Integrative single-cell multi-omics of CD19-CAR pos and CAR neg T cells suggest drivers of immunotherapy response in B cell neoplasias.

The impact of phenotypic, clonal, and functional heterogeneity of chimeric antigen receptor (CAR)-T cells on clinical outcome remains understudied. Here, we integrate clonal kinetics with transcriptomic heterogeneity resolved by single-cell omics to interrogate cellular dynamics of non-transduced (CAR ^neg ) and transduced (CAR ^pos ) T cells, in the infusion product (IP) and at the CAR-T cell expansion peak in five B cell acute lymphoblastic leukemia (B-ALL) patients treated with CD19CAR-T cells (varni-cel). We identify significant differences in cellular dynamics in response to therapy. CAR ^pos T cells at IP of complete response patients exhibit a significantly higher CD4:CD8 ratio, validated in a larger cohort B-ALL patients (n = 47). Conversely, at the expansion peak, there is a clonal expansion of CD8 ⁺ effector memory and cytotoxic T cells. Cytotoxic CAR ^pos γδ-T cells expansion correlates with treatment efficacy validated in a cohort of B-ALL (n = 18) and diffuse large B cell lymphoma (DLBCL) patients (n = 58). Our data provide insights into the complexity of T cell responses following CAR-T cell therapy and suggest drivers of immunotherapy response.
Competing Interests: Declaration of interests P.M. is a founder of the spin-off OneChain ImmunoTx, which has no connection with the present research. V.O.-M. reports honoraria and/or consulting fees from BMS/Celgene, Novartis, Gilead/Kite, Miltenyi Biomedicine, Pfizer, and Janssen. A.M.G.-S. reports honoraria and/or consulting fees from Roche, BMS/Celgene, Kyowa Kirin, Novartis, Gilead/Kite, Incyte, Lilly, ADC Therapeutics America, Miltenyi, Ideogen, AbbVie, and Sobi.
(Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)