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A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [bulkRNAseq]

ABSTRACT: A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [bulkRNAseq]

PROVIDER: PRJNA1294142 | ENA |

REPOSITORIES: ENA

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A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [bulkRNAseq]

Project description:Effective cancer immunotherapy relies on the clonal proliferation and expansion of CD8+ T cells in the tumor. However, our insights into clonal expansions are limited, owing to an inability to track the same clones in tumors over time. Here, we developed a multi-site tumor mouse model system to track hundreds of expanding and contracting CD8+ T cell clones over multiple timepoints in tumors of the same individual. Through coupling of clonal expansion dynamics and single-cell RNA/TCR-seq data, we identified a transcriptomic signature in PD-1+Ly108+ precursor exhausted cells that strongly predicts rates of intratumoral clone expansion. The signature correlates with expansion in mice, both with and without immunotherapies, and in patients undergoing PD-1 blockade therapy. Expression of the signature during treatment corresponds with positive clinical outcomes. Downregulation of the signature precedes clone contraction – a phase in which clones contract but maintain revivable precursor exhausted cells in the tumor. LAG-3 blockade re-activates the expansion signature, re-expanding pre-existing clones, including previously contracted clones. These findings reveal how the study of clonal expansion dynamics provide a powerful ‘pan-immunotherapy’ signature for monitoring immunotherapies with implications for their future development.

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A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [scTCR_immunotherapies]

Project description:A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [scTCR_immunotherapies]

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A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [bulkTCRseq_FTY]

Project description:A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [bulkTCRseq_FTY]

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Project description:A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [bulkTCR_control]

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Project description:A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [bulkTCR_Trilateral_similarity]