Integrative single-cell multi-omics of CD19CARpos and CARneg T cells suggest drivers of immunotherapy response in B-cell neoplasias

Abstract

How phenotypic, clonal, and functional heterogeneity of CAR-T-cells impact clinical outcomes remain understudied. Here, we integrated clonal kinetics with transcriptomic heterogeneity resolved by single-cell omics to explore cellular dynamics response of both non-transduced (CARneg) and transduced (CARpos)T-cells. CARneg and CARposT-cells were longitudinally interrogated in the manufactured infusion product (IP) and in-vivo at CAR-T cell expansion peak in five B-ALL patients treated with CD19CAR-T-cells (varni-cel). Significant differences were found in the cellular dynamics between CARpos and CARnegT-cells in response to therapy. CARposT-cells in the IP exhibited a significant higher CD4:CD8 ratio than CARnegT-cells, and the CD4:CD8 CARposT-cell composition impacted therapy outcome as confirmed in a larger cohort of 24 varni-cel-treated B-ALL patients. Conversely, an inverted trend in the CD4:CD8 CARposT-cell ratio was consistently observed at the expansion peak, with clonally expanding CD8+ effector memory and cytotoxic T-cells being the most abundant populations. Expanded cytotoxic CARpos{gamma}{delta}T cells emerged at the expansion peak, and the extent of their in-vivo expansion positively correlated with treatment efficacy, which was validated in a large cohort of B-ALL patients (n=18) treated with varni-cell and B-cell lymphoma patients (n=58) treated with either lisa-cel or axi-cel. Our data provide insights into the complexity and diversity of T-cell responses following CAR-T cell therapy and suggest drivers of immunotherapy response.