Kara Davis

All Publications

• The tidyomics ecosystem: enhancing omic data analyses. Nature methods Hutchison, W. J., Keyes, T. J., Crowell, H. L., Serizay, J., Soneson, C., Davis, E. S., Sato, N., Moses, L., Tarlinton, B., Nahid, A. A., Kosmac, M., Clayssen, Q., Yuan, V., Mu, W., Park, J. E., Mamede, I., Ryu, M. H., Axisa, P. P., Paiz, P., Poon, C. L., Tang, M., Gottardo, R., Morgan, M., Lee, S., Lawrence, M., Hicks, S. C., Nolan, G. P., Davis, K. L., Papenfuss, A. T., Love, M. I., Mangiola, S. 2024

  Abstract

  The growth of omic data presents evolving challenges in data manipulation, analysis and integration. Addressing these challenges, Bioconductor provides an extensive community-driven biological data analysis platform. Meanwhile, tidy R programming offers a revolutionary data organization and manipulation standard. Here we present the tidyomics software ecosystem, bridging Bioconductor to the tidy R paradigm. This ecosystem aims to streamline omic analysis, ease learning and encourage cross-disciplinary collaborations. We demonstrate the effectiveness of tidyomics by analyzing 7.5 million peripheral blood mononuclear cells from the Human Cell Atlas, spanning six data frameworks and ten analysis tools.

  View details for DOI 10.1038/s41592-024-02299-2

  View details for PubMedID 38877315

  View details for PubMedCentralID 545600

• Thetidyomicsecosystem: Enhancing omic data analyses. bioRxiv : the preprint server for biology Hutchison, W. J., Keyes, T. J., tidyomics Consortium, Crowell, H. L., Serizay, J., Soneson, C., Davis, E. S., Sato, N., Moses, L., Tarlinton, B., Nahid, A. A., Kosmac, M., Clayssen, Q., Yuan, V., Mu, W., Park, J., Mamede, I., Ryu, M. H., Axisa, P., Paiz, P., Poon, C., Tang, M., Gottardo, R., Morgan, M., Lee, S., Lawrence, M., Hicks, S. C., Nolan, G. P., Davis, K. L., Papenfuss, A. T., Love, M. I., Mangiola, S. 2024

  Abstract

  The growth of omic data presents evolving challenges in data manipulation, analysis, and integration. Addressing these challenges, Bioconductor1 provides an extensive community-driven biological data analysis platform. Meanwhile, tidy R programming2 offers a revolutionary standard for data organisation and manipulation. Here, we present the tidyomics software ecosystem, bridging Bioconductor to the tidy R paradigm. This ecosystem aims to streamline omic analysis, ease learning, and encourage cross-disciplinary collaborations. We demonstrate the effectiveness of tidyomics by analysing 7.5 million peripheral blood mononuclear cells from the Human Cell Atlas3, spanning six data frameworks and ten analysis tools.

  View details for DOI 10.1101/2023.09.10.557072

  View details for PubMedID 38826347

• Plasma microbial cell-free DNA following chimeric antigen receptor T cell therapy in pediatric patients with relapsed/refractory leukemia. European journal of haematology Aftandilian, C., Bito, X. R., Berman, D., Zhang, A., Duttagupta, R., Davis, K. L. 2024

  Abstract

  Chimeric antigen receptor (CAR) T cell therapy is a promising treatment for pediatric patients with relapsed or refractory B cell acute lymphoblastic leukemia (R/R B ALL). Cytokine release syndrome (CRS) is a common toxicity after CAR T cell therapy and fever is often the first symptom. Differentiating CRS from infection after CAR T cell therapy can be challenging. Plasma microbial cell free DNA (mcfDNA) is a novel diagnostic tool which allows for qualitative and quantitative assessment of over 1000 organisms. This pilot study sought to characterize mcfDNA results in pediatric patients with R/R B ALL in the first 2 months after CAR T cell therapy.

  View details for DOI 10.1111/ejh.14216

  View details for PubMedID 38658354

• CD22 CAR T cells demonstrate high response rates and safety in pediatric and adult B-ALL: Phase 1b results. Leukemia Schultz, L. M., Jeyakumar, N., Kramer, A. M., Sahaf, B., Srinagesh, H., Shiraz, P., Agarwal, N., Hamilton, M., Erickson, C., Jacobs, A., Moon, J., Baggott, C., Arai, S., Bharadwaj, S., Johnston, L. J., Liedtke, M., Lowsky, R., Meyer, E., Negrin, R., Rezvani, A., Shizuru, J., Sidana, S., Egeler, E., Mavroukakis, S., Tunuguntla, R., Gkitsas-Long, N., Retherford, A., Brown, A. K., Gramstrap-Petersen, A. L., Ibañez, R. M., Feldman, S. A., Miklos, D. B., Mackall, C. L., Davis, K. L., Frank, M., Ramakrishna, S., Muffly, L. 2024

  Abstract

  Chimeric antigen receptor (CAR) T cells targeting CD22 (CD22-CAR) provide a therapeutic option for patients with CD22+ malignancies with progression after CD19-directed therapies. Using on-site, automated, closed-loop manufacturing, we conducted parallel Phase 1b clinical trials investigating a humanized CD22-CAR with 41BB costimulatory domain in children and adults with heavily treated, relapsed/refractory (r/r) B-ALL. Of 19 patients enrolled, 18 had successful CD22-CAR manufacturing, and 16 patients were infused. High grade (3-4) cytokine release syndrome (CRS) and immune effector-cell-associated neurotoxicity syndrome (ICANS) each occurred in only one patient; however, three patients experienced immune-effector-cell-associated hemophagocytic lymphohistiocytosis-like syndrome (IEC-HS). Twelve of 16 patients (75%) achieved CR with an overall 56% MRD-negative CR rate. Duration of response was overall limited (median 77 days), and CD22 expression was downregulated in 4/12 (33%) available samples at relapse. In summary, we demonstrate that closed-loop manufacturing of CD22-CAR T cells is feasible and is associated with a favorable safety profile and high CR rates in pediatric and adult r/r B-ALL, a cohort with limited CD22-CAR reporting.

  View details for DOI 10.1038/s41375-024-02220-y

  View details for PubMedID 38491306

  View details for PubMedCentralID 4993814

• Inosine induces stemness features in CAR-T cells and enhances potency. Cancer cell Klysz, D. D., Fowler, C., Malipatlolla, M., Stuani, L., Freitas, K. A., Chen, Y., Meier, S., Daniel, B., Sandor, K., Xu, P., Huang, J., Labanieh, L., Keerthi, V., Leruste, A., Bashti, M., Mata-Alcazar, J., Gkitsas, N., Guerrero, J. A., Fisher, C., Patel, S., Asano, K., Patel, S., Davis, K. L., Satpathy, A. T., Feldman, S. A., Sotillo, E., Mackall, C. L. 2024

  Abstract

  Adenosine (Ado) mediates immune suppression in the tumor microenvironment and exhausted CD8+ CAR-T cells express CD39 and CD73, which mediate proximal steps in Ado generation. Here, we sought to enhance CAR-T cell potency by knocking out CD39, CD73, or adenosine receptor 2a (A2aR) but observed only modest effects. In contrast, overexpression of Ado deaminase (ADA-OE), which metabolizes Ado to inosine (INO), induced stemness and enhanced CAR-T functionality. Similarly, CAR-T cell exposure to INO augmented function and induced features of stemness. INO induced profound metabolic reprogramming, diminishing glycolysis, increasing mitochondrial and glycolytic capacity, glutaminolysis and polyamine synthesis, and reprogrammed the epigenome toward greater stemness. Clinical scale manufacturing using INO generated enhanced potency CAR-T cell products meeting criteria for clinical dosing. These results identify INO as a potent modulator of CAR-T cell metabolism and epigenetic stemness programming and deliver an enhanced potency platform for cell manufacturing.

  View details for DOI 10.1016/j.ccell.2024.01.002

  View details for PubMedID 38278150

• Stem cell transplantation for ALL: you've always got a donor, why not always use it? Hematology. American Society of Hematology. Education Program Shyr, D., Davis, K. L., Bertaina, A. 2023; 2023 (1): 84-90

  Abstract

  Hematopoietic stem cell transplantation (HSCT) represents a consolidated therapeutic strategy for high-risk pediatric acute lymphoblastic leukemia (ALL), offering the potential for curative treatment. This manuscript delves into the debate around the more universal application of HSCT for pediatric ALL in the modern era, considering the ubiquitous availability of suitable donors. In fact, despite significant advancements in chemotherapy, targeted therapy, and immunotherapy, a subset of pediatric patients with ALL with high-risk features or relapse continue to encounter poor prognostic outcomes. For this subgroup of patients, HSCT often remains the only potentially curative measure, leveraging the graft-versus- leukemia effect for long-term disease control. Nevertheless, the procedure's complexity and associated risks have traditionally curtailed its widespread use. However, the scenario is shifting with improvements in HLA matching, availability of alternative donor sources, less toxic conditioning regimens, and improved supportive care protocols. Concurrently, emerging therapies like CD19+ CAR T cells present new considerations for definitive therapy selection in relapsed/ refractory ALL. This article reviews critical current evidence and debates the potential of HSCT as a more universal treatment for ALL, reevaluating traditional treatment stratification in light of the constant availability of stem cell donors.

  View details for DOI 10.1182/hematology.2023000423

  View details for PubMedID 38066901

• CD22 CAR T Cell-Related IEC-HS Is Associated with an IFN-. Cytokine Signature Srinagesh, H., Baird, J. H., Agarwal, N., Su, Y., Kramer, A., Reschke, A., Jeyakumar, N., Bharadwaj, S., Schultz, L., Ramakrishna, S., Davis, K. L., Sahaf, B., Feldman, S., Mackall, C. L., Miklos, D. B., Muffly, L. S., Frank, M. J. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-178283

  View details for Web of Science ID 001159900800040

• Enrichment in Metabolic Pathway Activation Corresponds to Immunoglobulin Gene Diversity across B Cell Developmental Stages in B-Lymphoblastic Leukemia Simpson, C., Liu, Y., Stuani, L., Jager, A., Baker, C., Adlowitz, D. G., Rock, P. J., Burack, R., Davis, K. L. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-189313

  View details for Web of Science ID 001159740302081

• Uridine Synthesis Is the Metabolic Vulnerability in Relapse-Associated B-ALL Cells with Active Pre-BCR Signaling Liu, Y., Jiang, H., Stuani, L., Sarno, J., Domizi, P., Merchant, M., Jedoui, D., Jager, A., Huang, M., Lacayo, N. J., Sakamoto, K. M., Ye, J., Davis, K. L. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-186925

  View details for Web of Science ID 001159740307086

• Genome editing-induced t(4;11) chromosomal translocations model B cell precursor acute lymphoblastic leukemias with KMT2A-AFF1 fusion. The Journal of clinical investigation Pan, F., Sarno, J., Jeong, J., Yang, X., Jager, A., Gruber, T. A., Davis, K. L., Cleary, M. L. 2023

  View details for DOI 10.1172/JCI171030

  View details for PubMedID 37917159

• Prior Knowledge Integration Improves Relapse Prediction and Identifies Relapse Associated Mechanisms in Childhood B Cell Acute Lymphoblastic Leukemia Koladiya, A., Jager, A., Culos, A., Merchant, M., Liu, Y., Stuani, L., Sarno, J., Domizi, P., Mullighan, C. G., Aghaeepour, N., Bendall, S., Davis, K. L. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-187264

  View details for Web of Science ID 001159306706074

• Project Evolve, Evaluation of Lineage Switch (LS), an International Initiative: Preliminary Results Reveal Dismal Outcomes in Patients with LS Silbert, S. K., Harrison, C., Biery, N., Semchenkova, A., Zerkalenkova, E., Alonso-Saladrigues, A., Utley, K., Aldoss, I., Zhao, L., Fernandes, S., Rubinstein, J. D., Carapia, N., Chang, B. H., Vatsayan, A., De Moerloose, B., Pacenta, H. L., Kuo, D., Escherich, G., Lee, B. J., Redell, M. S., Fitzjohn, M. R., Larson, D. P., Duployez, N., Cuevo, R. S., He, R., Dickens, D., El Chaer, F., Reed, K., Wolfl, M., Raikar, S. S., Savasan, S., Puri, L., Gahvari, Z. J., Talleur, A. C., Abdel-Azim, H., Chamdin, A., Provost, M. M., Fabrizio, V. A., Mezger, K., Stevens, A., Hsieh, E. M., Wang, H., Yuan, C. M., Duffner, U. A., Pan, J., Ghorashian, S., Rives, S., Hoang, C., Davis, K. L., Jacoby, E., Popov, A., Lamble, A., Shah, N. N. AMER SOC HEMATOLOGY. 2023

  View details for DOI 10.1182/blood-2023-182293

  View details for Web of Science ID 001159740306248

• INSPIRED Symposium Part 4B: CAR T cell correlative studies-established findings and future priorities. Transplantation and cellular therapy Ligon, J. A., Ramakrishna, S., Ceppi, F., Calkoen, F. G., Diorio, C., Davis, K. L., Jacoby, E., Gottschalk, S., Schultz, L. M., Capitini, C. M. 2023

  Abstract

  Chimeric antigen receptor (CAR) T cells have revolutionized the treatment of B cell malignancies, with multiple CAR T cell products having received approval by regulatory agencies around the world for numerous indications. However, significant work remains to be done to enhance these treatments. In March 2023, a group of experts in CAR T cell therapy assembled at the National Institutes of Health in Bethesda, MD, USA at the Insights in Pediatric CAR T-cell Immunotherapy: Recent Advances and Future Directions (INSPIRED) Symposium to identify key areas for research for the coming years. In session 4B, correlative studies to be incorporated into future clinical trials and real-world settings were discussed. Active areas of research identified included: 1) optimization of CAR T cell product manufacturing; 2) ensuring adequate lymphodepletion prior to CAR T cell administration; 3) overcoming immunoregulatory cells and tumor stroma present in the tumor microenvironment, particularly in solid tumors; 4) understanding tumor intrinsic properties that lead to CAR T cell immunotherapy resistance; and 5) uncovering biomarkers predictive of treatment resistance, treatment durability or immune-related adverse events. Here we review the results of previously published clinical trials and real-world studies to outline what is currently understood on each of these topics. We then outline priorities for future research that we believe will be important for improving our understanding of CAR T cell therapy and ultimately leading to better outcomes for patients.

  View details for DOI 10.1016/j.jtct.2023.10.012

  View details for PubMedID 37863355

• CNS Repopulation by Hematopoietic-Derived Microglia-Like Cells Corrects Progranulin deficiency. Research square Colella, P., Sayana, R., Suarez-Nieto, M. V., Sarno, J., Nyame, K., Xiong, J., Vera, L. N., Basurto, J. A., Corbo, M., Limaye, A., Davis, K. L., Abu-Remaileh, M., Gomez-Ospina, N. 2023

  Abstract

  Hematopoietic stem cell transplantation can deliver therapeutic proteins to the CNS through donor-derived hematopoietic cells that become microglia-like cells. However, using standard conditioning approaches, hematopoietic stem cell transplantation is currently limited by low and slow engraftment of microglia-like cells. We report an efficient conditioning regimen based on Busulfan and a six-day course of microglia depletion using the colony-stimulating factor receptor 1 inhibitor PLX3397. Combining Busulfan-myeloablation and transient microglia depletion results in robust, rapid, and persistent microglia replacement by bone marrow-derived microglia-like cells throughout the CNS. Adding PLX3397 does not affect neurobehavior or has adverse effects on hematopoietic reconstitution. Through single-cell RNA sequencing and high-dimensional CyTOF mass cytometry, we show that microglia-like cells are a heterogeneous population and describe six distinct subpopulations. Though most bone-marrow-derived microglia-like cells can be classified as homeostatic microglia, their gene signature is a hybrid of homeostatic/embryonic microglia and border associated-macrophages. Busulfan-myeloablation and transient microglia depletion induce specific cytokines in the brain, ultimately combining myeloid proliferative and chemo-attractive signals that act locally to repopulate microglia from outside the niche. Importantly, this conditioning approach demonstrates therapeutic efficacy in a mouse model of GRN deficiency. Transplanting wild-type bone marrow into Grn-/- mice conditioned with Busulfan plus PLX3397 results in high engraftment of microglia-like cells in the brain and retina, restoring GRN levels and normalizing lipid metabolism.

