Pan-cancer assessment of the tumour and systemic T-cell receptor repertoire dynamics in patients treated with pembrolizumab
T-cells are the cellular underpinnings of response to immune checkpoint blockade (ICB) cancer treatments. Therefore, profiling the T-cell receptor (TCR) repertoires of both tumour and systemic immunity to characterize their pre- and on-ICB clonal composition and specificity landscape is required to identify features associated with clinical benefit from ICB. We sequenced TCR complementary determining region 3 (CDR3s) of 438 specimens collected from a cohort of 81 patients with advanced solid tumours before and during treatment with the ICB pembrolizumab (NCT02644369; 59 tumours, 306 peripheral blood mononuclear cell collections (PBMC), and 73 cell-free DNA samples). We demonstrated that head and neck squamous cell carcinoma (SCCHN) patients had a significantly lower PBMC diversity compared to other cancer types and demonstrated shorter persistence of ICB-induced clonal shifts compared to other cancer types. Tumours with low TCR diversity at baseline that remained unchanged or decreased while on treatment all failed to respond. Specificity analysis of tumour TCRs using the grouping of lymphocyte interactions with paratope hotspots II (GLIPHII) algorithm identified non-microbial specificity signatures that were shared among patients, highlighting convergence of CDR3 sequences in pan-cancer contexts. Tumour-derived CDR3s were significantly enriched in cfDNA repertoires compared to PBMCs (7.11% versus 1.72% at baseline, 16.2% versus 1.85% at cycle 3), despite the diversity of cell-free TCR repertories being a two orders of magnitude lower than PBMCs. Tumour/cfDNA overlapping TCRs were longitudinally persistent in PBMCs beyond 50 weeks of treatment with PD-1 blockade. In addition to exact CDR3s, we also showed sharing of GLIPHII-defined specificity signatures between tumour and cfDNA repertoires, suggesting cell-free DNA TCR repertoires are enriched for clonotypes contributing to anti-tumour immune surveillance. Future studies are warranted to establish clinical utility of cfDNA for non-invasive detection and monitoring of cancer-associated T-cells.