Research Identifies Cell Signatures of CAR T-Cells in Long Remission

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Cells from patients with ALL treated in the CARPALL study were analyzed and sequenced.

Recent research has elucidated characteristics of persistent chimeric antigen receptor (CAR) T-cells which contribute to long-lived responses in treated patients with relapsed and refractory childhood pre-B cell acute lymphoblastic leukemia (R/R B-ALL).1

“The molecular features underpinning CAR-T cell persistence in our study remain unknown. We reasoned that single-cell transcriptomic assays may help elucidate these features. To date, other CAR-T cell products in patients have been studied at the resolution of single cells. However, the persistence of CAR T-cells in these studies was generally limited to 3 months,” first author Nathaniel Anderson, PhD, Marie Skłodowska-Curie Fellow, Wellcome Sanger Institute, and colleagues wrote.1

Anderson and colleagues studied 15 consecutive patients with high-risk or relapsed CD19+ B-ALL treated with CD19 CAR-T cell therapy on the CARPALL study (NCT02443831) and in whom adequate CAR-T cells could be isolated for subsequent analyses from cryopreserved samples of blood or bone marrow by flow cytometry using CD3 and CAR expression, before single-cell sequencing. The researchers also obtained sufficient CAR-T cells were obtained for further interrogation by single-cell mRNA and T cell receptor sequencing at early, mid, and late timepoints in 10 children.The research used Chromium Single Cell Gene Expression technology from company 10x Genomics in their sequencing and analysis.

READ MORE: Multi-Base–Edited CAR T-Cell Therapy Trial Doses First Patient With R/R T-ALL/T-LL

"This study is a fantastic step forward in our understanding of CAR T-cell persistence and illustrates the power of collaborative science and combining pioneering clinical research with cutting-edge genomic science. It is crucial that we continue to develop and build on these new treatments to help more children with leukemia across the world,” cosenior author Sam Behjati, PhD, Group Lead and Wellcome Senior Research Fellow, Wellcome Sanger Institute and Honorary Consultant Paediatric Oncologist, Addenbrooke's Hospital, Cambridge, said in a statement issued by 10x Genomics.2

After studying around 50,000 CAR T-cells, the researchers found that CD8+ T cells were the predominant CAR-T cells in most cases, until late timepoints in which persisting CAR-T populations were predominantly double-negative (CD4- and CD8-) T cells.1 This persistence signature was dominant among circulating CAR-T cells in all 4 children evaluated with a long-lived treatment response for which sequencing data were sufficient. The signature was also present across different T cell subsets and clonotypes and was detected in 2 adult patients with chronic lymphocytic leukemia with decade-long remissions who received a different CD19 CAR-T cell product than what was used in the CARPALL study. This led the authors to conclude that persisting CAR-T cells converge transcriptionally and that there may be a universal transcriptional signature of clinically effective, persistent CD19 CAR-T cells

“A lack of CAR-T cell persistence leading to CD19+ relapse is the main cause of therapy failure after licensed CAR-T cell therapy for ALL and contributes to relapse in other B cell malignancies, such as myeloma. Therefore, a key question of CAR-T cell biology is why some cells persist whereas others perish. With this knowledge, we might better understand how to select patients, modify treatment phasing and optimize manufacturing protocols to support greater persistence and improve outcomes,” Anderson and colleagues concluded.1

REFERENCES
1. Anderson NA, Birch J, Accogli T, et al. Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia. Nat Med. (2023)29, 1700–1709. doi: 10.1038/s41591-023-02415-3
2. CAR T-Cell Study Enabled by 10x Genomics Single Cell Technology Published in Nature Medicine. News release. 10x Genomics. July 6, 2023. https://prnmedia.prnewswire.com/news-releases/car-t-cell-study-enabled-by-10x-genomics-single-cell-technology-published-in-nature-medicine-301870534.html
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