  View details for DOI 10.21203/rs.3.rs-3263412/v1

  View details for PubMedID 37790525

  View details for PubMedCentralID PMC10543302

• Advances in Clinical Mass Cytometry. Clinics in laboratory medicine Koladiya, A., Davis, K. L. 2023; 43 (3): 507-519

  Abstract

  The advent of high-dimensional single-cell technologies has enabled detection of cellular heterogeneity and functional diversity of immune cells during health and disease conditions. Because of its multiplexing capabilities and limited compensation requirements, mass cytometry or cytometry by time of flight (CyTOF) has played a superior role in immune monitoring compared with flow cytometry. Further, it has higher throughput and lower cost compared with other single-cell techniques. Several published articles have utilized CyTOF to identify cellular phenotypes and features associated with disease outcomes. This article introduces CyTOF-based assays to profile immune cell-types, cell-states, and their applications in clinical research.

  View details for DOI 10.1016/j.cll.2023.05.004

  View details for PubMedID 37481326

• TUMOR INFLAMMATION-ASSOCIATED NEUROTOXICITY (TIAN): A TOXICITY SYNDROME IN PATIENTS TREATED WITH IMMUNOTHERAPY FOR CENTRAL NERVOUS SYSTEM TUMORS Mahdi, J., Dietrich, J., Straathof, K., Roddie, C., Scott, B., Davidson, T., Prolo, L., Batchelor, T., Campen, C., Davis, K., Gust, J., Lim, M., Majzner, R., Park, J., Partap, S., Ramakrishna, S., Richards, R., Schultz, L., Vitanza, N., Wang, L., Mackall, C., Monje, M. OXFORD UNIV PRESS INC. 2023

  View details for DOI 10.1093/neuonc/noad073.192

  View details for Web of Science ID 001023504300193

• Dasatinib overcomes glucocorticoid resistance in B-cell acute lymphoblastic leukemia. Nature communications Sarno, J., Domizi, P., Liu, Y., Merchant, M., Pedersen, C. B., Jedoui, D., Jager, A., Nolan, G. P., Gaipa, G., Bendall, S. C., Bava, F., Davis, K. L. 2023; 14 (1): 2935

  Abstract

  Resistance to glucocorticoids (GC) is associated with an increased risk of relapse in B-cell progenitor acute lymphoblastic leukemia (BCP-ALL). Performing transcriptomic and single-cell proteomic studies in healthy B-cell progenitors, we herein identify coordination between the glucocorticoid receptor pathway with B-cell developmental pathways. Healthy pro-B cells most highly express the glucocorticoid receptor, and this developmental expression is conserved in primary BCP-ALL cells from patients at diagnosis and relapse. In-vitro and in vivo glucocorticoid treatment of primary BCP-ALL cells demonstrate that the interplay between B-cell development and the glucocorticoid pathways is crucial for GC resistance in leukemic cells. Gene set enrichment analysis in BCP-ALL cell lines surviving GC treatment show enrichment of B cell receptor signaling pathways. In addition, primary BCP-ALL cells surviving GC treatment in vitro and in vivo demonstrate a late pre-B cell phenotype with activation of PI3K/mTOR and CREB signaling. Dasatinib, a multi-kinase inhibitor, most effectively targets this active signaling in GC-resistant cells, and when combined with glucocorticoids, results in increased cell death in vitro and decreased leukemic burden and prolonged survival in an in vivo xenograft model. Targeting the active signaling through the addition of dasatinib may represent a therapeutic approach to overcome GC resistance in BCP-ALL.

  View details for DOI 10.1038/s41467-023-38456-y

  View details for PubMedID 37217509

• Inosine Induces Stemness Features in CAR T cells and Enhances Potency. bioRxiv : the preprint server for biology Klysz, D. D., Fowler, C., Malipatlolla, M., Stuani, L., Freitas, K. A., Meier, S., Daniel, B., Sandor, K., Xu, P., Huang, J., Labanieh, L., Leruste, A., Bashti, M., Keerthi, V., Mata-Alcazar, J., Gkitsas, N., Guerrero, J. A., Fisher, C., Patel, S., Asano, K., Patel, S., Davis, K. L., Satpathy, A. T., Feldman, S. A., Sotillo, E., Mackall, C. L. 2023

  Abstract

  Adenosine (Ado) mediates immune suppression in the tumor microenvironment and exhausted CD8+ CAR T cells mediate Ado-induced immunosuppression through CD39/73-dependent Ado production. Knockout of CD39, CD73 or A2aR had modest effects on exhausted CAR T cells, whereas overexpression of Ado deaminase (ADA), which metabolizes Ado to inosine (INO), induced stemness features and potently enhanced functionality. Similarly, and to a greater extent, exposure of CAR T cells to INO augmented CAR T cell function and induced hallmark features of T cell stemness. INO induced a profound metabolic reprogramming, diminishing glycolysis and increasing oxidative phosphorylation, glutaminolysis and polyamine synthesis, and modulated the epigenome toward greater stemness. Clinical scale manufacturing using INO generated enhanced potency CAR T cell products meeting criteria for clinical dosing. These data identify INO as a potent modulator of T cell metabolism and epigenetic stemness programming and deliver a new enhanced potency platform for immune cell manufacturing.

  View details for DOI 10.1101/2023.04.21.537859

  View details for PubMedID 37162847

  View details for PubMedCentralID PMC10168291

• Tumor inflammation-associated neurotoxicity. Nature medicine Mahdi, J., Dietrich, J., Straathof, K., Roddie, C., Scott, B. J., Davidson, T. B., Prolo, L. M., Batchelor, T. T., Campen, C. J., Davis, K. L., Gust, J., Lim, M., Majzner, R. G., Park, J. R., Partap, S., Ramakrishna, S., Richards, R., Schultz, L., Vitanza, N. A., Wang, L. D., Mackall, C. L., Monje, M. 2023

  Abstract

  Cancer immunotherapies have unique toxicities. Establishment of grading scales and standardized grade-based treatment algorithms for toxicity syndromes can improve the safety of these treatments, as observed for cytokine release syndrome (CRS) and immune effector cell associated neurotoxicity syndrome (ICANS) in patients with B cell malignancies treated with chimeric antigen receptor (CAR) T cell therapy. We have observed a toxicity syndrome, distinct from CRS and ICANS, in patients treated with cell therapies for tumors in the central nervous system (CNS), which we term tumor inflammation-associated neurotoxicity (TIAN). Encompassing the concept of 'pseudoprogression,' but broader than inflammation-induced edema alone, TIAN is relevant not only to cellular therapies, but also to other immunotherapies for CNS tumors. To facilitate the safe administration of cell therapies for patients with CNS tumors, we define TIAN, propose a toxicity grading scale for TIAN syndrome and discuss the potential management of this entity, with the goal of standardizing both reporting and management.

  View details for DOI 10.1038/s41591-023-02276-w

  View details for PubMedID 37024595

  View details for PubMedCentralID 7238960

• Role of peripheral blood MRD and 18F-FDG PET in the post-CAR relapse setting: a case study of discordant peripheral blood and bone marrow MRD. Journal for immunotherapy of cancer Schultz, L., Davis, K. L., Walkush, A., Baggott, C., Erickson, C., Ramakrishna, S., Aftandilian, C., Lacayo, N., Nadel, H. R., Oak, J., Mackall, C. L. 2023; 11 (2)

  Abstract

  Chimeric antigen receptor (CAR) T cell therapy is an effective salvage therapy for pediatric relapsed B-cell acute lymphoblastic leukemia (B-ALL), yet is challenged by high rates of post-CAR relapse. Literature describing specific relapse patterns and extramedullary (EM) sites of involvement in the post-CAR setting remains limited, and a clinical standard for post-CAR disease surveillance has yet to be established. We highlight the importance of integrating peripheral blood minimal residual disease (MRD) testing and radiologic imaging into surveillance strategies, to effectively characterize and capture post-CAR relapse.Here, we describe the case of a child with multiply relapsed B-ALL who relapsed in the post-CAR setting with gross non-contiguous medullary and EM disease. Interestingly, her relapse was identified first from peripheral blood flow cytometry MRD surveillance, in context of a negative bone marrow aspirate (MRD <0.01%). Positron emission tomography with 18F-fluorodeoxyglucose revealed diffuse leukemia with innumerable bone and lymph node lesions, interestingly sparing her sacrum, the site of her bone marrow aspirate sampling.We highlight this case as both peripheral blood MRD and 18F-fluorodeoxyglucose positron emission tomography imaging were more sensitive than standard bone marrow aspirate testing in detecting this patient's post-CAR relapse. Clinical/Biologic Insight: In the multiply relapsed B-ALL setting, where relapse patterns may include patchy medullary and/or EM disease, peripheral blood MRD and/or whole body imaging, may carry increased sensitivity at detecting relapse in patient subsets, as compared with standard bone marrow sampling.

  View details for DOI 10.1136/jitc-2022-004851

  View details for PubMedID 36849202

  View details for PubMedCentralID PMC9972424

• Single-cell technologies uncover intra-tumor heterogeneity in childhood cancers. Seminars in immunopathology Lo, Y., Liu, Y., Kammersgaard, M., Koladiya, A., Keyes, T. J., Davis, K. L. 2023

  Abstract

  Childhood cancer is the second leading cause of death in children aged 1 to 14. Although survival rates have vastly improved over the past 40years, cancer resistance and relapse remain a significant challenge. Advances in single-cell technologies enable dissection of tumors to unprecedented resolution. This facilitates unraveling the heterogeneity of childhood cancers to identify cell subtypes that are prone to treatment resistance. The rapid accumulation of single-cell data from different modalities necessitates the development of novel computational approaches for processing, visualizing, and analyzing single-cell data. Here, we review single-cell approaches utilized or under development in the context of childhood cancers. We review computational methods for analyzing single-cell data and discuss best practices for their application. Finally, we review the impact of several studies of childhood tumors analyzed with these approaches and future directions to implement single-cell studies into translational cancer research in pediatric oncology.

  View details for DOI 10.1007/s00281-022-00981-1

  View details for PubMedID 36625902

• SINGLE CELL METABOLIC CHARACTERIZATION AND TARGETING OF PAX5 REARRANGEMENTS IN A PRECLINICAL MODEL OF CHILDHOOD ACUTE LYMPHOBLASTIC LEUKEMIA Quadri, M., Sarno, J., Cazzaniga, G., Davis, K., Fazio, G. ELSEVIER SCIENCE INC. 2023: S128

  View details for Web of Science ID 001057881700198

• tidytof: a user-friendly framework for scalable and reproducible high-dimensional cytometry data analysis. Bioinformatics advances Keyes, T. J., Koladiya, A., Lo, Y., Nolan, G. P., Davis, K. L. 2023; 3 (1): vbad071

  Abstract

  Summary: While many algorithms for analyzing high-dimensional cytometry data have now been developed, the software implementations of these algorithms remain highly customized-this means that exploring a dataset requires users to learn unique, often poorly interoperable package syntaxes for each step of data processing. To solve this problem, we developed {tidytof}, an open-source R package for analyzing high-dimensional cytometry data using the increasingly popular 'tidy data' interface.Availability and implementation: {tidytof} is available at https://github.com/keyes-timothy/tidytof and is released under the MIT license. It is supported on Linux, MS Windows and MacOS. Additional documentation is available at the package website (https://keyes-timothy.github.io/tidytof/).Supplementary information: Supplementary data are available at Bioinformatics Advances online.

  View details for DOI 10.1093/bioadv/vbad071

  View details for PubMedID 37351311

• SARS-CoV-2 infections in pediatric and young adult recipients of chimeric antigen receptor T-cell therapy: an international registry report. Journal for immunotherapy of cancer McNerney, K. O., Richards, R. M., Aguayo-Hiraldo, P., Calkoen, F. G., Talano, J., Moskop, A., Balduzzi, A., Krajewski, J., Dave, H., Vatsayan, A., Callahan, C., Liu, H., Li, Y., Davis, K. L., Maude, S. L. 2023; 11 (1)

  Abstract

  BACKGROUND: Immunocompromised patients are at increased risk of SARS-CoV-2 infections. Patients undergoing chimeric antigen receptor (CAR) T-cell therapy for relapsed/refractory B-cell malignancies are uniquely immunosuppressed due to CAR T-mediated B-cell aplasia (BCA). While SARS-CoV-2 mortality rates of 33%-40% are reported in adult CAR T-cell recipients, outcomes in pediatric and young adult CAR T-cell recipients are limited.METHODS: We created an international retrospective registry of CAR T recipients aged 0-30 years infected with SARS-CoV-2 within 2 months prior to or any time after CAR T infusion. SARS-CoV-2-associated illness was graded as asymptomatic, mild, moderate, or severe COVID-19, or multisystem inflammatory syndrome in children (MIS-C). To assess for risk factors associated with significant SARS-CoV-2 infections (infections requiring hospital admission for respiratory distress or supplemental oxygen), univariate and multivariable regression analyses were performed.RESULTS: Nine centers contributed 78 infections in 75 patients. Of 70 SARS-CoV-2 infections occurring after CAR T infusion, 13 (18.6%) were classified as asymptomatic, 37 (52.9%) mild, 11 (15.7%) moderate, and 6 (8.6%) severe COVID-19. Three (4.3%) were classified as MIS-C. BCA was not significantly associated with infection severity. Prior to the emergence of the Omicron variant, of 47 infections, 19 (40.4%) resulted in hospital admission and 7 (14.9%) required intensive care, while after the emergence of the Omicron variant, of 23 infections, only 1 (4.3%) required admission and the remaining 22 (95.7%) had asymptomatic or mild COVID-19. Death occurred in 3 of 70 (4.3%); each death involved coinfection or life-threatening condition. In a multivariable model, factors associated with significant SARS-CoV-2 infection included having two or more comorbidities (OR 7.73, CI 1.05 to 74.8, p=0.048) and age ≥18 years (OR 9.51, CI 1.90 to 82.2, p=0.014). In the eight patients infected with SARS-CoV-2 before CAR T, half of these patients had their CAR T infusion delayed by 15-30days.CONCLUSIONS: In a large international cohort of pediatric and young adult CAR-T recipients, SARS-CoV-2 infections resulted in frequent hospital and intensive care unit admissions and were associated with mortality in 4.3%. Patients with two or more comorbidities or aged ≥18 years were more likely to experience significant illness. Suspected Omicron infections were associated with milder disease.

  View details for DOI 10.1136/jitc-2022-005957

  View details for PubMedID 36707090

• Development of clinical pathways to improve multidisciplinary care of high-risk pediatric oncology patients. Frontiers in oncology Reschke, A., Richards, R. M., Smith, S. M., Long, A. H., Marks, L. J., Schultz, L., Kamens, J. L., Aftandilian, C., Davis, K. L., Gruber, T., Sakamoto, K. M. 2022; 12: 1033993

  Abstract

  Clinical pathways are evidence-based tools that have been integrated into many aspects of pediatric hospital medicine and have proven effective at reducing in-hospital complications from a variety of diseases. Adaptation of similar tools for specific, high-risk patient populations in pediatric oncology has been slower, in part due to patient complexities and variations in management strategies. There are few published studies of clinical pathways for pediatric oncology patients. Pediatric patients with a new diagnosis of leukemia or lymphoma often present with one or more "oncologic emergencies" that require urgent intervention and deliberate multidisciplinary care to prevent significant consequences. Here, we present two clinical pathways that have recently been developed using a multidisciplinary approach at a single institution, intended for the care of patients who present with hyperleukocytosis or an anterior mediastinal mass. These clinical care pathways have provided a critical framework for the immediate care of these patients who are often admitted to the pediatric intensive care unit for initial management. The goal of the pathways is to facilitate multidisciplinary collaborations, expedite diagnosis, and streamline timely treatment initiation. Standardizing the care of high-risk pediatric oncology patients will ultimately decrease morbidity and mortality associated with these diseases to increase the potential for excellent outcomes.

