CD19-targeted CAR-T infusion products administered to pediatric B-ALL patients were transcriptionally heterogeneous and comprised two populations: HMGB2 (proliferating) and LTB (activated). CSF2 marked cells that expanded upon CAR stimulation. Low TH2 signaling (e.g., IL4, IL5, GATA3) in CAR-stimulated (but not TCR-stimulated or unstimulated) CAR+ cells predicted CD19+ disease relapse. Increased proportions of stem-like and central memory T cells and decreased effector memory cells associated with complete response. A model integrating these features displayed predictive potential (with ~70% sensitivity) of disease relapse in B-ALL.

Contributed by Alex Najibi

ABSTRACT: A notable number of acute lymphoblastic leukemia (ALL) patients develop CD19-positive relapse within 1 year after receiving chimeric antigen receptor (CAR) T cell therapy. It remains unclear if the long-term response is associated with the characteristics of CAR T cells in infusion products, hindering the identification of biomarkers to predict therapeutic outcomes. Here, we present 101,326 single-cell transcriptomes and surface protein landscape from the infusion products of 12 ALL patients. We observed substantial heterogeneity in the antigen-specific activation states, among which a deficiency of T helper 2 function was associated with CD19-positive relapse compared with durable responders (remission, >54 months). Proteomic data revealed that the frequency of early memory T cells, rather than activation or coinhibitory signatures, could distinguish the relapse. These findings were corroborated by independent functional profiling of 49 patients, and an integrative model was developed to predict the response. Our data unveil the molecular mechanisms that may inform strategies to boost specific T cell function to maintain long-term remission.

Author Info: (1) Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA. (2) Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania

Author Info: (1) Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA. (2) Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA. (3) Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA 19104, USA. Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA. (4) Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. (5) Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA. (6) Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA. (7) Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. (8) Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA. (9) Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. (10) Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA. (11) Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA. (12) Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. (13) Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. (14) Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA. (15) Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA 19104, USA. (16) Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA. Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA. Human and Translational Immunology, Yale School of Medicine, New Haven, CT 06520, USA. (17) Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA. (18) Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Parker Institute for Cancer Immunotherapy at University of Pennsylvania, Philadelphia, PA 19104, USA. Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA.