononuclear cells from 52 individuals: 29 patients with autoimmune adverse events (immune-related adverse events) on ICI, including 8 patients with ICI myocarditis, and 23 healthy control subjects. We also used multiomics single-cell technology to immunophenotype 30 patients/control subjects using single-cell RNA sequencing, single-cell T-cell receptor sequencing, and cellular indexing of transcriptomes and epitopes by sequencing with feature barcoding for surface marker expression confirmation. To correlate between the blood and the heart, we performed single-cell RNA sequencing/T-cell receptor sequencing/cellular indexing of transcriptomes and epitopes by sequencing on MRL/Pdcd1-/- (Murphy Roths large/programmed death-1-deficient) mice with spontaneous myocarditis.Using these complementary approaches, we found an expansion of cytotoxic CD8+ T effector cells re-expressing CD45RA (Temra CD8+ cells) in patients with ICI myocarditis compared with control subjects. T-cell receptor sequencing demonstrated that these CD8+ Temra cells were clonally expanded in patients with myocarditis compared with control subjects. Transcriptomic analysis of these Temra CD8+ clones confirmed a highly activated and cytotoxic phenotype. Longitudinal study demonstrated progression of these Temra CD8+ cells into an exhausted phenotype 2 months after treatment with glucocorticoids. Differential expression analysis demonstrated elevated expression levels of proinflammatory chemokines (CCL5/CCL4/CCL4L2) in the clonally expanded Temra CD8+ cells, and ligand receptor analysis demonstrated their interactions with innate immune cells, including monocytes/macrophages, dendritic cells, and neutrophils, as well as the absence of key anti-inflammatory signals. To complement the human study, we performed single-cell RNA sequencing/T-cell receptor sequencing/cellular indexing of transcriptomes and epitopes by sequencing in Pdcd1-/- mice with spontaneous myocarditis and found analogous expansions of cytotoxic clonal effector CD8+ cells in both blood and hearts of such mice compared with controls.Clonal cytotoxic Temra CD8+ cells are significantly increased in the blood of patients with ICI myocarditis, corresponding to an analogous increase in effector cytotoxic CD8+ cells in the blood/hearts of Pdcd1-/- mice with myocarditis. These expanded effector CD8+ cells have unique transcriptional changes, including upregulation of chemokines CCL5/CCL4/CCL4L2, which may serve as attractive diagnostic/therapeutic targets for reducing life-threatening cardiac immune-related adverse events in ICI-treated patients with cancer.

    View details for DOI 10.1161/CIRCULATIONAHA.121.056730

    View details for PubMedID 35762356

  • Full spectrum flow cytometry and mass cytometry: A 32-marker panel comparison. Cytometry. Part A : the journal of the International Society for Analytical Cytology Jaimes, M. C., Leipold, M., Kraker, G., Amir, E., Maecker, H., Lannigan, J. 2022


    High-dimensional single-cell data has become an important tool in unraveling the complexity of the immune system and its involvement in homeostasis and a large array of pathologies. As technological tools are developed, researchers are adopting them to answer increasingly complex biological questions. Up until recently, mass cytometry (MC) has been the main technology employed in cytometric assays requiring more than 29 markers. Recently, however, with the introduction of full spectrum flow cytometry (FSFC), it has become possible to break the fluorescence barrier and go beyond 29 fluorescent parameters. In this study, in collaboration with the Stanford Human Immune Monitoring Center (HIMC), we compared five patient samples using an established immune panel developed by the HIMC using their MC platform. Using split samples and the same antibody panel, we were able to demonstrate highly comparable results between the two technologies using multiple data analysis approaches. We report here a direct comparison of two technology platforms (MC and FSFC) using a 32-marker flow cytometric immune monitoring panel that can identify all the previously described and anticipated immune subpopulations defined by this panel.

    View details for DOI 10.1002/cyto.a.24565

    View details for PubMedID 35593221

  • Increases in ambient air pollutants during pregnancy are linked to increases in methylation of IL4, IL10, and IFNgamma. Clinical epigenetics Aguilera, J., Han, X., Cao, S., Balmes, J., Lurmann, F., Tyner, T., Lutzker, L., Noth, E., Hammond, S. K., Sampath, V., Burt, T., Utz, P. J., Khatri, P., Aghaeepour, N., Maecker, H., Prunicki, M., Nadeau, K. 2022; 14 (1): 40


    BACKGROUND: Ambient air pollutant (AAP) exposure is associated with adverse pregnancy outcomes, such as preeclampsia, preterm labor, and low birth weight. Previous studies have shown methylation of immune genes associate with exposure to air pollutants in pregnant women, but the cell-mediated response in the context of typical pregnancy cell alterations has not been investigated. Pregnancy causes attenuation in cell-mediated immunity with alterations in the Th1/Th2/Th17/Treg environment, contributing to maternal susceptibility. We recruited women (n=186) who were 20weeks pregnant from Fresno, CA, an area with chronically elevated AAP levels. Associations of average pollution concentration estimates for 1week, 1month, 3months, and 6months prior to blood draw were associated with Th cell subset (Th1, Th2, Th17, and Treg) percentages and methylation of CpG sites (IL4, IL10, IFNgamma, and FoxP3). Linear regression models were adjusted for weight, age, season, race, and asthma, using a Q value as the false-discovery-rate-adjusted p-value across all genes.RESULTS: Short-term and mid-term AAP exposures to fine particulate matter (PM2.5), nitrogen dioxide (NO2) carbon monoxide (CO), and polycyclic aromatic hydrocarbons (PAH456) were associated with percentages of immune cells. A decrease in Th1 cell percentage was negatively associated with PM2.5 (1 mo/3 mo: Q<0.05), NO2 (1 mo/3 mo/6 mo: Q<0.05), and PAH456 (1week/1 mo/3 mo: Q<0.05). Th2 cell percentages were negatively associated with PM2.5 (1week/1 mo/3 mo/6 mo: Q<0.06), and NO2 (1week/1 mo/3 mo/6 mo: Q<0.06). Th17 cell percentage was negatively associated with NO2 (3 mo/6 mo: Q<0.01), CO (1week/1 mo: Q<0.1), PM2.5 (3 mo/6 mo: Q<0.05), and PAH456 (1 mo/3 mo/6 mo: Q<0.08). Methylation of the IL10 gene was positively associated with CO (1week/1 mo/3 mo: Q<0.01), NO2 (1 mo/3 mo/6 mo: Q<0.08), PAH456 (1week/1 mo/3 mo: Q<0.01), and PM2.5 (3 mo: Q=0.06) while IL4 gene methylation was positively associated with concentrations of CO (1week/1 mo/3 mo/6 mo: Q<0.09). Also, IFNgamma gene methylation was positively associated with CO (1week/1 mo/3 mo: Q<0.05) and PAH456 (1week/1 mo/3 mo: Q<0.06).CONCLUSION: Exposure to several AAPs was negatively associated with T-helper subsets involved in pro-inflammatory and anti-inflammatory responses during pregnancy. Methylation of IL4, IL10, and IFNgamma genes with pollution exposure confirms previous research. These results offer insights into the detrimental effects of air pollution during pregnancy, the demand for more epigenetic studies, and mitigation strategies to decrease pollution exposure during pregnancy.

    View details for DOI 10.1186/s13148-022-01254-2

    View details for PubMedID 35287715

  • Single-Cell Immune Mapping of Melanoma Sentinel Lymph Nodes Reveals an Actionable Immunotolerant Microenvironment. Clinical cancer research : an official journal of the American Association for Cancer Research Yaddanapudi, K., Stamp, B. F., Subrahmanyam, P. B., Smolenkov, A., Waigel, S. J., Gosain, R., Egger, M. E., Martin, R. C., Buscaglia, R., Maecker, H. T., McMasters, K. M., Chesney, J. A. 1800


    PURPOSE: Improving our understanding of the immunological response to cancer cells within the sentinel lymph nodes (SLNs) of primary tumors is expected to identify new approaches to stimulate clinically meaningful cancer immunity.EXPERIMENTAL DESIGN: We used mass cytometry by time-of-flight (CyTOF), flow cytometry, and T cell receptor immunosequencing to conduct simultaneous single-cell analyses of immune cells in the SLNs of melanoma patients.RESULTS: We found increased effector-memory alphabeta T cells, TCR clonality, and gammadelta T cells selectively in the melanoma-bearing SLNs relative to non-melanoma-bearing SLNs, consistent with possible activation of an anti-tumor immune response. However, we also observed a markedly immunotolerant environment in the melanoma-bearing SLNs indicated by reduced and impaired NK cells and increased levels of CD8+CD57+PD-1+ cells which are known to display low melanoma killing capabilities. Other changes observed in melanoma-bearing SLNs when compared to non-melanoma bearing SLNs include: (i) reduced CD8+CD69+ T cells/T regulatory cells ratio; (ii) high PD-1 expression on CD4+ and CD8+ T cells; and (iii) high CTLA-4 expression on gammadelta T cells.CONCLUSIONS: Our data suggests that these immunological changes compromise anti-melanoma immunity and contribute to a high relapse rate. We propose the development of clinical trials to test the neo-adjuvant administration of anti-PD-1 antibodies prior to SLN resection in stage III melanoma patients.

    View details for DOI 10.1158/1078-0432.CCR-21-0664

    View details for PubMedID 35046061

  • 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


    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

  • Disease characteristics and serological responses in patients with differing severity of COVID-19 infection: A longitudinal cohort study in Dhaka, Bangladesh. PLoS neglected tropical diseases Akter, A., Ahmed, T., Tauheed, I., Akhtar, M., Rahman, S. I., Khaton, F., Ahmmed, F., Ferdous, J., Afrad, M. H., Kawser, Z., Hossain, M., Khondaker, R., Hasnat, M. A., Sumon, M. A., Rashed, A., Ghosh, S., Calderwood, S. B., Charles, R. C., Ryan, E. T., Khatri, P., Maecker, H. T., Obermoser, G., Pulendran, B., Clemens, J. D., Banu, S., Shirin, T., LaRocque, R. C., Harris, J. B., Bhuiyan, T. R., Chowdhury, F., Qadri, F. 2022; 16 (1): e0010102


    COVID-19 caused by SARS-CoV-2 ranges from asymptomatic to severe disease and can cause fatal and devastating outcome in many cases. In this study, we have compared the clinical, biochemical and immunological parameters across the different disease spectrum of COVID-19 in Bangladeshi patients.This longitudinal study was conducted in two COVID-19 hospitals and also around the community in Dhaka city in Bangladesh between November 2020 to March 2021. A total of 100 patients with COVID-19 infection were enrolled and classified into asymptomatic, mild, moderate and severe cases (n = 25/group). In addition, thirty age and sex matched healthy participants were enrolled and 21 were analyzed as controls based on exclusion criteria. After enrollment (study day1), follow-up visits were conducted on day 7, 14 and 28 for the cases. Older age, male gender and co-morbid conditions were the risk factors for severe COVID-19 disease. Those with moderate and severe cases of infection had low lymphocyte counts, high neutrophil counts along with a higher neutrophil-lymphocyte ratio (NLR) at enrollment; this decreased to normal range within 42 days after the onset of symptom. At enrollment, D-dimer, CRP and ferritin levels were elevated among moderate and severe cases. The mild, moderate, and severe cases were seropositive for IgG antibody by day 14 after enrollment. Moderate and severe cases showed significantly higher IgM and IgG levels of antibodies to SARS-CoV-2 compared to mild and asymptomatic cases.We report on the clinical, biochemical, and hematological parameters associated with the different severity of COVID-19 infection. We also show different profile of antibody response against SARS-CoV-2 in relation to disease severity, especially in those with moderate and severe disease manifestations compared to the mild and asymptomatic infection.

    View details for DOI 10.1371/journal.pntd.0010102

    View details for PubMedID 34982773

  • Mass Cytometry Assessment of Cell Phenotypes and Signaling States in Human Whole Blood. Methods in molecular biology (Clifton, N.J.) Sigal, N., Maecker, H. T. 2022; 2543: 113-128


    Phosphoflow is a powerful tool that allows researchers to measure distinct signaling responses to various stimuli in multiple subpopulations of cells. Extension of this technique to mass cytometry (cytometry by time-of-flight or CyTOF) allows many more cell phenotypes and signaling nodes to be interrogated in parallel. The use of fresh whole blood is ideal for capturing the in vivo signaling state of all leukocytes, including granulocytes. In this chapter, we provide a detailed protocol for performing CyTOF phosphoflow in human whole blood, using cytokines and other stimuli. Barcoding and combining of multiple samples and other techniques to reduce batch effects and provide optimal comparability between samples/stimulations are also described.

    View details for DOI 10.1007/978-1-0716-2553-8_10

    View details for PubMedID 36087263

  • Insulin Growth Factor Phenotypes in Heart Failure with Preserved Ejection Fraction, an INSPIRE Registry and CATHGEN Study: IGF axis in HFpEF. Journal of cardiac failure Haddad, F., Ataam, J. A., Amsallem, M., Cauwenberghs, N., Kuznetsova, T., Rosenberg-Hasson, Y., Zamanian, R. T., Karakikes, I., Horne, B. D., Muhlestein, J. B., Kwee, L., Shah, S., Maecker, H., Knight, S., Knowlton, K. 1800


    BACKGROUND: The insulin like growth factor (IGF) axis emerged as an important pathway in heart failure with preserved ejection (HFpEF). We aimed to identify IGF phenotypes associated with HFpEF in the context high-dimensional proteomic profiling.METHODS: From the Intermountain INSPIRE Registry, we identified 96 patients with HFpEF and matched controls. We performed targeted proteomics including IGF-1,2, IGF binding proteins (IGFBP) 1-7 and 111 other proteins (EMD Millipore and ELISA). We used partial least square discriminant analysis (PLS-DA) to identify a set of proteins associated with prevalent HFpEF, pulmonary hypertension (PH) and 5-year-all-cause mortality. K-mean clustering was used to identify IGF phenotypes.RESULTS: Patients with HFpEF had a high prevalence of systemic hypertension (95%) and coronary artery disease (74%). Using PLS-DA, we identified a set of biomarkers including IGF1,2 and IGFBP-1,2,7 that provided a strong discrimination of HFPEF, PH and mortality with an AUC of 0.91, 0.77 and 0.83, respectively. Using K mean clustering, we identified three IGF phenotypes that were independently associated with all-cause 5-year mortality after adjustment for age, NT-proBNP and kidney disease (p=0.004). Multivariable analysis validated the prognostic value of IGFBP-1 and 2 in the CATHGEN biorepository.CONCLUSION: IGF phenotypes were associated with PH and mortality in HFpEF.

    View details for DOI 10.1016/j.cardfail.2021.12.012

    View details for PubMedID 34979242

  • Inflammatory cytokines and callosal white matter microstructure in adolescents. Brain, behavior, and immunity Ho, T. C., Kulla, A., Teresi, G. I., Sisk, L. M., Rosenberg-Hasson, Y., Maecker, H. T., Gotlib, I. H. 1800


    Adolescent depression is characterized by heightened inflammation and altered connectivity of fronto-cingulate-limbic tracts, including the genu of the corpus callosum (CCG) and the uncinate fasciculus (UF). No studies, however, have yet examined the association between inflammation, measured by peripheral levels of cytokines, and white matter connectivity of fronto-cingulate-limbic tracts in adolescents. Here, 56 depressed adolescents (32 females, 3 non-binary; 16.23±1.28 years) and 19 controls (10 females; 15.72±1.17 years) completed a diffusion-weighted MRI scan at 3 Tesla. We conducted deterministic tractography to segment bilateral corpus callosum (genu and splenium) and UF and computed mean fractional anisotropy (FA) in each tract. A subset of participants (43 depressed and 17 healthy controls) also provided dried blood spot samples from which we assayed interleukin 6 (IL-6) and tumor necrosis alpha (TNF-ɑ) using a Luminex multiplex array. Depressed participants did not differ from controls in FA of the corpus callosum or UF (all FDR-corrected ps>0.056) but exhibited higher levels of inflammation than did controls (IL-6: beta=0.91, FDR-corrected p=0.006; TNF-alpha: beta=0.76, FDR-corrected p=0.006). Although diagnostic group did not moderate the associations between inflammatory cytokines and FA in the CCG and UF, across both groups, greater peripheral inflammation was associated with lower FA in the CCG (IL-6: beta=-0.38; FDR-corrected p=0.044; TNF-ɑ: beta=-0.41, FDR-corrected p=0.044). This study is the first to examine associations between peripheral inflammation and white matter microstructure of fronto-cingulate-limbic tracts in depressed and nondepressed adolescents. Future mechanistic studies are needed to confirm our findings; nevertheless, our results suggest that heightened inflammation is an important component of neurophenotypes that are relevant to adolescent depression.

    View details for DOI 10.1016/j.bbi.2021.12.003

    View details for PubMedID 34896593

  • Platelet transcriptome identifies progressive markers and potential therapeutic targets in chronic myeloproliferative neoplasms. Cell reports. Medicine Shen, Z., Du, W., Perkins, C., Fechter, L., Natu, V., Maecker, H., Rowley, J., Gotlib, J., Zehnder, J., Krishnan, A. 2021; 2 (10): 100425


    Predicting disease progression remains a particularly challenging endeavor in chronic degenerative disorders and cancer, thus limiting early detection, risk stratification, and preventive interventions. Here, profiling the three chronic subtypes of myeloproliferative neoplasms (MPNs), we identify the blood platelet transcriptome as a proxy strategy for highly sensitive progression biomarkers that also enables prediction of advanced disease via machine-learning algorithms. The MPN platelet transcriptome reveals an incremental molecular reprogramming that is independent of patient driver mutation status or therapy. Subtype-specific markers offer mechanistic and therapeutic insights, and highlight impaired proteostasis and a persistent integrated stress response. Using a LASSO model with validation in two independent cohorts, we identify the advanced subtype MF at high accuracy and offer a robust progression signature toward clinical translation. Our platelet transcriptome snapshot of chronic MPNs demonstrates a proof-of-principle for disease risk stratification and progression beyond genetic data alone, with potential utility in other progressive disorders.

    View details for DOI 10.1016/j.xcrm.2021.100425

    View details for PubMedID 34755136

    View details for PubMedCentralID PMC8561315

  • Development of immunosuppressive myeloid cells to induce tolerance in solid organ and hematopoietic cell transplant recipients. Blood advances Jensen, K. P., Hongo, D., Ji, X., Zheng, P., Pawar, R. D., Wu, H., Busque, S., Scandling, J. D., Shizuru, J. A., Lowsky, R., Shori, A., Dutt, S., Waters, J., Saraswathula, A., Baker, J., Tamaresis, J. S., Lavori, P., Negrin, R. S., Maecker, H. T., Engleman, E. G., Meyer, E., Strober, S. 2021


    Replacement of failed organs followed by safe withdrawal of immunosuppressive drugs have long been the goals of organ transplantation. We studied changes in the balance of T and myeloid cells in blood of HLA-matched and -mismatched patients given living donor kidney transplants (KTx) followed by total lymphoid irradiation (TLI), anti-thymocyte globulin (ATG) conditioning, and donor hematopoietic cell transplant (HCT) to induce mixed chimerism and immune tolerance. The clinical trials were based on a conditioning regimen used to establish mixed chimerism and tolerance in mice. In pre-clinical murine studies, there was a profound depletion of T cells and an increase in immunosuppressive, polymorphonuclear (pmn), myeloid derived suppressor cells (MDSCs) in the spleen and blood following transplant. Selective depletion of the pmn-MDSCs in mice abrogated mixed chimerism and tolerance. In our clinical trials, patients given an analogous tolerance conditioning regimen developed similar changes including profound depletion of T cells and a marked increase in MDSCs in blood post-transplant. Post-transplant pmn-MDSCs transiently increased expression of lectin-type, oxidized LDL receptor-1 (LOX-1), a marker of immunosuppression, and production of the T cell inhibitor, arginase-1. These post-transplant pmn-MDSCs suppressed the activation, proliferation, and inflammatory cytokine secretion of autologous, TCR microbead-stimulated, pre-transplant T cells when co-cultured in vitro. In conclusion, we elucidated changes in receptors, and function of immunosuppressive myeloid cells in patients enrolled in the tolerance protocol that were nearly identical to the that of MDSCs required for tolerance in mice. The clinical trials are registered in under NCT #s 00319657 and 01165762.

    View details for DOI 10.1182/bloodadvances.2020003669

    View details for PubMedID 34432869

  • Novel circulating and tissue monocytes as well as macrophages in pancreatitis and recovery. Gastroenterology Manohar, M., Jones, E. K., Rubin, S. J., Subrahmanyam, P. B., Swaminathan, G., Mikhail, D., Bai, L., Singh, G., Wei, Y., Sharma, V., Siebert, J. C., Maecker, H. T., Husain, S. Z., Park, W. G., Pandol, S. J., Habtezion, A. 2021


    BACKGROUND AND AIMS: Acute pancreatitis (AP) is an inflammatory disease with mild to severe course that is associated with local and systemic complications and significant mortality. Uncovering inflammatory pathways that lead to progression and recovery will inform ways to monitor and/or develop effective therapies.METHODS: We performed single-cell mass cytometry (CyTOF) analysis to identify pancreatic and systemic inflammatory signals during mild (referred as AP), severe AP (SAP) and recovery using two independent experimental models and blood from AP and recurrent AP (RAP) patients. Flowcytometric validation of monocytes subsets identified by CyTOF analysis was performed independently.RESULTS: Ly6C+ inflammatory monocytes were most altered cells in the pancreas during experimental AP, recovery, and SAP. Deep profiling uncovered heterogeneity among pancreatic and blood monocytes and identified seven novel subsets during AP and recovery, and six monocyte subsets during SAP. Notably, a dynamic shift in pancreatic CD206+ macrophage population was observed during AP and recovery. Deeper profiling of the CD206+ macrophage identified seven novel subsets during AP, recovery and SAP. DE analysis of these novel monocyte and CD206+ macrophage subsets revealed significantly altered surface (CD44, CD54, CD115, CD140a, CD196, PDPN) and functional markers (IFN-gamma, IL-4, IL-22, LAP-TGF-beta, TNF-alpha, T-bet, RoRgammat) that were associated with recovery and SAP. Moreover, a targeted functional analysis further revealed distinct expression of pro- and anti-inflammatory cytokines by pancreatic CD206+ macrophage subsets as the disease either progressed or resolved. Similarly, we identified heterogeneity among circulating classical inflammatory monocytes (CD14+CD16-) and novel subsets in patients with AP and RAP.CONCLUSION: We identified several novel monocyte/macrophage subsets with unique phenotype and functional characteristics that are associated with AP, recovery, and SAP. Our findings highlight differential innate immune responses during AP progression and recovery that can be leveraged for future disease monitoring and targeting.

    View details for DOI 10.1053/j.gastro.2021.08.033

    View details for PubMedID 34450180

  • Brief report: Tempol, a novel antioxidant, inhibits both activated T cell and antigen presenting cell derived cytokines in-vitro from COVID-19 patients. Clinical immunology (Orlando, Fla.) Mathi, K., Rosenberg-Hasson, Y., Maecker, H., Carlo, D. J., Moss, R. B. 2021: 108828


    COVID-19 is characterized by a dysregulation of inflammatory cytokines ultimately resulting a cytokine storm that can result in significant morbidity and mortality. We developed an in-vitro assay using activated peripheral blood mononuclear cells (PBMCs) stimulated with lipopolysaccharide (LPS) or CD3 + CD28 to examine secretion of cytokines from antigen presenting cells (APCs) and T cells, respectively, in donor patients with a history of COVID-19 (convalescent) and uninfected negative controls. We hypothesized that a novel antioxidant called Tempol may decrease cytokines from activated peripheral blood cells from both COVID-19 patients and normal donors. Preincubation of immune cells with Tempol resulted in a significant (P < 0.05) decrease in multiple T cell and APC-derived cytokines from both cells of COVID-19 (n = 7) and uninfected donors (n = 7). These preliminary results suggest that Tempol has strong in-vitro anti-cytokine activity and supports additional studies examining the use of Tempol for the treatment of COVID-19.

    View details for DOI 10.1016/j.clim.2021.108828

    View details for PubMedID 34425240

  • 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)


    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

  • IL-7 expands lymphocyte populations and enhances immune responses to sipuleucel-T in patients with metastatic castration-resistant prostate cancer (mCRPC). Journal for immunotherapy of cancer Pachynski, R. K., Morishima, C., Szmulewitz, R., Harshman, L., Appleman, L., Monk, P., Bitting, R. L., Kucuk, O., Millard, F., Seigne, J. D., Fling, S. P., Maecker, H. T., Duault, C., Ramchurren, N., Hess, B., D'Amico, L., Lacroix, A., Kaiser, J. C., Morre, M., Gregoire, A., Cheever, M., Yu, E. Y., Fong, L. 2021; 9 (8)


    BACKGROUND: Sipuleucel-T (sip-T) is a Food and Drug Administration (FDA)-approved autologous cellular immunotherapy for metastatic castration-resistant prostate cancer (mCRPC). We hypothesized that combining sip-T with interleukin (IL)-7, a homeostatic cytokine that enhances both B and T cell development and proliferation, would augment and prolong antigen-specific immune responses against both PA2024 (the immunogen for sip-T) and prostatic acid phosphatase (PAP).METHODS: Fifty-four patients with mCRPC treated with sip-T were subsequently enrolled and randomized 1:1 into observation (n=26) or IL-7 (n=28) arms of a phase II clinical trial (NCT01881867). Recombinant human (rh) IL-7 (CYT107) was given weekly*4. Immune responses were evaluated using flow cytometry, mass cytometry (CyTOF), interferon (IFN)-gamma ELISpot, 3H-thymidine incorporation, and ELISA.RESULTS: Treatment with rhIL-7 was well tolerated. For the rhIL-7-treated, but not observation group, statistically significant lymphocyte subset expansion was found, with 2.3-2.6-fold increases in CD4+T, CD8+T, and CD56bright NK cells at week 6 compared with baseline. No significant differences in PA2024 or PAP-specific T cell responses measured by IFN-gamma ELISpot assay were found between rhIL-7 and observation groups. However, antigen-specific T cell proliferative responses and humoral IgG and IgG/IgM responses significantly increased over time in the rhIL-7-treated group only. CyTOF analyses revealed pleiotropic effects of rhIL-7 on lymphocyte subsets, including increases in CD137 and intracellular IL-2 and IFN-gamma expression. While not powered to detect clinical outcomes, we found that 31% of patients in the rhIL-7 group had prostate specific antigen (PSA) doubling times of >6 months, compared with 14% in the observation group.CONCLUSIONS: Treatment with rhIL-7 led to a significant expansion of CD4+ and CD8+ T cells, and CD56bright natural killer (NK) cells compared with observation after treatment with sip-T. The rhIL-7 treatment also led to improved antigen-specific humoral and T cell proliferative responses over time as well as to increased expression of activation markers and beneficial cytokines. This is the first study to evaluate the use of rhIL-7 after sip-T in patients with mCRPC and demonstrates encouraging results for combination approaches to augment beneficial immune responses.