  View details for DOI 10.3389/fonc.2022.1033993

  View details for PubMedID 36523979

  View details for PubMedCentralID PMC9744920

• Three-Year Update of Tisagenlecleucel in Pediatric and Young Adult Patients With Relapsed/Refractory Acute Lymphoblastic Leukemia in the ELIANA Trial. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Laetsch, T. W., Maude, S. L., Rives, S., Hiramatsu, H., Bittencourt, H., Bader, P., Baruchel, A., Boyer, M., De Moerloose, B., Qayed, M., Buechner, J., Pulsipher, M. A., Myers, G. D., Stefanski, H. E., Martin, P. L., Nemecek, E., Peters, C., Yanik, G., Khaw, S. L., Davis, K. L., Krueger, J., Balduzzi, A., Boissel, N., Tiwari, R., O'Donovan, D., Grupp, S. A. 2022: JCO2200642

  Abstract

  Clinical trials frequently include multiple end points that mature at different times. The initial report, typically based on the primary end point, may be published when key planned co-primary or secondary analyses are not yet available. Clinical Trial Updates provide an opportunity to disseminate additional results from studies, published in JCO or elsewhere, for which the primary end point has already been reported.In the primary analysis of the global phase II ELIANA trial (ClinicalTrials.gov identifier: NCT02435849), tisagenlecleucel provided an overall remission rate of 81% in pediatric and young adult patients with relapsed or refractory B-cell acute lymphoblastic leukemia (R/R B-ALL), with 59% of responders remaining relapse-free at 12 months. Here, we report an update on efficacy, safety, and patient-reported quality of life in 79 pediatric and young adult patients with R/R B-ALL following a median follow-up of 38.8 months. The overall remission rate was 82%. The median event-free survival was 24 months, and the median overall survival was not reached. Event-free survival was 44% (95% CI, 31 to 57) and overall survival was 63% (95% CI, 51 to 73) at 3 years overall (most events occur within the first 2 years). The estimated 3-year relapse-free survival with and without censoring for subsequent therapy was 52% (95% CI, 37 to 66) and 48% (95% CI, 34 to 60), respectively. No new or unexpected long-term adverse events were reported. Grade 3/4 adverse events were reported in 29% of patients > 1 year after infusion; grade 3/4 infection rate did not increase > 1 year after infusion. Patients reported improvements in quality of life up to 36 months after infusion. These findings demonstrate favorable long-term safety and suggest tisagenlecleucel as a curative treatment option for heavily pretreated pediatric and young adult patients with R/R B-ALL.

  View details for DOI 10.1200/JCO.22.00642

  View details for PubMedID 36399695

• Improved Relapse Prediction in Pediatric Acute Myeloid Leukemia By Deconvolving Lineage-Specific and CancerSpecific Features in Single-Cell Data Keyes, T., Jager, A., Krueger, M., Plevritis, S., Tibshirani, R., Aplenc, R., Nolan, G. P., Redell, M. S., Davis, K. L. AMER SOC HEMATOLOGY. 2022: 6288-6289

  View details for DOI 10.1182/blood-2022-170939

  View details for Web of Science ID 000893223206132

• Plasma Microbial Cell-Free DNA to Characterize Infection Vs Cytokine Release Syndrome in Pediatric Patients with B ALL after CAR T Cell Therapy Aftandilian, C., Bito, X., Berman, D. M., Duttagupta, R., Davis, K. L. AMER SOC HEMATOLOGY. 2022: 4681-4683

  View details for DOI 10.1182/blood-2022-163662

  View details for Web of Science ID 000893223204306

• Single-Cell Proteomic Analysis Defines Metabolic Heterogeneity in Response to Venetoclax in AML Stuani, L., Jager, A., Sahal, A., Koladiya, A., Sarno, J., Domizi, P., Liu, Y., De Mas, V., Recher, C., Vergez, F., Sarry, J., Davis, K. L. AMER SOC HEMATOLOGY. 2022: 1028-1029

  View details for DOI 10.1182/blood-2022-171009

  View details for Web of Science ID 000893223201014

• Proof of Principle for Intracarotid Injection of Leukemia As Model for Late Stage Central Nervous System Leukemia Wang, C., Rodrigues, A., Chernikova, S., Davis, K. L., Gephart, M. AMER SOC HEMATOLOGY. 2022: 11522-11523

  View details for DOI 10.1182/blood-2022-158294

  View details for Web of Science ID 000893230304287

• Long-Term Follow-up of CD19/22 CAR Therapy in Children and Young Adults with B-ALL Reveals Efficacy, Tolerability and High Survival Rates When Coupled with Hematopoietic Stem Cell Transplantation Schultz, L. M., Ramakrishna, S., Baskar, R., Richards, R. M., Moon, J., Baggott, C., Fujimoto, M., Kunicki, M., Li, A., Jariwala, S., Erickson, C., Jacobs, A., Yamabe, K., Barsan, V., Majzner, R. G., Egeler, E. L., Mavroukakis, S., Ehlinger, Z., Reynolds, W. D., Sahaf, B., Muffly, L., Frank, M. J., Gramstrup, A., Chinnasamy, H., Patel, S., Miklos, D. B., Feldman, S. A., Mackall, C. L., Davis, K. L. AMER SOC HEMATOLOGY. 2022: 10300-10302

  View details for DOI 10.1182/blood-2022-167789

  View details for Web of Science ID 000893230303140

• CD22 CAR T Cells Demonstrate Favorable Safety Profile and High Response Rates in Pediatric and Adult B-ALL: Results of a Phase 1b Study Jeyakumar, N., Ramakrishna, S., Frank, M. J., Sahaf, B., Feldman, S. A., Miklos, D. B., Mackall, C. L., Davis, K. L., Muffly, L., Schultz, L. M. AMER SOC HEMATOLOGY. 2022: 2374-2375

  View details for DOI 10.1182/blood-2022-164456

  View details for Web of Science ID 000893223202157

• IKAROS MEDIATES ANTIGEN ESCAPE FOLLOWING CD19 CAR T CELL THERAPY IN R/R B-ALL Domizi, P., Sarno, J., Jager, A., Rotiroti, M., Baskar, R., Reynolds, W., Sahaf, B., Bendall, S., Mullighan, C., Leahy, A., Myers, R., Grupp, S., Majzner, R., Sotillo, E., Barrett, D., Davis, K. WILEY. 2022

  View details for Web of Science ID 000859203900105

• SARS-COV-2 INFECTIONS IN PEDIATRIC AND YOUNG ADULT (YA) RECIPIENTS OF CHIMERIC ANTIGEN RECEPTOR T-CELL THERAPY: AN INTERNATIONAL REGISTRY REPORT Mcnerney, K., Richards, R., Aguayo-Hiraldo, P., Calkoen, F., Talano, J., Moskop, A., Balduzzi, A., Krajewski, J., Dave, H., Callahan, C., Li, Y., Davis, K., Maude, S. WILEY. 2022: S327

  View details for Web of Science ID 000859203901291

• A Phase I/II Trial of Nivolumab Plus Ipilimumab in Children and Young Adults with Relapsed/Refractory Solid Tumors: A Children's Oncology Group Study ADVL1412. Clinical cancer research : an official journal of the American Association for Cancer Research Davis, K. L., Fox, E., Isikwei, E., Reid, J. M., Liu, X., Minard, C. G., Voss, S., Berg, S. L., Weigel, B. J., Mackall, C. L. 2022

  Abstract

  PURPOSE: In many cancers, nivolumab in combination with ipilimumab improves response rates compared to either agent alone, but the combination has not been evaluated in childhood cancer. We conducted a Phase I/II trial of nivolumab plus ipilimumab in children and young adults with recurrent/refractory solid tumors.EXPERIMENTAL DESIGN: ADVL1412, Part C assessed safety of nivolumab plus ipilimumab at two dose levels (DL): DL1 1mg/kg of each drug and DL2 3mg/kg nivolumab plus 1mg/kg Ipilimumab. Part D evaluated response at the recommended phase 2 dose (RP2D) in Ewing sarcoma, rhabdomyosarcoma, and osteosarcoma. Part E tested DL3 (1mg/kg nivolumab plus 3mg/kg Ipilimumab) in Ewing sarcoma and rhabdomyosarcoma. Tumor response was measured using RECIST v1.1. Pharmacokinetics and PD-L1 expression on archival tissues were assessed.RESULTS: Fifty-five eligible patients enrolled. Based upon safety, tolerability and similar drug exposure to the same doses administered in adults, DL2 was defined as the pediatric RP2D. Among 41 patients treated at the RP2D, 2 patients experienced dose-limiting toxicities during Cycle 1 and 4 patients experienced toxicities beyond that period. Two patients had clinically significant sustained partial responses (1 rhabdomyosarcoma, 1 Ewing sarcoma) and 4 had stable disease. Among 8 patients treated at DL3, 3 DLTs occurred, all immune related adverse events; no objective responses were observed.CONCLUSIONS: The RP2D of nivolumab (3mg/kg) plus ipilimumab (1mg/kg) is well-tolerated in children and young adults with solid tumors and shows some clinical activity. Increased dose of ipilimumab (3mg/kg) plus nivolumab (1mg/kg) was associated with increased toxicity without clinical benefit.

  View details for DOI 10.1158/1078-0432.CCR-22-2164

  View details for PubMedID 36190525

• Major tumor regressions in H3K27M-mutated diffuse midline glioma (DMG) following sequential intravenous (IV) and intracerebroventricular (ICV) delivery of GD2-CAR T cells Majzner, R. G., Mahdi, J., Ramakrishna, S., Patel, S., Chinnasamy, H., Yeom, K., Schultz, L., Barsan, V., Richards, R., Campen, C., Reschke, A., Toland, A., Baggott, C., Mavroukakis, S., Egeler, E., Moon, J., Jacobs, A., Yamabe-Kwong, K., Rasmussen, L., Nie, E., Green, S., Kunicki, M., Fujimoto, M., Ehlinger, Z., Reynolds, W., Prabhu, S., Warren, K. E., Cornell, T., Partap, S., Fisher, P., Grant, G., Vogel, H., Sahaf, B., Davis, K., Feldman, S., Monje, M., Mackall, C. L. AMER ASSOC CANCER RESEARCH. 2022

  View details for Web of Science ID 000892509500153

• MAJOR TUMOR REGRESSIONS IN H3K27M-MUTATED DIFFUSE MIDLINE GLIOMA (DMG) FOLLOWING SEQUENTIAL INTRAVENOUS (IV) AND INTRACEREBROVENTRICULAR (ICV) DELIVERY OF GD2-CAR T-CELLS Monje, M., Majzner, R., Mahdi, J., Ramakrishna, S., Patel, S., Chinnasamy, H., Yeom, K., Schultz, L., Barsan, V., Richards, R., Campen, C., Reschke, A., Toland, A., Baggott, C., Mavroukakis, S., Egeler, E., Moon, J., Jacobs, A., Yamabe-Kwong, K., Rasmussen, L., Nie, E., Green, S., Kunicki, M., Fujimoto, M., Ehlinger, Z., Reynolds, W., Prabhu, S., Warren, K. E., Cornell, T., Partap, S., Fisher, P., Grant, G., Vogel, H., Sahaf, B., Davis, K., Feldman, S., Mackall, C. OXFORD UNIV PRESS INC. 2022: 20-21

  View details for Web of Science ID 000840122400074

• Checkpoint Immunotherapy in Pediatrics: Here, Gone, and Back Again. American Society of Clinical Oncology educational book. American Society of Clinical Oncology. Annual Meeting Long, A. H., Morgenstern, D. A., Leruste, A., Bourdeaut, F., Davis, K. L. 2022; 42: 1-14

  Abstract

  The role of immune checkpoint inhibitors (ICIs) in the treatment of pediatric cancers continues to evolve. Such therapies function by augmenting existing antitumor T-cell responses that have been rendered ineffective by inhibitory pathways. Although ICIs have proven highly effective for adult cancers, initial phase I/II clinical trials using single-agent ICIs against unselected pediatric cancers have been overall disappointing. With the exception of pediatric classic Hodgkin lymphoma, responses to ICIs have been infrequent, likely stemming from an inherent difference in the immunogenicity of childhood cancers, which, on average, have far fewer neoantigens than adult cancers. Recently, however, hope has reemerged that certain subsets of children with cancer may benefit from ICI therapies. In preliminary studies, patients with both pediatric hypermutated and SMARCB1-deficient cancers have had impressive responses to ICI therapies, likely as a result of underlying biologies that enhance neoantigen expression and tumoral inflammation. Dedicated trials are ongoing to fully evaluate the efficacy of ICIs for patients with these subsets of pediatric cancer.

  View details for DOI 10.1200/EDBK_349799

  View details for PubMedID 35580293

• CytofIn enables integrated analysis of public mass cytometry datasets using generalized anchors. Nature communications Lo, Y., Keyes, T. J., Jager, A., Sarno, J., Domizi, P., Majeti, R., Sakamoto, K. M., Lacayo, N., Mullighan, C. G., Waters, J., Sahaf, B., Bendall, S. C., Davis, K. L. 2022; 13 (1): 934

  Abstract

  The increasing use of mass cytometry for analyzing clinical samples offers the possibility to perform comparative analyses across public datasets. However, challenges in batch normalization and data integration limit the comparison of datasets not intended to be analyzed together. Here, we present a data integration strategy, CytofIn, using generalized anchors to integrate mass cytometry datasets from the public domain. We show that low-variance controls, such as healthy samples and stable channels, are inherently homogeneous, robust against stimulation, and can serve as generalized anchors for batch correction. Single-cell quantification comparing mass cytometry data from 989 leukemia files pre- and post normalization with CytofIn demonstrates effective batch correction while recapitulating the gold-standard bead normalization. CytofIn integration of public cancer datasets enabled the comparison of immune features across histologies and treatments. We demonstrate the ability to integrate public datasets without necessitating identical control samples or bead standards for fast and robust analysis using CytofIn.

  View details for DOI 10.1038/s41467-022-28484-5

  View details for PubMedID 35177627

• GD2-CAR T cell therapy for H3K27M-mutated diffuse midline gliomas. Nature Majzner, R. G., Ramakrishna, S., Yeom, K. W., Patel, S., Chinnasamy, H., Schultz, L. M., Richards, R. M., Jiang, L., Barsan, V., Mancusi, R., Geraghty, A. C., Good, Z., Mochizuki, A. Y., Gillespie, S. M., Toland, A. M., Mahdi, J., Reschke, A., Nie, E., Chau, I. J., Rotiroti, M. C., Mount, C. W., Baggott, C., Mavroukakis, S., Egeler, E., Moon, J., Erickson, C., Green, S., Kunicki, M., Fujimoto, M., Ehlinger, Z., Reynolds, W., Kurra, S., Warren, K. E., Prabhu, S., Vogel, H., Rasmussen, L., Cornell, T. T., Partap, S., Fisher, P. G., Campen, C. J., Filbin, M. G., Grant, G., Sahaf, B., Davis, K. L., Feldman, S. A., Mackall, C. L., Monje, M. 2022

  Abstract

  Diffuse intrinsic pontine glioma (DIPG) and other H3K27M-mutated diffuse midline gliomas (DMG) are universally lethal paediatric central nervous system tumours1. We previously discovered that the disialoganglioside GD2 is highly expressed on H3K27M-mutant glioma cells and demonstrated promising preclinical efficacy of GD2-directed chimeric antigen receptor (CAR) T cells2, providing the rationale for a first-in-human Phase 1 clinical trial (NCT04196413). Because CAR T-cell-induced brainstem inflammation can result in obstructive hydrocephalus, increased intracranial pressure, and dangerous tissue shifts, neurocritical care precautions were incorporated. Here we present the clinical experience from the first four patients with H3K27M-mutant DIPG/DMG treated with GD2-CAR T cells (GD2-CART) at dose level 1 (1e6 GD2-CAR T cells/kg administered intravenously). Patients who exhibited clinical benefit were eligible for subsequent GD2-CAR T infusions administered intracerebroventricularly3. Toxicity was largely related to tumor location and reversible with intensive supportive care. On-target, off-tumor toxicity was not observed. Three of four patients exhibited clinical and radiographic improvement. Proinflammatory cytokines were increased in plasma and cerebrospinal fluid (CSF). Transcriptomic analyses of 65,598 single cells from CAR T cell products and CSF elucidate heterogeneity in response between subjects and administration routes. These early results underscore the promise of this approach for H3K27M+ DIPG/DMG therapy.

