Single-cell multiomics reveals regulatory mechanisms of CAR T-cell persistence and dysfunction in multiple myeloma.

Abstract

Understanding the mechanisms that drive chimeric antigen receptor (CAR) T-cell function and persistence in multiple myeloma (MM) remains a critical challenge for improving therapeutic outcomes. In this study, we applied single-cell multiomics and gene regulatory network analysis to characterize the transcriptional dynamics and clonal evolution of B-cell maturation antigen-targeted CAR T-cells in longitudinally collected bone marrow (BM) and peripheral blood (PB) samples from patients with MM. Our results revealed that CAR T cells infiltrating BM exhibited a more activated and exhausted phenotype than their PB counterparts, with key transcriptional regulators driving these changes. Dysregulation in the effector-to-memory transition led to increased presence of terminally differentiated CAR T-cells, correlating with poor persistence. Additionally, we identified a hyperexpanded CAR T-cell clone in the BM of a patient in partial response, marked by elevated interleukin-10 (IL-10) expression. Functional analyses demonstrated that stimulation of endogenous T-cell receptor (TCR) enhanced IL-10 production, potentially contributing to impaired CAR T-cell proliferation and persistence. These findings uncover regulatory mechanisms influencing CAR T-cell dynamics, offering new insights into improving CAR T-cell persistence and therapeutic efficacy in MM, and highlight potential molecular targets for optimizing CAR T-cell therapy in patients with MM.