    View details for DOI 10.1136/jitc-2021-002903

    View details for PubMedID 34452927

  • Novel Circulating and Tissue Monocytes As Well As Macrophages in Pancreatitis and Recovery Manohar, M., Jones, E. K., Rubin, S. S., Subrahmanyam, P. B., Mikhail, D., Bai, L., Singh, G., Wei, Y., Sharma, V., Swaminathan, G., Siebert, J. C., Maecker, H. T., Park, W., Pandol, S. J., Husain, S., Habtezion, A. LIPPINCOTT WILLIAMS & WILKINS. 2021: 1079-1080
  • Protective Effect of Saffron in Mouse Colitis Models Through Immune Modulation. Digestive diseases and sciences Singh, G., Haileselassie, Y., Ji, A. R., Maecker, H. T., Sinha, S. R., Brim, H., Habtezion, A., Ashktorab, H. 2021


    BACKGROUND: People with inflammatory bowel disease (IBD) including ulcerative colitis are at risk for colorectal cancer. Despite available effective drugs used to treat IBD, many patients fail or lose response over time with some displaying drug-induced adverse events. Saffron (Crocus sativus) has been reported to have anti-inflammatory properties. Its protective role in IBD has not been explored extensively.AIM: To establish whether saffron treatment alleviates inflammation in experimental colitis.METHODS: Colitis was induced in C57BL/6 mice with 3% DSS and treated with either saffron doses (7.5, 15, 20, 25mg/kg body weight) or vehicle through daily gavage. On day 11, mice were euthanized and analyzed for gross and microscopic inflammation. Distal colon segments were collected for mRNA and protein expression of HO-1 protein and GPX2, (the downstream targets of NRF-2). Nrf-2 translocation from cytosol to nucleus was confirmed by immunofluorescence, and further Nrf-2 protein expression in nuclear and cytosolic fraction of colon was analyzed by immunoblot. Immune cells were isolated from the lamina propria of mouse colon for flow cytometry-based immunophenotyping. Colitis was also induced in C57BL/6 Ahr knockout and wild type mice to explore the involvement of Ahr-dependent pathways in saffron's protective effect(s). The therapeutic effect of saffron was further validated in another TNBS model of colitis.RESULTS: Saffron 20mg/kg body weightshowed improved colon gross and histology features and led to better body weight, colon length, histology score, and reduced disease activity index (DAI). Saffron significantly decreased pro-inflammatory macrophages (M1), while increasing anti-inflammatory macrophages (M2) and IL10+dendritic cells. Saffron treatment also enhanced CD3+T and CD3+CD8+T cells followed by increase in different CD3+CD4+T cells subsets like CD25+T cells, FoxP3+CD25+regulatory T cells, and CD4+FOXP3+CD25-regulatory T cells. Immunoblot analysis showed a significant increase in HO-1/GPX2 protein expression. With saffron treatment, Nrf-2 translocation into nucleus from cytosol also supports the involvement of Nrf-2 and its downstream targets in the protective effect of saffron. Further, we demonstrated that saffron in part exert anti-inflammatory effect through activation of aryl hydrocarbon receptor (AhR)-nuclear factor erythroid 2-related factor 2 (Nrf2)-dependent pathways.CONCLUSION: These data demonstrate saffron's therapeutic potential and its protective role in part via Ahr/Nrf-2 pathways and regulatory innate and adaptive immune cells.

    View details for DOI 10.1007/s10620-021-07163-3

    View details for PubMedID 34275090

  • Multi-Center Immune Profiling Mass Cytometry Assay Harmonization. Clinical cancer research : an official journal of the American Association for Cancer Research Sahaf, B., Pichavant, M., Lee, B. H., Duault, C., Thrash, E. M., Davila, M., Fernandez, N., Millerchip, K., Bentebibel, S., Haymaker, C., Sigal, N., Del Valle, D. M., Ranasinghe, S., Fayle, S., Sanchez-Espiridion, B., Zhang, J., Bernatchez, C., Wu, C. J., Wistuba, I. I., Kim-Schulze, S., Gnjatic, S., Bendall, S. C., Song, M., Thurin, M., Lee, J. J., Maecker, H. T., Rahman, A. 2021


    PURPOSE: The Cancer Immune Monitoring and Analysis Centers - Cancer Immunologic Data Commons (CIMAC-CIDC) Network is supported by the National Cancer Institute to identify biomarkers of response to cancer immunotherapies across clinical trials using state-of-the-art assays. A primary platform for CIMAC-CIDC studies is cytometry by time-of-flight (CyTOF), performed at all CIMAC laboratories. To ensure the ability to generate comparable CyTOF data across labs, a multistep cross-site harmonization effort was undertaken.EXPERIMENTAL DESIGN: We first harmonized standard operating procedures (SOPs) across the CIMAC sites. Because of a new acquisition protocol comparing original narrow - or new wide bore injector introduced by the vendor (Fluidigm), we also tested this protocol across sites before finalizing the harmonized SOP. We then performed cross-site assay harmonization experiments using 5 shared cryopreserved and one lyophilized internal control PBMCs with a shared lyophilized antibody cocktail consisting of 14 isotype-tagged antibodies previously validated, plus additional liquid antibodies. These reagents and samples were distributed to the CIMAC sites and the data were centrally analyzed by manual gating and automated methods (Astrolabe).RESULTS: Average coefficients of variation (CVs) across sites for each cell population were reported and compared to a previous multisite CyTOF study. We reached an inter-site CV of under 20% for most cell subsets, similar to a previously published study.CONCLUSIONS: These results establish the ability to reproduce CyTOF data across sites in multi-center clinical trials, and also highlight the importance of quality control procedures, such as the use of spike-in control samples, for tracking variability in this assay.

    View details for DOI 10.1158/1078-0432.CCR-21-2052

    View details for PubMedID 34266889

  • 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


    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

  • The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination. Cell Wimmers, F., Donato, M., Kuo, A., Ashuach, T., Gupta, S., Li, C., Dvorak, M., Foecke, M. H., Chang, S. E., Hagan, T., De Jong, S. E., Maecker, H. T., van der Most, R., Cheung, P., Cortese, M., Bosinger, S. E., Davis, M., Rouphael, N., Subramaniam, S., Yosef, N., Utz, P. J., Khatri, P., Pulendran, B. 2021


    Emerging evidence indicates a fundamental role for the epigenome in immunity. Here, we mapped the epigenomic and transcriptional landscape of immunity to influenza vaccination in humans at the single-cell level. Vaccination against seasonal influenza induced persistently diminished H3K27ac in monocytes and myeloid dendritic cells (mDCs), which was associated with impaired cytokine responses to Toll-like receptor stimulation. Single-cell ATAC-seq analysis revealed an epigenomically distinct subcluster of monocytes with reduced chromatin accessibility at AP-1-targeted loci after vaccination. Similar effects were observed in response to vaccination with the AS03-adjuvanted H5N1 pandemic influenza vaccine. However, this vaccine also stimulated persistently increased chromatin accessibility at interferon response factor (IRF) loci in monocytes and mDCs. This was associated with elevated expression of antiviral genes and heightened resistance to the unrelated Zika and Dengue viruses. These results demonstrate that vaccination stimulates persistent epigenomic remodeling of the innate immune system and reveal AS03's potential as an epigenetic adjuvant.

    View details for DOI 10.1016/j.cell.2021.05.039

    View details for PubMedID 34174187

  • Dynamic Serial Cytokine Measurements During Intravenous Ca-DTPA Chelation in Gadolinium Deposition Disease and Gadolinium Storage Condition: A Pilot Study. Investigative radiology Maecker, H. T., Siebert, J. C., Rosenberg-Hasson, Y., Koran, L. M., Ramalho, M., Semelka, R. C. 2021


    PURPOSE: The aim of this study was to investigate the feasibility of measuring early changes in serum cytokine levels after intravenous diethylenetriaminepentaacetic acid (Ca-DTPA) chelation in patients manifesting either gadolinium deposition disease (GDD) or gadolinium storage condition (GSC) and the possible usefulness of this method in further research.METHODS: Four patients with recent-onset GDD (≤1 year) and 2 patients with long-standing GSC (4 and 9 years) underwent chelation with intravenous bolus administration of Ca-DTPA. Multiple blood draws were performed to measure serum cytokines: at T = 0 (before Ca-DTPA injection) and 1, 5, 10, 30, 60 minutes, and 24 hours after Ca-DTPA injection. Patients rated the severity of GDD symptom flare at 24 hours. The 24-hour urine Gd amounts were measured prechelation and for the 24 hours after chelation. Serum samples were analyzed blind to whether patients had GDD or GSC but with knowledge of the time points characterizing each sample.RESULTS: Urine samples for both GDD and GSC patients showed increases in Gd postchelation. All GDD patients experienced flare reactions postchelation; the 2 GSC patients did not. Two cytokines, EGF and sCD40L, peaked at 30 minutes postchelation in at least 4 of the 6 participants. Three cytokines, ENA78/CXCL5, EOTAXIN/CCL11, and LEPTIN, peaked at 24 hours in at least 4 of the 6 participants. Two participants were high outliers for a large number of cytokines across time points. No clear distinction between GDD and GSC was apparent from the cytokine patterns, although differences were present.CONCLUSIONS: This pilot study describes precise temporal resolution (in the range of minutes) after a cytokine-inciting event. Select cytokines exhibited peak values at different time points. At this preliminary stage of investigation, peak cytokine release seems to reflect the amount of Gd mobilized rather than the severity of the patient symptomatic reaction. Too few subjects were studied to support statistical analysis between GDD and GSC groups, although differences were observed through visual data analysis.

    View details for DOI 10.1097/RLI.0000000000000803

    View details for PubMedID 34120127

  • Activated Natural Killer Cells Predict Poor Clinical Prognosis in High-risk B- and T- cell Acute Lymphoblastic Leukemia. Blood Duault, C., Kumar, A., Taghi Khani, A., Lee, S. J., Yang, L., Huang, M., Hurtz, C., Manning, B., Ghoda, L. Y., McDonald, T., Lacayo, N. J., Sakamoto, K. M., Carroll, M. P., Tasian, S. K., Marcucci, G., Yu, J., Caligiuri, M. A., Maecker, H. T., Swaminathan, S. 2021


    B- and T- cell acute lymphoblastic leukemia (B/T-ALL) may be refractory or recur after therapy by suppressing host anti-cancer immune surveillance mediated specifically by natural killer (NK) cells. We delineated the phenotypic and functional defects in NK cells of high-risk B/T-ALL patients using mass, flow, and in silico cytometry, with the goal of further elucidating the role of NK cells in sustaining ALL regression. We found that, compared to normal counterparts, NK cells in B/T-ALL patients are less cytotoxic, but exhibit an activated signature characterized by high CD56, high CD69, production of activated NK-origin cytokines, and calcium signaling. We demonstrated that defective maturation of NK cells into cytotoxic effectors prevents NK cells of ALL patients from lysing NK-sensitive targets as efficiently as normal NK cells. Additionally, we showed that NK cells in ALL are exhausted, which is likely caused by their chronic activation. We found that increased frequencies of activated cytokine-producing NK cells are associated with increased disease severity and independently predict poor clinical outcome in ALL patients. Our studies highlight the benefits of developing NK cell profiling as a diagnostic tool to predict clinical outcome in patients with ALL and underscore the clinical potential of allogeneic NK infusions to prevent ALL recurrence.

    View details for DOI 10.1182/blood.2020009871

    View details for PubMedID 34077953

  • Association of Premature Immune Aging and Cytomegalovirus After Solid Organ Transplant. Frontiers in immunology Higdon, L. E., Gustafson, C. E., Ji, X., Sahoo, M. K., Pinsky, B. A., Margulies, K. B., Maecker, H. T., Goronzy, J., Maltzman, J. S. 2021; 12: 661551


    Immune function is altered with increasing age. Infection with cytomegalovirus (CMV) accelerates age-related immunological changes resulting in expanded oligoclonal memory CD8 T cell populations with impaired proliferation, signaling, and cytokine production. As a consequence, elderly CMV seropositive (CMV+) individuals have increased mortality and impaired responses to other infections in comparison to seronegative (CMV-) individuals of the same age. CMV is also a significant complication after organ transplantation, and recent studies have shown that CMV-associated expansion of memory T cells is accelerated after transplantation. Thus, we investigated whether immune aging is accelerated post-transplant, using a combination of telomere length, flow cytometry phenotyping, and single cell RNA sequencing. Telomere length decreased slightly in the first year after transplantation in a subset of both CMV+ and CMV- recipients with a strong concordance between CD57+ cells and short telomeres. Phenotypically aged cells increased post-transplant specifically in CMV+ recipients, and clonally expanded T cells were enriched for terminally differentiated cells post-transplant. Overall, these findings demonstrate a pattern of accelerated aging of the CD8 T cell compartment in CMV+ transplant recipients.

    View details for DOI 10.3389/fimmu.2021.661551

    View details for PubMedID 34122420

    View details for PubMedCentralID PMC8190404

  • Immune profiling of COVID-19: preliminary findings and implications for the pandemic. Journal for immunotherapy of cancer Maecker, H. T. 2021; 9 (5)


    SARS-CoV-2 infection can have widely diverse clinical outcomes, from asymptomatic infection to death, with many possible clinical symptoms and syndromes. It is thus essential to understand how the virus interacts with the host immune system to bring about these varied outcomes and to inform vaccine development. We now know that both antibody and T cell responses are induced in the majority of infected individuals, and that cross-reactive responses from other coronaviruses also exist in the uninfected population. Innate immune responses are a key focus of research and may influence the course of disease and the character of subsequent adaptive responses. Finally, baseline immune profiles and changes during early acute infection may be key to predicting the course of disease. Understanding all these aspects can help to create better immune monitoring tools for COVID-19, including tools for predicting disease severity or specific sequelae, perhaps even prior to infection.

    View details for DOI 10.1136/jitc-2021-002550

    View details for PubMedID 33963016

  • Immune Changes Beyond Th2 Pathways During Rapid Multifood Immunotherapy enabled with Omalizumab. Allergy Manohar, M., Dunham, D., Gupta, S., Yan, Z., Zhang, W., Minnicozzi, S., Kirkey, M., Bunning, B., Chowdhury, R. R., Galli, S. J., Boyd, S. D., Kost, L. E., Chinthrajah, R. S., Desai, M., Oettgen, H. C., Maecker, H. T., Yu, W., DeKruyff, R. H., Andorf, S., Nadeau, K. C. 2021


    BACKGROUND: Multifood Oral Immunotherapy (mOIT) with adjunctive anti-IgE (omalizumab, Xolair ) treatment affords safe, effective, and rapid desensitization to multiple foods, although the specific immune mechanisms mediating this desensitization remain to be fully elucidated.METHODS: Participants in our phase 2 mOIT trial (NCT02643862) received omalizumab from baseline to week 16 and mOIT from week 8 to week 36. We compared the immune profile of PBMCs and plasma taken at baseline, week 8 and week 36 using high-dimensional mass cytometry, component-resolved diagnostics, the indirect basophil activation test, and Luminex.RESULTS: We found (i) decreased frequency of IL4+ peanut-reactive CD4+ T cells and a marked downregulation of GPR15 expression and CXCR3 frequency among gammadelta and CD8+ T cell subsets at week 8 during the initial, omalizumab-alone induction phase; (ii) significant upregulation of the skin-homing receptor CCR4 in peanut-reactive CD4+ T and Th2 effector memory (EM) cells and of cutaneous lymphocyte-associated antigen (CLA) in peanut-reactive CD8+ T and CD8+ EM cells (iii) downregulation of CD86 expression among antigen-presenting cell subsets; and (iv) reduction in pro-inflammatory cytokines, notably IL-17, at week 36 post-OIT. We also observed significant attenuation of the Th2 phenotype post-OIT, defined by downregulation of IL-4 peanut-reactive T cells and OX40 in Th2EM cells, increased allergen component-specific IgG4/IgE ratio, and decreased allergen-driven activation of indirectly sensitized basophils.CONCLUSIONS: This exploratory study provides novel comprehensive insight into the immune underpinnings of desensitization through omalizumab-facilitated mOIT. Moreover, this study provides encouraging results to support the complex immune changes that can be induced by OIT.

    View details for DOI 10.1111/all.14833

    View details for PubMedID 33782956

  • Functional monocytic myeloid-derived suppressor cells increase in blood but not airways and predict COVID-19 severity JOURNAL OF CLINICAL INVESTIGATION Falck-Jones, S., Vangeti, S., Yu, M., Falck-Jones, R., Cagigi, A., Badolati, I., Osterberg, B., Lautenbach, M., Ahlberg, E., Lin, A., Lepzien, R., Szurgot, I., Lenart, K., Hellgren, F., Maecker, H., Salde, J., Albert, J., Johansson, N., Bell, M., Lore, K., Farnert, A., Smed-Sorensen, A. 2021; 131 (6)

    View details for DOI 10.1172/JCI144734.

    View details for Web of Science ID 000663119400001

  • Safety and Efficacy of B-Cell Depletion with Rituximab for the Treatment of Systemic Sclerosis Associated Pulmonary Arterial Hypertension: A Multi-center, Double-blind, Randomized, Placebo-controlled Trial. American journal of respiratory and critical care medicine Zamanian, R. T., Badesch, D., Chung, L., Domsic, R. T., Medsger, T., Pinckney, A., Keyes-Elstein, L., D'Aveta, C., Spychala, M., White, R. J., Hassoun, P. M., Torres, F., Sweatt, A. J., Molitor, J. A., Khanna, D., Maecker, H., Welch, B., Goldmuntz, E., Nicolls, M. R., NIH ASC01 Study Group 2021


    RATIONALE: Systemic sclerosis-pulmonary arterial hypertension (SSc-PAH) is one of the most prevalent and deadly forms of PAH. B cells may contribute to SSc pathogenesis.OBJECTIVE: We investigated the safety and efficacy of B-cell depletion for SSc-PAH.METHODS AND MEASUREMENTS: In an NIH-sponsored, multi-center, double-blinded, randomized, placebo-controlled, proof-of-concept trial, 57 SSc-PAH patients on stable-dose standard medical therapy received two infusions of 1000 mg of rituximab or placebo administered two weeks apart. The primary outcome measure was the change in six-minute walk distance (6MWD) at 24 weeks. Secondary endpoints included safety and invasive hemodynamics. We applied a machine learning approach to predict drug-responsiveness.MAIN RESULTS: We randomized 57 subjects from 2010-2018. In the primary analysis, using data through week 24, the adjusted mean change in 6MWD at 24 weeks favored the treatment arm but did not reach statistical significance (23.6±11.1m vs. 0.5±9.7m, p=0.12). While a negative study, when data through week 48 were also considered, the estimated change in 6MWD at week 24 was 25.5±8.8m for rituximab and 0.4±7.4m for placebo (p=0.03). Rituximab treatment appeared to be safe and well tolerated. Low levels of rheumatoid factor (RF), IL-12, and IL-17 were sensitive and specific as favorable predictors of a rituximab response as measured by an improved 6MWD (ROC AUC 0.88-0.95).CONCLUSIONS: B cell depletion therapy is a potentially effective and safe adjuvant treatment for SSc-PAH. Future studies in these patients can confirm whether the identified biomarkers predict rituximab-responsiveness. Clinical trial registration available at, ID: NCT01086540.

    View details for DOI 10.1164/rccm.202009-3481OC

    View details for PubMedID 33651671

  • 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


    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

  • Network for biomarker immunoprofiling for cancer immunotherapy: Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Commons (CIMAC-CIDC). Clinical cancer research : an official journal of the American Association for Cancer Research Chen, H. X., Song, M., Maecker, H. T., Gnjatic, S., Patton, D., Lee, J. J., Adam, S. J., Moravec, R., Liu, X. S., Cerami, E., Lindsay, J., Hodi, F. S., Wu, C., Wistuba, I. I., Al-Atrash, G., Bernatchez, C., Bendall, S. C., Hewitt, S. M., Sharon, E., Streicher, H., Enos, R. A., Bowman, M. D., Tatard-Leitman, V. M., Sanchez-Espiridion, B., Ranasinghe, S., Pichavant, M., Del Valle, D. M., Yu, J., Janssens, S., Peterson-Klaus, J., Rowe, C., Bongers, G., Jenq, R. R., Chang, C., Abrams, J. S., Mooney, M., Doroshow, J. H., Harris, L. N., Thurin, M. 2021


    Immunoprofiling to identify biomarkers and integration with clinical trials outcome are critical to improve immunotherapy approaches for cancer patients. However, the translational potential of individual studies is often limited by small sample size of trials and the complexity of immuno-oncology biomarkers. Variability in assays further limits comparison and interpretation of data across studies and laboratories. To enable a systematic approach to biomarker identification and correlation with clinical outcome across trials, the Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Commons (CIMAC-CIDC) Network was established through support of the Cancer MoonshotSM Initiative of the National Cancer Institute and the Partnership for Accelerating Cancer Therapies (PACT) with industry partners via the Foundation for the National Institutes of Health. The CIMAC-CIDC Network is composed of four academic centers (CIMACs) with multidisciplinary expertise in the field of cancer immunotherapy that provide validated and harmonized assays for immune profiling. A data coordinating center (CIDC) provides the computational expertise and resources for biomarker data storage and analysis platforms for correlation with clinical data. This overview highlights strategies for assay harmonization to enable cross-trial and cross-site data analysis and describes key elements for establishing a network to enhance immuno-oncology biomarker development. These include an operational infrastructure; validation and harmonization of core immunoprofiling assays; platforms for data ingestion and integration; and access to specimens from clinical trials. Published in the same volume are reports of harmonization for core analyses: whole exome sequencing, RNA sequencing, cytometry by time of flight, and immunohistochemistry/immunofluorescence.

    View details for DOI 10.1158/1078-0432.CCR-20-3241

    View details for PubMedID 33419780

  • Acute Chelation Therapy-Associated Changes in Urine Gadolinium, Self-reported Flare Severity, and Serum Cytokines in Gadolinium Deposition Disease. Investigative radiology Maecker, H. T., Siebert, J. C., Rosenberg-Hasson, Y. n., Koran, L. M., Ramalho, M. n., Semelka, R. C. 2021


    The aim of this study was to determine the following in patients who have undergone magnetic resonance imaging with gadolinium-based contrast agents (GBCAs) and meet the proposed diagnostic criteria for gadolinium deposition disease (GDD): (1) the effectiveness of chelation therapy (CT) with intravenous Ca-diethylenetriaminepentaacetic acid in removing retained gadolinium (Gd) and factors affecting the amount removed; (2) the frequency of CT-induced Flare, that is, GDD diagnostic symptom worsening, and factors affecting Flare intensity; (3) whether, as reported in a separate cohort, GDD patients' serum cytokine levels differ significantly from those in healthy normal controls and change significantly in response to CT; and (4) whether urine Gd, Flare reaction, and serum cytokine findings in GDD patients are mimicked in non-ill patients described as having gadolinium storage condition (GSC).Twenty-one GDD subjects and 3 GSC subjects underwent CT. Patients provided pre-CT and post-CT 24-hour urine samples for Gd content determination along with pre-CT and 24-hour post-CT serum samples for cytokine analysis. Patients rated potential Flare 24 hours after CT. Pre-CT and post-CT 24-hour urine Gd analyses and Luminex serum cytokine assays were performed blind to patients' GDD and GSC status and all other data except age and sex. Serum cytokine levels in a healthy normal control group of age- and sex-matched subjects drawn from Stanford influenza vaccination studies were measured once, contemporaneously with those of GDD and GSC patients, using the same Luminex assay.Urine Gd amounts increased post-CT by 4 times or more after 87% of the 30 CT sessions. The most important factors appeared to be the time since the last GBCA dose and the cumulative dose received. Urine Gd amounts for GDD and GSC patients fell in the same ranges. All GDD patients, and no GSC patient, reported a Flare 24 hours post-CT. Linear regression found that Flare intensity was significantly predicted by a model including pre- and post-CT Gd amounts and the number of GBCA-enhanced magnetic resonance imaging. Post-CT, multiple cytokines showed strong positive relationships with GDD patients' Flare intensity in multivariable models. The pre-CT serum levels of 12 cytokines were significantly different in GDD patients compared with healthy flu vaccine controls. The small number of GSC patients precluded analogous statistical testing. Post-CT, GDD patients' serum levels of 20 cytokines were significantly decreased, and 2 cytokines significantly increased. These cytokines did not exhibit the same change pattern in the 3 GSC patients. The small number of GSC patients precluded statistical comparisons of GSC to GDD patients' results.In this preliminary study, 24-hour urine Gd content increased markedly and similarly in GDD and GSC patients after Ca-diethylenetriaminepentaacetic acid CT. Post-CT Flare reaction developed only in GDD patients. The current study is the second finding significantly different serum cytokine levels in GDD patients compared with healthy normal controls. These differences and the difference between GDD and GSC patients' Flare and cytokine responses to CT suggest some inflammatory, immunologic, or other physiological differences in patients with GDD. Further research into the treatment and physiological underpinnings of GDD is warranted.

