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TCRs enable traceability of CAR-T cells but impair function in dual target cell contexts [car_post_infusion]

GSE299416 Homo sapiens Expression profiling by high throughput sequencing; Other 9 samples Submitted 2025/10/06 Platform GPL24676
Summary
Chimeric antigen receptor (CAR) T cells are powerful tools against cancer and autoimmunity. CARs are typically introduced into T cells with endogenous T cell receptors (TCRs), enabling clonotype tracking. Also, CAR expression in T cells with virus-specific TCRs may enhance CAR-T efficacy. However, the functional impact of endogenous TCR activity on CAR-T behavior remains unclear. We here traced anti-CD19 CAR-T clonotypes in patients with B-cell malignancies using single-cell RNA-, TCR-, and CITE-seq. An IFNG-positive phenotype, but not short-term reactivity, predicted clinical CAR-T persistence. To test intrinsic TCR effects, we combined CAR transduction with orthotopic TCR replacement in human T cells. Inactive TCRs did not alter CAR-T function and may serve as molecular barcodes. In contrast, active TCRs modulated CAR signaling as agonists and CAR cytotoxicity as antagonists in an avidity-dependent manner, while CAR activity had no effect on TCR cytotoxicity. Therefore, spatial antigen separation alters TCR/CAR interplay with implications for therapeutic CAR-T design.
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Direct links to NCBI, no account and no request form: the whole study as GSE299416_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 9 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA1274394 and SRA study SRP591027. Searching any of these in the dataset finder brings you back here.

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