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Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remission

Nature, 2024

Bai Z., Feng B., McClory S., de Oliveira B., Diorio C., Gregoire C., Tao B., Yang L., Zhao Z., Peng L., Sferruzza G., Zhou L., Zhou X., Kerr J., Baysoy A., Su G., Yang M., Camara P., Chen S., Tang L., June C., Melenhorst J., Grupp S., Fan R.

Disease areaApplication areaSample typeProducts
Oncology
Immunotherapy
Pathophysiology
Serum
Olink Explore 3072/384

Olink Explore 3072/384

Abstract

Despite a high response rate in chimeric antigen receptor (CAR) T cell therapy for acute lymphocytic leukaemia (ALL)1–3, approximately 50% of patients relapse within the first year4–6, representing an urgent question to address in the next stage of cellular immunotherapy. Here, to investigate the molecular determinants of ultralong CAR T cell persistence, we obtained a single-cell multi-omics atlas from 695,819 pre-infusion CAR T cells at the basal level or after CAR-specific stimulation from 82 paediatric patients with ALL enrolled in the first two CAR T ALL clinical trials and 6 healthy donors. We identified that elevated type 2 functionality in CAR T infusion products is significantly associated with patients maintaining a median B cell aplasia duration of 8.4 years. Analysis of ligand–receptor interactions revealed that type 2 cells regulate a dysfunctional subset to maintain whole-population homeostasis, and the addition of IL-4 during antigen-specific activation alleviates CAR T cell dysfunction while enhancing fitness at both transcriptomic and epigenomic levels. Serial proteomic profiling of sera after treatment revealed a higher level of circulating type 2 cytokines in 5-year or 8-year relapse-free responders. In a leukaemic mouse model, type 2high CAR T cell products demonstrated superior expansion and antitumour activity, particularly after leukaemia rechallenge. Restoring antitumour efficacy in type 2low CAR T cells was attainable by enhancing their type 2 functionality, either through incorporating IL-4 into the manufacturing process or by priming manufactured CAR T products with IL-4 before infusion. Our findings provide insights into the mediators of durable CAR T therapy response and suggest potential therapeutic strategies to sustain long-term remission by boosting type 2 functionality in CAR T cells.

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