    View details for DOI 10.1097/RLI.0000000000000752

    View details for PubMedID 33449576

  • Altered Functional Mitochondrial Protein Levels in Plasma Neuron-Derived Extracellular Vesicles of Patients With Gadolinium Deposition. Frontiers in toxicology Goetzl, E. J., Maecker, H. T., Rosenberg-Hasson, Y., Koran, L. M. 2021; 3: 797496


    The retention of the heavy metal, gadolinium, after a Gadolinium-Based Contrast Agent-assisted MRI may lead to a symptom cluster termed Gadolinium Deposition Disease. Little is known of the disorder's underlying pathophysiology, but a recent study reported abnormally elevated serum levels of pro-inflammatory cytokines compared to normal controls. As a calcium channel blocker in cellular plasma and mitochondrial membranes, gadolinium also interferes with mitochondrial function. We applied to sera from nine Gadolinium Deposition Disease and two Gadolinium Storage Condition patients newly developed methods allowing isolation of plasma neuron-derived extracellular vesicles that contain reproducibly quantifiable levels of mitochondrial proteins of all major classes. Patients' levels of five mitochondrial functional proteins were statistically significantly lower and of two significantly higher than the levels in normal controls. The patterns of differences between study patients and controls for mitochondrial dynamics and mitochondrial proteins encompassing neuronal energy generation, metabolic regulation, ion fluxes, and survival differed from those seen for patients with first episode psychosis and those with Major Depressive Disorder compared to their controls. These findings suggest that mitochondrial dysfunction due to retained gadolinium may play a role in causing Gadolinium Deposition Disease. Larger samples of both GDD and GSC patients are needed to allow not only testing the repeatability of our findings, but also investigation of relationships of specific mitochondrial protein deficiencies or excesses and concurrent cytokine, genetic, or other factors to GDD's neurological and cognitive symptoms. Studies of neuronal mitochondrial proteins as diagnostic markers or indicators of treatment effectiveness are also warranted.

    View details for DOI 10.3389/ftox.2021.797496

    View details for PubMedID 35295151

  • 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


    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)


    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

  • Mass Cytometry Analysis of T-Helper Cells. Methods in molecular biology (Clifton, N.J.) Subrahmanyam, P. B., Maecker, H. T. 2021; 2285: 49–63


    CD4+ T cells or helper T cells play various roles in the immune response to pathogens, tumors, as well as in asthma, allergy, and autoimmunity. Consequently, there is great interest in the comprehensive investigation of different T helper cell subsets. Here, we use mass cytometry (CyTOF), which is similar to flow cytometry but uses metal ion-tagged antibodies, which are detected using time-of-flight mass spectrometry. CyTOF allows the simultaneous detection of over 40 different antibodies, allowing us to collect high-dimensional single-cell proteomic data on T helper subsets. We use an extensive staining panel with a large number of lineage markers, cytokines, and other functional markers to identify and characterize CD4+ T cell subsets. In this method, human peripheral blood mononuclear cells are stimulated ex vivo with PMA and ionomycin, which activates T cells. Theactivated CD4+ T cells can then be identified as Th1, Th2, or Th17 cells based on their production of IFNgamma, IL-4, and IL-17, respectively. Tregs are identified as CD4+CD25+CD127lo. Once Th1, Th2, Th17, and Tregs have been identified, they can be characterized in more detail using the large number of phenotypic and functional markers included in the CyTOF staining panel. Finally, automated and unbiased high-dimensional data analysis tools can be employed to comprehensively characterize T helper cells and discover novel features.

    View details for DOI 10.1007/978-1-0716-1311-5_4

    View details for PubMedID 33928542

  • Higher Levels of Pro-inflammatory Cytokines Are Associated With Higher Levels of Glutamate in the Anterior Cingulate Cortex in Depressed Adolescents. Frontiers in psychiatry Ho, T. C., Teresi, G. I., Segarra, J. R., Ojha, A., Walker, J. C., Gu, M., Spielman, D. M., Sacchet, M. D., Jiang, F., Rosenberg-Hasson, Y., Maecker, H., Gotlib, I. H. 2021; 12: 642976


    Animal models of stress and related conditions, including depression, have shown that elevated peripheral levels of inflammatory cytokines have downstream consequences on glutamate (Glu) in the brain. Although studies in human adults with depression have reported evidence of higher inflammation but lower Glu in the anterior cingulate cortex (ACC), the extent to which peripheral inflammation contributes to glutamatergic abnormalities in adolescents with depression is not well-understood. It is also unclear whether antioxidants, such as ascorbate (Asc), may buffer against the effects of inflammation on Glu metabolism. Fifty-five depressed adolescents were recruited in the present cross-sectional study and provided blood samples, from which we assayed pro-inflammatory cytokines, and underwent a short-TE proton magnetic spectroscopy scan at 3T, from which we estimated Glu and Asc in the dorsal ACC. In the 31 adolescents with usable cytokine and Glu data, we found that IL-6 was significantly positively associated with dorsal ACC Glu (beta = 0.466 ± 0.199, p = 0.029). Of the 16 participants who had usable Asc data, we found that at higher levels of dorsal ACC Asc, there was a negative association between IL-6 and Glu (interaction effect: beta = -0.906 ± 0.433, p = 0.034). Importantly, these results remained significant when controlling for age, gender, percentage of gray matter in the dorsal ACC voxel, BMI, and medication (antidepressant and anti-inflammatory) usage. While preliminary, our results underscore the importance of examining both immune and neural contributors to depression and highlight the potential role of anti-inflammatory compounds in mitigating the adverse effects of inflammation (e.g., glutamatergic neuroexcitotoxicity). Future studies that experimentally manipulate levels of inflammation, and of ascorbate, and that characterize these effects on cortical glutamate concentrations and subsequent behavior in animals and in humans are needed.

    View details for DOI 10.3389/fpsyt.2021.642976

    View details for PubMedID 33935833

  • 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


    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

  • Vi-Vaccinations Induce Heterogeneous Plasma Cell Responses That Associate With Protection From Typhoid Fever FRONTIERS IN IMMUNOLOGY Cross, D. L., Verheul, M. K., Leipold, M. D., Obermoser, G., Jin, C., Jones, E., Starr, J. S., Mohorianu, I., Blohmke, C. J., Maecker, H. T., Napolitani, G., Hill, J., Pollard, A. J. 2020; 11
  • SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. Journal for immunotherapy of cancer Hu-Lieskovan, S., Bhaumik, S., Dhodapkar, K., Grivel, J. J., Gupta, S., Hanks, B. A., Janetzki, S., Kleen, T. O., Koguchi, Y., Lund, A. W., Maccalli, C., Mahnke, Y. D., Novosiadly, R. D., Selvan, S. R., Sims, T., Zhao, Y., Maecker, H. T. 2020; 8 (2)


    Since the publication of the Society for Immunotherapy of Cancer's (SITC) original cancer immunotherapy biomarkers resource document, there have been remarkable breakthroughs in cancer immunotherapy, in particular the development and approval of immune checkpoint inhibitors, engineered cellular therapies, and tumor vaccines to unleash antitumor immune activity. The most notable feature of these breakthroughs is the achievement of durable clinical responses in some patients, enabling long-term survival. These durable responses have been noted in tumor types that were not previously considered immunotherapy-sensitive, suggesting that all patients with cancer may have the potential to benefit from immunotherapy. However, a persistent challenge in the field is the fact that only a minority of patients respond to immunotherapy, especially those therapies that rely on endogenous immune activation such as checkpoint inhibitors and vaccination due to the complex and heterogeneous immune escape mechanisms which can develop in each patient. Therefore, the development of robust biomarkers for each immunotherapy strategy, enabling rational patient selection and the design of precise combination therapies, is key for the continued success and improvement of immunotherapy. In this document, we summarize and update established biomarkers, guidelines, and regulatory considerations for clinical immune biomarker development, discuss well-known and novel technologies for biomarker discovery and validation, and provide tools and resources that can be used by the biomarker research community to facilitate the continued development of immuno-oncology and aid in the goal of durable responses in all patients.

    View details for DOI 10.1136/jitc-2020-000705

    View details for PubMedID 33268350

  • Study Protocol for Teen Inflammation Glutamate Emotion Research (TIGER) FRONTIERS IN HUMAN NEUROSCIENCE Walker, J. C., Teresi, G. I., Weisenburger, R. L., Segarra, J. R., Ojha, A., Kulla, A., Sisk, L., Gu, M., Spielman, D. M., Rosenberg-Hasson, Y., Maecker, H. T., Singh, M. K., Gotlib, I. H., Ho, T. C. 2020; 14
  • Immune biomarkers link air pollution exposure to blood pressure in adolescents. Environmental health : a global access science source Prunicki, M., Cauwenberghs, N., Ataam, J. A., Movassagh, H., Kim, J. B., Kuznetsova, T., Wu, J. C., Maecker, H., Haddad, F., Nadeau, K. 2020; 19 (1): 108


    BACKGROUND: Childhood exposure to air pollution contributes to cardiovascular disease in adulthood. Immune and oxidative stress disturbances might mediate the effects of air pollution on the cardiovascular system, but the underlying mechanisms are poorly understood in adolescents. Therefore, we aimed to identify immune biomarkers linking air pollution exposure and blood pressure levels in adolescents.METHODS: We randomly recruited 100 adolescents (mean age, 16years) from Fresno, California. Using central-site data, spatial-temporal modeling, and distance weighting exposures to the participant's home, we estimated average pollutant levels [particulate matter (PM), polyaromatic hydrocarbons (PAH), ozone (O3), carbon monoxide (CO) and nitrogen oxides (NOx)]. We collected blood samples and vital signs on health visits. Using proteomic platforms, we quantitated markers of inflammation, oxidative stress, coagulation, and endothelial function. Immune cellular characterization was performed via mass cytometry (CyTOF). We investigated associations between pollutant levels, cytokines, immune cell types, and blood pressure (BP) using partial least squares (PLS) and linear regression, while adjusting for important confounders.RESULTS: Using PLS, biomarkers explaining most of the variance in air pollution exposure included markers of oxidative stress (GDF-15 and myeloperoxidase), acute inflammation (C-reactive protein), hemostasis (ADAMTS, D-dimer) and immune cell types such as monocytes. Most of these biomarkers were independently associated with the air pollution levels in fully adjusted regression models. In CyTOF analyses, monocytes were enriched in participants with the highest versus the lowest PM2.5 exposure. In both PLS and linear regression, diastolic BP was independently associated with PM2.5, NO, NO2, CO and PAH456 pollution levels (P≤0.009). Moreover, monocyte levels were independently related to both air pollution and diastolic BP levels (P≤0.010). In in vitro cell assays, plasma of participants with high PM2.5 exposure induced endothelial dysfunction as evaluated by eNOS and ICAM-1 expression and tube formation.CONCLUSIONS: For the first time in adolescents, we found that ambient air pollution levels were associated with oxidative stress, acute inflammation, altered hemostasis, endothelial dysfunction, monocyte enrichment and diastolic blood pressure. Our findings provide new insights on pollution-related immunological and cardiovascular disturbances and advocate preventative measures of air pollution exposure.

    View details for DOI 10.1186/s12940-020-00662-2

    View details for PubMedID 33066786

  • An initial investigation of serum cytokine levels in patients with gadolinium retention. Radiologia brasileira Maecker, H. T., Wang, W., Rosenberg-Hasson, Y., Semelka, R. C., Hickey, J., Koran, L. M. 2020; 53 (5): 306–13


    Objective: To determine whether individuals with proposed gadolinium deposition disease (GDD) have elevated serum levels of pro-inflammatory and pro-fibrotic cytokines, and whether specific cytokines are correlated with certain symptoms.Materials and Methods: Twenty-four participants recruited between May 2016 and June 2017 met GDD diagnostic criteria. The 64 control subjects provided serum samples before prophylactic flu vaccination. Serum cytokine levels were obtained with Luminex serum cytokine assay using eBiosciences/Affymetrix human 62-plex kits. Wilcoxon rank-sum tests were performed to assess the difference between the median fluorescence intensity values for the participants and the control group. Generalized linear models were built to evaluate the association between each cytokine of interest and selected participant symptoms.Results: Serum levels of 14 cytokines, including nine pro-inflammatory cytokines, were statistically significantly elevated compared to controls (p ≤ 0.05). Hypotheses regarding pro-fibrotic cytokines and cytokine links to specific symptoms' intensity were not confirmed.Conclusion: The statistically significantly elevated cytokines may be markers of susceptibility to GDD or agents of symptom induction. These findings suggest that individuals developing symptoms characteristic of GDD after a contrast-assisted magnetic resonance imaging should be studied to investigate whether gadolinium retention and elevated cytokines may be related to their symptoms.

    View details for DOI 10.1590/0100-3984.2019.0075

    View details for PubMedID 33071374

  • Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science (New York, N.Y.) Arunachalam, P. S., Wimmers, F., Mok, C. K., Perera, R. A., Scott, M., Hagan, T., Sigal, N., Feng, Y., Bristow, L., Tak-Yin Tsang, O., Wagh, D., Coller, J., Pellegrini, K. L., Kazmin, D., Alaaeddine, G., Leung, W. S., Chan, J. M., Chik, T. S., Choi, C. Y., Huerta, C., Paine McCullough, M., Lv, H., Anderson, E., Edupuganti, S., Upadhyay, A. A., Bosinger, S. E., Maecker, H. T., Khatri, P., Rouphael, N., Peiris, M., Pulendran, B. 2020


    COVID-19 represents a global crisis, yet major knowledge gaps remain about human immunity to SARS-CoV-2. We analyzed immune responses in 76 COVID-19 patients and 69 healthy individuals from Hong Kong and Atlanta. In PBMCs of COVID-19 patients, there was reduced expression of HLA-DR and pro-inflammatory cytokines by myeloid cells, and impaired mTOR-signaling and IFN-alpha production by plasmacytoid DCs. In contrast, there were enhanced plasma levels of inflammatory mediators, including EN-RAGE, TNFSF14, and oncostatin-M, which correlated with disease severity and increased bacterial products in human plasma. Single-cell transcriptomics revealed no type-I IFN, reduced HLA-DR in myeloid cells of severe patients, and transient expression of IFN-stimulated genes. This was consistent with bulk PBMC transcriptomics, and transient, low plasma IFN-alpha levels during infection. These results reveal mechanisms and potential therapeutic targets for COVID-19.

    View details for DOI 10.1126/science.abc6261

    View details for PubMedID 32788292

  • Transcriptional changes in peanut-specific CD4+ T cells over the course of oral immunotherapy. Clinical immunology (Orlando, Fla.) Wang, W., Lyu, S., Ji, X., Gupta, S., Manohar, M., Dhondalay, G. K., Chinthrajah, S., Andorf, S., Boyd, S. D., Tibshirani, R., Galli, S. J., Nadeau, K. C., Maecker, H. T. 2020: 108568


    Oral immunotherapy (OIT) can successfully desensitize allergic individuals to offending foods such as peanut. Our recent clinical trial (NCT02103270) of peanut OIT allowed us to monitor peanut-specific CD4+ T cells, using MHC-peptide Dextramers, over the course of OIT. We used a single-cell targeted RNAseq assay to analyze these cells at 0, 12, 24, 52, and 104 weeks of OIT. We found a transient increase in TGFbeta-producing cells at 52 weeks in those with successful desensitization, which lasted until 117 weeks. We also performed clustering and identified 5 major clusters of Dextramer+ cells, which we tracked over time. One of these clusters appeared to be anergic, while another was consistent with recently described TFH13 cells. The other 3 clusters appeared to be Th2 cells by their coordinated production of IL-4 and IL-13, but they varied in their expression of STAT signaling proteins and other markers. A cluster with high expression of STAT family members also showed a possible transient increase at week 24 in those with successful desensitization. Single cell TCRalphabeta repertoire sequences were too diverse to track clones over time. Together with increased TGFbeta production, these changes may be mechanistic predictors of successful OIT that should be further investigated.

    View details for DOI 10.1016/j.clim.2020.108568

    View details for PubMedID 32783912

  • Cytokine profile in plasma of severe COVID-19 does not differ from ARDS and sepsis. JCI insight Wilson, J. G., Simpson, L. J., Ferreira, A., Rustagi, A., Roque, J. A., Asuni, A., Ranganath, T., Grant, P. M., Subramanian, A. K., Rosenberg-Hasson, Y., Maecker, H., Holmes, S., Levitt, J. E., Blish, C., Rogers, A. J. 2020


    BACKGROUND: Elevated levels of inflammatory cytokines have been associated with poor outcomes among COVID-19 patients. It is unknown, however, how these levels compare to those observed in critically ill patients with ARDS or sepsis due to other causes.METHODS: We used a luminex assay to determine expression of 76 cytokines from plasma of hospitalized COVID-19 patients and banked plasma samples from ARDS and sepsis patients. Our analysis focused on detecting statistical differences in levels of 6 cytokines associated with cytokine storm (IL-1b, IL-1RA, IL-6, IL-8, IL-18, and TNFalpha) between patients with moderate COVID-19, severe COVID-19, and ARDS or sepsis.RESULTS: 15 hospitalized COVID-19 patients, 9 of whom were critically ill, were compared to critically ill patients with ARDS (n = 12) or sepsis (n = 16). There were no statistically significant differences in baseline levels of IL-1b, IL-1RA, IL-6, IL-8, IL-18, and TNFalpha between patients with COVID-19 and critically ill controls with ARDS or sepsis.CONCLUSIONS: Levels of inflammatory cytokines were not higher in severe COVID-19 patients than in moderate COVID-19 or critically ill patients with ARDS or sepsis in this small cohort. Broad use of immunosuppressive therapies in ARDS has failed in numerous Phase 3 studies; use of these therapies in unselected patients with COVID-19 may be unwarranted.FUNDING: A.J.R.: Stanford ICU Biobank NHLBI K23 HL125663. C.A.B.: Burroughs Wellcome Fund Investigators in the Pathogenesis of Infectious Diseases #1016687; NIH/NIAID U19AI057229-16 (PI MM Davis); Stanford Maternal Child Health Research Institute; Chan Zuckerberg Biohub.

    View details for DOI 10.1172/jci.insight.140289

    View details for PubMedID 32706339

  • MYC functions as a switch for natural killer cell-mediated immune surveillance of lymphoid malignancies. Nature communications Swaminathan, S., Hansen, A. S., Heftdal, L. D., Dhanasekaran, R., Deutzmann, A., Fernandez, W. D., Liefwalker, D. F., Horton, C., Mosley, A., Liebersbach, M., Maecker, H. T., Felsher, D. W. 2020; 11 (1): 2860


    The MYC oncogene drives T- and B- lymphoid malignancies, including Burkitt's lymphoma (BL) and Acute Lymphoblastic Leukemia (ALL). Here, we demonstrate a systemic reduction in natural killer (NK) cell numbers in SRalpha-tTA/Tet-O-MYCON mice bearing MYC-driven T-lymphomas. Residual mNK cells in spleens of MYCON T-lymphoma-bearing mice exhibit perturbations in the terminal NK effector differentiation pathway. Lymphoma-intrinsic MYC arrests NK maturation by transcriptionally repressing STAT1/2 and secretion of Type I Interferons (IFNs). Treating T-lymphoma-bearing mice with Type I IFN improves survival by rescuing NK cell maturation. Adoptive transfer of mature NK cells is sufficient to delay both T-lymphoma growth and recurrence post MYC inactivation. In MYC-driven BL patients, low expression of both STAT1 and STAT2 correlates significantly with the absence of activated NK cells and predicts unfavorable clinical outcomes. Our studies thus provide a rationale for developing NK cell-based therapies to effectively treat MYC-driven lymphomas in the future.

    View details for DOI 10.1038/s41467-020-16447-7

    View details for PubMedID 32503978

  • A Novel Utility to Correct for Plate/Batch/Lot and Nonspecific Binding Artifacts in Luminex Data. Journal of immunology (Baltimore, Md. : 1950) Maecker, H. T., Rosenberg-Hasson, Y., Kolstad, K. D., Steen, V. D., Chung, L. S. 2020


    Cytokines and other secreted soluble proteins are routinely assayed as fluorescence intensities on the Luminex (Luminex, Austin, TX) platform. As with any immunoassay, a portion of the measured Ab binding can be nonspecific. Use of spiked-in microbead controls (e.g., AssayChex Process, Control Panel; Radix Biosolutions, Georgetown, TX) can determine the level of nonspecific binding on a per specimen basis. A statistical approach for correction of this assay's nonspecific binding artifact was first described in earlier work. The current paper describes a novel utility written in the R language (, that refines correction for nonspecific binding in three important ways: 1) via local polynomial regression, the utility allows for curvature in relationships between soluble protein median fluorescence intensities and nonspecific binding median fluorescence intensities; 2) to stabilize correction, the fit of the nonlinear regression function is obtained via repeated cross-validation; and 3) the utility addresses possible bias due to technical error in measured nonspecific binding. The utility first logarithm transforms and then removes plate/batch/lot artifacts from median fluorescence intensities prior to correction for nonspecific binding, even when plates/batches/lots are unbalanced with respect to experimental factors of interest. Continuous (e.g., age) and categorical (e.g., diagnosis) covariates are accommodated in plate/batch/lot artifact correction. We present application of the utility to a panel of 62 cytokines in a sample of human patients diagnosed with systemic sclerosis and to an experiment that examined multiple lots of a human 51-cytokine panel. The R script for our new utility is publicly available for download from the web.

    View details for DOI 10.4049/jimmunol.2000017

    View details for PubMedID 32376648

  • JAK-STAT Activity in Peripheral Blood Cells and Kidney Tissue in IgA Nephropathy. Clinical journal of the American Society of Nephrology : CJASN Tao, J., Mariani, L., Eddy, S., Maecker, H., Kambham, N., Mehta, K., Hartman, J., Wang, W., Kretzler, M., Lafayette, R. A. 2020


    BACKGROUND AND OBJECTIVES: IgA nephropathy is the most common primary glomerular disease in the world. Marked by mesangial inflammation and proliferation, it generally leads to progressive kidney fibrosis. As the Janus kinase signal transducer and activator of transcription pathway has been implicated as an important mediator of diabetic kidney disease and FSGS, detailed investigation of this pathway in IgA nephropathy was undertaken to establish the basis for targeting this pathway across glomerular diseases.DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: Well characterized patients with IgA nephropathy and controls were studied, allowing us to compare 77 patients with biopsy-proven IgA nephropathy with 45 healthy subjects. STAT phosphorylation was assessed in peripheral blood monocytes (PBMCs) by phosphoflow before and after cytokine stimulation. Kidney Janus kinase signal transducer and activator of transcription activity was studied by immunofluorescence and by transcriptomic studies. An STAT1 activity score was established using downstream transcriptional targets of pSTAT1 and associated with disease and clinical outcomes.RESULTS: We found PBMCs to have upregulated pSTAT production at baseline in patients with IgA nephropathy with a limited reserve to respond to cytokine stimulation compared with controls. Increased staining in glomerular mesangium and endothelium was seen for Jak-2 and pSTAT1 and in the tubulointerstitial for JAK2, pSTAT1, and pSTAT3. Activation of the Janus kinase signal transducer and activator of transcription pathway was further supported by increased pSTAT1 and pSTAT3 scores in glomerular and tubulointerstitial sections of the kidney (glomerular activation Z scores: 7.1 and 4.5, respectively; P values: <0.001 and <0.001, respectively). Clinically, phosphoflow results associated with proteinuria and kidney function, and STAT1 activation associated with proteinuria but was not associated with progression.CONCLUSIONS: Janus kinase signal transducer and activator of transcription signaling was activated in patients with IgA nephropathy compared with controls. There were altered responses in peripheral immune cells and increased message and activated proteins in the kidney. These changes variably related to proteinuria and kidney function.

    View details for DOI 10.2215/CJN.11010919

    View details for PubMedID 32354727

  • A Prospective, Phase 1 Trial of Nivolumab, Ipilimumab, and Radiotherapy in Patients with Advanced Melanoma. Clinical cancer research : an official journal of the American Association for Cancer Research Postow, M. A., Knox, S. J., Goldman, D. A., Elhanati, Y., Mavinkurve, V., Wong, P., Halpenny, D. F., Reddy, S. A., Vado, K. P., McCabe, D., Ramirez, K. A., Macri, M., Schwarzenberger, P., Ricciardi, T., Ryan, A., Venhaus, R. R., Momtaz, P., Shoushtari, A. N., Callahan, M. K., Chapman, P. B., Wolchok, J. D., Subrahmanyam, P. B., Maecker, H. T., Panageas, K. S., Barker, C. A. 2020


    PURPOSE: Preclinical data suggests radiotherapy is beneficial in combination with immune checkpoint blockade. Clinical trials have explored radiotherapy with single agent immune checkpoint blockade, but no trials have reported radiotherapy with the combination of nivolumab and ipilimumab.EXPERIMENTAL DESIGN: We conducted a phase 1 study of patients with stage IV melanoma receiving nivolumab and ipilimumab with two different dose-fractionation schemes of radiotherapy. Patients had at least one melanoma metastasis that would benefit from palliative radiotherapy and one metastasis that would not be irradiated. Nivolumab 1mg/kg + ipilimumab 3mg/kg and extracranial radiotherapy with a dose of 30 Gy in 10 fractions was administered in Cohort A, and then 27 Gy in 3 fractions was administered in Cohort B. The primary outcome was safety.RESULTS: Twenty patients were treated (10 in each cohort). The rates of treatment related grade 3-4 adverse events in Cohort A and Cohort B were 40% and 30%, respectively. There were no grade ≥3 adverse events attributed to radiation. Patients responded to treatment outside of the irradiated volume (Cohort A 5/10; Cohort B 1/9). No evaluable patients had progression of irradiated metastases. Immunologic changes were seen in the peripheral blood with increases in T cell receptor diversity in some responding patients.CONCLUSIONS: Radiotherapy with nivolumab and ipilimumab was safe compared to historical data of nivolumab and ipilimumab alone. Immunologic effects were observed in the peripheral blood. Randomized studies are ongoing to assess whether RT increases the efficacy of nivolumab and ipilimumab.

    View details for DOI 10.1158/1078-0432.CCR-19-3936

    View details for PubMedID 32205463

  • Impaired Immune Health in Survivors of Diffuse Large B-Cell Lymphoma. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Shree, T., Li, Q., Glaser, S. L., Brunson, A., Maecker, H. T., Haile, R. W., Levy, R., Keegan, T. H. 2020: JCO1901937


    PURPOSE: Therapeutic advances for diffuse large B-cell lymphoma (DLBCL) have led to an increasing number of survivors. Both DLBCL and its treatments perturb the immune system, yet little is known about immune health during extended survivorship.METHODS: In this retrospective cohort study, we compared 21,690 survivors of DLBCL from the California Cancer Registry (CCR) to survivors of breast, prostate, head and neck, and melanoma cancers. We linked their CCR records to a statewide database documenting hospital, emergency room, and ambulatory surgery visits and investigated the incidence of autoimmune conditions, immune deficiencies, and infections 1-10 years after cancer diagnosis.RESULTS: We found elevated incidence rate ratios (IRRs) for many immune-related conditions in survivors of DLBCL compared with other cancer survivors, including significantly and consistently elevated IRRs for viral and fungal pneumonias (up to 10.8-fold), meningitis (up to 5.3-fold), as well as humoral deficiency (up to 17.6-fold) and autoimmune cytopenias (up to 12-fold). IRRs for most conditions remained high even in the late survivorship period (5-10 years after cancer diagnosis). The elevated risks could not be explained by exposure to chemotherapy, stem-cell transplantation, or rituximab, except for IRRs for humoral deficiency, which were consistently higher after the incorporation of rituximab into DLBCL treatments.CONCLUSION: To our knowledge, this is the largest cohort study with extended follow-up to demonstrate impaired immune health in survivors of DLBCL. The observed persistent, elevated risks for autoimmune diseases, immune deficiencies, and infectious conditions may reflect persistent immune dysregulation caused by lymphoma or treatment and may lead to excess morbidity and mortality during survivorship. Improved understanding of these risks could meaningfully improve long-term care of patients with DLBCL.