  View details for DOI 10.1038/s41586-022-04489-4

  View details for PubMedID 35130560

• An instructive role for Interleukin-7 receptor alpha in the development of human B-cell precursor leukemia. Nature communications Geron, I., Savino, A. M., Fishman, H., Tal, N., Brown, J., Turati, V. A., James, C., Sarno, J., Hameiri-Grossman, M., Lee, Y. N., Rein, A., Maniriho, H., Birger, Y., Zemlyansky, A., Muler, I., Davis, K. L., Marcu-Malina, V., Mattson, N., Parnas, O., Wagener, R., Fischer, U., Barata, J. T., Jamieson, C. H., Muschen, M., Chen, C., Borkhardt, A., Kirsch, I. R., Nagler, A., Enver, T., Izraeli, S. 1800; 13 (1): 659

  Abstract

  Kinase signaling fuels growth of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Yet its role in leukemia initiation is unclear and has not been shown in primary human hematopoietic cells. We previously described activating mutations in interleukin-7 receptor alpha (IL7RA) in poor-prognosis "ph-like" BCP-ALL. Here we show that expression of activated mutant IL7RA in human CD34+ hematopoietic stem and progenitor cells induces a preleukemic state in transplanted immunodeficient NOD/LtSz-scid IL2Rgammanull mice, characterized by persistence of self-renewing Pro-B cells with non-productive V(D)J gene rearrangements. Preleukemic CD34+CD10highCD19+ cells evolve into BCP-ALL with spontaneously acquired Cyclin Dependent Kinase Inhibitor 2A (CDKN2A) deletions, as commonly observed in primary human BCP-ALL. CRISPR mediated gene silencing of CDKN2A in primary human CD34+ cells transduced with activated IL7RA results in robust development of BCP-ALLs in-vivo. Thus, we demonstrate that constitutive activation of IL7RA can initiate preleukemia in primary human hematopoietic progenitors and cooperates with CDKN2A silencing in progression into BCP-ALL.

  View details for DOI 10.1038/s41467-022-28218-7

  View details for PubMedID 35115489

• Understanding the hematopoietic factory during acute lymphoblastic leukemia. Pediatric research Davis, K. L. 1800

  View details for DOI 10.1038/s41390-022-01957-5

  View details for PubMedID 35079114

• Comparison of the Transcriptomic Signatures in Pediatric and Adult CML. Cancers Youn, M., Smith, S. M., Lee, A. G., Chae, H., Spiteri, E., Erdmann, J., Galperin, I., Jones, L. M., Donato, M., Abidi, P., Bittencourt, H., Lacayo, N., Dahl, G., Aftandilian, C., Davis, K. L., Matthews, J. A., Kornblau, S. M., Huang, M., Sumarsono, N., Redell, M. S., Fu, C. H., Chen, I., Alonzo, T. A., Eklund, E., Gotlib, J., Khatri, P., Sweet-Cordero, E. A., Hijiya, N., Sakamoto, K. M. 1800; 13 (24)

  Abstract

  Children with chronic myeloid leukemia (CML) tend to present with higher white blood counts and larger spleens than adults with CML, suggesting that the biology of pediatric and adult CML may differ. To investigate whether pediatric and adult CML have unique molecular characteristics, we studied the transcriptomic signature of pediatric and adult CML CD34+ cells and healthy pediatric and adult CD34+ control cells. Using high-throughput RNA sequencing, we found 567 genes (207 up- and 360 downregulated) differentially expressed in pediatric CML CD34+ cells compared to pediatric healthy CD34+ cells. Directly comparing pediatric and adult CML CD34+ cells, 398 genes (258 up- and 140 downregulated), including many in the Rho pathway, were differentially expressed in pediatric CML CD34+ cells. Using RT-qPCR to verify differentially expressed genes, VAV2 and ARHGAP27 were significantly upregulated in adult CML CD34+ cells compared to pediatric CML CD34+ cells. NCF1, CYBB, and S100A8 were upregulated in adult CML CD34+ cells but not in pediatric CML CD34+ cells, compared to healthy controls. In contrast, DLC1 was significantly upregulated in pediatric CML CD34+ cells but not in adult CML CD34+ cells, compared to healthy controls. These results demonstrate unique molecular characteristics of pediatric CML, such as dysregulation of the Rho pathway, which may contribute to clinical differences between pediatric and adult patients.

  View details for DOI 10.3390/cancers13246263

  View details for PubMedID 34944883

• Chromatin Content Capture Reveals Acute Leukaemia Oncogenic Vulnerability Point in Human B Cell Development Baskar, R., Favaro, P., Reynolds, W. D., Domizi, P., Tsai, A. G., Davis, K. L., Bendall, S. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-153114

  View details for Web of Science ID 000736398802212

• Ikaros Mediates Antigen Escape Following CD19 CAR T Cell Therapy in r/r B-ALL Domizi, P., Sarno, J., Jager, A., Baskar, R., Reynolds, W. D., Sahaf, B., Bendall, S., Mullighan, C. G., Leahy, A., Myers, R. M., Grupp, S. A., Sotillo, E., Barrett, D., Davis, K. L. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-151002

  View details for Web of Science ID 000736398802154

• Inhibition of Pre-BCR Signaling Mediates a Metabolic Switch in B-Cell Progenitor Acute Lymphoblastic Leukemia Liu, Y., Stuani, L., Jedoui, D., Merchant, M., Jager, A., Sarno, J., Mullighan, C. G., Hartmann, F. J., Bendall, S., Davis, K. L. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-145956

  View details for Web of Science ID 000736398802156

• Glucocorticoid-Resistant B-Cell Acute Lymphoblastic Leukemic Cells Can be Targeted By BCR-Signaling Inhibition Sarno, J., Domizi, P., Liu, Y., Merchant, M., Jedoui, D., Jager, A., Biondi, A., Gaipa, G., Bava, A., Davis, K. L. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-150356

  View details for Web of Science ID 000736398802158

• CD22-CAR T-Cell Therapy Mediates High Durable Remission Rates in Adults with Large B-Cell Lymphoma Who Have Relapsed after CD19-CAR T-Cell Therapy Frank, M. J., Baird, J. H., Patel, S., Craig, J., Spiegel, J. Y., Ehlinger, Z., Chinnasamy, H., Younes, S. F., Oak, J. S., Natkunam, Y., Reynolds, W. D., Iglesias, M., Crawford, E., Srinagesh, H. K., Egeler, E. L., Arai, S., Johnston, L. J., Lowsky, R., Negrin, R. S., Rezvani, A. R., Shiraz, P., Sidana, S., Weng, W., Schultz, L. M., Ramakrishna, S., Davis, K. L., Sahaf, B., Feldman, S. A., Mackall, C. L., Miklos, D. B., Muffl, L. AMER SOC HEMATOLOGY. 2021

  View details for DOI 10.1182/blood-2021-152145

  View details for Web of Science ID 000736398803041

• Evaluating Efficacy and Safety of Tisagenlecleucel Reinfusion Following Loss of B-Cell Aplasia in Pediatric and Young Adult Patients with Acute Lymphoblastic Leukemia: HESTER Phase II Study Boyer, M. W., Chaudhury, S., Davis, K. L., Driscoll, T., Grupp, S. A., Hermiston, M., John, S., Keating, A. K., Kovacs, C., Myers, G., Phillips, C. L., Pulsipher, M. A., Talano, J., Kari, G., Willert, J. CIG MEDIA GROUP, LP. 2021: S262-S263

  View details for Web of Science ID 000691910500082

• CAR T cells with dual targeting of CD19 and CD22 in adult patients with recurrent or refractory B cell malignancies: a phase 1 trial. Nature medicine Spiegel, J. Y., Patel, S., Muffly, L., Hossain, N. M., Oak, J., Baird, J. H., Frank, M. J., Shiraz, P., Sahaf, B., Craig, J., Iglesias, M., Younes, S., Natkunam, Y., Ozawa, M. G., Yang, E., Tamaresis, J., Chinnasamy, H., Ehlinger, Z., Reynolds, W., Lynn, R., Rotiroti, M. C., Gkitsas, N., Arai, S., Johnston, L., Lowsky, R., Majzner, R. G., Meyer, E., Negrin, R. S., Rezvani, A. R., Sidana, S., Shizuru, J., Weng, W., Mullins, C., Jacob, A., Kirsch, I., Bazzano, M., Zhou, J., Mackay, S., Bornheimer, S. J., Schultz, L., Ramakrishna, S., Davis, K. L., Kong, K. A., Shah, N. N., Qin, H., Fry, T., Feldman, S., Mackall, C. L., Miklos, D. B. 2021

  Abstract

  Despite impressive progress, more than 50% of patients treated with CD19-targeting chimeric antigen receptor T cells (CAR19) experience progressive disease. Ten of 16 patients with large B cell lymphoma (LBCL) with progressive disease after CAR19 treatment had absent or low CD19. Lower surface CD19 density pretreatment was associated with progressive disease. To prevent relapse with CD19- or CD19lo disease, we tested a bispecific CAR targeting CD19 and/or CD22 (CD19-22.BB.z-CAR) in a phase I clinical trial ( NCT03233854 ) of adults with relapsed/refractory B cell acute lymphoblastic leukemia (B-ALL) and LBCL. The primary end points were manufacturing feasibility and safety with a secondary efficacy end point. Primary end points were met; 97% of products met protocol-specified dose and no dose-limiting toxicities occurred during dose escalation. In B-ALL (n=17), 100% of patients responded with 88% minimal residual disease-negative complete remission (CR); in LBCL (n=21), 62% of patients responded with 29% CR. Relapses were CD19-/lo in 50% (5 out of 10) of patients with B-ALL and 29% (4 out of 14) of patients with LBCL but were not associated with CD22-/lo disease. CD19/22-CAR products demonstrated reduced cytokine production when stimulated with CD22 versus CD19. Our results further implicate antigen loss as a major cause of CAR T cell resistance, highlight the challenge of engineering multi-specific CAR T cells with equivalent potency across targets and identify cytokine production as an important quality indicator for CAR T cell potency.

  View details for DOI 10.1038/s41591-021-01436-0

  View details for PubMedID 34312556

• GD2 CAR T cells mediate clinical activity and manageable toxicity in children and young adults with DIPG and H3K27M-mutated diffuse midline gliomas. Majzner, R. G., Ramakrishna, S., Mochizuki, A., Patel, S., Chinnasamy, H., Yeom, K., Schultz, L., Richards, R., Campen, C., Reschke, A., Mahdi, J., Toland, A., Baggott, C., Mavroukakis, S., Egeler, E., Moon, J., Landrum, K., Erickson, C., Rasmussen, L., Barsan, V., Tamaresis, J. S., Marcy, A., Kunicki, M., Fujimoto, M., Ehlinger, Z., Kurra, S., Cornell, T., Partap, S., Fisher, P., Grant, G., Vogel, H., Sahaf, B., Davis, K., Feldman, S., Mackall, C. L., Monje, M. AMER ASSOC CANCER RESEARCH. 2021

  View details for Web of Science ID 000680263501014

• SINGLE CELL RNA SEQUENCING FROM THE CSF OF SUBJECTS WITH H3K27M+DIPG/DMG TREATED WITH GD2 CAR T-CELLULAR THERAPY Mochizuki, A., Ramakrishna, S., Good, Z., Patel, S., Chinnasamy, H., Yeom, K., Schultz, L., Richards, R., Campen, C., Reschke, A., Mahdi, J., Toland, A., Baggot, C., Mavroukakis, S., Egeler, E., Moon, J., Landrum, K., Erickson, C., Rasmussen, L., Barsan, V., Tamaresis, J., Marcy, A., Kunicki, M., Celones, M., Ehlinger, Z., Kurra, S., Cornell, T., Partap, S., Fisher, P., Grant, G., Vogel, H., Davis, K., Feldman, S., Sahaf, B., Majzner, R., Mackall, C., Monje, M. OXFORD UNIV PRESS INC. 2021: 39

  View details for DOI 10.1093/neuonc/noab090.158

  View details for Web of Science ID 000671540600159

• GD2 CAR T-CELLS MEDIATE CLINICAL ACTIVITY AND MANAGEABLE TOXICITY IN CHILDREN AND YOUNG ADULTS WITH H3K27M-MUTATED DIPG AND SPINAL CORD DMG Majzner, R., Ramakrishna, S., Mochizuki, A., Patel, S., Chinnasamy, H., Yeom, K., Schultz, L., Richards, R., Campen, C., Reschke, A., Mahdi, J., Martin, A., Toland, S., Baggott, C., Mavroukakis, S., Egeler, E., Moon, J., Landrum, K., Erickson, C., Rasmussen, L., Barsan, V., Tamaresis, J., Marcy, A., Kunicki, M., Fujimoto, M., Ehlinger, Z., Kurra, S., Cornell, T., Partap, S., Fisher, P., Grant, G., Vogel, H., Sahaf, B., Davis, K., Feldman, S., Mackall, C., Monje, M. OXFORD UNIV PRESS INC. 2021: 49-50

  View details for DOI 10.1093/neuonc/noab090.200

  View details for Web of Science ID 000671540600201

• Systemic Bevacizumab for Treatment of Respiratory Papillomatosis: International Consensus Statement. The Laryngoscope Sidell, D. R., Balakrishnan, K., Best, S. R., Zur, K., Buckingham, J., De Alarcon, A., Baroody, F. M., Bock, J. M., Boss, E. F., Bower, C. M., Campisi, P., Chen, S. F., Clarke, J. M., Clarke, K. D., Cocciaglia, A., Cotton, R. T., Cuestas, G., Davis, K. L., DeFago, V. H., Dikkers, F. G., Dossans, I., Florez, W., Fox, E., Friedman, A. D., Grant, N., Hamdi, O., Hogikyan, N. D., Johnson, K., Johnson, L. B., Johnson, R. F., Kelly, P., Klein, A. M., Lawlor, C. M., Leboulanger, N., Levy, A. G., Lam, D., Licameli, G. R., Long, S., Lott, D. G., Manrique, D., McMurray, J. S., Meister, K. D., Messner, A. H., Mohr, M., Mudd, P., Mortelliti, A. J., Novakovic, D., Ongkasuwan, J., Peer, S., Piersiala, K., Prager, J. D., Pransky, S. M., Preciado, D., Raynor, T., Rinkel, R. N., Rodriguez, H., Rodriguez, V. P., Russell, J., Scatolini, M. L., Scheffler, P., Smith, D. F., Smith, L. P., Smith, M. E., Smith, R. J., Sorom, A., Steinberg, A., Stith, J. A., Thompson, D., Thompson, J. W., Varela, P., White, D. R., Wineland, A. M., Yang, C. J., Zdanski, C. J., Derkay, C. S. 2021

  Abstract

  OBJECTIVES/HYPOTHESIS: The purpose of this study is to develop consensus on key points that would support the use of systemic bevacizumab for the treatment of recurrent respiratory papillomatosis (RRP), and to provide preliminary guidance surrounding the use of this treatment modality.STUDY DESIGN: Delphi method-based survey series.METHODS: A multidisciplinary, multi-institutional panel of physicians with experience using systemic bevacizumab for the treatment of RRP was established. The Delphi method was used to identify and obtain consensus on characteristics associated with systemic bevacizumab use across five domains: 1) patient characteristics; 2) disease characteristics; 3) treating center characteristics; 4) prior treatment characteristics; and 5) prior work-up.RESULTS: The international panel was composed of 70 experts from 12 countries, representing pediatric and adult otolaryngology, hematology/oncology, infectious diseases, pediatric surgery, family medicine, and epidemiology. A total of 189 items were identified, of which consensus was achieved on Patient Characteristics (9), Disease Characteristics (10), Treatment Center Characteristics (22), and Prior Workup Characteristics (18).CONCLUSION: This consensus statement provides a useful starting point for clinicians and centers hoping to offer systemic bevacizumab for RRP and may serve as a framework to assess the components of practices and centers currently using this therapy. We hope to provide a strategy to offer the treatment and also to provide a springboard for bevacizumab's use in combination with other RRP treatment protocols. Standardized delivery systems may facilitate research efforts and provide dosing regimens to help shape best-practice applications of systemic bevacizumab for patients with early-onset or less-severe disease phenotypes.LEVEL OF EVIDENCE: 5. Laryngoscope, 2021.

  View details for DOI 10.1002/lary.29343

  View details for PubMedID 33405268

• Mass Cytometry of Hematopoietic Cells. Methods in molecular biology (Clifton, N.J.) Jager, A., Sarno, J., Davis, K. L. 2021; 2185: 65–76

  Abstract

  Mass cytometry is now a well-established method that enables the measurement of 40-50 markers (generally proteins but transcripts are also possible) in single cells. Analytes are detected via antibodies tagged with heavy metal and detected by using a time-of-flight mass spectrometer. Over the past decade, mass cytometry has proven to be a valuable method for immunophenotyping hematopoietic cells with remarkable precision in both healthy and malignant scenarios. This chapter explains in detail how to profile hematopoietic cells by using this high-dimensional multiplexed approach.

