Lewis Au, Emine Hatipoglu, Marc Robert de Massy, Kevin Litchfield, Andrew Rowan, Rachael Thompson, Desiree Schnidrig, Fiona Byrne, Gordon Beattie, Stuart Horswell, Nicos Fotiadis, Steve Hazell, David Nicol, Scott Shepherd, Annika Fendler, Robert Mason, Jan Attig, Kroopa Joshi, Imran Uddin, Pablo Becker, Mariana Werner Sunderland, Ayse Akarca, Ignazio Puccio, William Yang, Tom Lund, Kim Dhillon, Marcos Duran Vasquez, Ehsan Ghorani, Hang Xu, José Ignacio López, Anna Green, Ula Mahadeva, Elaine Borg, Miriam Mitchinson, David Moore, Ian Proctor, Mary Falzon, Andrew Furness, Lisa Pickering, James L. Reading, Roberto Salgado, Teresa Marafioti, Mariam Jamal-Hanjani, PEACE Consortium, George Kassiotis, Benny Chain, James Larkin, Charles Swanton, Sergio A. Quezada, Samra Turajlic, and TRACERx Renal Consortium
Antigen recognition and T-cell mediated cytotoxicity in clear-cell renal cell carcinoma (ccRCC) remains incompletely understood. To address this knowledge gap, we analysed 115 multiregion tumour samples collected from 15 treatment-naive patients pre- and post-nivolumab therapy, and at autopsy in three patients. We performed whole-exome sequencing, RNAseq, TCRseq, multiplex immunofluorescence and flow cytometry analyses and correlated with clinical response. We observed pre-treatment intratumoural TCR clonal expansions suggesting pre-existing immunity. Nivolumab maintained pre-treatment expanded, clustered TCR clones in responders, suggesting ongoing antigen-driven stimulation of T-cells. T-cells in responders were enriched for expanded TCF7+CD8+ T-cells and upregulated GZMK/B upon nivolumab-binding. By contrast, nivolumab promoted accumulation of new TCR clones in non-responders, replacing pre-treatment expanded clonotypes. In this dataset, mutational features did not correlate with response to nivolumab and human endogenous retrovirus expression correlated indirectly. Our data suggests that nivolumab potentiates clinical responses in ccRCC by binding pre-existing expanded CD8+ T-cells to enhance cytotoxicity.