    View details for DOI 10.1200/JCO.19.01937

    View details for PubMedID 32083991

  • High-Parametric Evaluation of Human Invariant Natural Killer T Cells to Delineate Heterogeneity in Allo- and Autoimmunity. Blood Erkers, T., Xie, B., Kenyon, L. J., Smith, B., Rieck, M., Jensen, K. P., Ji, X., Basina, M., Strober, S., Negrin, R. S., Maecker, H. T., Meyer, E. 2020


    Human invariant natural killer T cells (iNKTs) are a rare innate-like lymphocyte population that recognize glycolipids presented on CD1d. Studies in mice have shown that these cells are heterogenous and capable of enacting diverse functions, and the composition of iNKT subsets can alter disease outcomes. In contrast, far less is known about how heterogeneity in human iNKTs relates to disease. To address this, we use a high-dimensional, data-driven approach to devise a framework to parse human iNKT heterogeneity. Our data revealed novel and previously described iNKT phenotypes with distinct functions. In particular, we found two phenotypes of interest: 1) a population with Th1 function that was increased with iNKT activation characterized by HLA-II+CD161- expression, and 2) a population with enhanced cytotoxic function characterized by CD4-CD94+ expression. These populations, respectively, correlate with acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation and with new onset type 1 diabetes. Our study identifies human iNKT phenotypes associated with human disease that could aid in the development of biomarkers or therapeutics targeting iNKTs.

    View details for DOI 10.1182/blood.2019001903

    View details for PubMedID 31935280

  • The Application of Cytokine Expression Assays to Differentiate Active From Previously Treated Syphilis. The Journal of infectious diseases Kojima, N. n., Siebert, J. C., Maecker, H. n., Rosenberg-Hasson, Y. n., Leon, S. R., Vargas, S. K., Konda, K. A., Caceres, C. F., Klausner, J. D. 2020; 222 (4): 690–94


    To investigate the role of serum cytokine assays to distinguish between active from treated syphilis among serofast patients, we recruited individuals into a prospective cohort study. Participants underwent routine syphilis screening. We selected specimens from a majority cohort of serofast participants with treated and active syphilis. We analyzed specimens with a 62-cytokine multiplex bead-based enzyme-linked immunosorbent assay. Cytokines, brain-derived neurotrophic factor and tumor necrosis factor β, were most predictive. We built a decision tree that was 82.4% accurate, 100% (95% confidence interval, 82%-100%) sensitive, and 45% (18%-75%) specific. Our decision tree differentiated between serum specimens from serofast participants with treated syphilis versus active syphilis.

    View details for DOI 10.1093/infdis/jiaa127

    View details for PubMedID 32189000

  • Autoantibody-positive healthy individuals with lower lupus risk display a unique immune endotype. The Journal of allergy and clinical immunology Slight-Webb, S. n., Smith, M. n., Bylinska, A. n., Macwana, S. n., Guthridge, C. n., Lu, R. n., Merrill, J. T., Chakravarty, E. n., Arriens, C. n., Munroe, M. E., Maecker, H. T., Utz, P. J., Guthridge, J. M., James, J. A. 2020


    Autoimmune diseases comprise a spectrum of illnesses and are on the rise worldwide. Although anti-nuclear antibodies (ANA) are detected in many autoimmune diseases, up to 20% of healthy women are ANA+ and most will never develop clinical symptoms. Further, disease transition is higher among ANA+ African Americans compared to European Americans.To determine the immune features that might define and prevent transition to clinical autoimmunity in ANA+ healthy individuals.We comprehensively phenotype immune profiles of African Americans and European Americans who are ANA- healthy, ANA+ healthy, or have systemic lupus erythematosus (SLE) using single cell mass cytometry, next-generation RNA sequencing, multiplex cytokine profiling, and phospho-signaling analyses.We found that SLE patients of both races displayed T cell expansion and elevated expression of Type I and II interferon pathways compared to both ANA- and ANA+ healthy individuals. We discovered a unique immune signature that suggests a suppressive immune phenotype and reduced CD11C+ autoimmunity-associated B cells in healthy ANA+ European Americans that is absent in their SLE or even healthy ANA- counterparts, or among African American cohorts. In contrast, ANA+ healthy African Americans exhibited elevated expression of T cell activation markers and higher plasma levels of IL-6 compared to healthy ANA+ European Americans.We propose that this novel immune signature identified in ANA+ healthy European Americans protects them from T cell expansion, heightened activation of interferon pathways, and disease transition.

    View details for DOI 10.1016/j.jaci.2020.04.047

    View details for PubMedID 32446964

  • 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)
  • High-Parameter Immune Profiling with CyTOF. Methods in molecular biology (Clifton, N.J.) Sahaf, B., Rahman, A., Maecker, H. T., Bendall, S. C. 2020; 2055: 351–68


    Mass cytometry, or CyTOF, is a useful technology for high-parameter single-cell phenotyping, especially from suspension cells such as blood or PBMC. It is particularly appealing to monitor the systemic immune changes that could accompany cancer immunotherapy. Here we present a reference panel for identification of all major immune cell populations, with flexibility for addition of trial-specific markers. We also describe best-practice measures for minimizing and tracking batch variability. These include: sample barcoding, use of spiked-in reference cells, and lyophilization of the antibody cocktail. Our protocol assumes the use of cryopreserved PBMC, both for convenience of batching samples and for maximum comparability across patients and time points. Finally, we show an option for automated analysis using the Astrolabe platform (Astrolabe Diagnostics, Inc.).

    View details for DOI 10.1007/978-1-4939-9773-2_16

    View details for PubMedID 31502160

  • Immunologic effects of forest fire exposure show increases in IL-1β and CRP. Allergy Prunicki, M. M., Dant, C. C., Cao, S. n., Maecker, H. n., Haddad, F. n., Kim, J. B., Snyder, M. n., Wu, J. n., Nadeau, K. n. 2020

    View details for DOI 10.1111/all.14251

    View details for PubMedID 32112439

  • 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


    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

  • Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition). European journal of immunology Cossarizza, A., Chang, H., Radbruch, A., Acs, A., Adam, D., Adam-Klages, S., Agace, W. W., Aghaeepour, N., Akdis, M., Allez, M., Almeida, L. N., Alvisi, G., Anderson, G., Andra, I., Annunziato, F., Anselmo, A., Bacher, P., Baldari, C. T., Bari, S., Barnaba, V., Barros-Martins, J., Battistini, L., Bauer, W., Baumgart, S., Baumgarth, N., Baumjohann, D., Baying, B., Bebawy, M., Becher, B., Beisker, W., Benes, V., Beyaert, R., Blanco, A., Boardman, D. A., Bogdan, C., Borger, J. G., Borsellino, G., Boulais, P. E., Bradford, J. A., Brenner, D., Brinkman, R. R., Brooks, A. E., Busch, D. H., Buscher, M., Bushnell, T. P., Calzetti, F., Cameron, G., Cammarata, I., Cao, X., Cardell, S. L., Casola, S., Cassatella, M. A., Cavani, A., Celada, A., Chatenoud, L., Chattopadhyay, P. K., Chow, S., Christakou, E., Cicin-Sain, L., Clerici, M., Colombo, F. S., Cook, L., Cooke, A., Cooper, A. M., Corbett, A. J., Cosma, A., Cosmi, L., Coulie, P. G., Cumano, A., Cvetkovic, L., Dang, V. D., Dang-Heine, C., Davey, M. S., Davies, D., De Biasi, S., Del Zotto, G., Dela Cruz, G. V., Delacher, M., Della Bella, S., Dellabona, P., Deniz, G., Dessing, M., Di Santo, J. P., Diefenbach, A., Dieli, F., Dolf, A., Dorner, T., Dress, R. J., Dudziak, D., Dustin, M., Dutertre, C., Ebner, F., Eckle, S. B., Edinger, M., Eede, P., Ehrhardt, G. R., Eich, M., Engel, P., Engelhardt, B., Erdei, A., Esser, C., Everts, B., Evrard, M., Falk, C. S., Fehniger, T. A., Felipo-Benavent, M., Ferry, H., Feuerer, M., Filby, A., Filkor, K., Fillatreau, S., Follo, M., Forster, I., Foster, J., Foulds, G. A., Frehse, B., Frenette, P. S., Frischbutter, S., Fritzsche, W., Galbraith, D. W., Gangaev, A., Garbi, N., Gaudilliere, B., Gazzinelli, R. T., Geginat, J., Gerner, W., Gherardin, N. A., Ghoreschi, K., Gibellini, L., Ginhoux, F., Goda, K., Godfrey, D. I., Goettlinger, C., Gonzalez-Navajas, J. M., Goodyear, C. S., Gori, A., Grogan, J. L., Grummitt, D., Grutzkau, A., Haftmann, C., Hahn, J., Hammad, H., Hammerling, G., Hansmann, L., Hansson, G., Harpur, C. M., Hartmann, S., Hauser, A., Hauser, A. E., Haviland, D. L., Hedley, D., Hernandez, D. C., Herrera, G., Herrmann, M., Hess, C., Hofer, T., Hoffmann, P., Hogquist, K., Holland, T., Hollt, T., Holmdahl, R., Hombrink, P., Houston, J. P., Hoyer, B. F., Huang, B., Huang, F., Huber, J. E., Huehn, J., Hundemer, M., Hunter, C. A., Hwang, W. Y., Iannone, A., Ingelfinger, F., Ivison, S. M., Jack, H., Jani, P. K., Javega, B., Jonjic, S., Kaiser, T., Kalina, T., Kamradt, T., Kaufmann, S. H., Keller, B., Ketelaars, S. L., Khalilnezhad, A., Khan, S., Kisielow, J., Klenerman, P., Knopf, J., Koay, H., Kobow, K., Kolls, J. K., Kong, W. T., Kopf, M., Korn, T., Kriegsmann, K., Kristyanto, H., Kroneis, T., Krueger, A., Kuhne, J., Kukat, C., Kunkel, D., Kunze-Schumacher, H., Kurosaki, T., Kurts, C., Kvistborg, P., Kwok, I., Landry, J., Lantz, O., Lanuti, P., LaRosa, F., Lehuen, A., LeibundGut-Landmann, S., Leipold, M. D., Leung, L. Y., Levings, M. K., Lino, A. C., Liotta, F., Litwin, V., Liu, Y., Ljunggren, H., Lohoff, M., Lombardi, G., Lopez, L., Lopez-Botet, M., Lovett-Racke, A. E., Lubberts, E., Luche, H., Ludewig, B., Lugli, E., Lunemann, S., Maecker, H. T., Maggi, L., Maguire, O., Mair, F., Mair, K. H., Mantovani, A., Manz, R. A., Marshall, A. J., Martinez-Romero, A., Martrus, G., Marventano, I., Maslinski, W., Matarese, G., Mattioli, A. V., Maueroder, C., Mazzoni, A., McCluskey, J., McGrath, M., McGuire, H. M., McInnes, I. B., Mei, H. E., Melchers, F., Melzer, S., Mielenz, D., Miller, S. D., Mills, K. H., Minderman, H., Mjosberg, J., Moore, J., Moran, B., Moretta, L., Mosmann, T. R., Muller, S., Multhoff, G., Munoz, L. E., Munz, C., Nakayama, T., Nasi, M., Neumann, K., Ng, L. G., Niedobitek, A., Nourshargh, S., Nunez, G., O'Connor, J., Ochel, A., Oja, A., Ordonez, D., Orfao, A., Orlowski-Oliver, E., Ouyang, W., Oxenius, A., Palankar, R., Panse, I., Pattanapanyasat, K., Paulsen, M., Pavlinic, D., Penter, L., Peterson, P., Peth, C., Petriz, J., Piancone, F., Pickl, W. F., Piconese, S., Pinti, M., Pockley, A. G., Podolska, M. J., Poon, Z., Pracht, K., Prinz, I., Pucillo, C. E., Quataert, S. A., Quatrini, L., Quinn, K. M., Radbruch, H., Radstake, T. R., Rahmig, S., Rahn, H., Rajwa, B., Ravichandran, G., Raz, Y., Rebhahn, J. A., Recktenwald, D., Reimer, D., Reis E Sousa, C., Remmerswaal, E. B., Richter, L., Rico, L. G., Riddell, A., Rieger, A. M., Robinson, J. P., Romagnani, C., Rubartelli, A., Ruland, J., Saalmuller, A., Saeys, Y., Saito, T., Sakaguchi, S., Sala-de-Oyanguren, F., Samstag, Y., Sanderson, S., Sandrock, I., Santoni, A., Sanz, R. B., Saresella, M., Sautes-Fridman, C., Sawitzki, B., Schadt, L., Scheffold, A., Scherer, H. U., Schiemann, M., Schildberg, F. A., Schimisky, E., Schlitzer, A., Schlosser, J., Schmid, S., Schmitt, S., Schober, K., Schraivogel, D., Schuh, W., Schuler, T., Schulte, R., Schulz, A. R., Schulz, S. R., Scotta, C., Scott-Algara, D., Sester, D. P., Shankey, T. V., Silva-Santos, B., Simon, A. K., Sitnik, K. M., Sozzani, S., Speiser, D. E., Spidlen, J., Stahlberg, A., Stall, A. M., Stanley, N., Stark, R., Stehle, C., Steinmetz, T., Stockinger, H., Takahama, Y., Takeda, K., Tan, L., Tarnok, A., Tiegs, G., Toldi, G., Tornack, J., Traggiai, E., Trebak, M., Tree, T. I., Trotter, J., Trowsdale, J., Tsoumakidou, M., Ulrich, H., Urbanczyk, S., van de Veen, W., van den Broek, M., van der Pol, E., Van Gassen, S., Van Isterdael, G., van Lier, R. A., Veldhoen, M., Vento-Asturias, S., Vieira, P., Voehringer, D., Volk, H., von Borstel, A., von Volkmann, K., Waisman, A., Walker, R. V., Wallace, P. K., Wang, S. A., Wang, X. M., Ward, M. D., Ward-Hartstonge, K. A., Warnatz, K., Warnes, G., Warth, S., Waskow, C., Watson, J. V., Watzl, C., Wegener, L., Weisenburger, T., Wiedemann, A., Wienands, J., Wilharm, A., Wilkinson, R. J., Willimsky, G., Wing, J. B., Winkelmann, R., Winkler, T. H., Wirz, O. F., Wong, A., Wurst, P., Yang, J. H., Yang, J., Yazdanbakhsh, M., Yu, L., Yue, A., Zhang, H., Zhao, Y., Ziegler, S. M., Zielinski, C., Zimmermann, J., Zychlinsky, A. 2019; 49 (10): 1457–1973


    These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.

    View details for DOI 10.1002/eji.201970107

    View details for PubMedID 31633216

  • Reversal of epigenetic aging and immunosenescent trends in humans. Aging cell Fahy, G. M., Brooke, R. T., Watson, J. P., Good, Z., Vasanawala, S. S., Maecker, H., Leipold, M. D., Lin, D. T., Kobor, M. S., Horvath, S. 2019: e13028


    Epigenetic "clocks" can now surpass chronological age in accuracy for estimating biological age. Here, we use four such age estimators to show that epigenetic aging can be reversed in humans. Using a protocol intended to regenerate the thymus, we observed protective immunological changes, improved risk indices for many age-related diseases, and a mean epigenetic age approximately 1.5years less than baseline after 1year of treatment (-2.5-year change compared to no treatment at the end of the study). The rate of epigenetic aging reversal relative to chronological age accelerated from -1.6year/year from 0-9month to -6.5year/year from 9-12month. The GrimAge predictor of human morbidity and mortality showed a 2-year decrease in epigenetic vs. chronological age that persisted six months after discontinuing treatment. This is to our knowledge the first report of an increase, based on an epigenetic age estimator, in predicted human lifespan by means of a currently accessible aging intervention.

    View details for DOI 10.1111/acel.13028

    View details for PubMedID 31496122

  • Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy. Cell reports Hartmann, F. J., Babdor, J., Gherardini, P. F., Amir, E. D., Jones, K., Sahaf, B., Marquez, D. M., Krutzik, P., O'Donnell, E., Sigal, N., Maecker, H. T., Meyer, E., Spitzer, M. H., Bendall, S. C. 2019; 28 (3): 819


    The success of immunotherapy has led to a myriad of clinical trials accompanied by efforts to gain mechanistic insight and identify predictive signatures for personalization. However, many immune monitoring technologies face investigator bias, missing unanticipated cellular responses in limited clinical material. We present here a mass cytometry (CyTOF) workflow for standardized, systems-level biomarker discovery in immunotherapy trials. To broadly enumerate immune cell identity and activity, we established and extensively assessed a reference panel of 33 antibodies to cover major cell subsets, simultaneously quantifying activation and immune checkpoint molecules in a single assay. This assay enumerates ≥98% of peripheral immune cells with ≥4 positively identifying antigens. Robustness and reproducibility are demonstrated on multiple samples types, across two research centers and by orthogonal measurements. Using automated analysis, we identify stratifying immune signatures in bone marrow transplantation-associated graft-versus-host disease. Together, this validated workflow ensures comprehensive immunophenotypic analysis and data comparability and will accelerate biomarker discovery.

    View details for DOI 10.1016/j.celrep.2019.06.049

    View details for PubMedID 31315057

  • Diminished B-Cell Response After Repeat Influenza Vaccination JOURNAL OF INFECTIOUS DISEASES Sanyal, M., Holmes, T. H., Maecker, H. T., Albrecht, R. A., Dekker, C. L., He, X., Greenberg, H. B. 2019; 219 (10): 1586–95
  • Vaccine-Induced Memory CD8(+) T Cells Provide Clinical Benefit in HER2 Expressing Breast Cancer: A Mouse to Human Translational Study CLINICAL CANCER RESEARCH Crosby, E. J., Gwin, W. R., Blackwell, K., Marcom, P., Chang, S., Maecker, H. T., Broadwater, G., Hyslop, T. M., Kim, S., Rogatko, A., Lubkov, V., Snyder, J. C., Osada, T., Hobeika, A. C., Morse, M. A., Lyerly, H., Hartman, Z. C. 2019; 25 (9): 2725–36
  • Getting the Most from Your High-Dimensional Cytometry Data. Immunity Olsen, L. R., Pedersen, C. B., Leipold, M. D., Maecker, H. T. 2019; 50 (3): 535–36

    View details for PubMedID 30893579

  • 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


    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

  • Penalized Supervised Star Plots: Example Application in Influenza-Specific CD4+T Cells VIRAL IMMUNOLOGY Holmes, T. H., Subrahmanyam, P. B., Wang, W., Maecker, H. T. 2019; 32 (2): 102–9
  • The anatomy of single cell mass cytometry data CYTOMETRY PART A Olsen, L. R., Leipold, M. D., Pedersen, C. B., Maecker, H. 2019; 95A (2): 156–72
  • Mycophenolate mofetil reduces STAT3 phosphorylation in systemic lupus erythematosus patients. JCI insight Slight-Webb, S., Guthridge, J. M., Chakravarty, E. F., Chen, H., Lu, R., Macwana, S., Bean, K., Maecker, H. T., Utz, P. J., James, J. A. 2019; 4 (2)


    Systemic lupus erythematosus (SLE) is a highly variable autoimmune disease that can involve severe organ-threatening symptoms, such as lupus nephritis. Certain drugs, such as mycophenolate mofetil (MMF), are effective at reducing morbidity associated with nephritis; however, the immune pathways associated with disease suppression are poorly defined. Here, we provide evidence that MMF inhibits phosphorylation of STAT3 and other associated immune pathways. Using mass cytometry and bead-based or ELISA assays, the systemic phenotype of SLE patients not taking (MMF-) or taking (MMF+) MMF were studied. MMF+ SLE patients had significant reductions in total numbers of transitional B cells, plasmablasts, and T cells, specifically CD4+ Th17-type and CD4+ Treg-type cells, compared with MMF- patients. Plasma soluble mediators were decreased in MMF+ patients including chemokines (MIG/CXCL9 and SDF-1alpha/CXCL12) and growth factors (VEGF-A and PDGF-BB). Soluble mediators and cell subsets grouped by functional properties revealed significant modifications associated with STAT3 and B cell pathways. Further, healthy PBMCs treated with IL-6 revealed a reduction in p-STAT3 following the addition of mycophenolic acid (the active metabolite of MMF). In conclusion, the inhibition of STAT3 phosphorylation by MMF may explain the effectiveness of this treatment in SLE patients, since increased levels of p-STAT3 are associated with disease pathology.

    View details for PubMedID 30674728

  • Value of Neutrophil to Lymphocyte Ratio and Its Trajectory in Patients Hospitalized With Acute Heart Failure and Preserved Ejection Fraction. The American journal of cardiology Boralkar, K. A., Kobayashi, Y. n., Amsallem, M. n., Ataam, J. A., Moneghetti, K. J., Cauwenberghs, N. n., Horne, B. D., Knowlton, K. U., Maecker, H. n., Kuznetsova, T. n., Heidenreich, P. A., Haddad, F. n. 2019


    The neutrophil to lymphocyte ratio (NLR) has been proposed as a simple and routinely obtained marker of inflammation. This study sought to determine whether the NLR on admission as well as NLR trajectory would be complementary to the Get with the Guidelines Heart Failure (GWTG-HF) risk score in patients hospitalized with acute heart failure with preserved ejection fraction (HFpEF).Using the Stanford Translational Research Database, we identified 443 patients between January 2002 and December 2013 hospitalized with acute HFpEF and with complete data of NLR both on admission and at discharge. The primary endpoint was all-cause mortality. Mean age was 77 ± 16 years, 58% were female, with a high prevalence of diabetes mellitus (35.4%), coronary artery disease (58.2%), systemic hypertension (96.6%) and history of atrial fibrillation (57.5%). Over a median follow-up of 2.2 years, 121 (27.3%) patients died. The median NLR on admission was 6.5 (IQR 3.6 - 11.1); a majority of patients decreased their NLR during the course of hospitalization. On multivariable Cox modeling, both NLR on admission (HR 1.18 95% CI (1.00 - .38), p = 0.04) and absolute NLR trajectory (HR 1.26 95% CI (1.10 - 1.45), p = 0.001) were shown to be incremental to GWTG-HF risk score (p < 0.05) for outcome prediction. Adding the NLR or absolute NLR trajectory to the GWTG-HF risk score significantly improved the area under the operator-receiver curve and the reclassification up to 3 years after admission.This simple, readily available marker of inflammation may be useful when stratifying the risk of patients hospitalized with HFpEF.

    View details for DOI 10.1016/j.amjcard.2019.10.020

    View details for PubMedID 31753313

  • Pembrolizumab in Relapsed and Refractory Mycosis Fungoides and Sézary Syndrome: A Multicenter Phase II Study. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Khodadoust, M. S., Rook, A. H., Porcu, P. n., Foss, F. n., Moskowitz, A. J., Shustov, A. n., Shanbhag, S. n., Sokol, L. n., Fling, S. P., Ramchurren, N. n., Pierce, R. n., Davis, A. n., Shine, R. n., Li, S. n., Fong, S. n., Kim, J. n., Yang, Y. n., Blumenschein, W. M., Yearley, J. H., Das, B. n., Patidar, R. n., Datta, V. n., Cantu, E. n., McCutcheon, J. N., Karlovich, C. n., Williams, P. M., Subrahmanyam, P. B., Maecker, H. T., Horwitz, S. M., Sharon, E. n., Kohrt, H. E., Cheever, M. A., Kim, Y. H. 2019: JCO1901056


    To assess the efficacy of pembrolizumab in patients with advanced relapsed or refractory mycosis fungoides (MF) or Sézary syndrome (SS).CITN-10 is a single-arm, multicenter phase II trial of 24 patients with advanced MF or SS. Patients were treated with pembrolizumab 2 mg/kg every 3 weeks for up to 24 months. The primary end point was overall response rate by consensus global response criteria.Patients had advanced-stage disease (23 of 24 with stage IIB to IV MF/SS) and were heavily pretreated with a median of four prior systemic therapies. The overall response rate was 38% with two complete responses and seven partial responses. Of the nine responding patients, six had 90% or more improvement in skin disease by modified Severity Weighted Assessment Tool, and eight had ongoing responses at last follow-up. The median duration of response was not reached, with a median response follow-up time of 58 weeks. Immune-related adverse events led to treatment discontinuation in four patients. A transient worsening of erythroderma and pruritus occurred in 53% of patients with SS. This cutaneous flare reaction did not result in treatment discontinuation for any patient. The flare reaction correlated with high PD-1 expression on Sézary cells but did not associate with subsequent clinical responses or lack of response. Treatment responses did not correlate with expression of PD-L1, total mutation burden, or an interferon-γ gene expression signature.Pembrolizumab demonstrated significant antitumor activity with durable responses and a favorable safety profile in patients with advanced MF/SS.

    View details for DOI 10.1200/JCO.19.01056

    View details for PubMedID 31532724

  • Guidelines for Gating Flow Cytometry Data for Immunological Assays. Methods in molecular biology (Clifton, N.J.) Staats, J. n., Divekar, A. n., McCoy, J. P., Maecker, H. T. 2019; 2032: 81–104


    "Gating" refers to the selection of successive subpopulations of cells for analysis in flow cytometry. It is usually performed manually, based on expert knowledge of cell characteristics. However, there can be considerable disagreement in how gates should be applied, even between individuals experienced in the field. While clinical software often automates gating, and some guidelines do exist (especially for clinical assays), there are no comprehensive guidelines across the various types of immunological assays performed using flow cytometry. Here we attempt to provide such guidelines, focused on the most general and pervasive types of gates, why they are important, and what recommendations can be made regarding their use. We do so through the display of example data, collected by academic, government, and industry representatives. These guidelines should be of value to both novice and experienced flow cytometrists analyzing a wide variety of immunological assays.

