Abstract 882: Harnessing single cell multi-omics data to identify predictors of clinical outcome in CD19 CAR T cell therapy

Abstract

Abstract Background: Chimeric antigen receptor (CAR) T cell therapy is effective in treating B-cell malignancies, but factors influencing the persistence of functional CAR+ T cells, such as product composition, patients’ lymphodepletion, and immune reconstitution, are not well understood. To shed light on this issue, we conducted single-cell multi-omics analysis of transcriptional, clonal, and phenotypic profiles from pre- to 1-month post-infusion of CAR+ and CAR− T cells from patients who received a donor-derived 4-1BB CAR product targeting CD19. Methods: Longitudinal blood samples and infusion products were obtained from 10 individuals with large B cell lymphoma or B-cell acute lymphoblastic leukemia (CARTELL cohort in Sydney Australia1). CD45+ cells and enriched CAR+ T cells were single cell sorted for simultaneous scRNA-seq, 41 barcoded proteins (N=41) and T cell receptors, n= 115,000 cells across 21 samples. Machine learning methods were used to identify subsets of immune cells associated with clinically relevant parameters. Results: Following infusion, CAR+ and CAR− T cells showed similar differentiation profiles with clonally expanded populations across heterogeneous phenotypes, demonstrating clonal lineages and phenotypic plasticity. These findings were validated by performing the same analysis on two publicly available scRNA-seq data sets from two cohorts 2, 3 of paediatric (N=18) and adult (N=32) individual with large B cell lymphoma who received CAR19 T cells. Analysis of mass-cytometry data from our cohort and from 28 patients with B cell lymphoma treated with commercial CAR19 T cells (axi-cel)4, identified an association of CAR− and also CAR+ T cells, both expressing an 2B4− CD11b+ CD8+ phenotype, with complete remission or progressive disease at 3 and 6 months post-infusion. Finally, we report additional analysis on the immunogenomics of circulating CAR T cells in two patients who developed CAR T cell induced lymphoma and compared it with ascites and CAR-Lymphoma cells. Discussion: These results suggest that CAR+ and CAR− CD8+ T cells share a differentiation trajectory terminating in an NK-like phenotype that is associated with clinical outcome, and that non-CAR-derived signals may influence patients’ immune recovery and outcomes.