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

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. Overall design: Lewis lung carcinoma (LLC) cells (5 × 10^5 cells /mouse) were inoculated subcutaneously (s.c.) into the left flank, right flank and the left hip of C57BL/6 mice (untreated : n=5, aLAG3 : n=6). tumors were excised sequentially in the order of left flank tumor, right flank tumor and left hip on days 14, 21 and 28. CD8+ T cells obtained from each tumor were analyzed by bulk TCR-sequencing.