    View details for DOI 10.1007/978-1-4939-9650-6_5

    View details for PubMedID 31522414

  • Sustained outcomes in oral immunotherapy for peanut allergy (POISED study): a large, randomised, double-blind, placebo-controlled, phase 2 study. Lancet (London, England) Chinthrajah, R. S., Purington, N. n., Andorf, S. n., Long, A. n., O'Laughlin, K. L., Lyu, S. C., Manohar, M. n., Boyd, S. D., Tibshirani, R. n., Maecker, H. n., Plaut, M. n., Mukai, K. n., Tsai, M. n., Desai, M. n., Galli, S. J., Nadeau, K. C. 2019


    Dietary avoidance is recommended for peanut allergies. We evaluated the sustained effects of peanut allergy oral immunotherapy (OIT) in a randomised long-term study in adults and children.In this randomised, double-blind, placebo-controlled, phase 2 study, we enrolled participants at the Sean N Parker Center for Allergy and Asthma Research at Stanford University (Stanford, CA, USA) with peanut allergy aged 7-55 years with a positive result from a double-blind, placebo-controlled, food challenge (DBPCFC; ≤500 mg of peanut protein), a positive skin-prick test (SPT) result (≥5 mm wheal diameter above the negative control), and peanut-specific immunoglobulin (Ig)E concentration of more than 4 kU/L. Participants were randomly assigned (2·4:1·4:1) in a two-by-two block design via a computerised system to be built up and maintained on 4000 mg peanut protein through to week 104 then discontinued on peanut (peanut-0 group), to be built up and maintained on 4000 mg peanut protein through to week 104 then to ingest 300 mg peanut protein daily (peanut-300 group) for 52 weeks, or to receive oat flour (placebo group). DBPCFCs to 4000 mg peanut protein were done at baseline and weeks 104, 117, 130, 143, and 156. The pharmacist assigned treatment on the basis of a randomised computer list. Peanut or placebo (oat) flour was administered orally and participants and the study team were masked throughout by use of oat flour that was similar in look and feel to the peanut flour and nose clips, as tolerated, to mask taste. The statistician was also masked. The primary endpoint was the proportion of participants who passed DBPCFCs to a cumulative dose of 4000 mg at both 104 and 117 weeks. The primary efficacy analysis was done in the intention-to-treat population. Safety was assessed in the intention-to-treat population. This trial is registered at, NCT02103270.Between April 15, 2014, and March 2, 2016, of 152 individuals assessed, we enrolled 120 participants, who were randomly assigned to the peanut-0 (n=60), peanut-300 (n=35), and placebo groups (n=25). 21 (35%) of peanut-0 group participants and one (4%) placebo group participant passed the 4000 mg challenge at both 104 and 117 weeks (odds ratio [OR] 12·7, 95% CI 1·8-554·8; p=0·0024). Over the entire study, the most common adverse events were mild gastrointestinal symptoms, which were seen in 90 of 120 patients (50/60 in the peanut-0 group, 29/35 in the peanut-300 group, and 11/25 in the placebo group) and skin disorders, which were seen in 50/120 patients (26/60 in the peanut-0 group, 15/35 in the peanut-300 group, and 9/25 in the placebo group). Adverse events decreased over time in all groups. Two participants in the peanut groups had serious adverse events during the 3-year study. In the peanut-0 group, in which eight (13%) of 60 participants passed DBPCFCs at week 156, higher baseline peanut-specific IgG4 to IgE ratio and lower Ara h 2 IgE and basophil activation responses were associated with sustained unresponsiveness. No treatment-related deaths occurred.Our study suggests that peanut OIT could desensitise individuals with peanut allergy to 4000 mg peanut protein but discontinuation, or even reduction to 300 mg daily, could increase the likelihood of regaining clinical reactivity to peanut. Since baseline blood tests correlated with week 117 treatment outcomes, this study might aid in optimal patient selection for this therapy.National Institute of Allergy and Infectious Diseases.

    View details for DOI 10.1016/S0140-6736(19)31793-3

    View details for PubMedID 31522849

  • 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


    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

  • Autoimmunity to hypocretin and molecular mimicry to flu in type 1 narcolepsy. Proceedings of the National Academy of Sciences of the United States of America Luo, G., Ambati, A., Lin, L., Bonvalet, M., Partinen, M., Ji, X., Maecker, H. T., Mignot, E. J. 2018


    Type 1 narcolepsy (T1N) is caused by hypocretin/orexin (HCRT) neuronal loss. Association with the HLA DQB1*06:02/DQA1*01:02 (98% vs. 25%) heterodimer (DQ0602), T cell receptors (TCR) and other immune loci suggest autoimmunity but autoantigens are unknown. Onset is seasonal and associated with influenza A, notably pandemic 2009 H1N1 (pH1N1) infection and vaccination (Pandemrix). Peptides derived from HCRT and influenza A, including pH1N1, were screened for DQ0602 binding and presence of cognate DQ0602 tetramer-peptide-specific CD4+ T cells tested in 35 T1N cases and 22 DQ0602 controls. Higher reactivity to influenza pHA273-287 (pH1N1 specific), PR8 (H1N1 pre-2009 and H2N2)-specific NP17-31 and C-amidated but not native version of HCRT54-66 and HCRT86-97 (HCRTNH2) were observed in T1N. Single-cell TCR sequencing revealed sharing of CDR3beta TRBV4-2-CASSQETQGRNYGYTF in HCRTNH2 and pHA273-287-tetramers, suggesting molecular mimicry. This public CDR3beta uses TRBV4-2, a segment modulated by T1N-associated SNP rs1008599, suggesting causality. TCR-alpha/beta CDR3 motifs of HCRT54-66-NH2 and HCRT86-97-NH2 tetramers were extensively shared: notably public CDR3alpha, TRAV2-CAVETDSWGKLQF-TRAJ24, that uses TRAJ24, a chain modulated by T1N-associated SNPs rs1154155 and rs1483979. TCR-alpha/beta CDR3 sequences found in pHA273-287, NP17-31, and HCRTNH2 tetramer-positive CD4+ cells were also retrieved in single INF-gamma-secreting CD4+ sorted cells stimulated with Pandemrix, independently confirming these results. Our results provide evidence for autoimmunity and molecular mimicry with flu antigens modulated by genetic components in the pathophysiology of T1N.

    View details for PubMedID 30541895

  • Baseline Gastrointestinal Eosinophilia Is Common in Oral Immunotherapy Subjects With IgE-Mediated Peanut Allergy. Frontiers in immunology Wright, B. L., Fernandez-Becker, N. Q., Kambham, N., Purington, N., Tupa, D., Zhang, W., Rank, M. A., Kita, H., Shim, K. P., Bunning, B. J., Doyle, A. D., Jacobsen, E. A., Boyd, S. D., Tsai, M., Maecker, H., Manohar, M., Galli, S. J., Nadeau, K. C., Chinthrajah, R. S. 2018; 9: 2624


    Rationale: Oral immunotherapy (OIT) is an emerging treatment for food allergy. While desensitization is achieved in most subjects, many experience gastrointestinal symptoms and few develop eosinophilic gastrointestinal disease. It is unclear whether these subjects have subclinical gastrointestinal eosinophilia (GE) at baseline. We aimed to evaluate the presence of GE in subjects with food allergy before peanut OIT. Methods: We performed baseline esophagogastroduodenoscopies on 21 adults before undergoing peanut OIT. Subjects completed a detailed gastrointestinal symptom questionnaire. Endoscopic findings were assessed using the Eosinophilic Esophagitis (EoE) Endoscopic Reference Score (EREFS) and biopsies were obtained from the esophagus, gastric antrum, and duodenum. Esophageal biopsies were evaluated using the EoE Histologic Scoring System. Immunohistochemical staining for eosinophil peroxidase (EPX) was also performed. Hematoxylin and eosin and EPX stains of each biopsy were assessed for eosinophil density and EPX/mm2 was quantified using automated image analysis. Results: All subjects were asymptomatic. Pre-existing esophageal eosinophilia (>5 eosinophils per high-power field [eos/hpf]) was present in five participants (24%), three (14%) of whom had >15 eos/hpf associated with mild endoscopic findings (edema, linear furrowing, or rings; median EREFS = 0, IQR 0-0.25). Some subjects also demonstrated basal cell hyperplasia, dilated intercellular spaces, and lamina propria fibrosis. Increased eosinophils were noted in the gastric antrum (>12 eos/hpf) or duodenum (>26 eos/hpf) in 9 subjects (43%). EPX/mm2 correlated strongly with eosinophil counts (r = 0.71, p < 0.0001). Conclusions: Pre-existing GE is common in adults with IgE-mediated peanut allergy. Eosinophilic inflammation (EI) in these subjects may be accompanied by mild endoscopic and histologic findings. Longitudinal data collection during OIT is ongoing.

    View details for DOI 10.3389/fimmu.2018.02624

    View details for PubMedID 30524424

    View details for PubMedCentralID PMC6261984

  • Interleukin 4 is inactivated via selective disulfide-bond reduction by extracellular thioredoxin. Proceedings of the National Academy of Sciences of the United States of America Plugis, N. M., Weng, N., Zhao, Q., Palanski, B. A., Maecker, H. T., Habtezion, A., Khosla, C. 2018


    Thioredoxin 1 (TRX), an essential intracellular redox regulator, is also secreted by mammalian cells. Recently, we showed that TRX activates extracellular transglutaminase 2 via reduction of an allosteric disulfide bond. In an effort to identify other extracellular substrates of TRX, macrophages derived from THP-1 cells were treated with NP161, a small-molecule inhibitor of secreted TRX. NP161 enhanced cytokine outputs of alternatively activated macrophages, suggesting that extracellular TRX regulated the activity of interleukin 4 (IL-4) and/or interleukin 13 (IL-13). To test this hypothesis, the C35S mutant of human TRX was shown to form a mixed disulfide bond with recombinant IL-4 but not IL-13. Kinetic analysis revealed a kcat/KM value of 8.1 muM-1min-1 for TRX-mediated recognition of IL-4, which established this cytokine as the most selective partner of extracellular TRX to date. Mass spectrometry identified the C46-C99 bond of IL-4 as the target of TRX, consistent with the essential role of this disulfide bond in IL-4 activity. To demonstrate the physiological relevance of our biochemical findings, recombinant TRX was shown to attenuate IL-4-dependent proliferation of cultured TF-1 erythroleukemia cells and also to inhibit the progression of chronic pancreatitis in an IL-4-driven mouse model of this disease. By establishing that IL-4 is posttranslationally regulated by TRX-promoted reduction of a disulfide bond, our findings highlight a novel regulatory mechanism of the type 2 immune response that is specific to IL-4 over IL-13.

    View details for PubMedID 30104382

  • JAK-STAT signaling is activated in the kidney and peripheral blood cells of patients with focal segmental glomerulosclerosis. Kidney international Tao, J., Mariani, L., Eddy, S., Maecker, H., Kambham, N., Mehta, K., Hartman, J., Wang, W., Kretzler, M., Lafayette, R. A. 2018


    Focal segmental glomerular sclerosis (FSGS) is a devastating disease with limited treatment options and poor prognosis. Activated JAK-STAT signaling has been implicated in other kidney diseases. Since new technologies allow us to better evaluate changes in systemic and renal JAK-STAT activity as it relates to kidney function, we examined this in 106 patients with biopsy-proven FSGS compared to 47 healthy control individuals. Peripheral immune function was assessed in peripheral blood mononuclear cells by phosphoflow studies before and after cytokine stimulation. Kidney JAK-STAT activity was measured by immunofluorescence and by transcriptomics. A STAT1 activity score was calculated by evaluating message status of downstream targets of pSTAT1. Peripheral blood mononuclear cells were found to be upregulated in terms of pSTAT production at baseline in FSGS and to have limited reserve to respond to various cytokines. Increased staining for components of the JAK-STAT system in FSGS by microscopy was found. Furthermore, we found transcriptomic evidence for activation of JAK-STAT that increased pSTAT 1 and pSTAT 3 in glomerular and tubulointerstitial sections of the kidney. Some of these changes were associated with the likelihood of remission of proteinuria and progression of disease. JAK-STAT signaling is altered in patients with FSGS as compared to healthy controls with activated peripheral immune cells, increased message in the kidney and increased activated proteins in the kidney. Thus, our findings support immune activation in this disease and point to the JAK-STAT pathway as a potential target for treatment of FSGS.

    View details for PubMedID 30093081

  • Baseline immune profile by CyTOF can predict response to an investigational adjuvanted vaccine in elderly adults. Journal of translational medicine Lingblom, C. M., Kowli, S., Swaminathan, N., Maecker, H. T., Lambert, S. L. 2018; 16 (1): 153


    BACKGROUND: Mass cytometry, or CyTOF (Cytometry by Time-of-Flight), permits the simultaneous detection of over 40 phenotypic and functional immune markers in individual cells without the issues of spectral overlap seen in traditional flow cytometry.METHODS: In this study, we applied CyTOF to comprehensively characterize the circulating immune cell populations in elderly individuals both before and after administration of an investigational adjuvanted protein vaccine against respiratory syncytial virus (RSV) in a Phase 1a trial. Antigen-specific T cell responses to RSV by IFNgamma ELISPOT had been observed in most but not all recipients in the highest dose cohort in this trial. Here, CyTOF was used to characterize the cellular response profile of ELISPOT responders and non-responders in this vaccine dose cohort.RESULTS: Both CD4+ and CD8+ T cell antigen-specific IFNgamma responses were observed. Principal components analysis revealed baseline differences between responders and non-responders, including differences in activated (HLA-DR+) CD4+ and CD8+ T cells, which were higher in non-responders versus responders. Using viSNE to analyze RSV-responsive CD4+ and CD8+ T cells, we also found increased expression of HLA-DR, CCR7, CD127 and CD69 in non-responders versus responders.CONCLUSIONS: High parameter CyTOF can help profile immune components associated with differential vaccine responsiveness.

    View details for PubMedID 29866115

  • 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


    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

  • Food allergy and omics. The Journal of allergy and clinical immunology Dhondalay, G. K., Rael, E. n., Acharya, S. n., Zhang, W. n., Sampath, V. n., Galli, S. J., Tibshirani, R. n., Boyd, S. D., Maecker, H. n., Nadeau, K. C., Andorf, S. n. 2018; 141 (1): 20–29


    Food allergy (FA) prevalence has been increasing over the last few decades and is now a global health concern. Current diagnostic methods for FA result in a high number of false-positive results, and the standard of care is either allergen avoidance or use of epinephrine on accidental exposure, although currently with no other approved treatments. The increasing prevalence of FA, lack of robust biomarkers, and inadequate treatments warrants further research into the mechanism underlying food allergies. Recent technological advances have made it possible to move beyond traditional biological techniques to more sophisticated high-throughput approaches. These technologies have created the burgeoning field of omics sciences, which permit a more systematic investigation of biological problems. Omics sciences, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, and exposomics, have enabled the construction of regulatory networks and biological pathway models. Parallel advances in bioinformatics and computational techniques have enabled the integration, analysis, and interpretation of these exponentially growing data sets and opens the possibility of personalized or precision medicine for FA.

    View details for PubMedID 29307411

  • Differences in multiple immune parameters between Indian and U.S. infants. PloS one Rathore, D. K., Holmes, T. H., Nadeau, K. C., Mittal, P., Batra, A., Rosenberg-Hasson, Y., Sopory, S., Gupta, R., Chellani, H. K., Aggarwal, K. C., Bal, V., Natchu, U. C., Bhatnagar, S., Tavassoli, M., Lyell, D. J., Rath, S., Wadhwa, N., Maecker, H. T. 2018; 13 (11): e0207297


    To compare immune phenotypes across two geographic and ethnic communities, we examined umbilical cord blood by flow cytometry and Luminex in parallel cohorts of 53 newborns from New Delhi, India, and 46 newborns from Stanford, California. We found that frequencies of a B cell subset suggested to be B-1-like, and serum IgM concentration were both significantly higher in the Stanford cohort, independent of differences in maternal age. While serum IgA levels were also significantly higher in the Stanford cohort, IgG1, IgG2, and IgG4 were significantly higher in the New Delhi samples. We found that neutrophils, plasmacytoid dendritic cells, CD8+ T cells, and total T cells were higher in the U.S. cohort, while dendritic cells, patrolling monocytes (CD14dimCD16+), natural killer cells, CD4+ T cells, and naive B cells were higher in the India cohort. Within the India cohort, we also identified cell types whose frequency was positively or negatively predictive of occurrence of infection(s) in the first six months of life. Monocytes, total T cells, and memory CD4+ T cells were most prominent in having an inverse relationship with infection. We suggest that these data provide impetus for follow-up studies linking phenotypic differences to environmental versus genetic factors, and to infection outcomes.

    View details for PubMedID 30444901

  • Multiparameter Intracellular Cytokine Staining FLOW CYTOMETRY PROTOCOLS, 4TH EDITION Lovelace, P., Maecker, H. T., Hawley, T. S., Hawley, R. G. 2018; 1678: 151–66


    Intracellular cytokine staining is a popular method for visualizing cellular responses, most often T-cell responses to antigenic or mitogenic stimulation. It can be coupled with staining for other functional markers, such as upregulation of CD107 or CD154, as well as phenotypic markers that define specific cellular subsets, e.g., effector and memory T-cell compartments, NK cells, or monocytes. Recent advances in multicolor flow cytometry instrumentation and software have allowed the routine combination of 12 or more markers, creating some technical and analytical challenges along the way, and exposing a need for standardization in the field. Here, we will review best practices for antibody panel design and procedural variables for multicolor intracellular cytokine staining, and present an optimized protocol with variations designed for use with specific markers and sample types.

    View details for PubMedID 29071680

  • Mass Cytometry Assays for Antigen-Specific T Cells Using CyTOF FLOW CYTOMETRY PROTOCOLS, 4TH EDITION Lin, D., Maecker, H. T., Hawley, T. S., Hawley, R. G. 2018; 1678: 37–47


    T Cells specific for a single antigen tend to be rare, even after expansion of memory cells. They are commonly detected by in vitro stimulation with peptides or protein, followed by staining for intracellular cytokines. In this protocol, we use CyTOF® mass cytometry to collect single-cell data on a large number of cytokines/chemokines, as well as cell-surface proteins that characterize T cells and other immune cells. We also include a method for magnetic bead enrichment of antigen-stimulated T cells, based on their expression of CD154 and CD69. Coupling magnetic enrichment with highly multi-parameter mass cytometry, this method enables the ability to dissect the frequency, phenotype, and function of antigen-specific T cells in greater detail than previously possible. Rare cell subsets can be examined, while minimizing run times on the CyTOF.

    View details for PubMedID 29071674

    View details for PubMedCentralID PMC5798871

  • Distinct predictive biomarker candidates for response to anti-CTLA-4 and anti-PD-1 immunotherapy in melanoma patients. Journal for immunotherapy of cancer Subrahmanyam, P. B., Dong, Z. n., Gusenleitner, D. n., Giobbie-Hurder, A. n., Severgnini, M. n., Zhou, J. n., Manos, M. n., Eastman, L. M., Maecker, H. T., Hodi, F. S. 2018; 6 (1): 18


    While immune checkpoint blockade has greatly improved clinical outcomes in diseases such as melanoma, there remains a need for predictive biomarkers to determine who will likely benefit most from which therapy. To date, most biomarkers of response have been identified in the tumors themselves. Biomarkers that could be assessed from peripheral blood would be even more desirable, because of ease of access and reproducibility of sampling.We used mass cytometry (CyTOF) to comprehensively profile peripheral blood of melanoma patients, in order to find predictive biomarkers of response to anti-CTLA-4 or anti-PD-1 therapy. Using a panel of ~ 40 surface and intracellular markers, we performed in-depth phenotypic and functional immune profiling to identify potential predictive biomarker candidates.Immune profiling of baseline peripheral blood samples using CyTOF revealed that anti-CTLA-4 and anti-PD-1 therapies have distinct sets of candidate biomarkers. The distribution of CD4+ and CD8+ memory/non-memory cells and other memory subsets was different between responders and non-responders to anti-CTLA-4 therapy. In anti-PD-1 (but not anti-CTLA-4) treated patients, we discovered differences in CD69 and MIP-1β expressing NK cells between responders and non-responders. Finally, multivariate analysis was used to develop a model for the prediction of response.Our results indicate that anti-CTLA-4 and anti-PD-1 have distinct predictive biomarker candidates. CD4+ and CD8+ memory T cell subsets play an important role in response to anti-CTLA-4, and are potential biomarker candidates. For anti-PD-1 therapy, NK cell subsets (but not memory T cell subsets) correlated with clinical response to therapy. These functionally active NK cell subsets likely play a critical role in the anti-tumor response triggered by anti-PD-1.

    View details for PubMedID 29510697

    View details for PubMedCentralID PMC5840795

  • 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


    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

  • Lupus Nephritis in Isolation or Accompanied By Extra-Renal Manifestations: Early Lessons from the Accelerating Medicines Partnership James, J. A., Petri, M., Putterman, C., Diamond, B., Wofsy, D., Lee, C., Fine, D., Broder, A. R., Clancy, R. M., Izmirly, P. M., Belmont, M., Bornkamp, N., Davidson, A., Tosta, P., Kalunian, K. C., Park, M., Dall'Era, M., Furie, R., Massarotti, E., Hernandez, G. T., Payan-Schober, F., Connery, S. M., Kamen, D. L., Lee, I., Pendergraft, W., Anolik, J. H., Shah, U., Raychaudhuri, S., Lee, Y. C., Guthridge, J. M., Holers, V., Utz, P. J., Pichavant, M., Gupta, R., Maecker, H. T., Weisman, M., Buyon, J. P. WILEY. 2017
  • 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


    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

  • Cord blood T cell subpopulations and associations with maternal cadmium and arsenic exposures PLOS ONE Nygaard, U. C., Li, Z., Palys, T., Jackson, B., Subbiah, M., Malipatlolla, M., Sampath, V., Maecker, H., Karagas, M. R., Nadeau, K. C. 2017; 12 (6): e0179606


    Arsenic and cadmium are environmental pollutants, and although the evidence for adverse immune effects after prenatal arsenic and cadmium exposures is increasing, little is known about the underlying immunological mechanisms.We investigated the relationship between prenatal arsenic and cadmium exposures and a variety of T cell subpopulations measured in cord blood for 63 participants in the New Hampshire Birth Cohort Study. Post-partum toenail concentrations of arsenic and cadmium were used as an estimate of maternal exposure during pregnancy. The characteristics of cord blood proportions of T lymphocytes and subpopulations (expression of markers for Th1, Th2, Th17, Th1Th17, induced and natural regulatory T cells and NKTs) are presented.In regression analyses, maternal arsenic exposure levels were inversely associated with cord blood T helper memory cells (-21%, 95% CI: -36%, -3%) and the association was found to be stronger in females. They were also inversely associated with activated T helper memory cells, particularly in males (-26%, 95% CI: -43%, -3%). Similarly, inverse associations were observed between cadmium exposure levels and activated T helper memory cells (-16%, 95% CI: -30%, -1%) and also for T helper memory cells in females (-20%, 95% CI: -35%, -3%).The results suggest that prenatal exposures to relatively low levels of arsenic and cadmium may contribute to altered distribution of T cell populations at birth. These changes in theory, could have contributed to the previously reported immunosuppressive effects observed later in infancy/childhood.

    View details for PubMedID 28662050

  • Antigen Availability Shapes T Cell Differentiation and Function during Tuberculosis CELL HOST & MICROBE Moguche, A. O., Musvosvi, M., Penn-Nicholson, A., Plumlee, C. R., Mearns, H., Geldenhuys, H., Smit, E., Abrahams, D., Rozot, V., Dintwe, O., Hoff, S. T., Kromann, I., Ruhwald, M., Bang, P., Larson, R. P., Shafiani, S., Ma, S., Sherman, D. R., Sette, A., Arlehamn, C., McKinney, D. M., Maecker, H., Hanekom, W. A., Hatherill, M., Andersen, P., Scriba, T. J., Urdahl, K. B. 2017; 21 (6): 695-+


    CD4 T cells are critical for protective immunity against Mycobacterium tuberculosis (Mtb), the cause of tuberculosis (TB). Yet to date, TB vaccine candidates that boost antigen-specific CD4 T cells have conferred little or no protection. Here we examined CD4 T cell responses to two leading TB vaccine antigens, ESAT-6 and Ag85B, in Mtb-infected mice and in vaccinated humans with and without underlying Mtb infection. In both species, Mtb infection drove ESAT-6-specific T cells to be more differentiated than Ag85B-specific T cells. The ability of each T cell population to control Mtb in the lungs of mice was restricted for opposite reasons: Ag85B-specific T cells were limited by reduced antigen expression during persistent infection, whereas ESAT-6-specific T cells became functionally exhausted due to chronic antigenic stimulation. Our findings suggest that different vaccination strategies will be required to optimize protection mediated by T cells recognizing antigens expressed at distinct stages of Mtb infection.

    View details for PubMedID 28618268

    View details for PubMedCentralID PMC5533182

  • Immune Checkpoint Function of CD85j in CD8 T Cell Differentiation and Aging FRONTIERS IN IMMUNOLOGY Gustafson, C. E., Qi, Q., Hutter-Saunders, J., Gupta, S., Jadhav, R., Newell, E., Maecker, H., Weyand, C. M., Goronzy, J. J. 2017; 8: 692


    Aging is associated with an increased susceptibility to infection and a failure to control latent viruses thought to be driven, at least in part, by alterations in CD8 T cell function. The aging T cell repertoire is characterized by an accumulation of effector CD8 T cells, many of which express the negative regulatory receptor CD85j. To define the biological significance of CD85j expression on CD8 T cells and to address the question whether presence of CD85j in older individuals is beneficial or detrimental for immune function, we examined the specific attributes of CD8 T cells expressing CD85j as well as the functional role of CD85j in antigen-specific CD8 T cell responses during immune aging. Here, we show that CD85j is mainly expressed by terminally differentiated effector (TEMRAs) CD8 T cells, which increase with age, in cytomegalovirus (CMV) infection and in males. CD85j+ CMV-specific cells demonstrate clonal expansion. However, TCR diversity is similar between CD85j+ and CD85j- compartments, suggesting that CD85j does not directly impact the repertoire of antigen-specific cells. Further phenotypic and functional analyses revealed that CD85j identifies a specific subset of CMV-responsive CD8 T cells that coexpress a marker of senescence (CD57) but retain polyfunctional cytokine production and expression of cytotoxic mediators. Blocking CD85j binding enhanced proliferation of CMV-specific CD8 T cells upon antigen stimulation but did not alter polyfunctional cytokine production. Taken together, these data demonstrate that CD85j characterizes a population of "senescent," but not exhausted antigen-specific effector CD8 T cells and indicates that CD85j is an important checkpoint regulator controlling expansion of virus-specific T cells during aging. Inhibition of CD85j activity may be a mechanism to promote stronger CD8 T cell effector responses during immune aging.