  View details for DOI 10.1007/978-1-0716-0810-4_5

  View details for PubMedID 33165843

• Cancer Informatics for Cancer Centers: Scientific Drivers for Informatics, Data Science, and Care in Pediatric, Adolescent, and Young Adult Cancer. JCO clinical cancer informatics Kerlavage, A. R., Kirchhoff, A. C., Guidry Auvil, J. M., Sharpless, N. E., Davis, K. L., Reilly, K., Reaman, G., Penberthy, L., Deapen, D., Hwang, A., Durbin, E. B., Gallotto, S. L., Aplenc, R., Volchenboum, S. L., Heath, A. P., Aronow, B. J., Zhang, J., Vaske, O., Alonzo, T. A., Nathan, P. C., Poynter, J. N., Armstrong, G., Hahn, E. E., Wernli, K. J., Greene, C., DiGiovanna, J., Resnick, A. C., Shalley, E. R., Nadaf, S., Kibbe, W. A. 2021; 5: 881-896

  Abstract

  Cancer Informatics for Cancer Centers (CI4CC) is a grassroots, nonprofit 501c3 organization intended to provide a focused national forum for engagement of senior cancer informatics leaders, primarily aimed at academic cancer centers anywhere in the world but with a special emphasis on the 70 National Cancer Institute-funded cancer centers. This consortium has regularly held topic-focused biannual face-to-face symposiums. These meetings are a place to review cancer informatics and data science priorities and initiatives, providing a forum for discussion of the strategic and pragmatic issues that we faced at our respective institutions and cancer centers. Here, we provide meeting highlights from the latest CI4CC Symposium, which was delayed from its original April 2020 schedule because of the COVID-19 pandemic and held virtually over three days (September 24, October 1, and October 8) in the fall of 2020. In addition to the content presented, we found that holding this event virtually once a week for 6 hours was a great way to keep the kind of deep engagement that a face-to-face meeting engenders. This is the second such publication of CI4CC Symposium highlights, the first covering the meeting that took place in Napa, California, from October 14-16, 2019. We conclude with some thoughts about using data science to learn from every child with cancer, focusing on emerging activities of the National Cancer Institute's Childhood Cancer Data Initiative.

  View details for DOI 10.1200/CCI.21.00040

  View details for PubMedID 34428097

• Use of cardiac radiation therapy as bridging therapy to CAR-T for relapsed pediatric B-cell acute lymphoblastic leukemia. Pediatric blood & cancer Marquez, C. P., Montiel-Esparza, R., Hui, C., Schultz, L. M., Davis, K. L., Hoppe, R. T., Donaldson, S. S., Ramakrishna, S., Hiniker, S. M. 2020: e28870

  Abstract

  The use of radiotherapy as bridging therapy to chimeric antigen receptor T-cell therapy (CAR-T) in pre-B acute lymphoblastic leukemia (B-ALL) has been minimally explored. Here, we present a boy with B-ALL who relapsed after allogeneic bone marrow transplant with disseminated disease, including significant symptomatic cardiovascular and gastrointestinal (GI) involvement. The cardiac and GI leukemic infiltrates were successfully treated with bridging radiation therapy (BRT) prior to CAR-T infusion. Using this approach, he successfully tolerated CAR-T with no evidence of disease or sequelae on 3-month follow-up. This is the first reported case of safe and effective delivery of cardiac BRT in B-ALL.

  View details for DOI 10.1002/pbc.28870

  View details for PubMedID 33355997

• Use of Chimeric Antigen Receptor Modified T Cells With Extensive Leukemic Myocardial Involvement JACC: CARDIOONCOLOGY Han, B., Montiel-Esparza, R., Chubb, H., Kache, S., Schultz, L. M., Davis, K. L., Ramakrishna, S., Su, L. 2020; 2 (4): 666–70

  View details for DOI 10.1016/j.jaccao.2020.08.009

  View details for Web of Science ID 000613114700018

• Multiplexed ion beam imaging to describe tumor-immune microenvironment and tumor heterogeneity in neuroblastoma. Kammersgaard, M. B., Bosse, M., Martinez, D., Bosse, K. R., Maris, J. M., Mackall, C. L., Angelo, R. M., Davis, K. L. AMER ASSOC CANCER RESEARCH. 2020

  View details for Web of Science ID 000587913100053

• Use of Chimeric Antigen Receptor Modified T Cells With Extensive Leukemic Myocardial Involvement. JACC. CardioOncology Han, B., Montiel-Esparza, R., Chubb, H., Kache, S., Schultz, L. M., Davis, K. L., Ramakrishna, S., Su, L. 2020; 2 (4): 666-670

  View details for DOI 10.1016/j.jaccao.2020.08.009

  View details for PubMedID 34396279

  View details for PubMedCentralID PMC8352108

• Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions NATURE MACHINE INTELLIGENCE Culos, A., Tsai, A. S., Stanley, N., Becker, M., Ghaemi, M. S., McIlwain, D. R., Fallahzadeh, R., Tanada, A., Nassar, H., Espinosa, C., Xenochristou, M., Ganio, E., Peterson, L., Han, X., Stelzer, I. A., Ando, K., Gaudilliere, D., Phongpreecha, T., Maric, I., Chang, A. L., Shaw, G. M., Stevenson, D. K., Bendall, S., Davis, K. L., Fantl, W., Nolan, G. P., Hastie, T., Tibshirani, R., Angst, M. S., Gaudilliere, B., Aghaeepour, N. 2020

  View details for DOI 10.1038/s42256-020-00232-8

  View details for Web of Science ID 000579336000001

• Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions. Nature machine intelligence Culos, A., Tsai, A. S., Stanley, N., Becker, M., Ghaemi, M. S., McIlwain, D. R., Fallahzadeh, R., Tanada, A., Nassar, H., Espinosa, C., Xenochristou, M., Ganio, E., Peterson, L., Han, X., Stelzer, I. A., Ando, K., Gaudilliere, D., Phongpreecha, T., Marić, I., Chang, A. L., Shaw, G. M., Stevenson, D. K., Bendall, S., Davis, K. L., Fantl, W., Nolan, G. P., Hastie, T., Tibshirani, R., Angst, M. S., Gaudilliere, B., Aghaeepour, N. 2020; 2 (10): 619-628

  Abstract

  The dense network of interconnected cellular signalling responses that are quantifiable in peripheral immune cells provides a wealth of actionable immunological insights. Although high-throughput single-cell profiling techniques, including polychromatic flow and mass cytometry, have matured to a point that enables detailed immune profiling of patients in numerous clinical settings, the limited cohort size and high dimensionality of data increase the possibility of false-positive discoveries and model overfitting. We introduce a generalizable machine learning platform, the immunological Elastic-Net (iEN), which incorporates immunological knowledge directly into the predictive models. Importantly, the algorithm maintains the exploratory nature of the high-dimensional dataset, allowing for the inclusion of immune features with strong predictive capabilities even if not consistent with prior knowledge. In three independent studies our method demonstrates improved predictions for clinically relevant outcomes from mass cytometry data generated from whole blood, as well as a large simulated dataset. The iEN is available under an open-source licence.

  View details for DOI 10.1038/s42256-020-00232-8

  View details for PubMedID 33294774

  View details for PubMedCentralID PMC7720904

• Identification of dual positive CD19+/CD3+ T cells in a leukapheresis product undergoing CAR transduction: a case report. Journal for immunotherapy of cancer Schultz, L., Patel, S., Davis, K. L., Ramakrishna, S., Sahaf, B., Bhatia, N., Baggott, C., Erickson, C., Majzner, R. G., Oak, J., Bertaina, A., Mackall, C., Feldman, S. 2020; 8 (2)

  Abstract

  BACKGROUND: Chimeric antigen receptor (CAR) therapy and hematopoietic stem cell transplantation (HSCT) are therapeutics for relapsed acute lymphocytic leukemia (ALL) that are increasingly being used in tandem. We identified a non-physiologic CD19+/CD3+ T-cell population in the leukapheresis product of a patient undergoing CAR T-cell manufacturing who previously received a haploidentical HSCT, followed by infusion of a genetically engineered T-cell addback product. We confirm and report the origin of these CD19+/CD3+ T cells that have not previously been described in context of CAR T-cell manufacturing. We additionally interrogate the fate of these CD19-expressing cells as they undergo transduction to express CD19-specific CARs.MAIN BODY: We describe the case of a preteen male with multiply relapsed B-ALL who was treated with sequential cellular therapies. He received an alphabeta T-cell depleted haploidentical HSCT followed by addback of donor-derived T cells genetically modified with a suicide gene for iCaspase9 and truncated CD19 for cell tracking (RivoCel). He relapsed 6months following HSCT and underwent leukapheresis and CAR T-cell manufacturing. During manufacturing, we identified an aberrant T-cell population dually expressing CD19 and CD3. We hypothesized that these cells were RivoCel cells and confirmed using flow cytometry and PCR that the identified cells were in fact RivoCel cells and were eliminated with iCaspase9 activation. We additionally tracked these cells through CD19-specific CAR transduction and notably did not detect T cells dually positive for CD19 and CD19-directed CARs. The most likely rationale for this is in vitro fratricide of the CD19+ 'artificial' T-cell population by the CD19-specific CAR+ T cells in culture.CONCLUSIONS: We report the identification of CD19+/CD3+ cells in an apheresis product undergoing CAR transduction derived from a patient previously treated with a haploidentical transplant followed by RivoCel addback. We aim to bring attention to this cell phenotype that may be recognized with greater frequency as CAR therapy and engineered alphabetahaplo-HSCT are increasingly coupled. We additionally suggest consideration towards using alternative markers to CD19 as a synthetic identifier for post-transplant addback products, as CD19-expression on effector T cells may complicate subsequent treatment using CD19-directed therapy.

  View details for DOI 10.1136/jitc-2020-001073

  View details for PubMedID 32929049

• Progressive B Cell Loss in Revertant X-SCID. Journal of clinical immunology Lin, C. H., Kuehn, H. S., Thauland, T. J., Lee, C. M., De Ravin, S. S., Malech, H. L., Keyes, T. J., Jager, A., Davis, K. L., Garcia-Lloret, M. I., Rosenzweig, S. D., Butte, M. J. 2020

  Abstract

  We report the case of a patient with X-linked severe combined immunodeficiency (X-SCID) who survived for over 20years without hematopoietic stem cell transplantation (HSCT) because of a somatic reversionmutation. An important feature of this rare case included the strategy to validate the pathogenicity of a variant of the IL2RG gene when the T and B cell lineages comprised only revertant cells. We studied the X-inactivation of sorted T cells from the mother to show that the pathogenic variant was indeed the cause of his SCID. One interesting feature was a progressive loss of B cells over 20years. CyTOF (cytometry time of flight) analysis of bone marrow offered a potential explanation of the B cell failure, with expansions of progenitor populations that suggest a developmental block. Another interesting feature was that the patient bore extensive granulomatous disease and skin cancers that contained T cells, despite severe T cell lymphopenia in the blood. Finally, the patient had a few hundred T cells on presentation but his TCRs comprised a very limited repertoire, supporting the important conclusion that repertoire size trumps numbers of T cells.

  View details for DOI 10.1007/s10875-020-00825-3

  View details for PubMedID 32681206

• Using single-cell, high-dimensional approaches to unravel tumor heterogeneity in pediatric cancer Davis, K. L. AMER ASSOC CANCER RESEARCH. 2020: 29–30

  View details for Web of Science ID 000551367400027

• Validation of a model of pediatric leukemia based on pluripotent stem cells using mass cytometry Domingo-Reines, J., Kimmey, S., Vijayaragavan, K., Bosse, M., Bendall, S., Davis, K., Ramos-Mejia, V. AMER ASSOC CANCER RESEARCH. 2020: 95

  View details for Web of Science ID 000551367400138

• A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry. Cytometry. Part A : the journal of the International Society for Analytical Cytology Keyes, T. J., Domizi, P., Lo, Y., Nolan, G. P., Davis, K. L. 2020

  Abstract

  The application of machine learning and artificial intelligence to high-dimensional cytometry data sets has increasingly become a staple of bioinformatic data analysis over the past decade. This is especially true in the field of cancer biology, where protocols for collecting multiparameter single-cell data in a high-throughput fashion are rapidly developed. As the use of machine learning methodology in cytometry becomes increasingly common, there is a need for cancer biologists to understand the basic theory and applications of a variety of algorithmic tools for analyzing and interpreting cytometry data. We introduce the reader to several keystone machine learning-based analytic approaches with an emphasis on defining key terms and introducing a conceptual framework for making translational or clinically relevant discoveries. The target audience consists of cancer cell biologists and physician-scientists interested in applying these tools to their own data, but who may have limited training in bioinformatics. © 2020 International Society for Advancement of Cytometry.

  View details for DOI 10.1002/cyto.a.24158

  View details for PubMedID 32602650

• Immunotherapy for the Treatment of Acute Lymphoblastic Leukemia. Current oncology reports Barsan, V., Ramakrishna, S., Davis, K. L. 2020; 22 (2): 11

  Abstract

  PURPOSE OF REVIEW: Immunotherapy for the treatment of acute lymphoblastic leukemia (ALL) broadens therapeutic options beyond chemotherapy and targeted therapy. Here, we review the use of monoclonal antibody-based drugs and cellular therapies to treat ALL. We discuss the challenges facing the field regarding the optimal timing and sequencing of these therapies in relation to other treatment options as well as considerations of cost effectiveness.RECENT FINDINGS: By early identification of patients at risk for leukemic relapse, monoclonal antibody and cellular immunotherapies can be brought to the forefront of treatment options. Novel CAR design and manufacturing approaches may enhance durable patient response. Multiple clinical trials are now underway to evaluate the sequence and timing of monoclonal antibody, cellular therapy, and/or stem cell transplantation. The biologic and clinical contexts in which immunotherapies have advanced the treatment of ALL confer optimism that more patients will achieve durable remissions. Immunotherapy treatments in ALL will expand through rationally targeted approaches alongside advances in CAR T cell therapy design and clinical experience.

  View details for DOI 10.1007/s11912-020-0875-2

  View details for PubMedID 31997022

• Nivolumab in children and young adults with relapsed or refractory solid tumours or lymphoma (ADVL1412): a multicentre, open-label, single-arm, phase 1-2 trial. The Lancet. Oncology Davis, K. L., Fox, E. n., Merchant, M. S., Reid, J. M., Kudgus, R. A., Liu, X. n., Minard, C. G., Voss, S. n., Berg, S. L., Weigel, B. J., Mackall, C. L. 2020

  Abstract

  Immune checkpoint inhibitors targeting PD-1 have shown clinical benefit in adults with cancer, but data on these drugs in children are scarce. We did a phase 1-2 study of nivolumab, a PD-1 blocking monoclonal antibody, to determine its safety, pharmacokinetics, and antitumour activity in children and young adults with recurrent or refractory non-CNS solid tumours or lymphoma.We did a multicentre, open-label, single-arm, dose-confirmation and dose-expansion, phase 1-2 trial in 23 hospitals in the USA. Eligible patients for part A (dose-confirmation phase) of the study were aged 1-18 years with solid tumours with measurable or evaluable disease (by Response Evaluation Criteria in Solid Tumors [RECIST] version 1.1) regardless of histology. Eligible patients for part B (dose-expansion phase) were aged 1-30 years with measurable disease (by RECIST criteria) in the following disease cohorts: rhabdomyosarcoma, Ewing sarcoma, osteosarcoma, neuroblastoma, Hodgkin lymphoma, non-Hodgkin lymphoma, and melanoma. Patients in part A and were given nivolumab 3 mg/kg intravenously over 60 min on days 1 and 15 of a 28-day cycle in a rolling 6 study design with de-escalation upon dose-limiting toxicities to establish the recommended phase 2 dose. Patients in part B were given the recommended phase 2 dose. The primary outcomes were the tolerability, systemic exposure, maximum tolerated dose, and the antitumour activity of nivolumab at the adult recommended dose in children and young adults. This trial is registered with ClinicalTrials.gov, NCT02304458, with follow-up ongoing and is closed to new participants.85 patients were enrolled between Feb 22, 2015, and Dec 31, 2018, and 75 patients were fully evaluable for toxicity. Median follow-up was 30 days (IQR 27-83). In part A, 13 patients were enrolled and 12 were evaluable for toxicity. There were no dose de-escalations or dose-limiting toxicities and nivolumab 3 mg/kg was confirmed as the paediatric recommended phase 2. 72 patients were enrolled in part B and 63 were evaluable for toxicity. Five (7%) patients in part B had dose-limiting toxicities. The most common overall toxicity was anaemia (35 [47%] of 75 patients; five patients had grade 3 or grade 4) and non-haematological toxicity was fatigue (28 [37%] patients; none had grade 3 or grade 4). Responses were observed in patients with lymphoma (three [30%] of ten with Hodgkin lymphoma and one [10%] of ten with non-Hodgkin lymphoma; all responders had PD-L1 expression). Objective responses were not observed in other tumour types.Nivolumab was safe and well tolerated in children and young adults and showed clinical activity in lymphoma. Nivolumab showed no significant single-agent activity in the common paediatric solid tumours. This study defines the recommended phase 2 dose and establishes a favourable safety profile for nivolumab in children and young adults, which can serve as the basis for its potential study in combinatorial regimens for childhood cancer.Bristol-Myers Squibb, Children's Oncology Group, National Institutes of Health, Cookies for Kids Cancer Foundation.

