Immune checkpoint blockade sensitivity and progression-free survival associates with baseline CD8 T cell clone size and cytotoxicity.

The antitumor action of immune checkpoint blockade (ICB) is primarily mediated by CD8 T cells. How sensitivity to ICB varies across CD8 T cell subsets and clonotypes and the relationship of these with clinical outcome is unclear. To explore this, we used single-cell V(D)J and RNA-sequencing to track gene expression changes elicited by ICB across individual peripheral CD8 T cell clones, identify baseline markers of CD8 T cell clonal sensitivity, and chart how CD8 T cell transcriptional changes vary according to phenotypic subset and clonal size. We identified seven subsets of CD8 T cells with divergent reactivity to ICB and found that the cytotoxic effector subset showed the greatest number of differentially expressed genes while remaining stable in clonal size after ICB. At the level of CD8 T cell clonotypes, we found a relationship between transcriptional changes and clone size, with large clones showing a greater number of differentially regulated genes enriched for pathways including T cell receptor (TCR) signaling. Cytotoxic CD8 effector clones were more likely to persist following ICB and were more likely to correspond with public tumor-infiltrating lymphocyte clonotypes. Last, we demonstrated that individuals whose CD8 T cell pretreatment showed low cytotoxicity and had fewer expanded clones typically had worse outcomes after ICB treatment. This work further advances understanding of the molecular determinants of ICB response, assisting in the search for peripheral prognostic biomarkers and highlighting the importance of the baseline CD8 immune landscape in determining ICB response in metastatic melanoma.