Immune Checkpoint Blockade induces peripheral cytotoxicity and persistence of large effector CD8⁺ T cell clones

ABSTRACT

Immune checkpoint blockers (ICB) exert their anti-cancer effects via CD8⁺ T cells, although how responses vary over sub-populations and across clones is incompletely understood. We performed single-cell RNA-sequencing of CD8⁺ T cells and their receptors pre and post ICB across eight patients, integrating results with bulk-sequencing data (n=169). We identify seven phenotypic subsets with divergent sensitivity to ICB, finding the effector subset demonstrates the most pronounced changes. ICB response was related to clone size, with small and large clones markedly differing in the magnitude and immunological relevance of regulated genes. ICB upregulates mitotic pathways and promotes expansion and survival of larger, more cytotoxic clones. Notably, baseline cytotoxicity, but not correlates of mitosis, associated with progression-free survival; highlighting the importance of the pre-treatment CD8⁺ immune landscape in long-term response. This work further advances understanding of the molecular determinants of ICB response and assists in the search for peripheral prognostic biomarkers.