  View details for DOI 10.1016/S1470-2045(20)30023-1

  View details for PubMedID 32192573

• RSK inhibitor BI-D1870 inhibits acute myeloid leukemia cell proliferation by targeting mitotic exit. Oncotarget Chae, H. D., Dutta, R. n., Tiu, B. n., Hoff, F. W., Accordi, B. n., Serafin, V. n., Youn, M. n., Huang, M. n., Sumarsono, N. n., Davis, K. L., Lacayo, N. J., Pigazzi, M. n., Horton, T. M., Kornblau, S. M., Sakamoto, K. M. 2020; 11 (25): 2387–2403

  Abstract

  The 90 kDa Ribosomal S6 Kinase (RSK) drives cell proliferation and survival in cancers, although its oncogenic mechanism has not been well characterized. Phosphorylated level of RSK (T573) was increased in acute myeloid leukemia (AML) patients and associated with poor survival. To examine the role of RSK in AML, we analyzed apoptosis and the cell cycle profile following treatment with BI-D1870, a potent inhibitor of RSK. BI-D1870 treatment increased the G2/M population and induced apoptosis in AML cell lines and patient AML cells. Characterization of mitotic phases showed that the metaphase/anaphase transition was significantly inhibited by BI-D1870. BI-D1870 treatment impeded the association of activator CDC20 with APC/C, but increased binding of inhibitor MAD2 to CDC20, preventing mitotic exit. Moreover, the inactivation of spindle assembly checkpoint or MAD2 knockdown released cells from BI-D1870-induced metaphase arrest. Therefore, we investigated whether BI-D1870 potentiates the anti-leukemic activity of vincristine by targeting mitotic exit. Combination treatment of BI-D1870 and vincristine synergistically increased mitotic arrest and apoptosis in acute leukemia cells. These data show that BI-D1870 induces apoptosis of AML cells alone and in combination with vincristine through blocking mitotic exit, providing a novel approach to overcoming vincristine resistance in AML cells.

  View details for DOI 10.18632/oncotarget.27630

  View details for PubMedID 32637030

  View details for PubMedCentralID PMC7321696

• Supercharging your CAR. Blood Ramakrishna, S. n., Davis, K. L. 2020; 135 (9): 593–94

  View details for DOI 10.1182/blood.2019004469

  View details for PubMedID 32106308

• CD22-Directed CAR T-Cell Therapy Induces Complete Remissions in CD19-Directed CAR-Refractory Large B-Cell Lymphoma. Blood Baird, J. H., Frank, M. J., Craig, J. n., Patel, S. n., Spiegel, J. Y., Sahaf, B. n., Oak, J. S., Younes, S. n., Ozawa, M. n., Yang, E. n., Natkunam, Y. n., Tamaresis, J. S., Ehlinger, Z. n., Reynolds, W. D., Arai, S. n., Johnston, L. n., Lowsky, R. n., Meyer, E. n., Negrin, R. S., Rezvani, A. R., Shiraz, P. n., Sidana, S. n., Weng, W. K., Davis, K. L., Ramakrishna, S. n., Schultz, L. n., Mullins, C. D., Jacob, A. P., Kirsch, I. R., Feldman, S. A., Mackall, C. L., Miklos, D. B., Muffly, L. n. 2020

  Abstract

  The prognosis for patients with large B-cell lymphoma (LBCL) progressing after treatment with chimeric antigen receptor (CAR) T-cell therapy targeting CD19 (CAR19) is poor. We report on the first three consecutive patients with autologous CAR19-refractory LBCL treated with a single infusion of autologous 1×106 CAR+ T-cells/kg targeting CD22 (CAR22) as part of a phase I dose escalation study. CAR22 therapy was relatively well tolerated, without any observed non-hematologic adverse events higher than grade 2. Following infusion, all three patients achieved complete remission, with all responses ongoing at the time of last follow up (mean 7.8 months, range 6-9.3). Circulating CAR22 cells demonstrated robust expansion (peak range 85.4-350 cells/µL), and persisted beyond three months in all patients with continued radiographic responses and corresponding decreases in circulating tumor DNA (ctDNA) beyond six months post-infusion. Further accrual at a higher dose level in this phase 1 dose-escalation study is ongoing and will explore the role of this therapy in patients who have failed prior CAR T-cell therapies. (Funded by the National Cancer Institute and others; ClinicalTrials.gov number, NCT04088890).

  View details for DOI 10.1182/blood.2020009432

  View details for PubMedID 33512414

• Patient-reported quality of life after tisagenlecleucel infusion in children and young adults with relapsed or refractory B-cell acute lymphoblastic leukaemia: a global, single-arm, phase 2 trial. The Lancet. Oncology Laetsch, T. W., Myers, G. D., Baruchel, A., Dietz, A. C., Pulsipher, M. A., Bittencourt, H., Buechner, J., De Moerloose, B., Davis, K. L., Nemecek, E., Driscoll, T., Mechinaud, F., Boissel, N., Rives, S., Bader, P., Peters, C., Sabnis, H. S., Grupp, S. A., Yanik, G. A., Hiramatsu, H., Stefanski, H. E., Rasouliyan, L., Yi, L., Shah, S., Zhang, J., Harris, A. C. 2019

  Abstract

  BACKGROUND: The ELIANA trial showed that 61 (81%) of 75 paediatric and young adult patients with relapsed or refractory B-cell acute lymphoblastic leukaemia achieved overall remission after treatment with tisagenlecleucel, a chimeric antigen receptor targeted against the CD19 antigen. We aimed to evaluate patient-reported quality of life in these patients before and after tisagenlecleucel infusion.METHODS: ELIANA, a global, single-arm, open-label, phase 2 trial, was done in 25 hospitals across Australia, Austria, Belgium, Canada, France, Germany, Italy, Japan, Norway, Spain, and the USA. Patients with B-cell acute lymphoblastic leukaemia aged at least 3 years at the time of screening and 21 years or younger at the time of initial diagnosis who were in second or greater bone marrow relapse, chemorefractory, relapsed after allogeneic stem-cell transplantation, or were otherwise ineligible for allogeneic stem-cell transplantation were enrolled. Patients received a single intravenous administration of a target dose of 0·2-5 * 106 transduced viable T cells per kg for patients weighing 50 kg or less or 0·1-2·5 * 108 transduced viable T cells for patients weighing more than 50 kg. The primary outcome, reported previously, was the proportion of patients who achieved remission. A prespecified secondary endpoint, reported here, was patient-reported quality of life measured with the Pediatric Quality of Life Inventory (PedsQL) and European Quality of Life-5 Dimensions questionnaire (EQ-5D). Patients completed the questionnaires at baseline, day 28, and months 3, 6, 9, and 12 after treatment. The data collected were summarised using descriptive statistics and post-hoc mixed models for repeated measures. Change from baseline response profiles were illustrated with cumulative distribution function plots. The proportion of patients achieving the minimal clinically important difference and normative mean value were reported. Analysis was per protocol. This study is registered with ClinicalTrials.gov, NCT02435849.FINDINGS: Between April 8, 2015, and April 25, 2017, 107 patients were screened, 92 were enrolled, and 75 received tisagenlecleucel. 58 patients aged 8-23 years were included in the analysis of quality of life. At baseline, 50 (86%) patients had completed the PedsQL questionnaire and 48 (83%) had completed the EQ-5D VAS. Improvements in patient-reported quality-of-life scores were observed for all measures at month 3 after tisagenlecleucel infusion (mean change from baseline to month 3 was 13·3 [95% CI 8·9-17·6] for the PedsQL total score and 16·8 [9·4-24·3] for the EQ-5D visual analogue scale). 30 (81%) of 37 patients achieved the minimal clinically important difference at month 3 for the PedsQL total score and 24 (67%) of 36 patients achieved this for the EQ-5D visual analogue scale.INTERPRETATION: These findings, along with the activity and safety results of ELIANA, suggest a favourable benefit-risk profile of tisagenlecleucel in the treatment of paediatric and young adult patients with relapsed or refractory B-cell acute lymphoblastic leukaemia.FUNDING: Novartis.

  View details for DOI 10.1016/S1470-2045(19)30493-0

  View details for PubMedID 31606419

• Bcl-2 Is a Therapeutic Target for Hypodiploid B-Lineage Acute Lymphoblastic Leukemia CANCER RESEARCH Diaz-Flores, E., Comeaux, E. Q., Kim, K. L., Melnik, E., Beckman, K., Davis, K. L., Wu, K., Akutagawa, J., Bridges, O., Marino, R., Wohlfeil, M., Braun, B. S., Mullighan, C. G., Loh, M. L. 2019; 79 (9): 2339–51

  View details for DOI 10.1158/0008-5472.CAN-18-0236

  View details for Web of Science ID 000466765900024

• BCL-2 is a Therapeutic Target For Hypodiploid B-Lineage Acute Lymphoblastic Leukemia. Cancer research Diaz-Flores, E., Comeaux, E. Q., Kim, K. L., Melnik, E. M., Beckman, K., Davis, K. L., Wu, K., Akutagawa, J., Bridges, O., Marino, R., Wohlfeil, M., Braun, B. S., Mullighan, C. G., Loh, M. L. 2019

  Abstract

  Acute lymphoblastic leukemia (ALL) is the most common cancer in children. The highest rates of treatment failure occur in specific genetic subsets of acute lymphoblastic leukemia (ALL), including hypodiploid B cell ALL for which effective alternative therapies to current intensive chemotherapy treatments have yet to be developed. Here we integrated biochemical and genomic profiling with functional drug assays to select effective agents with therapeutic potential against hypodiploid B-ALL. ABT-199, a selective Bcl-2 inhibitor was effective in reducing leukemic burden in vitro and in vivo in patient-derived xenograft models of hypodiploid B-ALL. Daily oral treatment with ABT-199 significantly increased survival in xenografted mice. The unexpected efficacy of ABT-199 observed in hypodiploid leukemias lacking BIM expression (the major reported mediator of ABT-199-induced apoptosis) led us to investigate the mechanism of action of ABT-199 in the absence of BIM. Treatment with ABT-199 elicited responses in a dose-dependent manner, from cell cycle arrest at low nanomolar concentrations to cell death at concentrations above 100 nM. Collectively, these results demonstrate the efficacy of Bcl-2 inhibition and potential therapeutic strategy in hypodiploid B-ALL.

  View details for PubMedID 30862722

• High-efficiency CRISPR induction of t(9;11) chromosomal translocations and acute leukemias in human blood stem cells. Blood advances Jeong, J. n., Jager, A. n., Domizi, P. n., Pavel-Dinu, M. n., Gojenola, L. n., Iwasaki, M. n., Wei, M. C., Pan, F. n., Zehnder, J. L., Porteus, M. H., Davis, K. L., Cleary, M. L. 2019; 3 (19): 2825–35

  Abstract

  Chromosomal rearrangements involving the mixed lineage leukemia (MLL) gene, also known as KMT2A, are often observed in human leukemias and are generally associated with a poor prognosis. To model these leukemias, we applied clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing to induce MLL chromosomal rearrangements in human hematopoietic stem and progenitor cells purified from umbilical cord blood. Electroporation of ribonucleoprotein complexes containing chemically modified synthetic single guide RNAs and purified Cas9 protein induced translocations between chromosomes 9 and 11 [t(9;11)] at an efficiency >1%. Transplantation of gene-edited cells into immune-compromised mice rapidly induced acute leukemias of different lineages and often with multiclonal origins dictated by the duration of in vitro culture prior to transplantation. Breakpoint junction sequences served as biomarkers to monitor clonal selection and progression in culture and in vivo. High-dimensional cell surface and intracellular protein analysis by mass cytometry (CyTOF) revealed that gene-edited leukemias recapitulated disease-specific protein expression observed in human patients and showed that MLL-rearranged (MLLr) mixed phenotype acute leukemias (MPALs) were more similar to acute myeloid leukemias (AMLs) than to acute lymphoblastic leukemias (ALLs). Therefore, highly efficient generation of MLL chromosomal translocations in primary human blood stem cells using CRISPR/Cas9 reliably models human acute MLLr leukemia and provides an experimental platform for basic and translational studies of leukemia biology and therapeutics.

  View details for DOI 10.1182/bloodadvances.2019000450

  View details for PubMedID 31582391

• A novel platform for isotype-specific testing of autoantibodies. PloS one Carter, K. L., Treurnicht, A., Davis, K. L., Kumar, R. B., Feldman, B. J. 2019; 14 (2): e0211596

  Abstract

  The objective of this study was to test if a novel platform could be used for isotype-specific autoantibody testing in humans. Further, we evaluated if testing with this novel platform enables earlier detection of insulin autoantibodies in individuals that have first-degree relatives with type-1 diabetes than currently used approaches. Longitudinal serum samples from participants were collected before and after they converted to become positive for insulin autoantibodies by the current standardly used assays. Using a novel plasmonic gold chip platform, we tested these samples for IgM isotype-specific autoantibodies. Serial serum samples from individuals without diabetes were also tested as a comparison control cohort. Our results demonstrate proof-of-concept that a plasmonic gold chip can specifically detect the IgM insulin autoantibody. Five out of the six individuals that converted to being positive for insulin autoantibodies by standard testing had significant IgM autoantibodies on the plasmonic chip platform. The plasmonic chip platform detected IgM autoantibodies earlier than standard testing by up to 4 years. Our results indicate that the plasmonic gold platform can specifically detect the IgM isotype autoantibodies and suggest that combining isotype-specific testing with currently used approaches enables earlier detection of insulin autoantibodies in individuals that have first-degree relatives with type 1 diabetes.