    View details for PubMedID 28659925

  • Reconstitution of immune cell populations in multiple sclerosis patients after autologous stem cell transplantation. Clinical and experimental immunology Karnell, F. G., LIN, D., Motley, S., Duhen, T., Lim, N., Campbell, D. J., Turka, L. A., Maecker, H. T., Harris, K. M. 2017


    Multiple sclerosis is an inflammatory T cell-mediated autoimmune disease. In a Phase II clinical trial, high-dose immunosuppressive therapy combined with autologous CD34(+) haematopoietic stem cell transplant resulted in 69·2% of subjects remaining disease-free without evidence of relapse, loss of neurological function or new magnetic resonance imaging (MRI) lesions to year 5 post-treatment. A combination of CyTOF mass cytometry and multi-parameter flow cytometry was used to explore the reconstitution kinetics of immune cell subsets in the periphery post-haematopoietic cell transplant (HSCT) and the impact of treatment on the phenotype of circulating T cells in this study population. Repopulation of immune cell subsets progressed similarly for all patients studied 2 years post-therapy, regardless of clinical outcome. At month 2, monocytes and natural killer (NK) cells were proportionally more abundant, while CD4 T cells and B cells were reduced, relative to baseline. In contrast to the changes observed at earlier time-points in the T cell compartment, B cells were proportionally more abundant and expansion in the proportion of naive B cells was observed 1 and 2 years post-therapy. Within the T cell compartment, the proportion of effector memory and late effector subsets of CD4 and CD8 T cells was increased, together with transient increases in proportions of CD45RA-regulatory T cells (Tregs ) and T helper type 1 (Th1 cells) and a decrease in Th17·1 cells. While none of the treatment effects studied correlated with clinical outcome, patients who remained healthy throughout the 5-year study had significantly higher absolute numbers of memory CD4 and CD8 T cells in the periphery prior to stem cell transplantation.

    View details for DOI 10.1111/cei.12985

    View details for PubMedID 28498568

  • Systems approach to uncover signaling networks in primary immunodeficiency diseases. journal of allergy and clinical immunology Choi, J., Fernandez, R., Maecker, H. T., Butte, M. J. 2017

    View details for DOI 10.1016/j.jaci.2017.03.025

    View details for PubMedID 28412396

  • Immunotherapy biomarkers 2016: overcoming the barriers JOURNAL FOR IMMUNOTHERAPY OF CANCER Gulley, J. L., Berzofsky, J. A., Butler, M. O., Cesano, A., Fox, B. A., Gnjatic, S., Janetzki, S., Kalavar, S., Karanikas, V., Khleif, S. N., Kirsch, I., Lee, P. P., Maccalli, C., Maecker, H., Schlom, J., Seliger, B., Siebert, J., Stroncek, D. F., Thurin, M., Yuan, J., Butterfield, L. H. 2017; 5: 29


    This report summarizes the symposium, 'Immunotherapy Biomarkers 2016: Overcoming the Barriers', which was held on April 1, 2016 at the National Institutes of Health in Bethesda, Maryland. The symposium, cosponsored by the Society for Immunotherapy of Cancer (SITC) and the National Cancer Institute (NCI), focused on emerging immunotherapy biomarkers, new technologies, current hurdles to further progress, and recommendations for advancing the field of biomarker development.

    View details for PubMedID 28653584

  • Assessing basophil activation by using flow cytometry and mass cytometry in blood stored 24 hours before analysis JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY Mukai, K., Gaudenzio, N., Gupta, S., Vivanco, N., Bendall, S. C., Maecker, H. T., Chinthrajah, R. S., Tsai, M., Nadeau, K. C., Galli, S. J. 2017; 139 (3): 889-?


    Basophil activation tests (BATs) have promise for research and for clinical monitoring of patients with allergies. However, BAT protocols vary in blood anticoagulant used and temperature and time of storage before testing, complicating comparisons of results from various studies.We attempted to establish a BAT protocol that would permit analysis of blood within 24 hours of obtaining the sample.Blood from 46 healthy donors and 120 patients with peanut allergy was collected into EDTA or heparin tubes, and samples were stored at 4°C or room temperature for 4 or 24 hours before performing BATs.Stimulation with anti-IgE or IL-3 resulted in strong upregulation of basophil CD203c in samples collected in EDTA or heparin, stored at 4°C, and analyzed 24 hours after sample collection. However, a CD63(hi) population of basophils was not observed in any conditions in EDTA-treated samples unless exogenous calcium/magnesium was added at the time of anti-IgE stimulation. By contrast, blood samples collected in heparin tubes were adequate for quantification of upregulation of basophil CD203c and identification of a population of CD63(hi) basophils, irrespective of whether the specimens were analyzed by means of conventional flow cytometry or cytometry by time-of-flight mass spectrometry, and such tests could be performed after blood was stored for 24 hours at 4°C.BATs to measure upregulation of basophil CD203c and induction of a CD63(hi) basophil population can be conducted with blood obtained in heparin tubes and stored at 4°C for 24 hours.

    View details for DOI 10.1016/j.jaci.2016.04.060

    View details for Web of Science ID 000397295800022

    View details for PubMedCentralID PMC5237629

  • Opening the Door on the CMV Immune Response in Aging. journal of infectious diseases Maecker, H. T. 2017

    View details for DOI 10.1093/infdis/jix081

    View details for PubMedID 28199686

  • Isolation of Peripheral Blood Mononuclear Cells Using Vacutainer® Cellular Preparation Tubes (CPTTM). Bio-protocol Puleo, A., Carroll, C., Maecker, H. T., Gupta, R. 2017; 7 (2): e2103


    Peripheral blood mononuclear cell (PBMC) isolation is commonly done via density gradient centrifugation over Ficoll-Hypaque, a labor-intensive procedure that requires skilled technicians and can contribute to sample variability. Cellular Preparation Tubes (CPTs) are Vacutainer blood draw tubes that contain Ficoll-Hypaque and a gel plug that separates the Ficoll solution from the blood to be drawn. Once blood is drawn into CPTs, they can be centrifuged to separate the PBMC, then shipped (if desired) to a processing lab. The processing lab removes the PBMC from the upper compartment of the tube (above the gel plug), washes the PBMC, and can cryopreserve them using DMSO-containing media, as detailed in this protocol.

    View details for DOI 10.21769/BioProtoc.2103

    View details for PubMedID 34458433

    View details for PubMedCentralID PMC8376597

  • Wild immunology assessed by multidimensional mass cytometry. Cytometry. Part A : the journal of the International Society for Analytical Cytology Japp, A. S., Hoffmann, K., Schlickeiser, S., Glauben, R., Nikolaou, C., Maecker, H. T., Braun, J., Matzmohr, N., Sawitzki, B., Siegmund, B., Radbruch, A., Volk, H., Frentsch, M., Kunkel, D., Thiel, A. 2017; 91 (1): 85-95


    A great part of our knowledge on mammalian immunology has been established in laboratory settings. The use of inbred mouse strains enabled controlled studies of immune cell and molecule functions in defined settings. These studies were usually performed in specific-pathogen free (SPF) environments providing standardized conditions. In contrast, mammalians including humans living in their natural habitat are continuously facing pathogen encounters throughout their life. The influences of environmental conditions on the signatures of the immune system and on experimental outcomes are yet not well defined. Thus, the transferability of results obtained in current experimental systems to the physiological human situation has always been a matter of debate. Studies elucidating the diversity of "wild immunology" imprintings in detail and comparing it with those of "clean" lab mice are sparse. Here, we applied multidimensional mass cytometry to dissect phenotypic and functional differences between distinct groups of laboratory and pet shop mice as a source for "wild mice". For this purpose, we developed a 31-antibody panel for murine leukocyte subsets identification and a 35-antibody panel assessing various cytokines. Established murine leukocyte populations were easily identified and diverse immune signatures indicative of numerous pathogen encounters were classified particularly in pet shop mice and to a lesser extent in quarantine and non-SPF mice as compared to SPF mice. In addition, unsupervised analysis identified distinct clusters that associated strongly with the degree of pathogenic priming, including increased frequencies of activated NK cells and antigen-experienced B- and T-cell subsets. Our study unravels the complexity of immune signatures altered under physiological pathogen challenges and highlights the importance of carefully adapting laboratory settings for immunological studies in mice, including drug and therapy testing. © 2016 International Society for Advancement of Cytometry.

    View details for DOI 10.1002/cyto.a.22906

    View details for PubMedID 27403624

  • Isolation of PBMCs Using Vacutainer® Cellular Preparation Tubes Bio-protocol Puleo, A., Carroll, C., Maecker, H., Gupta, R. 2017; 7 (2)

    View details for DOI 10.21769/BioProtoc.2103

  • Autoantibody profiling on a plasmonic nano-gold chip for the early detection of hypertensive heart disease. Proceedings of the National Academy of Sciences of the United States of America Li, X. n., Kuznetsova, T. n., Cauwenberghs, N. n., Wheeler, M. n., Maecker, H. n., Wu, J. C., Haddad, F. n., Dai, H. n. 2017; 114 (27): 7089–94


    The role of autoimmunity in cardiovascular (CV) diseases has been increasingly recognized. Autoimmunity is most commonly examined by the levels of circulating autoantibodies in clinical practices. Measurement of autoantibodies remains, however, challenging because of the deficiency of reproducible, sensitive, and standardized assays. The lack of multiplexed assays also limits the potential to identify a CV-specific autoantibody profile. To overcome these challenges, we developed a nanotechnology-based plasmonic gold chip for autoantibody profiling. This approach allowed simultaneous detection of 10 CV autoantibodies targeting the structural myocardial proteins, the neurohormonal regulatory proteins, the vascular proteins, and the proteins associated with apoptosis and coagulation. Autoantibodies were measured in four groups of participants across the continuum of hypertensive heart diseases. We observed higher levels of all 10 CV autoantibodies in hypertensive subjects (n= 77) compared with healthy participants (n= 30), and the autoantibodies investigated were related to each other, forming a highly linked network. In addition, we established that autoantibodies to troponin I, annexin-A5, and beta 1-adrenegic receptor best discriminated hypertensive subjects with adverse left ventricular (LV) remodeling or dysfunction (n= 49) from hypertensive subjects with normal LV structure and function (n= 28). By further linking these three significant CV autoantibodies to the innate and growth factors, we revealed a positive but weak association between autoantibodies to troponin I and proinflammatory cytokine IL-18. Overall, we demonstrated that this platform can be used to evaluate autoantibody profiles in hypertensive subjects at risk for heart failure.

    View details for PubMedID 28630342

  • 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


    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

  • CyTOF Measurement of Immunocompetence Across Major Immune Cell Types. Current protocols in cytometry Subrahmanyam, P. B., Maecker, H. T. 2017; 82: 9.54.1–9.54.12


    The central role of the immune system is becoming appreciated in a wide variety of diseases. Cancer immunotherapy is one area that has yielded much recent success, although not all patients benefit equally. At the same time, recent studies have highlighted the heterogeneity of the human immune system. Despite this heterogeneity, we do not routinely measure immune competence in clinical practice, and there are no consensus assays of healthy immune function. Using mass cytometry (CyTOF), we can simultaneously detect ∼40 markers to identify various cell subsets and determine their function by the expression of cytokines, cytotoxicity, and activation markers. This can help assess 'immunocompetence' and facilitate better implementation of immunotherapies, both in specific disease settings and perhaps eventually as a prognostic tool in healthy subjects. Here we introduce the concepts behind this assay and provide a protocol that we have successfully implemented to identify possible predictive biomarkers of immunotherapy outcome. © 2017 by John Wiley & Sons, Inc.

    View details for PubMedID 28967988

    View details for PubMedCentralID PMC5678938

  • Characterizing CD137 Upregulation on NK cells in Patients Receiving Monoclonal Antibody Therapy. Annals of oncology MAKKOUK, A., Sundaram, V., Chester, C., Chang, S., Colevas, A. D., Sunwoo, J. B., Maecker, H., Desai, M., Kohrt, H. E. 2016


    In the era of personalized cancer medicine, identifying techniques for effectively matching patients to efficacious treatments is a critical step in the treatment process. The advent of anti-cancer immunotherapies necessitates novel approaches to biomarker identification beyond traditional genomic profiling. One promising approach is incorporation of nomograms into treatment decisions. Nomograms are prediction tools, based on statistical modeling, designed to predict treatment outcomes. As a first step toward developing a nomogram, we conducted analyses to predict CD137 expression of natural killer cells after monoclonal antibody (mAb) treatment.Patient, tumor and immune characteristics were collected from 199 patients with breast cancer (N = 62), head/neck cancers (N = 46) and non-Hodgkin's lymphoma (NHL) (N = 91), who were receiving mAb therapy as part of clinical trials. The difference in CD137 expression before and after mAb therapy was assessed by flow cytometry. To evaluate those who respond to mAb therapy via increased CD137 expression, we applied classification and regression trees (CART), multivariable lasso regression tools and Random Forest.The CD137 expression was significantly different for each cancer type [mean (SD): Breast: 6.6 (6.5); Head/Neck: 11.0 (7.0); NHL: 7.5 (7.1), P < 0.0001]. For breast cancer and NHL, FcR polymorphism and baseline CD137 expression were significant predictors of increased CD137 expression; for head/neck cancer, FcR polymorphism and age were significant predictors of increased expression.Our preliminary results suggest that FcR polymorphism, pre-treatment CD137 expression and age are significant predictors of CD137 upregulation in patients. This study demonstrates that the development of a nomogram for therapy response is feasible. Further work validating our models in an independent cohort will provide the next steps in developing a nomogram that may be used to individualize this therapeutic approach for patients (NCT01114256).

    View details for PubMedID 27831501

  • Cytokine profiles in patients with toxoplasmic lymphadenitis in the setting of pregnancy. Cytokine Pomares, C., Holmes, T. H., Estran, R., Press, C. J., Ramirez, R., Talucod, J., Maecker, H., Rosenberg-Hasson, Y., Montoya, J. G. 2016; 90: 14-20


    Majority of Toxoplasma gondii infections are benign and asymptomatic; however, some patients experience toxoplasmic lymphadenitis (TL). Factors associated as to whether infection will be symptomatic or not are unknown.Dye test titers of patients with acute toxoplasmosis (pregnant and not pregnant) with TL (TL+) were compared with those in patients with asymptomatic acute infection (TL-). Additionally, mean levels of 62 serum cytokines were compared between TL+ and TL- pregnant women and between TL+ pregnant and non-pregnant women.During acute infection, mean dye test titer was higher in TL+ than in TL- patients (p=0.021). In addition, out of 62 cytokines, CXCL9andCXCL10 levels were higher (p<0.05) and resistin mean levels were lower (p<0.05) in pregnant women with TL+ compared to TL-. Among patients with TL+, levels of VCAM1andCCL2 were lower (p<0.05) in pregnant women than in non-pregnant women.Here we report differences in dye test titers in patients with acute infection. Cytokine responses vary according to the presence of TL+ and to the pregnancy status. Factors underlying these differences are presently unknown and require further studies to define individual and combined roles of cytokines in TL+.

    View details for DOI 10.1016/j.cyto.2016.09.021

    View details for PubMedID 27744174

  • 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)


    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

  • Immune Profiles to Predict Response to Desensitization Therapy in Highly HLA-Sensitized Kidney Transplant Candidates PLOS ONE Yabu, J. M., Siebert, J. C., Maecker, H. T. 2016; 11 (4)


    Kidney transplantation is the most effective treatment for end-stage kidney disease. Sensitization, the formation of human leukocyte antigen (HLA) antibodies, remains a major barrier to successful kidney transplantation. Despite the implementation of desensitization strategies, many candidates fail to respond. Current progress is hindered by the lack of biomarkers to predict response and to guide therapy. Our objective was to determine whether differences in immune and gene profiles may help identify which candidates will respond to desensitization therapy.Single-cell mass cytometry by time-of-flight (CyTOF) phenotyping, gene arrays, and phosphoepitope flow cytometry were performed in a study of 20 highly sensitized kidney transplant candidates undergoing desensitization therapy. Responders to desensitization therapy were defined as 5% or greater decrease in cumulative calculated panel reactive antibody (cPRA) levels, and non-responders had 0% decrease in cPRA. Using a decision tree analysis, we found that a combination of transitional B cell and regulatory T cell (Treg) frequencies at baseline before initiation of desensitization therapy could distinguish responders from non-responders. Using a support vector machine (SVM) and longitudinal data, TRAF3IP3 transcripts and HLA-DR-CD38+CD4+ T cells could also distinguish responders from non-responders. Combining all assays in a multivariate analysis and elastic net regression model with 72 analytes, we identified seven that were highly interrelated and eleven that predicted response to desensitization therapy.Measuring baseline and longitudinal immune and gene profiles could provide a useful strategy to distinguish responders from non-responders to desensitization therapy. This study presents the integration of novel translational studies including CyTOF immunophenotyping in a multivariate analysis model that has potential applications to predict response to desensitization, select candidates, and personalize medicine to ultimately improve overall outcomes in highly sensitized kidney transplant candidates.

    View details for DOI 10.1371/journal.pone.0153355

    View details for Web of Science ID 000374131700042

    View details for PubMedID 27078882

    View details for PubMedCentralID PMC4831845

  • 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


    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

  • Platinum-conjugated antibodies for application in mass cytometry. Cytometry. Part A : the journal of the International Society for Analytical Cytology Mei, H. E., Leipold, M. D., Maecker, H. T. 2016; 89 (3): 292-300


    Mass cytometry has overcome limitations of fluorescent single cell cytometry by allowing for the measurement of up to currently ∼40 different parameters on a single cell level. However, the cellular proteome comprises many more potential analytes, and current mass cytometry instrumentation allows for theoretically up to 121 different mass detection channels. The labeling of specific probes with appropriate metal ions is a significant hurdle for exploiting more of mass cytometry's analytical capacity. To this end, we here describe the labeling of antibody with natural abundance or isotopically purified platinum as formulated in cisplatin and circumventing the use of chelator-loaded polymers. We confirm the utility of cisplatin-antibody-conjugates for surface, intracellular, and phosphoepitope-specific immunophenotyping, as well as for application in cell surface CD45-based barcoding. Cisplatin-labeling of antibody increases the analytical capacity of the CyTOF(®) platform by two channels based on available reagents, and has the potential to add a total of six channels for detection of specific probes, thus helping to better extend the analytical mass range of mass cytometers. © 2015 International Society for Advancement of Cytometry.

    View details for DOI 10.1002/cyto.a.22778

    View details for PubMedID 26355391

  • Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium SCIENTIFIC REPORTS Finak, G., Langweiler, M., Jaimes, M., Malek, M., Taghiyar, J., Korin, Y., Raddassi, K., Devine, L., Obermoser, G., Pekalski, M. L., Pontikos, N., Diaz, A., Heck, S., Villanova, F., Terrazzini, N., Kern, F., Qian, Y., Stanton, R., Wang, K., Brandes, A., Ramey, J., Aghaeepour, N., Mosmann, T., Scheuermann, R. H., Reed, E., Palucka, K., pascual, V., Blomberg, B. B., Nestle, F., Nussenblatt, R. B., Brinkman, R. R., Gottardo, R., Maecker, H., McCoy, J. P. 2016; 6


    Standardization of immunophenotyping requires careful attention to reagents, sample handling, instrument setup, and data analysis, and is essential for successful cross-study and cross-center comparison of data. Experts developed five standardized, eight-color panels for identification of major immune cell subsets in peripheral blood. These were produced as pre-configured, lyophilized, reagents in 96-well plates. We present the results of a coordinated analysis of samples across nine laboratories using these panels with standardized operating procedures (SOPs). Manual gating was performed by each site and by a central site. Automated gating algorithms were developed and tested by the FlowCAP consortium. Centralized manual gating can reduce cross-center variability, and we sought to determine whether automated methods could streamline and standardize the analysis. Within-site variability was low in all experiments, but cross-site variability was lower when central analysis was performed in comparison with site-specific analysis. It was also lower for clearly defined cell subsets than those based on dim markers and for rare populations. Automated gating was able to match the performance of central manual analysis for all tested panels, exhibiting little to no bias and comparable variability. Standardized staining, data collection, and automated gating can increase power, reduce variability, and streamline analysis for immunophenotyping.

    View details for DOI 10.1038/srep20686

    View details for PubMedID 26861911

  • Immunodynamics: a cancer immunotherapy trials network review of immune monitoring in immuno-oncology clinical trials. Journal for immunotherapy of cancer Kohrt, H. E., Tumeh, P. C., Benson, D., Bhardwaj, N., Brody, J., Formenti, S., Fox, B. A., Galon, J., June, C. H., Kalos, M., Kirsch, I., Kleen, T., Kroemer, G., Lanier, L., Levy, R., Lyerly, H. K., Maecker, H., Marabelle, A., Melenhorst, J., Miller, J., Melero, I., Odunsi, K., Palucka, K., Peoples, G., Ribas, A., Robins, H., Robinson, W., Serafini, T., Sondel, P., Vivier, E., Weber, J., Wolchok, J., Zitvogel, L., Disis, M. L., Cheever, M. A. 2016; 4: 15-?


    The efficacy of PD-1/PD-L1 targeted therapies in addition to anti-CTLA-4 solidifies immunotherapy as a modality to add to the anticancer arsenal. Despite raising the bar of clinical efficacy, immunologically targeted agents raise new challenges to conventional drug development paradigms by highlighting the limited relevance of assessing standard pharmacokinetics (PK) and pharmacodynamics (PD). Specifically, systemic and intratumoral immune effects have not consistently correlated with standard relationships between systemic dose, toxicity, and efficacy for cytotoxic therapies. Hence, PK and PD paradigms remain inadequate to guide the selection of doses and schedules, both starting and recommended Phase 2 for immunotherapies. The promise of harnessing the immune response against cancer must also be considered in light of unique and potentially serious toxicities. Refining immune endpoints to better inform clinical trial design represents a high priority challenge. The Cancer Immunotherapy Trials Network investigators review the immunodynamic effects of specific classes of immunotherapeutic agents to focus immune assessment modalities and sites, both systemic and importantly intratumoral, which are critical to the success of the rapidly growing field of immuno-oncology.

    View details for DOI 10.1186/s40425-016-0118-0

    View details for PubMedID 26981245

  • Similarities in the Markers of Inflammation Between Men With Syphilis and Women With Increased Risk of HIV Acquisition. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Kojima, N. n., Bristow, C. C., Maecker, H. n., Rosenberg-Hasson, Y. n., Leon, S. R., Vargas, S. K., Konda, K. A., Caceres, C. F., Klausner, J. D. 2016; 62 (2): 265–66

    View details for PubMedID 26394671

  • Novel technologies and emerging biomarkers for personalized cancer immunotherapy. Journal for immunotherapy of cancer Yuan, J., Hegde, P. S., Clynes, R., Foukas, P. G., Harari, A., Kleen, T. O., Kvistborg, P., Maccalli, C., Maecker, H. T., Page, D. B., Robins, H., Song, W., Stack, E. C., Wang, E., Whiteside, T. L., Zhao, Y., Zwierzina, H., Butterfield, L. H., Fox, B. A. 2016; 4: 3-?


    The culmination of over a century's work to understand the role of the immune system in tumor control has led to the recent advances in cancer immunotherapies that have resulted in durable clinical responses in patients with a variety of malignancies. Cancer immunotherapies are rapidly changing traditional treatment paradigms and expanding the therapeutic landscape for cancer patients. However, despite the current success of these therapies, not all patients respond to immunotherapy and even those that do often experience toxicities. Thus, there is a growing need to identify predictive and prognostic biomarkers that enhance our understanding of the mechanisms underlying the complex interactions between the immune system and cancer. Therefore, the Society for Immunotherapy of Cancer (SITC) reconvened an Immune Biomarkers Task Force to review state of the art technologies, identify current hurdlers, and make recommendations for the field. As a product of this task force, Working Group 2 (WG2), consisting of international experts from academia and industry, assembled to identify and discuss promising technologies for biomarker discovery and validation. Thus, this WG2 consensus paper will focus on the current status of emerging biomarkers for immune checkpoint blockade therapy and discuss novel technologies as well as high dimensional data analysis platforms that will be pivotal for future biomarker research. In addition, this paper will include a brief overview of the current challenges with recommendations for future biomarker discovery.

    View details for DOI 10.1186/s40425-016-0107-3

    View details for PubMedID 26788324

    View details for PubMedCentralID PMC4717548

  • Computationally efficient multidimensional analysis of complex flow cytometry data using second order polynomial histograms CYTOMETRY PART A Zaunders, J., Jing, J., Leipold, M., Maecker, H., Kelleher, A. D., Koch, I. 2016; 89A (1): 44-58


    Many methods have been described for automated clustering analysis of complex flow cytometry data, but so far the goal to efficiently estimate multivariate densities and their modes for a moderate number of dimensions and potentially millions of data points has not been attained. We have devised a novel approach to describing modes using second order polynomial histogram estimators (SOPHE). The method divides the data into multivariate bins and determines the shape of the data in each bin based on second order polynomials, which is an efficient computation. These calculations yield local maxima and allow joining of adjacent bins to identify clusters. The use of second order polynomials also optimally uses wide bins, such that in most cases each parameter (dimension) need only be divided into 4-8 bins, again reducing computational load. We have validated this method using defined mixtures of up to 17 fluorescent beads in 16 dimensions, correctly identifying all populations in data files of 100,000 beads in <10 s, on a standard laptop. The method also correctly clustered granulocytes, lymphocytes, including standard T, B, and NK cell subsets, and monocytes in 9-color stained peripheral blood, within seconds. SOPHE successfully clustered up to 36 subsets of memory CD4 T cells using differentiation and trafficking markers, in 14-color flow analysis, and up to 65 subpopulations of PBMC in 33-dimensional CyTOF data, showing its usefulness in discovery research. SOPHE has the potential to greatly increase efficiency of analysing complex mixtures of cells in higher dimensions.

