Figure 2.

CD8⁺ T cell exhaustion states are differentially remodeled by ICB

(A) UMAP of lymphoid cells captured across all lesions, colored and labeled by cell type. Bar plots show cell-type proportions grouped by ICB treatment history.

(B) Heatmap of scaled normalized expression for cell-type-defining genes as determined by two-sided Wilcoxon rank-sum test with Bonferroni FDR correction (q < 0.01).

(C) UMAP of CD8⁺ T cell subtypes, followed by expression heatmaps in UMAP space of co-inhibitory receptors, exhaustion markers, and memory-associated genes.

(D) Heatmaps in UMAP space of VISION signature scores for terminally exhausted and progenitor exhausted CD8⁺ T cells.

(E) Signature score distributions for terminally exhausted and progenitor exhausted CD8⁺ T cell signatures within each CD8⁺ T cell subtype. Significance of differential signature enrichment (p value) between subtypes was determined by two-sided Wilcoxon rank-sum test. Boxplots include centerline, median; box limits, upper and lower quartiles; and whiskers extending at most 1.5× the interquartile range past upper and lower quartiles.

(F) Heatmap of differential gene expression q values (two-sided Wilcoxon rank-sum test with Bonferroni FDR correction) for comparisons of cells within each CD8⁺ T cell cluster from ICB-exposed versus ICB-naive patients.

(G) Gene set enrichment analysis (GSEA) of terminally exhausted and progenitor exhausted signatures in 4-1BB-Lo CD8⁺ T cells from ICB PR patients compared with ICB SD/PD patients.

(H) Signature scores for an ICB-exposed 4-1BB-Lo CD8⁺ T cell signature and expression values for individual genes in paired pre-/on-ICB bulk RNA-seq samples in the Checkmate 009 RCC cohort. Expression values for individual genes were normalized against total CD8 fraction per sample as inferred by CIBERSORTx. Significance of differential signature enrichment or expression (p value) was determined by paired two-sided Wilcoxon rank-sum test. Boxplots include centerline, median; box limits, upper and lower quartiles; and whiskers extending at most 1.5× the interquartile range past upper and lower quartiles.

^∗∗∗p < 0.001, two-sided Wilcoxon rank-sum test. See also Figures S2 and S3, Table S2.