  View details for DOI 10.1371/journal.pone.0211596

  View details for PubMedID 30730939

• Comparison of the Transcriptomic Signature of Pediatric Vs. Adult CML and Normal Bone Marrow Stem Cells Chae, H., Murphy, L. C., Donato, M., Lee, A. G., Sweet-Cordero, E., Abidi, P., Bittencourt, H., Lacayo, N. J., Dahl, G., Aftandilian, C., Davis, K. L., Huang, M., Sumarsono, N., Redell, M., Fu, C. H., Chen, I. L., Alonzo, T. A., Eklund, E. A., Gotlib, J. R., Khatri, P., Hijiya, N., Sakamoto, K. M. AMER SOC HEMATOLOGY. 2018

  View details for DOI 10.1182/blood-2018-99-119974

  View details for Web of Science ID 000454842803255

• Updated Analysis of the Efficacy and Safety of Tisagenlecleucel in Pediatric and Young Adult Patients with Relapsed/Refractory (r/r) Acute Lymphoblastic Leukemia Grupp, S. A., Maude, S. L., Rives, S., Baruchel, A., Boyer, M. W., Bittencourt, H., Bader, P., Buchner, J., Laetsch, T. W., Stefanski, H., Myers, G., Qayed, M., Pulsipher, M. A., De Moerloose, B., Yanik, G. A., Davis, K. L., Martin, P. L., Nemecek, E. R., Peters, C., Krueger, J., Balduzzi, A., Boissel, N., Mechinaud, F., Leung, M., Eldjerou, L. K., Yi, L., Mueller, K., Bleickardt, E., Hiramatsu, H. AMER SOC HEMATOLOGY. 2018

  View details for DOI 10.1182/blood-2018-99-112599

  View details for Web of Science ID 000454837602271

• 1 Study of CD19/CD22 Bispecific Chimeric Antigen Receptor (CAR) Therapy in Children and Young Adults with B Cell Acute Lymphoblastic Leukemia (ALL) Schultz, L. M., Davis, K. L., Baggott, C., Chaudry, C., Marcy, A., Mavroukakis, S., Sahaf, B., Kong, K. A., Muffly, L. S., Kim, S., Meyer, E. H., Fry, T. J., Qin, H., Miklos, D. B., Mackall, C. L. AMER SOC HEMATOLOGY. 2018

  View details for DOI 10.1182/blood-2018-99-117445

  View details for Web of Science ID 000454837602274

• Glucocorticoids-Resistant Leukemic B-Cells Undergo a Phenotypic Change That Increases Sensitivity to SRC/ABL Inhibition Sarno, J., Pedersen, C., Jager, A., Burns, T., Gaipa, G., Nolan, G. P., Bava, A., Davis, K. L. AMER SOC HEMATOLOGY. 2018

  View details for DOI 10.1182/blood-2018-99-117443

  View details for Web of Science ID 000454837604217

• Chromation Remodeling Therapy and Capizzi Methotrexate in Treatment-Related MDS/AML Aftandilian, C., Sakamoto, K. M., Davis, K. L., Dahl, G., Lacayo, N. J. AMER SOC HEMATOLOGY. 2018

  View details for DOI 10.1182/blood-2018-99-110481

  View details for Web of Science ID 000454842806106

• Cost Effectiveness of Chimeric Antigen Receptor T-Cell Therapy in Relapsed or Refractory Pediatric B-Cell Acute Lymphoblastic Leukemia. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Lin, J. K., Lerman, B. J., Barnes, J. I., Boursiquot, B. C., Tan, Y. J., Robinson, A. Q., Davis, K. L., Owens, D. K., Goldhaber-Fiebert, J. D. 2018: JCO2018790642

  Abstract

  Purpose The anti-CD19 chimeric antigen receptor T-cell therapy tisagenlecleucel was recently approved to treat relapsed or refractory pediatric acute lymphoblastic leukemia. With a one-time infusion cost of $475,000, tisagenlecleucel is currently the most expensive oncologic therapy. We aimed to determine whether tisagenlecleucel is cost effective compared with currently available treatments. Methods Markov modeling was used to evaluate tisagenlecleucel in pediatric relapsed or refractory acute lymphoblastic leukemia from a US health payer perspective over a lifetime horizon. The model was informed by recent multicenter, single-arm clinical trials. Tisagenlecleucel (under a range of plausible long-term effectiveness) was compared with blinatumomab, clofarabine combination therapy (clofarabine, etoposide, and cyclophosphamide), and clofarabine monotherapy. Scenario and probabilistic sensitivity analyses were used to explore uncertainty. Main outcomes were life-years, discounted lifetime costs, discounted quality-adjusted life-years (QALYs), and incremental cost-effectiveness ratio (3% discount rate). Results With an assumption of a 40% 5-year relapse-free survival rate, tisagenlecleucel increased life expectancies by 12.1 years and cost $61,000/QALY gained. However, at a 20% 5-year relapse-free survival rate, life-expectancies were more modest (3.8 years) and expensive ($151,000/QALY gained). At a 0% 5-year relapse-free survival rate and with use as a bridge to transplant, tisagenlecleucel increased life expectancies by 5.7 years and cost $184,000/QALY gained. Reduction of the price of tisagenlecleucel to $200,000 or $350,000 would allow it to meet a $100,000/QALY or $150,000/QALY willingness-to-pay threshold in all scenarios. Conclusion The long-term effectiveness of tisagenlecleucel is a critical but uncertain determinant of its cost effectiveness. At its current price, tisagenlecleucel represents reasonable value if it can keep a substantial fraction of patients in remission without transplantation; however, if all patients ultimately require a transplantation to remain in remission, it will not be cost effective at generally accepted thresholds. Price reductions would favorably influence cost effectiveness even if long-term clinical outcomes are modest.

  View details for DOI 10.1200/JCO.2018.79.0642

  View details for PubMedID 30212291

• Individualized drug combination based on single-cell drug perturbations Anchang, B., Davis, K., Fienberg, H., Bendall, S., Karacosta, L., Nolan, G., Plevritis, S. K. AMER ASSOC CANCER RESEARCH. 2018

  View details for DOI 10.1158/1538-7445.AM2018-2275

  View details for Web of Science ID 000468818905139

• False-positive results with select HIV-1 NAT methods following lentivirus-based tisagenlecleucel therapy BLOOD Laetsch, T. W., Maude, S. L., Milone, M. C., Davis, K. L., Krueger, J., Cardenas, A., Eldjerou, L. K., Keir, C. H., Wood, P. A., Grupp, S. A. 2018; 131 (23): 2596–98

  View details for PubMedID 29669777

• SRC/ABL inhibition disrupts CRLF2-driven signaling to induce cell death in B-cell acute lymphoblastic leukemia. Oncotarget Sarno, J., Savino, A. M., Buracchi, C., Palmi, C., Pinto, S., Bugarin, C., Jager, A., Bresolin, S., Barber, R. C., Silvestri, D., Israeli, S., Dyer, M. J., Cazzaniga, G., Nolan, G. P., Biondi, A., Davis, K. L., Gaipa, G. 2018; 9 (33): 22872–85

  Abstract

  Children with B-cell precursor acute lymphoblastic leukemia (BCP-ALL) overexpressing the CRLF2 gene (hiCRLF2) have poor prognosis. CRLF2 protein overexpression leads to activated JAK/STAT signaling and trials are underway using JAK inhibitors to overcome treatment failure. Pre-clinical studies indicated limited efficacy of single JAK inhibitors, thus additional pathways must be targeted in hiCRLF2 cells. To identify additional activated networks, we used single-cell mass cytometry to examine 15 BCP-ALL primary patient samples. We uncovered a coordinated signaling network downstream of CRLF2 characterized by co-activation of JAK/STAT, PI3K, and CREB pathways. This CRLF2-driven network could be more effectively disrupted by SRC/ABL inhibition than single-agent JAK or PI3K inhibition, and this could be demonstrated even in primary minimal residual disease (MRD) cells. Our study suggests SCR/ABL inhibition as effective in disrupting the cooperative functional networks present in hiCRLF2 BCP-ALL patients, supporting further investigation of this strategy in pre-clinical studies.

  View details for PubMedID 29796158

• Single-cell developmental classification of B cell precursor acute lymphoblastic leukemia at diagnosis reveals predictors of relapse. Nature medicine Good, Z., Sarno, J., Jager, A., Samusik, N., Aghaeepour, N., Simonds, E. F., White, L., Lacayo, N. J., Fantl, W. J., Fazio, G., Gaipa, G., Biondi, A., Tibshirani, R., Bendall, S. C., Nolan, G. P., Davis, K. L. 2018; 24 (4): 474–83

  Abstract

  Insight into the cancer cell populations that are responsible for relapsed disease is needed to improve outcomes. Here we report a single-cell-based study of B cell precursor acute lymphoblastic leukemia at diagnosis that reveals hidden developmentally dependent cell signaling states that are uniquely associated with relapse. By using mass cytometry we simultaneously quantified 35 proteins involved in B cell development in 60 primary diagnostic samples. Each leukemia cell was then matched to its nearest healthy B cell population by a developmental classifier that operated at the single-cell level. Machine learning identified six features of expanded leukemic populations that were sufficient to predict patient relapse at diagnosis. These features implicated the pro-BII subpopulation of B cells with activated mTOR signaling, and the pre-BI subpopulation of B cells with activated and unresponsive pre-B cell receptor signaling, to be associated with relapse. This model, termed 'developmentally dependent predictor of relapse' (DDPR), significantly improves currently established risk stratification methods. DDPR features exist at diagnosis and persist at relapse. By leveraging a data-driven approach, we demonstrate the predictive value of single-cell 'omics' for patient stratification in a translational setting and provide a framework for its application to human cancer.

  View details for PubMedID 29505032

• Publisher Correction: High-resolution myogenic lineage mapping by single-cell mass cytometry. Nature cell biology Porpiglia, E., Samusik, N., Van Ho, A. T., Cosgrove, B. D., Mai, T., Davis, K. L., Jager, A., Nolan, G. P., Bendall, S. C., Fantl, W. J., Blau, H. M. 2018

  Abstract

  In the version of this Article originally published, the name of author Andrew Tri Van Ho was coded wrongly, resulting in it being incorrect when exported to citation databases. This has been corrected, though no visible changes will be apparent.

  View details for PubMedID 29507406

• Tisagenlecleucel in Children and Young Adults with B-Cell Lymphoblastic Leukemia NEW ENGLAND JOURNAL OF MEDICINE Maude, S. L., Laetsch, T. W., Buechner, J., Rives, S., Boyer, M., Bittencourt, H., Bader, P., Verneris, M. R., Stefanski, H. E., Myers, G. D., Qayed, M., De Moerloose, B., Hiramatsu, H., Schlis, K., Davis, K. L., Martin, P. L., Nemecek, E. R., Yanik, G. A., Peters, C., Baruchel, A., Boissel, N., Mechinaud, F., Balduzzi, A., Krueger, J., June, C. H., Levine, B. L., Wood, P., Taran, T., Leung, M., Mueller, K. T., Zhang, Y., Sen, K., Lebwohl, D., Pulsipher, M. A., Grupp, S. A. 2018; 378 (5): 439–48

  Abstract

  In a single-center phase 1-2a study, the anti-CD19 chimeric antigen receptor (CAR) T-cell therapy tisagenlecleucel produced high rates of complete remission and was associated with serious but mainly reversible toxic effects in children and young adults with relapsed or refractory B-cell acute lymphoblastic leukemia (ALL).We conducted a phase 2, single-cohort, 25-center, global study of tisagenlecleucel in pediatric and young adult patients with CD19+ relapsed or refractory B-cell ALL. The primary end point was the overall remission rate (the rate of complete remission or complete remission with incomplete hematologic recovery) within 3 months.For this planned analysis, 75 patients received an infusion of tisagenlecleucel and could be evaluated for efficacy. The overall remission rate within 3 months was 81%, with all patients who had a response to treatment found to be negative for minimal residual disease, as assessed by means of flow cytometry. The rates of event-free survival and overall survival were 73% (95% confidence interval [CI], 60 to 82) and 90% (95% CI, 81 to 95), respectively, at 6 months and 50% (95% CI, 35 to 64) and 76% (95% CI, 63 to 86) at 12 months. The median duration of remission was not reached. Persistence of tisagenlecleucel in the blood was observed for as long as 20 months. Grade 3 or 4 adverse events that were suspected to be related to tisagenlecleucel occurred in 73% of patients. The cytokine release syndrome occurred in 77% of patients, 48% of whom received tocilizumab. Neurologic events occurred in 40% of patients and were managed with supportive care, and no cerebral edema was reported.In this global study of CAR T-cell therapy, a single infusion of tisagenlecleucel provided durable remission with long-term persistence in pediatric and young adult patients with relapsed or refractory B-cell ALL, with transient high-grade toxic effects. (Funded by Novartis Pharmaceuticals; ClinicalTrials.gov number, NCT02435849 .).

  View details for PubMedID 29385370

• Niclosamide suppresses acute myeloid leukemia cell proliferation through inhibition of CREB-dependent signaling pathways ONCOTARGET Chae, H., Cox, N., Dahl, G. V., Lacayo, N. J., Davis, K. L., Capolicchio, S., Smith, M., Sakamoto, K. M. 2018; 9 (4): 4301–17

  Abstract

  CREB (cAMP Response Element Binding protein) is a transcription factor that is overexpressed in primary acute myeloid leukemia (AML) cells and associated with a decreased event-free survival and increased risk of relapse. We recently reported a small molecule inhibitor of CREB, XX-650-23, which inhibits CREB activity in AML cells. Structure-activity relationship analysis for chemical compounds with structures similar to XX-650-23 led to the identification of the anthelminthic drug niclosamide as a potent anti-leukemic agent that suppresses cell viability of AML cell lines and primary AML cells without a significant decrease in colony forming activity of normal bone marrow cells. Niclosamide significantly inhibited CREB function and CREB-mediated gene expression in cells, leading to apoptosis and G1/S cell cycle arrest with reduced phosphorylated CREB levels. CREB knockdown protected cells from niclosamide treatment-mediated cytotoxic effects. Furthermore, treatment with a combination of niclosamide and CREB inhibitor XX-650-23 showed an additive anti-proliferative effect, consistent with the hypothesis that niclosamide and XX-650-23 regulate the same targets or pathways to inhibit proliferation and survival of AML cells. Niclosamide significantly inhibited the progression of disease in AML patient-derived xenograft (PDX) mice, and prolonged survival of PDX mice. Niclosamide also showed synergistic effects with chemotherapy drugs to inhibit AML cell proliferation. While chemotherapy antagonized the cytotoxic potential of niclosamide, pretreatment with niclosamide sensitized cells to chemotherapeutic drugs, cytarabine, daunorubicin, and vincristine. Therefore, our results demonstrate niclosamide as a potential drug to treat AML by inducing apoptosis and cell cycle arrest through inhibition of CREB-dependent pathways in AML cells.

  View details for PubMedID 29435104

• DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity. Proceedings of the National Academy of Sciences of the United States of America Anchang, B. n., Davis, K. L., Fienberg, H. G., Williamson, B. D., Bendall, S. C., Karacosta, L. G., Tibshirani, R. n., Nolan, G. P., Plevritis, S. K. 2018; 115 (18): E4294–E4303

  Abstract

  An individual malignant tumor is composed of a heterogeneous collection of single cells with distinct molecular and phenotypic features, a phenomenon termed intratumoral heterogeneity. Intratumoral heterogeneity poses challenges for cancer treatment, motivating the need for combination therapies. Single-cell technologies are now available to guide effective drug combinations by accounting for intratumoral heterogeneity through the analysis of the signaling perturbations of an individual tumor sample screened by a drug panel. In particular, Mass Cytometry Time-of-Flight (CyTOF) is a high-throughput single-cell technology that enables the simultaneous measurements of multiple ([Formula: see text]40) intracellular and surface markers at the level of single cells for hundreds of thousands of cells in a sample. We developed a computational framework, entitled Drug Nested Effects Models (DRUG-NEM), to analyze CyTOF single-drug perturbation data for the purpose of individualizing drug combinations. DRUG-NEM optimizes drug combinations by choosing the minimum number of drugs that produce the maximal desired intracellular effects based on nested effects modeling. We demonstrate the performance of DRUG-NEM using single-cell drug perturbation data from tumor cell lines and primary leukemia samples.

  View details for PubMedID 29654148

• Single-cell mass cytometry and machine learning predict relapse in childhood leukemia. Molecular & cellular oncology Sarno, J., Davis, K. L. 2018; 5 (5): e1472057

  Abstract

  Improved insight into cancer cell populations responsible for treatment failure will lead to better outcomes for patients. We herein highlight a single-cell study of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) at diagnosis that revealed hidden developmentally dependent cell signaling states uniquely associated with relapse.