    View details for DOI 10.1002/cyto.a.22704

    View details for Web of Science ID 000369061600007

  • Cytokines profile in hypertensive patients with left ventricular remodeling and dysfunction. Journal of the American Society of Hypertension Kuznetsova, T., Haddad, F., Knez, J., Rosenberg-Hasson, Y., Sung, J., Cauwenberghs, N., Thijs, L., Karakikes, I., Maecker, H., Mahaffey, K. W., Wu, J. C., Staessen, J. A. 2015; 9 (12): 975-984 e3


    There is strong evidence that inflammatory mediators play a key role in the progression to heart failure in patients with systemic hypertension (HTN). The present study aimed to identify a set of cytokines that are associated with early left ventricular (LV) remodeling and dysfunction as captured by echocardiography in patients with HTN in a cross-sectional case-control study nested within the FLEMish study on ENvironment, Genes and Health Outcome. We identified three groups of participants from the cohort: normotensive subjects (normotension; n = 30), HTN with normal LV structure and function (HTN [LV-]; n = 30), and HTN with evidence of adverse LV remodeling (HTN [LV+]; n = 50). We measured cytokines using a 63-plex Luminex platform. Using partial least squares-discriminant analysis, we constructed three latent variables from the measured cytokines that explained 35%-45% of the variance between groups. We identified five common cytokines (interleukin 18, monokine induced by gamma interferon, hepatocyte growth factor, epithelial neutrophil-activating peptide 78, and vascular endothelial growth factor D) with a stable signal which had a major impact on the construction of the latent variables. Among these cytokines, after adjustment for confounders, interleukin 18 remained significantly different between HTN participants with and without LV involvement (P = .02). Moreover, granulocyte-macrophage colony-stimulating factor and leptin showed a consistent upward trend in all HTN patients compared with normotensive subjects. In conclusion, in HTN patients with LV remodeling or/and dysfunction, we identified a set of cytokines strongly associated with LV maladaptation. We also found a distinct profile of inflammatory biomarkers that characterize HTN.

    View details for DOI 10.1016/j.jash.2015.10.003

    View details for PubMedID 26565110

  • Algorithmic Tools for Mining High-Dimensional Cytometry Data. Journal of immunology (Baltimore, Md. : 1950) Chester, C., Maecker, H. T. 2015; 195 (3): 773-9


    The advent of mass cytometry has led to an unprecedented increase in the number of analytes measured in individual cells, thereby increasing the complexity and information content of cytometric data. Although this technology is ideally suited to the detailed examination of the immune system, the applicability of the different methods for analyzing such complex data is less clear. Conventional data analysis by manual gating of cells in biaxial dot plots is often subjective, time consuming, and neglectful of much of the information contained in a highly dimensional cytometric dataset. Algorithmic data mining has the promise to eliminate these concerns, and several such tools have been applied recently to mass cytometry data. We review computational data mining tools that have been used to analyze mass cytometry data, outline their differences, and comment on their strengths and limitations. This review will help immunologists to identify suitable algorithmic tools for their particular projects.

    View details for DOI 10.4049/jimmunol.1500633

    View details for PubMedID 26188071

    View details for PubMedCentralID PMC4507289

  • Large-Scale and Comprehensive Immune Profiling and Functional Analysis of Normal Human Aging PLOS ONE Whiting, C. C., Siebert, J., Newman, A. M., Du, H., Alizadeh, A. A., Goronzy, J., Weyand, C. M., Krishnan, E., Fathman, C. G., Maecker, H. T. 2015; 10 (7)


    While many age-associated immune changes have been reported, a comprehensive set of metrics of immune aging is lacking. Here we report data from 243 healthy adults aged 40-97, for whom we measured clinical and functional parameters, serum cytokines, cytokines and gene expression in stimulated and unstimulated PBMC, PBMC phenotypes, and cytokine-stimulated pSTAT signaling in whole blood. Although highly heterogeneous across individuals, many of these assays revealed trends by age, sex, and CMV status, to greater or lesser degrees. Age, then sex and CMV status, showed the greatest impact on the immune system, as measured by the percentage of assay readouts with significant differences. An elastic net regression model could optimally predict age with 14 analytes from different assays. This reinforces the importance of multivariate analysis for defining a healthy immune system. These data provide a reference for others measuring immune parameters in older people.

    View details for DOI 10.1371/journal.pone.0133627

    View details for Web of Science ID 000358547600123

  • Immunologic Network and Response to Intramyocardial CD34(+) Stem Cell Therapy in Patients With Dilated Cardiomyopathy JOURNAL OF CARDIAC FAILURE Haddad, F., Sever, M., Poglajen, G., Lezaic, L., Yang, P., Maecker, H., Davis, M., Kuznetsova, T., Wu, J. C., Vrtovec, B. 2015; 21 (7): 572-582


    Although stem cell therapy (SCT) is emerging as a potential treatment for patients with dilated cardiomyopathy (DCM), clinical response remains variable. Our objective was to determine whether baseline differences in circulating immunologic and nonimmunologic biomarkers may help to identify patients more likely to respond to intramyocardial injection of CD34(+)-based SCT.We enrolled from January 3, 2011 to March 5, 2012 37 patients with longstanding DCM (left ventricular ejection fraction [LVEF] <40%, New York Heart Association functional class III) who underwent peripheral CD34(+) stem cell mobilization with granulocyte colony-stimulating factor (G-CSF) and collection by means of apheresis. CD34(+) cells were labeled with (99m)Tc-hexamethylpropyleneamine oxime to allow assessment of stem cell retention at 18 hours. Response to SCT was predefined as an increase in LVEF of ≥5% at 3 months. The majority (84%) of patients were male with an overall mean LVEF of 27 ± 7% and a median N-terminal pro-B-type natriuretic peptide (NT-proBNP) level of 2,774 pg/mL. Nineteen patients (51%) were responders to SCT. There was no significant difference between responders and nonresponders regarding to age, sex, baseline LVEF, NT-proBNP levels, or 6-minute walking distance. With the use of a partial least squares (PLS) predictive model, we identified 9 baseline factors that were associated with both stem cell response and stem cell retention (mechanistic validation). Among the baseline factors positively associated with both clinical response and stem cell retention were G-CSF, SDF-1, LIF, MCP-1, and MCP-3. Among baseline factors negatively associated with both clinical response and retention were IL-12p70, FASL, ICAM-1, and GGT. A decrease in G-CSF at 3-month follow-up was also observed in responders compared with nonresponders (P = .02).If further validated, baseline immunologic and nonimmunologic biomarkers may help to identify patients with DCM who are more likely to respond to CD34(+)-based SCT.

    View details for DOI 10.1016/j.cardfail.2015.03.011

    View details for Web of Science ID 000358105900007

    View details for PubMedID 25863169

  • Cytokine-stimulated Phosphoflow of PBMC Using CyTOF Mass Cytometry. Bio-protocol Fernandez, R., Maecker, H. 2015; 5 (11)


    Phosphorylation of tyrosine, serine, and threonine residues is critical for the control of protein activity involved in various cellular events. An assortment of kinases and phosphatases regulate intracellular protein phosphorylation in many different cell signaling pathways. These pathways include T and B cell signaling, regulating growth and cell cycle control, plus cytokine, chemokine, and stress responses. Phosphoflow assays combine phosphoprotein-specific antibodies with the power of flow cytometry to enhance phosphoprotein study. In our assay, peripheral blood mononuclear cells are stimulated by cytokines, fixed, surface-stained with a cocktail of antibodies labeled with MAXPAR (brand name) metal-chelating polymers and permeabilized with methanol. They are then stained with intracellular phospho-specific antibodies. We use a CyTOF(™) mass cytometer to acquire the ICP-MS (inductively coupled plasma mass spectrometry) data. The current mass window selected is approximately AW 103-203, which includes the lanthanides used for most antibody labeling, as well as iridium and rhodium for DNA intercalators. Subsequent analysis of the dual count signal data using FlowJo software allows for cell types to be analyzed based on the dual count signal in each mass channel. The percentage of each cell type is determined and reported as a percent of the parent cell type. Median values are reported to quantitate the level of phosphorylation of each protein in response to stimulation. Comparing the level of phosphorylation between samples can offer insight to the status of the immune system.

    View details for PubMedID 27446979

  • Cytokine-Stimulated Phosphoflow of Whole Blood Using CyTOF Mass Cytometry. Bio-protocol Fernandez, R., Maecker, H. 2015; 5 (11)


    The ability to assess the function of a range of cytokine, antigen receptor, and Toll-like receptor (TLR) signaling pathways in a range of immune cells could provide a kind of fingerprint of the state of the human immune system. The mass cytometry or CyTOF, platform allows for the parallel application of about 40 labeled antibodies to a single sample, creating the possibility to read out many cell types and signaling pathways in a single small blood sample. We developed such a mass cytometry panel, consisting of 22 antibodies to cell surface lineage markers and 8 antibodies to phospho-specific epitopes of signaling proteins. These antibodies were chosen to discriminate all major white blood cell lineages, to a level of detail that includes subsets such as naïve, central memory, effector memory, and late effector CD4+ and CD8+T cells, naïve, transitional, and switched memory B cells, plasmablasts, myeloid and plasmacytoid dendritic cells, CD16+ and CD16+CD56+ NK cells, CD16+ and classical monocytes etc. 32 such cell subsets are defined in our standard gating scheme. The eight phospho-specific antibodies were chosen to represent major signaling nodes responsive to cytokine, TLR, and antigen receptor signaling. This antibody panel is used with 8 standard stimulation conditions (unstimulated, IFNa, IL-6, IL-7, IL-10, IL-21, LPS, PMA+ ionomycin), although other stimuli can be added. Comparison of healthy controls to subjects with immune deficiencies of unknown etiology may help elucidate the mechanisms of such deficiencies. Phosphorylation of tyrosine, serine, and threonine residues is critical for the control of protein activity involved in various cellular events. An assortment of kinases and phosphatases regulate intracellular protein phosphorylation in many different cell signaling pathways, such as T and B cell signaling, those regulating apoptosis, growth and cell cycle control, plus those involved with cytokine, chemokine, and stress responses. Phosphoflow assays combine phospho-specific antibodies with the power of flow cytometry to enhance phospho protein study. In our assay, peripheral blood mononuclear cells are stimulated by cytokines, fixed, surface-stained with a cocktail of antibodies labeled with MAXPAR (Brand Name) metal-chelating polymers and permeabilized with methanol. They are then stained with intracellular phospho-specific antibodies. We use a CyTOF™ mass cytometer to acquire the ICP-MS data. The current mass window selected is approximately AW 103-203, which includes the lanthanides used for most antibody labeling, as well as iridium and rhodium for DNA intercalators. Subsequent analysis of the dual count signal data using FlowJo software allows for cell types to be analyzed based on the dual count signal in each mass channel. The percentage of each cell type is determined and reported as a percent of the parent cell type. Median values are reported to quantitate the level of phosphorylation of each protein in response to stimulation. Comparing the level of phosphorylation between samples can offer insight to the status of the immune system. Whole blood stimulation is the closest to the in vivo condition and it allows for assessment of granulocyte population as well as lymphocytes and monocytes.

    View details for PubMedID 27135045

  • Mass cytometry as a platform for the discovery of cellular biomarkers to guide effective rheumatic disease therapy ARTHRITIS RESEARCH & THERAPY Nair, N., Mei, H. E., Chen, S., Hale, M., Nolan, G. P., Maecker, H. T., Genovese, M., Fathman, C. G., Whiting, C. C. 2015; 17


    The development of biomarkers for autoimmune diseases has been hampered by a lack of understanding of disease etiopathogenesis and of the mechanisms underlying the induction and maintenance of inflammation, which involves complex activation dynamics of diverse cell types. The heterogeneous nature and suboptimal clinical response to treatment observed in many autoimmune syndromes highlight the need to develop improved strategies to predict patient outcome to therapy and personalize patient care. Mass cytometry, using CyTOF®, is an advanced technology that facilitates multiparametric, phenotypic analysis of immune cells at single-cell resolution. In this review, we outline the capabilities of mass cytometry and illustrate the potential of this technology to enhance the discovery of cellular biomarkers for rheumatoid arthritis, a prototypical autoimmune disease.

    View details for DOI 10.1186/s13075-015-0644-z

    View details for Web of Science ID 000354850500001

    View details for PubMedID 25981462

    View details for PubMedCentralID PMC4436107

  • flowCL: ontology-based cell population labelling in flow cytometry BIOINFORMATICS Courtot, M., Meskas, J., Diehl, A. D., Droumeva, R., Gottardo, R., Jalali, A., Taghiyar, M. J., Maecker, H. T., McCoy, J. P., Ruttenberg, A., Scheuermann, R. H., Brinkman, R. R. 2015; 31 (8): 1337-1339


    Finding one or more cell populations of interest, such as those correlating to a specific disease, is critical when analysing flow cytometry data. However, labelling of cell populations is not well defined, making it difficult to integrate the output of algorithms to external knowledge sources.We developed flowCL, a software package that performs semantic labelling of cell populations based on their surface markers and applied it to labelling of the Federation of Clinical Immunology Societies Human Immunology Project Consortium lyoplate populations as a use case.By providing automated labelling of cell populations based on their immunophenotype, flowCL allows for unambiguous and reproducible identification of standardized cell types.Code, R script and documentation are available under the Artistic 2.0 license through Bioconductor ( data are available at Bioinformatics online.

    View details for DOI 10.1093/bioinformatics/btu807

    View details for Web of Science ID 000354453700035

    View details for PubMedID 25481008

    View details for PubMedCentralID PMC4393520

  • Intracellular Cytokine Staining (ICS) on Human Lymphocytes or Peripheral Blood Mononuclear Cells (PBMCs). Bio-protocol Gupta, S., Maecker, H. 2015; 5 (5): e1442


    Production of cytokines plays an important role in the immune response. Cytokines are involved in many different pathways including the induction of many anti-viral proteins by IFN gamma, the induction of T cell proliferation by IL-2 and the inhibition of viral gene expression and replication by TNF alpha. Cytokines are not preformed factors but are rapidly produced and secreted in response to cellular activation. Intracellular cytokine detection by flow cytometry has emerged as the premier technique for studying cytokine production at the single-cell level. It detects the production and accumulation of cytokines within the endoplasmic reticulum after cell stimulation, allowing direct TH1 versus TH2 determination. It can also be used in combination with other flow cytometry protocols for immunophenotyping using cell surface markers or with MHC multimers to detect an antigen specific response, making it an extremely flexible and versatile method. This capability, combined with the high throughput nature of the instrumentation, gives intracellular cytokine staining an enormous advantage over existing single-cell techniques such as ELISPOT, limiting dilution, and T cell cloning. The principle steps of intracellular cytokine staining is as follows: Cells are activated for a few hours using either a specific peptide or a non-specific activation cocktail; An inhibitor of protein transport (e.g. Brefeldin A) is added to retain the cytokines within the cell; Next, EDTA is added to remove adherent cells from the activation vessel;After washing, antibodies to cell surface markers can be added to the cells;The cells are then fixed in paraformaldehyde and permeabilized;The anti-cytokine antibody is added and the cells can be analyzed by flow cytometer.

    View details for DOI 10.21769/BioProtoc.1442

    View details for PubMedID 34604458

    View details for PubMedCentralID PMC8443452

  • 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-?


    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

  • Barcoding of live human peripheral blood mononuclear cells for multiplexed mass cytometry. Journal of immunology Mei, H. E., Leipold, M. D., Schulz, A. R., Chester, C., Maecker, H. T. 2015; 194 (4): 2022-2031


    Mass cytometry is developing as a means of multiparametric single-cell analysis. In this study, we present an approach to barcoding separate live human PBMC samples for combined preparation and acquisition on a cytometry by time of flight instrument. Using six different anti-CD45 Ab conjugates labeled with Pd104, Pd106, Pd108, Pd110, In113, and In115, respectively, we barcoded up to 20 samples with unique combinations of exactly three different CD45 Ab tags. Cell events carrying more than or less than three different tags were excluded from analyses during Boolean data deconvolution, allowing for precise sample assignment and the electronic removal of cell aggregates. Data from barcoded samples matched data from corresponding individually stained and acquired samples, at cell event recoveries similar to individual sample analyses. The approach greatly reduced technical noise and minimizes unwanted cell doublet events in mass cytometry data, and it reduces wet work and Ab consumption. It also eliminates sample-to-sample carryover and the requirement of instrument cleaning between samples, thereby effectively reducing overall instrument runtime. Hence, CD45 barcoding facilitates accuracy of mass cytometric immunophenotyping studies, thus supporting biomarker discovery efforts, and it should be applicable to fluorescence flow cytometry as well.

    View details for DOI 10.4049/jimmunol.1402661

    View details for PubMedID 25609839

    View details for PubMedCentralID PMC4323739

  • 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


    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

  • Mass cytometry as a platform for the discovery of cellular biomarkers to guide effective rheumatic disease therapy. Arthritis research & therapy Nair, N., Mei, H. E., Chen, S., Hale, M., Nolan, G. P., Maecker, H. T., Genovese, M., Fathman, C. G., Whiting, C. C. 2015; 17: 127-?


    The development of biomarkers for autoimmune diseases has been hampered by a lack of understanding of disease etiopathogenesis and of the mechanisms underlying the induction and maintenance of inflammation, which involves complex activation dynamics of diverse cell types. The heterogeneous nature and suboptimal clinical response to treatment observed in many autoimmune syndromes highlight the need to develop improved strategies to predict patient outcome to therapy and personalize patient care. Mass cytometry, using CyTOF®, is an advanced technology that facilitates multiparametric, phenotypic analysis of immune cells at single-cell resolution. In this review, we outline the capabilities of mass cytometry and illustrate the potential of this technology to enhance the discovery of cellular biomarkers for rheumatoid arthritis, a prototypical autoimmune disease.

    View details for DOI 10.1186/s13075-015-0644-z

    View details for PubMedID 25981462

  • Thinking outside the gate: single-cell assessments in multiple dimensions. Immunity Kvistborg, P. n., Gouttefangeas, C. n., Aghaeepour, N. n., Cazaly, A. n., Chattopadhyay, P. K., Chan, C. n., Eckl, J. n., Finak, G. n., Hadrup, S. R., Maecker, H. T., Maurer, D. n., Mosmann, T. n., Qiu, P. n., Scheuermann, R. H., Welters, M. J., Ferrari, G. n., Brinkman, R. R., Britten, C. M. 2015; 42 (4): 591–92

    View details for PubMedID 25902473

  • Intracellular Cytokine Staining on PBMCs Using CyTOF™ Mass Cytometry. Bio-protocol Lin, D. n., Gupta, S. n., Maecker, H. T. 2015; 5 (1)


    In this protocol, we use a CyTOF™ mass cytometry to collect single-cell data on a large number of cytokines/chemokines as well as cell-surface proteins that characterize T cells and other immune cells. The current selected mass window in AW 103-203 includes the lanthanides used for most antibody labeling, along with iridium and rhodium for DNA intercalators. The output data are in the format as .txt and .fcs files, which is compatible with many analysis programs. This protocol could be adapted to include tetramers into the staining panel, but we have not optimized for that purpose. The principal steps of intracellular cytokine staining are as follows: First, cells are activated for a few hours using either a specific peptide or a non-specific activation cocktail. An inhibitor of protein transport (e.g. Brefeldin A) is added to retain the cytokines within the cell. Next, EDTA is added to remove adherent cells from the activation vessel. After washing, antibodies to cell surface markers are added to the cells. The cells are then fixed in paraformaldehyde and permeabilized. We use a gentle detergent, saponin, as the permealization buffer because it is less destructive to surface and intracellular epitopes compared to harsh detergents or methanol. After permeabilization, the metal-conjugated anti-cytokine antibodies are added into the cell suspension. The stained cells are then sequentially introduced into the mass cytometry for signal intensity analysis.

    View details for PubMedID 29104886

  • Predictors of clinical response to immunotherapy with or without radiotherapy. Journal of radiation oncology Hiniker, S. M., Maecker, H. T., Knox, S. J. 2015; 4: 339-345


    Success with recent immunotherapies has resulted in previously unattainable response rates, as well as durable responses in diseases with historically poor prognoses. The combination of radiation therapy and immunotherapy has been a recent area of active investigation, with exciting results in a subset of patients. However, patient characteristics predictive of probable benefit from therapy and clinically meaningful biomarkers indicative of the early development of an antitumor immune response have yet to be identified. What is needed is a better way to predict which patients are likely to benefit from therapy, which would allow those patients unlikely to benefit from immunotherapy to be spared potentially futile therapies, thereby avoiding unnecessary risks of toxicity and costly treatment. Here, we summarize the early data on predictors of clinical response to immunotherapy, and to immunotherapy in combination with radiation.

    View details for PubMedID 26709361

  • Phenotyping of Live Human PBMC using CyTOF™ Mass Cytometry. Bio-protocol Leipold, M. D., Maecker, H. T. 2015; 5 (2)


    Single-cell analysis has become an method of importance in immunology. Fluorescence flow cytometry has been a major player. However, due to issues such as autofluorescence and emission spillover between different fluorophores, alternative techniques are being developed. In recent years, mass cytometry has emerged, wherein antibodies labeled with metal ions are detected by ICP-MS. In order for a cell to be seen, a metal in the mass window must be present; there is no analogous parameter to forward or side scatter. The current mass window selected is approximately AW 103-196, which includes the lanthanides used for most antibody labeling, as well as iridium and rhodium for DNA intercalators. In this protocol, we use a cocktail of antibodies labeled with MAXPAR metal-chelating polymers to surface-stain live PBMC that have been previously cryopreserved. Many of these markers were taken from a standard fluorescence phenotyping panel (Maecker et al., 2012). No intracellular antibodies are used. We use a CyTOF™ (Cytometry by Time-Of-Flight) mass cytometer to acquire the ICP-MS data. Subsequent analysis of the dual count signal data using FlowJo software allows for cell types to be analyzed based on the dual count signal in each mass channel. The percentage of each cell type is determined and reported as a percent of the parent cell type.

    View details for PubMedID 27390767

  • Multiparameter Phenotyping of Human PBMCs Using Mass Cytometry. Methods in molecular biology (Clifton, N.J.) Leipold, M. D., Newell, E. W., Maecker, H. T. 2015; 1343: 81-95


    The standard for single-cell analysis of phenotype and function in recent decades has been fluorescence flow cytometry. Mass cytometry is a newer technology that uses heavy metal ions, rather than fluorochromes, as labels for probes such as antibodies. The binding of these ion-labeled probes to cells is quantitated by mass spectrometry. This greatly increases the number of phenotypic and functional markers that can be probed simultaneously. Here, we review topics that must be considered when adapting existing flow cytometry panels to mass cytometry analysis. We present a protocol and representative panels for surface phenotyping and intracellular cytokine staining (ICS) assays.

    View details for DOI 10.1007/978-1-4939-2963-4_7

    View details for PubMedID 26420710

    View details for PubMedCentralID PMC4748856

  • Immune monitoring technology primer: flow and mass cytometry. Journal for immunotherapy of cancer Maecker, H. T., Harari, A. 2015; 3: 44-?

    View details for DOI 10.1186/s40425-015-0085-x

    View details for PubMedID 26380089

    View details for PubMedCentralID PMC4570613

  • mTOR inhibition improves immune function in the elderly SCIENCE TRANSLATIONAL MEDICINE Mannick, J. B., Del Giudice, G., Lattanzi, M., Valiante, N. M., Praestgaard, J., Huang, B., Lonetto, M. A., Maecker, H. T., Kovarik, J., Carson, S., Glass, D. J., Klickstein, L. B. 2014; 6 (268)


    Inhibition of the mammalian target of rapamycin (mTOR) pathway extends life span in all species studied to date, and in mice delays the onset of age-related diseases and comorbidities. However, it is unknown if mTOR inhibition affects aging or its consequences in humans. To begin to assess the effects of mTOR inhibition on human aging-related conditions, we evaluated whether the mTOR inhibitor RAD001 ameliorated immunosenescence (the decline in immune function during aging) in elderly volunteers, as assessed by their response to influenza vaccination. RAD001 enhanced the response to the influenza vaccine by about 20% at doses that were relatively well tolerated. RAD001 also reduced the percentage of CD4 and CD8 T lymphocytes expressing the programmed death-1 (PD-1) receptor, which inhibits T cell signaling and is more highly expressed with age. These results raise the possibility that mTOR inhibition may have beneficial effects on immunosenescence in the elderly.

    View details for DOI 10.1126/scitranslmed.3009892

    View details for Web of Science ID 000346844100005

    View details for PubMedID 25540326

  • In utero arsenic exposure and fetal immune repertoire in a US pregnancy cohort CLINICAL IMMUNOLOGY Nadeau, K. C., Li, Z., Farzan, S., Koestler, D., Robbins, D., Fei, D. L., Malipatlolla, M., Maecker, H., Enelow, R., Korrick, S., Karagas, M. R. 2014; 155 (2): 188-197


    Arsenic has wide-ranging effects on human health and there is evidence that it alters the immune response by influencing CD4+/CD8+ T cell ratios, IL-2 cytokine levels, and the expression of immune-response genes. We investigated the impact of in utero environmental arsenic exposure on immune development and function in newborns participating in a pregnancy cohort in New Hampshire, U.S., where arsenic levels have exceeded the current EPA maximum contaminant level of 10 μg/L. Our results showed that maternal urinary arsenic concentrations were inversely related to absolute total CD45RA+ CD4+ cord blood CD69+ T cell counts (N=116, p=0.04) and positively associated with CD45RA+ CD69- CD294+ cell counts (p=0.01). In placental samples (N=70), higher in utero urinary arsenic concentrations were positively associated with the expression of IL1β (p=0.03). These data provide evidence that relatively low-level arsenic exposure in utero may alter the fetal immune system and lead to immune dysregulation.

    View details for DOI 10.1016/j.clim.2014.09.004

    View details for Web of Science ID 000346114300004

    View details for PubMedID 25229165

    View details for PubMedCentralID PMC4309995

  • 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


    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

  • Monitoring the immune competence of cancer patients to predict outcome CANCER IMMUNOLOGY IMMUNOTHERAPY Chang, S., Kohrt, H., Maecker, H. T. 2014; 63 (7): 713-719


    A new era of cancer immunotherapy has brought not only successful cancer vaccines but also immunomodulators, such as those that target checkpoint blockade in order to induce endogenous host immune responses. However, the immune system of cancer patients can be compromised through multiple means, including immune suppression by the tumor and by prior therapies such as chemotherapy and radiation. Therefore, a comprehensive means of assessing patient immunocompetence would seem helpful for determining whether patients are ready to benefit from immunotherapy, and perhaps even which immunotherapy might be most appropriate for them. Unfortunately, there are no standardized tests for immune competence, nor is there agreement on what to measure and what will be predictive of outcome. In this review, we will discuss the technologies and assays that might be most useful for this purpose. We argue for a comprehensive approach that should maximize the chances of developing predictive biomarkers for eventual clinical use.