  View details for PubMedID 30263942

• Cost-Effectiveness of Chimeric Antigen Receptor T-Cell Therapy in Relapsed or Refractory Pediatric B-Cell Acute Lymphoblastic Leukemia Journal of Clinical Oncology Lin, J., Lerman, B. J., Barnes, J., Boursiquot, B., Tan, Y., Robinson, A., Davis, K., Owens, D., Goldhaber-Fiebert, J. 2018

  View details for DOI 10.1200/JCO.2018.79.0642

• Identity and Diversity of Human Peripheral Th and T Regulatory Cells Defined by Single-Cell Mass Cytometry JOURNAL OF IMMUNOLOGY Kunicki, M. A., Hernandez, L., Davis, K. L., Bacchetta, R., Roncarolo, M. 2018; 200 (1): 336–46

  Abstract

  Human CD3+CD4+ Th cells, FOXP3+ T regulatory (Treg) cells, and T regulatory type 1 (Tr1) cells are essential for ensuring peripheral immune response and tolerance, but the diversity of Th, Treg, and Tr1 cell subsets has not been fully characterized. Independent functional characterization of human Th1, Th2, Th17, T follicular helper (Tfh), Treg, and Tr1 cells has helped to define unique surface molecules, transcription factors, and signaling profiles for each subset. However, the adequacy of these markers to recapitulate the whole CD3+CD4+ T cell compartment remains questionable. In this study, we examined CD3+CD4+ T cell populations by single-cell mass cytometry. We characterize the CD3+CD4+ Th, Treg, and Tr1 cell populations simultaneously across 23 memory T cell-associated surface and intracellular molecules. High-dimensional analysis identified several new subsets, in addition to the already defined CD3+CD4+ Th, Treg, and Tr1 cell populations, for a total of 11 Th cell, 4 Treg, and 1 Tr1 cell subsets. Some of these subsets share markers previously thought to be selective for Treg, Th1, Th2, Th17, and Tfh cells, including CD194 (CCR4)+FOXP3+ Treg and CD183 (CXCR3)+T-bet+ Th17 cell subsets. Unsupervised clustering displayed a phenotypic organization of CD3+CD4+ T cells that confirmed their diversity but showed interrelation between the different subsets, including similarity between Th1-Th2-Tfh cell populations and Th17 cells, as well as similarity of Th2 cells with Treg cells. In conclusion, the use of single-cell mass cytometry provides a systems-level characterization of CD3+CD4+ T cells in healthy human blood, which represents an important baseline reference to investigate abnormalities of different subsets in immune-mediated pathologies.

  View details for PubMedID 29180490

• High-resolution myogenic lineage mapping by single-cell mass cytometry NATURE CELL BIOLOGY Porpiglia, E., Samusik, N., Van Ho, A. T., Cosgrove, B. D., Mai, T., Davis, K. L., Jager, A., Nolan, G. P., Bendall, S. C., Fantl, W. J., Blau, H. M. 2017; 19 (5): 558-?

  Abstract

  Muscle regeneration is a dynamic process during which cell state and identity change over time. A major roadblock has been a lack of tools to resolve a myogenic progression in vivo. Here we capitalize on a transformative technology, single-cell mass cytometry (CyTOF), to identify in vivo skeletal muscle stem cell and previously unrecognized progenitor populations that precede differentiation. We discovered two cell surface markers, CD9 and CD104, whose combined expression enabled in vivo identification and prospective isolation of stem and progenitor cells. Data analysis using the X-shift algorithm paired with single-cell force-directed layout visualization defined a molecular signature of the activated stem cell state (CD44(+)/CD98(+)/MyoD(+)) and delineated a myogenic trajectory during recovery from acute muscle injury. Our studies uncover the dynamics of skeletal muscle regeneration in vivo and pave the way for the elucidation of the regulatory networks that underlie cell-state transitions in muscle diseases and ageing.

  View details for DOI 10.1038/ncb3507

  View details for Web of Science ID 000400376100019

  View details for PubMedID 28414312

• New developments in immunotherapy for pediatric solid tumors. Current opinion in pediatrics Schultz, L. M., Majzner, R. n., Davis, K. L., Mackall, C. n. 2017

  Abstract

  Building upon preclinical advances, we are uncovering immunotherapy strategies that are translating into improved outcomes in tumor subsets. Advanced pediatric solid tumors carry poor prognoses and resultant robust efforts to apply immunotherapy advances to pediatric solid tumors are in progress. Here, we discuss recent developments in the field using mAb and mAb-based therapies including checkpoint blockade and chimeric antigen receptors (CARs).The pediatric solid tumor mAb experience targeting the diganglioside, GD2, for patients with neuroblastoma has been the most compelling to date. GD2 and alternative antigen-specific mAbs are now being incorporated into antibody-drug conjugates, bispecific antibodies and CARs for treatment of solid tumors. CARs in pediatric solid tumors have not yet achieved comparative responses to the hematologic CAR experience; however, novel strategies such as bispecific targeting, intratumoral administration and improved understanding of T-cell biology may yield enhanced CAR-efficacy. Therapeutic effect using single-agent checkpoint blocking antibodies in pediatric solid tumors also remains limited to date. Combinatorial strategies continue to hold promise and the clinical effect in tumor subsets with high antigenic burden is being explored.Pediatric immunotherapy remains at early stages of translation, yet we anticipate that with advanced technology, we will achieve widespread, efficacious use of immunotherapy for pediatric solid tumors.

  View details for DOI 10.1097/MOP.0000000000000564

  View details for PubMedID 29189429

• Checkpoint inhibition in pediatric hematologic malignancies PEDIATRIC HEMATOLOGY AND ONCOLOGY Davis, K. L., Agarwal, A. M., Verma, A. R. 2017; 34 (6-7): 379–94

  Abstract

  Immune surveillance comprising of adaptive and innate immune systems is naturally designed to eliminate cancer development; overexpression of inhibitory receptors and their ligands prevent this check and lead to evasion and hence cancer progression and metastasis. The use of tumor-specific monoclonal antibodies (MAbs) targeting these checkpoint regulators is promising and has led to this novel field of cancer immunotherapy. The first antibody directed against cytotoxic T-lymphocyte associated protein 4 (CTLA-4), ipilimumab, showed promising results in clinical trials and was approved by the US Food and Drug Administration (FDA) for the treatment of metastatic melanoma in 2011. Since then, various other immune checkpoint inhibitors are being studied in preclinical and clinical trial phases, targeting programmed-death-1 (PD-1) and its ligand programmed death ligand 1 (PD-L1), T cell lymphocyte activation gene-3 (LAG-3), and others. Results from clinical trials are promising, and currently this approach has proven effective and safe in patients with solid tumors and some hematological malignancies in adults. In general, CTLA-4 and PD-1 inhibitors are well tolerated; however, the augmented immune response enabled by this class of agents is associated with a unique group of side effects called immune-related adverse events (irAEs). Experience in pediatrics using immune checkpoint inhibitors for hematological malignancies is limited to Hodgkin's disease and non-Hodgkin's lymphoma as in the ongoing Children's Oncology Group (COG) protocol ADVL1412. Therapeutic advances in childhood leukemia and lymphoma (TACL) consortium will initiate an early phase clinical trial with PD-1 inhibitor nivolumab in relapsed/refractory acute myeloid leukemia (AML) in the next few months.

  View details for PubMedID 29190182

• Immunotherapy for acute lymphoblastic leukemia: from famine to feast BLOOD ADVANCES Davis, K. L., Mackall, C. L. 2016; 1 (3): 265–69

  Abstract

  Publisher's Note: This article has a companion Point by Jabbour and Kantarjian. Publisher's Note: Join in the discussion of these articles at Blood Advances Community Conversations.

  View details for PubMedID 29296941

  View details for PubMedCentralID PMC5737176

• Automated mapping of phenotype space with single-cell data NATURE METHODS Samusik, N., Good, Z., Spitzer, M. H., Davis, K. L., Nolan, G. P. 2016; 13 (6): 493-?

  Abstract

  Accurate identification of cell subsets in complex populations is key to discovering novelty in multidimensional single-cell experiments. We present X-shift (http://web.stanford.edu/~samusik/vortex/), an algorithm that processes data sets using fast k-nearest-neighbor estimation of cell event density and arranges populations by marker-based classification. X-shift enables automated cell-subset clustering and access to biological insights that 'prior knowledge' might prevent the researcher from discovering.

  View details for DOI 10.1038/NMETH.3863

  View details for Web of Science ID 000377480100015

  View details for PubMedID 27183440

  View details for PubMedCentralID PMC4896314

• Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis CELL Levine, J. H., Simonds, E. F., Bendall, S. C., Davis, K. L., Amir, E. D., Tadmor, M. D., Litvin, O., Fienberg, H. G., Jager, A., Zunder, E. R., Finck, R., Gedman, A. L., Radtke, I., Downing, J. R., Pe'er, D., Nolan, G. P. 2015; 162 (1): 184-197

  Abstract

  Acute myeloid leukemia (AML) manifests as phenotypically and functionally diverse cells, often within the same patient. Intratumor phenotypic and functional heterogeneity have been linked primarily by physical sorting experiments, which assume that functionally distinct subpopulations can be prospectively isolated by surface phenotypes. This assumption has proven problematic, and we therefore developed a data-driven approach. Using mass cytometry, we profiled surface and intracellular signaling proteins simultaneously in millions of healthy and leukemic cells. We developed PhenoGraph, which algorithmically defines phenotypes in high-dimensional single-cell data. PhenoGraph revealed that the surface phenotypes of leukemic blasts do not necessarily reflect their intracellular state. Using hematopoietic progenitors, we defined a signaling-based measure of cellular phenotype, which led to isolation of a gene expression signature that was predictive of survival in independent cohorts. This study presents new methods for large-scale analysis of single-cell heterogeneity and demonstrates their utility, yielding insights into AML pathophysiology.

  View details for DOI 10.1016/j.cell.2015.05.047

  View details for Web of Science ID 000357542300019

  View details for PubMedID 26095251

  View details for PubMedCentralID PMC4508757

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

  Abstract

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

  View details for DOI 10.1016/j.vaccine.2014.07.115

  View details for Web of Science ID 000343629900016

  View details for PubMedCentralID PMC4191649

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

  Abstract

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

  View details for DOI 10.1016/j.vaccine.2014.07.115

  View details for PubMedID 25203448

• Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development CELL Bendall, S. C., Davis, K. L., Amir, E. D., Tadmor, M. D., Simonds, E. F., Chen, T. J., Shenfeld, D. K., Nolan, G. P., Pe'er, D. 2014; 157 (3): 714-725

  Abstract

  Tissue regeneration is an orchestrated progression of cells from an immature state to a mature one, conventionally represented as distinctive cell subsets. A continuum of transitional cell states exists between these discrete stages. We combine the depth of single-cell mass cytometry and an algorithm developed to leverage this continuum by aligning single cells of a given lineage onto a unified trajectory that accurately predicts the developmental path de novo. Applied to human B cell lymphopoiesis, the algorithm (termed Wanderlust) constructed trajectories spanning from hematopoietic stem cells through to naive B cells. This trajectory revealed nascent fractions of B cell progenitors and aligned them with developmentally cued regulatory signaling including IL-7/STAT5 and cellular events such as immunoglobulin rearrangement, highlighting checkpoints across which regulatory signals are rewired paralleling changes in cellular state. This study provides a comprehensive analysis of human B lymphopoiesis, laying a foundation to apply this approach to other tissues and "corrupted" developmental processes including cancer.

  View details for DOI 10.1016/j.cell.2014.04.005

  View details for Web of Science ID 000335392100019

  View details for PubMedID 24766814

  View details for PubMedCentralID PMC4045247

• viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nature biotechnology Amir, E. D., Davis, K. L., Tadmor, M. D., Simonds, E. F., Levine, J. H., Bendall, S. C., Shenfeld, D. K., Krishnaswamy, S., Nolan, G. P., Pe'er, D. 2013; 31 (6): 545-552

  Abstract

  New high-dimensional, single-cell technologies offer unprecedented resolution in the analysis of heterogeneous tissues. However, because these technologies can measure dozens of parameters simultaneously in individual cells, data interpretation can be challenging. Here we present viSNE, a tool that allows one to map high-dimensional cytometry data onto two dimensions, yet conserve the high-dimensional structure of the data. viSNE plots individual cells in a visual similar to a scatter plot, while using all pairwise distances in high dimension to determine each cell's location in the plot. We integrated mass cytometry with viSNE to map healthy and cancerous bone marrow samples. Healthy bone marrow automatically maps into a consistent shape, whereas leukemia samples map into malformed shapes that are distinct from healthy bone marrow and from each other. We also use viSNE and mass cytometry to compare leukemia diagnosis and relapse samples, and to identify a rare leukemia population reminiscent of minimal residual disease. viSNE can be applied to any multi-dimensional single-cell technology.

  View details for DOI 10.1038/nbt.2594

  View details for PubMedID 23685480

• Pediatric Acute Myeloid Leukemia as Classified Using 2008 WHO Criteria: A Single-Center Experience. American journal of clinical pathology Davis, K. L., Marina, N., Arber, D. A., Ma, L., Cherry, A., Dahl, G. V., Heerema-McKenney, A. 2013; 139 (6): 818-825

  Abstract

  The classification of acute myeloid leukemia (AML) has evolved to the most recent World Health Organization (WHO) schema, which integrates genetic, morphologic, and prognostic data into a single system. However, this system was devised using adult data and how this system applies to a pediatric cohort is unknown. Performing a retrospective chart review, we examined our single-center experience with AML in 115 children and classified their leukemia using the WHO 2008 schema. We examined patient samples for mutations of FLT3, NPM1, and CEBPA. Overall survival was calculated within categories. In our pediatric population, most cases of AML had recurrent genetic abnormalities of favorable prognosis. More than 10% of patients in our series were categorized as AML, with myelodysplasia-related changes, an entity not well-described in pediatric patients. In addition, a large proportion of patients were categorized with secondary, therapy-related AML. To our knowledge, this is the first application of the WHO 2008 classification to a pediatric cohort. In comparison to adult studies, AML in the pediatric population shows a distinct distribution within the WHO 2008 classification.

  View details for DOI 10.1309/AJCP59WKRZVNHETN

  View details for PubMedID 23690127

• Ikaros: master of hematopoiesis, agent of leukemia. Therapeutic advances in hematology Davis, K. L. 2011; 2 (6): 359-368

  Abstract

  Ikaros is the founding member of a family of zinc finger transcription factors whose function during early hematopoietic development is required for differentiation into the three major hematopoietic lineages. Ikaros deletions have been described in human malignancies, particularly precursor B-cell leukemia. Deletions of this transcription factor appear to mediate leukemogenesis, although the exact mechanism is unclear. This article reviews the structure and function of Ikaros proteins in chromatin remodeling and gene expression as well as the current knowledge of Ikaros deletions in human malignancies. A new proteomic platform, mass cytometry, is introduced which allows measurements of greater than 30 parameters at the single-cell level and should thus provide a greater level of detail to unravel the mechanistic consequences of Ikaros dysfunction in leukemia.

  View details for DOI 10.1177/2040620711412419

  View details for PubMedID 23556102

  View details for PubMedCentralID PMC3573420

• Speeding the Flow Toward Personalized Therapy in Childhood Acute Leukemia PEDIATRIC BLOOD & CANCER Simonds, E. F., Davis, K. L., Lacayo, N. J. 2009; 53 (4): 525-526

  View details for DOI 10.1002/pbc.22180

  View details for Web of Science ID 000269295500001

  View details for PubMedID 19642213

• Why Are Young Infants Tested for Herpes Simplex Virus? PEDIATRIC EMERGENCY CARE Davis, K. L., Shah, S. S., Frank, G., Eppes, S. C. 2008; 24 (10): 673-678

  Abstract

  The polymerase chain reaction (PCR)-based test to detect herpes simplex virus (HSV) genome in cerebrospinal fluid (CSF) has become the test of choice for diagnosing this infection. The utility of this test in young infants undergoing sepsis evaluations is unknown.We sought to identify the factors that prompted physicians to include HSV PCR in their evaluation of young infants undergoing lumbar puncture. In addition, the impact of ordering this test on patient management was assessed.This case-control study included infants 0 to 60 days who were evaluated by lumbar puncture at the Alfred I. duPont Hospital for Children over a 5-year period. Case patients had CSF HSV PCR ordered as part of their evaluation and control patients did not.Eighty-eight case patients and 83 control patients were identified. The median patient age was 12 days and most patients (55%) were male. Both groups were similar in demographics. Herpes simplex virus infection was diagnosed by PCR in 3.4% of cases. The occurrence of a seizure (adjusted odds ratio [OR], 8.3; 95% confidence interval [CI], 1.7-41.0), the performance of CSF enteroviral PCR testing (adjusted OR, 4.7; 95% CI, 1.4-15.8), and the decision to obtain hepatic transaminases (adjusted OR, 5.6; 95% CI, 2.7-11.8) were associated with the decision to perform CSF HSV PCR testing. Use of health care resources associated with PCR testing was considerable.The occurrence of a seizure, the performance of CSF enteroviral PCR testing, and the decision to obtain hepatic transaminases were independently associated with the decision to perform CSF HSV PCR testing. Features traditionally associated with neonatal HSV infection, such as elevated numbers of CSF white blood cells or red blood cells, did not appear to influence the decision to perform CSF HSV PCR testing. The yield of testing in this population was low. Clinicians should weigh the benefits of early diagnosis in a few patients against the consequences of excessive testing in this population.

  View details for Web of Science ID 000260157500006

  View details for PubMedID 19242136