    View details for DOI 10.1007/s00262-014-1521-3

    View details for Web of Science ID 000339873300006

    View details for PubMedID 24487923

    View details for PubMedCentralID PMC4058358

  • IFN Priming Is Necessary but Not Sufficient To Turn on a Migratory Dendritic Cell Program in Lupus Monocytes JOURNAL OF IMMUNOLOGY Rodriguez-Pla, A., Patel, P., Maecker, H. T., Rossello-Urgell, J., Baldwin, N., Bennett, L., Cantrell, V., Baisch, J., Punaro, M., Gotte, A., Nassi, L., Wright, T., Palucka, A. K., Banchereau, J., Pascual, V. 2014; 192 (12): 5586-5598


    Blood monocytes from children with systemic lupus erythematosus (SLE) behave similar to dendritic cells (DCs), and SLE serum induces healthy monocytes to differentiate into DCs in a type I IFN-dependent manner. In this study, we found that these monocytes display significant transcriptional changes, including a prominent IFN signature, compared with healthy controls. Few of those changes, however, explain DC function. Exposure to allogeneic T cells in vitro reprograms SLE monocytes to acquire DC phenotype and function, and this correlates with both IFN-inducible (IP10) and proinflammatory cytokine (IL-1β and IL6) expression. Furthermore, we found that both IFN and SLE serum induce the upregulation of CCR7 transcription in these cells. CCR7 protein expression, however, requires a second signal provided by TLR agonists such as LPS. Thus, SLE serum "primes" a subset of monocytes to readily (<24 h) respond to TLR agonists and acquire migratory DC properties. Our findings might explain how microbial infections exacerbate lupus.

    View details for DOI 10.4049/jimmunol.1301319

    View details for Web of Science ID 000337172100018

    View details for PubMedID 24829414

  • Effects of serum and plasma matrices on multiplex immunoassays. Immunologic research Rosenberg-Hasson, Y., Hansmann, L., Liedtke, M., Herschmann, I., Maecker, H. T. 2014; 58 (2-3): 224-233


    Multiplexed fluorescence or electrochemiluminescence immunoassays of soluble cytokines are commonly performed in the context of human serum or plasma, to look for disease biomarkers and to monitor the immune system in a simple and minimally invasive way. These assays provide challenges due to the complexities of the matrix (serum or plasma) and the presence of many cytokines near the limit of detection of the assay. Here, we compare the readout of matched serum and plasma samples, which are generally correlated. However, a subset of cytokines usually have higher levels in serum, and the non-specific background is significantly increased in serum versus plasma. Presumably as a result of this non-specific background, disease-related decreases in low-abundance cytokines can sometimes be detected in plasma but not in serum. We further show, through spike recovery experiments, that both serum and plasma inhibit the readout of many cytokines, with some variability between donors, but with serum causing greater inhibition than plasma in many cases. Standard diluents from different vendors can partially reverse this inhibition to varying degrees. Dilution of samples can also partly overcome the inhibitory effect of the matrix. We also show that dilution is nonlinear and differentially affects various cytokines. Together, these data argue that (1) plasma is a more sensitive matrix for detecting changes in certain low-abundance cytokines; (2) calculation of concentrations in serum or plasma matrices is inherently inaccurate; and (3) dilution of samples should not be assumed to be linear, i.e., all comparisons need to be made among similarly diluted samples.

    View details for DOI 10.1007/s12026-014-8491-6

    View details for PubMedID 24522699

  • Vitamin D Deficiency in a Multiethnic Healthy Control Cohort and Altered Immune Response in Vitamin D Deficient European-American Healthy Controls PLOS ONE Ritterhouse, L. L., Lu, R., Shah, H. B., Robertson, J. M., Fife, D. A., Maecker, H. T., Du, H., Fathman, C. G., Chakravarty, E. F., Scofield, R. H., Kamen, D. L., Guthridge, J. M., James, J. A. 2014; 9 (4)


    In recent years, vitamin D has been shown to possess a wide range of immunomodulatory effects. Although there is extensive amount of research on vitamin D, we lack a comprehensive understanding of the prevalence of vitamin D deficiency or the mechanism by which vitamin D regulates the human immune system. This study examined the prevalence and correlates of vitamin D deficiency and the relationship between vitamin D and the immune system in healthy individuals.Healthy individuals (n = 774) comprised of European-Americans (EA, n = 470), African-Americans (AA, n = 125), and Native Americans (NA, n = 179) were screened for 25-hydroxyvitamin D [25(OH)D] levels by ELISA. To identify the most noticeable effects of vitamin D on the immune system, 20 EA individuals with severely deficient (<11.3 ng/mL) and sufficient (>24.8 ng/mL) vitamin D levels were matched and selected for further analysis. Serum cytokine level measurement, immune cell phenotyping, and phosphoflow cytometry were performed.Vitamin D sufficiency was observed in 37.5% of the study cohort. By multivariate analysis, AA, NA, and females with a high body mass index (BMI, >30) demonstrate higher rates of vitamin D deficiency (p<0.05). Individuals with vitamin D deficiency had significantly higher levels of serum GM-CSF (p = 0.04), decreased circulating activated CD4+ (p = 0.04) and CD8+ T (p = 0.04) cell frequencies than individuals with sufficient vitamin D levels.A large portion of healthy individuals have vitamin D deficiency. These individuals have altered T and B cell responses, indicating that the absence of sufficient vitamin D levels could result in undesirable cellular and molecular alterations ultimately contributing to immune dysregulation.

    View details for DOI 10.1371/journal.pone.0094500

    View details for Web of Science ID 000336736200083

    View details for PubMedID 24727903

    View details for PubMedCentralID PMC3984168

  • Cytokine and chemokine patterns across 100 days after hematopoietic stem cell transplantation in children. Biology of blood and marrow transplantation DiCarlo, J., Agarwal-Hashmi, R., Shah, A., Kim, P., Craveiro, L., Killen, R., Rosenberg-Hasson, Y., Maecker, H. 2014; 20 (3): 361-369


    We mapped the cytokine response to hematopoietic stem cell transplantation (HSCT) by assaying 51 cytokines and chemokines each week for 100 days in 51 children receiving allogeneic (n = 44) or autologous HSCT (n = 7). Assay values were reported as mean fluorescence intensity (MFI). Log transformation converted MFI to clinically relevant measures (ie, pg/mL). We searched for potential markers of transplant complications by using mixed treatment by subject analysis of variance. Global cytokine secretion in HSCT recipients was significantly lower than in concurrent control patients (n = 11). Coincident with the nadir in WBC count, the concentration of many cytokines declined further by the second and third week. All analytes (except monokine induced by gamma interferon [MIG]) subsequently rebounded by week 4 (coincident with engraftment and recovery of WBC count) but often still remained well below control levels. Concurrent with the collective nadir of multiple cytokines, monocyte chemoattractant protein 1 (MCP-1), growth-regulated oncogene alpha (GRO-a), and leptin surged during weeks 2 to 4. High levels of leptin persisted throughout the 100 post-transplant days. Also during weeks 2 to 4, hepatocyte growth factor (HGF) and IL-6 surged in children with complications but not in those without complications. The peak in HGF was more pronounced in veno-occlusive disease (VOD). HGF and IL-6 secretion rose at least 2 weeks before the clinical diagnosis of VOD or graft-versus-host disease (GVHD). From week 4 onward in all groups, the MFI of the cytokine resistin increased to 5 to 15 times above concurrent control. HGF has now emerged in 3 or more biomarker discovery efforts for GVHD (and in our population for VOD as well). HGF (with or without IL-6) should be investigated as a potential predictive biomarker of VOD or GVHD. Alternatively, the hyperinflammatory "signature" provided by a multicytokine assay may be predictive.

    View details for DOI 10.1016/j.bbmt.2013.11.026

    View details for PubMedID 24316459

  • Influence of Frequent Infectious Exposures on General and Varicella-Zoster Virus-Specific Immune Responses in Pediatricians CLINICAL AND VACCINE IMMUNOLOGY Ogunjimi, B., Smits, E., Heynderickx, S., Van Den Bergh, J., Bilcke, J., Jansens, H., Malfait, R., Ramet, J., Maecker, H. T., Cools, N., Beutels, P., Van Damme, P. 2014; 21 (3): 417-426


    Reexposure to viruses is assumed to strengthen humoral and cellular immunity via the secondary immune response. We studied the effects of frequent exposure to viral infectious challenges on immunity. Furthermore, we assessed whether repetitive exposures to varicella-zoster virus (VZV) elicited persistently high immune responses. Blood samples from 11 pediatricians and matched controls were assessed at 3 time points and 1 time point, respectively. Besides the assessment of general immunity by means of measuring T-cell subset percentages, antibody titers and gamma interferon (IFN-γ)/interleukin 2 (IL-2)-producing T-cell percentages against adenovirus type 5 (AdV-5), cytomegalovirus (CMV), tetanus toxin (TT), and VZV were determined. Pediatricians had lower levels of circulating CD4(+)-naive T cells and showed boosting of CD8(+) effector memory T cells. Although no effect on humoral immunity was seen, repetitive exposures to VZV induced persistently higher percentages of IFN-γ-positive T cells against all VZV antigens tested (VZV glycoprotein E [gE], VZV intermediate-early protein 62 [IE62], and VZV IE63) than in controls. T cells directed against latency-associated VZV IE63 benefitted the most from natural exogenous boosting. Although no differences in cellular or humoral immunity were found between the pediatricians and controls for AdV-5 or TT, we did find larger immune responses against CMV antigens in pediatricians. Despite the high infectious burden, we detected a robust and diverse immune system in pediatricians. Repetitive exposures to VZV have been shown to induce a stable increased level of VZV-specific cellular but not humoral immunity. Based on our observations, VZV IE63 can be considered a candidate for a zoster vaccine.

    View details for DOI 10.1128/CVI.00818-13

    View details for Web of Science ID 000332036900019

    View details for PubMedID 24429070

    View details for PubMedCentralID PMC3957663

  • Peanut oral immunotherapy results in increased antigen-induced regulatory T-cell function and hypomethylation of forkhead box protein 3 (FOXP3). journal of allergy and clinical immunology Syed, A., Garcia, M. A., Lyu, S., Bucayu, R., Kohli, A., Ishida, S., Berglund, J. P., Tsai, M., Maecker, H., O'Riordan, G., Galli, S. J., Nadeau, K. C. 2014; 133 (2): 500-510


    The mechanisms contributing to clinical immune tolerance remain incompletely understood. This study provides evidence for specific immune mechanisms that are associated with a model of operationally defined clinical tolerance.Our overall objective was to study laboratory changes associated with clinical immune tolerance in antigen-induced T cells, basophils, and antibodies in subjects undergoing oral immunotherapy (OIT) for peanut allergy.In a phase 1 single-site study, we studied participants (n = 23) undergoing peanut OIT and compared them with age-matched allergic control subjects (n = 20) undergoing standard of care (abstaining from peanut) for 24 months. Participants were operationally defined as clinically immune tolerant (IT) if they had no detectable allergic reactions to a peanut oral food challenge after 3 months of therapy withdrawal (IT, n = 7), whereas those who had an allergic reaction were categorized as nontolerant (NT; n = 13).Antibody and basophil activation measurements did not statistically differentiate between NT versus IT participants. However, T-cell function and demethylation of forkhead box protein 3 (FOXP3) CpG sites in antigen-induced regulatory T cells were significantly different between IT versus NT participants. When IT participants were withdrawn from peanut therapy for an additional 3 months (total of 6 months), only 3 participants remained classified as IT participants, and 4 participants regained sensitivity along with increased methylation of FOXP3 CpG sites in antigen-induced regulatory T cells.In summary, modifications at the DNA level of antigen-induced T-cell subsets might be predictive of a state of operationally defined clinical immune tolerance during peanut OIT.

    View details for DOI 10.1016/j.jaci.2013.12.1037

    View details for PubMedID 24636474

  • Vitamin d deficiency in a multiethnic healthy control cohort and altered immune response in vitamin D deficient European-American healthy controls. PloS one Ritterhouse, L. L., Lu, R., Shah, H. B., Robertson, J. M., Fife, D. A., Maecker, H. T., Du, H., Fathman, C. G., Chakravarty, E. F., Scofield, R. H., Kamen, D. L., Guthridge, J. M., James, J. A. 2014; 9 (4)


    In recent years, vitamin D has been shown to possess a wide range of immunomodulatory effects. Although there is extensive amount of research on vitamin D, we lack a comprehensive understanding of the prevalence of vitamin D deficiency or the mechanism by which vitamin D regulates the human immune system. This study examined the prevalence and correlates of vitamin D deficiency and the relationship between vitamin D and the immune system in healthy individuals.Healthy individuals (n = 774) comprised of European-Americans (EA, n = 470), African-Americans (AA, n = 125), and Native Americans (NA, n = 179) were screened for 25-hydroxyvitamin D [25(OH)D] levels by ELISA. To identify the most noticeable effects of vitamin D on the immune system, 20 EA individuals with severely deficient (<11.3 ng/mL) and sufficient (>24.8 ng/mL) vitamin D levels were matched and selected for further analysis. Serum cytokine level measurement, immune cell phenotyping, and phosphoflow cytometry were performed.Vitamin D sufficiency was observed in 37.5% of the study cohort. By multivariate analysis, AA, NA, and females with a high body mass index (BMI, >30) demonstrate higher rates of vitamin D deficiency (p<0.05). Individuals with vitamin D deficiency had significantly higher levels of serum GM-CSF (p = 0.04), decreased circulating activated CD4+ (p = 0.04) and CD8+ T (p = 0.04) cell frequencies than individuals with sufficient vitamin D levels.A large portion of healthy individuals have vitamin D deficiency. These individuals have altered T and B cell responses, indicating that the absence of sufficient vitamin D levels could result in undesirable cellular and molecular alterations ultimately contributing to immune dysregulation.

    View details for DOI 10.1371/journal.pone.0094500

    View details for PubMedID 24727903

    View details for PubMedCentralID PMC3984168

  • 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-?


    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

  • A harmonized approach to intracellular cytokine staining gating: Results from an international multiconsortia proficiency panel conducted by the Cancer Immunotherapy Consortium (CIC/CRI). Cytometry. Part A : the journal of the International Society for Analytical Cytology McNeil, L. K., Price, L., Britten, C. M., Jaimes, M., Maecker, H., Odunsi, K., Matsuzaki, J., Staats, J. S., Thorpe, J., Yuan, J., Janetzki, S. 2013; 83 (8): 728-738


    Previous results from two proficiency panels of intracellular cytokine staining (ICS) from the Cancer Immunotherapy Consortium and panels from the National Institute of Allergy and Infectious Disease and the Association for Cancer Immunotherapy highlight the variability across laboratories in reported % CD8+ or % CD4+ cytokine-positive cells. One of the main causes of interassay variability in flow cytometry-based assays is due to differences in gating strategies between laboratories, which may prohibit the generation of robust results within single centers and across institutions. To study how gating strategies affect the variation in reported results, a gating panel was organized where all participants analyzed the same set of Flow Cytometry Standard (FCS) files from a four-color ICS assay using their own gating protocol (Phase I) and a gating protocol drafted by consensus from the organizers of the panel (Phase II). Focusing on analysis removed donor, assay, and instrument variation, enabling us to quantify the variability caused by gating alone. One hundred ten participating laboratories applied 110 different gating approaches. This led to high variability in the reported percentage of cytokine-positive cells and consequently in response detection in Phase I. However, variability was dramatically reduced when all laboratories used the same gating strategy (Phase II). Proximity of the cytokine gate to the negative population most impacted true-positive and false-positive response detection. Recommendations are provided for the (1) placement of the cytokine-positive gate, (2) identification of CD4+ CD8+ double-positive T cells, (3) placement of lymphocyte gate, (4) inclusion of dim cells, (5) gate uniformity, and 6) proper adjustment of the biexponential scaling. © 2013 International Society for Advancement of Cytometry.

    View details for DOI 10.1002/cyto.a.22319

    View details for PubMedID 23788464

  • 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-?


    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

  • Daily cytokine fluctuations, driven by leptin, are associated with fatigue severity in chronic fatigue syndrome: evidence of inflammatory pathology. Journal of translational medicine Stringer, E. A., Baker, K. S., Carroll, I. R., Montoya, J. G., Chu, L., Maecker, H. T., Younger, J. W. 2013; 11: 93-?


    Chronic fatigue syndrome (CFS) is a debilitating disorder characterized by persistent fatigue that is not alleviated by rest. The lack of a clearly identified underlying mechanism has hindered the development of effective treatments. Studies have demonstrated elevated levels of inflammatory factors in patients with CFS, but findings are contradictory across studies and no biomarkers have been consistently supported. Single time-point approaches potentially overlook important features of CFS, such as fluctuations in fatigue severity. We have observed that individuals with CFS demonstrate significant day-to-day variability in their fatigue severity.Therefore, to complement previous studies, we implemented a novel longitudinal study design to investigate the role of cytokines in CFS pathophysiology. Ten women meeting the Fukuda diagnostic criteria for CFS and ten healthy age- and body mass index (BMI)-matched women underwent 25 consecutive days of blood draws and self-reporting of symptom severity. A 51-plex cytokine panel via Luminex was performed for each of the 500 serum samples collected. Our primary hypothesis was that daily fatigue severity would be significantly correlated with the inflammatory adipokine leptin, in the women with CFS and not in the healthy control women. As a post-hoc analysis, a machine learning algorithm using all 51 cytokines was implemented to determine whether immune factors could distinguish high from low fatigue days.Self-reported fatigue severity was significantly correlated with leptin levels in six of the participants with CFS and one healthy control, supporting our primary hypothesis. The machine learning algorithm distinguished high from low fatigue days in the CFS group with 78.3% accuracy.Our results support the role of cytokines in the pathophysiology of CFS.

    View details for DOI 10.1186/1479-5876-11-93

    View details for PubMedID 23570606

  • Experimental pain and opioid analgesia in volunteers at high risk for obstructive sleep apnea. PloS one Doufas, A. G., Tian, L., Padrez, K. A., Suwanprathes, P., Cardell, J. A., Maecker, H. T., Panousis, P. 2013; 8 (1)


    Obstructive sleep apnea (OSA) is characterized by recurrent nocturnal hypoxia and sleep disruption. Sleep fragmentation caused hyperalgesia in volunteers, while nocturnal hypoxemia enhanced morphine analgesic potency in children with OSA. This evidence directly relates to surgical OSA patients who are at risk for airway compromise due to postoperative use of opioids. Using accepted experimental pain models, we characterized pain processing and opioid analgesia in male volunteers recruited based on their risk for OSA.After approval from the Intitutional Review Board and informed consent, we assessed heat and cold pain thresholds and tolerances in volunteers after overnight polysomnography (PSG). Three pro-inflammatory and 3 hypoxia markers were determined in the serum. Pain tests were performed at baseline, placebo, and two effect site concentrations of remifentanil (1 and 2 µg/ml), an μ-opioid agonist. Linear mixed effects regression models were employed to evaluate the association of 3 PSG descriptors [wake after sleep onset, number of sleep stage shifts, and lowest oxyhemoglobin saturation (SaO(2)) during sleep] and all serum markers with pain thresholds and tolerances at baseline, as well as their changes under remifentanil.Forty-three volunteers (12 normal and 31 with a PSG-based diagnosis of OSA) were included in the analysis. The lower nadir SaO(2) and higher insulin growth factor binding protein-1 (IGFBP-1) were associated with higher analgesic sensitivity to remifentanil (SaO(2), P = 0.0440; IGFBP-1, P = 0.0013). Other pro-inflammatory mediators like interleukin-1β and tumor necrosis factor-α (TNF-α) were associated with an enhanced sensitivity to the opioid analgesic effect (IL-1β, P = 0.0218; TNF-α, P = 0.0276).Nocturnal hypoxemia in subjects at high risk for OSA was associated with an increased potency of opioid analgesia. A serum hypoxia marker (IGFBP-1) was associated with hypoalgesia and increased potency to opioid analgesia; other pro-inflammatory mediators also predicted an enhanced opioid NCT00672737.

    View details for DOI 10.1371/journal.pone.0054807

    View details for PubMedID 23382975

    View details for PubMedCentralID PMC3558510

  • The phenotypic distribution and functional profile of tuberculin-specific CD4 T-cells characterizes different stages of TB infection. Cytometry. Part B, Clinical cytometry Streitz, M., Fuhrmann, S., Thomas, D., Cheek, E., Nomura, L., Maecker, H., Martus, P., Aghaeepour, N., Brinkman, R. R., Volk, H., Kern, F. 2012; 82 (6): 360-368


    Recent publications have suggested that altered proportions of functional CD4 T-cell subsets correlate with active pulmonary TB. Also, CD27-expression on tuberculin-activated IFN-γ(+) CD4 T-cells is known to differ significantly between patients with active pulmonary TB and healthy TB-unexposed BCG vaccinees. Here, we explore links between CD4 T-cell phenotype, multiple functional subsets, and control of TB.We examined ex-vivo overnight tuberculin activated CD4 T-cells in regards to CD27-expression and the activation markers, CD154 upregulation, IFN-γ, TNF-α, IL-2, and degranulation in 44 individuals, including cases of clinically active pulmonary TB, and hospital staff with prolonged TB exposure, some of whom had latent TB.Active pulmonary TB generally showed an excess of TNF-α(+) subsets over IFN-γ(+) subsets, paralleled by decreased CD27 expression on activated IFN-γ(+) or CD154(+) CD4 T-cells. The single subset distinguishing best between active pulmonary TB and high TB exposure was CD154(+) /TNF-α(+) / IFN-γ(-) /IL-2(-) /degranulation(-) (AUROC 0.90). The ratio between the frequencies of TNF-α(+) /IFN-γ(+) CD4 T-cells was an effective alternative parameter (AUROC 0.87).Functional subsets and phenotype of tuberculin induced CD4 T-cells differ between stages of TB infection. Predominance of TNF-α(+) CD4 T-cells in active infection suggests an increased effort of the immune system to contain disease.

    View details for DOI 10.1002/cyto.b.21041

    View details for PubMedID 22961735

  • 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

  • New tools for classification and monitoring of autoimmune diseases NATURE REVIEWS RHEUMATOLOGY Maecker, H. T., Lindstrom, T. M., Robinson, W. H., Utz, P. J., Hale, M., Boyd, S. D., Shen-Orr, S. S., Fathman, C. G. 2012; 8 (6): 317-328


    Rheumatologists see patients with a range of autoimmune diseases. Phenotyping these diseases for diagnosis, prognosis and selection of therapies is an ever increasing problem. Advances in multiplexed assay technology at the gene, protein, and cellular level have enabled the identification of 'actionable biomarkers'; that is, biological metrics that can inform clinical practice. Not only will such biomarkers yield insight into the development, remission, and exacerbation of a disease, they will undoubtedly improve diagnostic sensitivity and accuracy of classification, and ultimately guide treatment. This Review provides an introduction to these powerful technologies that could promote the identification of actionable biomarkers, including mass cytometry, protein arrays, and immunoglobulin and T-cell receptor high-throughput sequencing. In our opinion, these technologies should become part of routine clinical practice for the management of autoimmune diseases. The use of analytical tools to deconvolve the data obtained from use of these technologies is also presented here. These analyses are revealing a more comprehensive and interconnected view of the immune system than ever before and should have an important role in directing future treatment approaches for autoimmune diseases.

    View details for DOI 10.1038/nrrheum.2012.66

    View details for PubMedID 22647780

  • 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


    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

  • NK cells are dysfunctional in human chronic myelogenous leukemia before and on imatinib treatment and in BCR-ABL-positive mice LEUKEMIA Chen, C., Koschmieder, S., KERSTIENS, L., Schemionek, M., Altvater, B., Pscherer, S., Gerss, J., Maecker, H. T., Berdel, W. E., Juergens, H., Lee, P. P., Rossig, C. 2012; 26 (3): 465-474


    Although BCR-ABL+ stem cells in chronic myeloid leukemia (CML) resist elimination by targeted pharmacotherapy in most patients, immunological graft-versus-leukemia effects can cure the disease. Besides cytotoxic T cells, natural killer (NK) cells may have a role in immune control of CML. Here, we explored the functionality of NK cells in CML patients and in a transgenic inducible BCR-ABL mouse model. Compared with controls, NK-cell proportions among lymphocytes were decreased at diagnosis of CML and did not recover during imatinib-induced remission for 10-34 months. Functional experiments revealed limited in vitro expansion of NK cells from CML patients and a reduced degranulation response to K562 target cells both at diagnosis and during imatinib therapy. Consistent with the results in human CML, relative numbers of NK1.1+ NK cells were reduced following induction of BCR-ABL expression in mice, and the defects persisted after BCR-ABL reversion. Moreover, target-induced degranulation by expanded BCR-ABL+ NK cells was compromised. We conclude that CML is associated with quantitative and functional defects within the NK-cell compartment, which is reproduced by induced BCR-ABL expression in mice. Further work will aim at identifying the mechanisms of NK-cell deficiency in CML and at developing strategies to exploit NK cells for immunotherapy.

    View details for DOI 10.1038/leu.2011.239

    View details for Web of Science ID 000301290300012

    View details for PubMedID 21904381

  • Standardizing immunophenotyping for the Human Immunology Project NATURE REVIEWS IMMUNOLOGY Maecker, H. T., McCoy, J. P., Nussenblatt, R. 2012; 12 (3): 191-200


    The heterogeneity in the healthy human immune system, and the immunological changes that portend various diseases, have been only partially described. Their comprehensive elucidation has been termed the 'Human Immunology Project'. The accurate measurement of variations in the human immune system requires precise and standardized assays to distinguish true biological changes from technical artefacts. Thus, to be successful, the Human Immunology Project will require standardized assays for immunophenotyping humans in health and disease. A major tool in this effort is flow cytometry, which remains highly variable with regard to sample handling, reagents, instrument setup and data analysis. In this Review, we outline the current state of standardization of flow cytometry assays and summarize the steps that are required to enable the Human Immunology Project.

    View details for DOI 10.1038/nri3158

    View details for Web of Science ID 000300790600013

    View details for PubMedID 22343568

    View details for PubMedCentralID PMC3409649