Extended Data Fig. 1: Characterization of tumor-specific CD8 T cells.
a, Volcano plot showing differentially expressed genes between bystander CD8 T cells and tumor-reactive CD8 T cells from post-ICB non-responsive tumors; N = 6 tumors. Each red dot denotes an individual gene with adjusted P value < 0.01 (two-sided t-test) and fold change ≥ 0.2. b, Volcano plot showing differentially expressed genes between bystander CD8 T cells and tumor-reactive CD8 T cells from N = 13 treatment-naïve tumors. Each red dot denotes an individual gene with adjusted P value < 0.01 (two-sided t-test) and fold change ≥ 0.2. c, Gene expression heatmap for tumor-specific and bystander CD8 T cells. The tumor-reactive CD8 T cells shown here were from N = 13 treatment-naive tumors. d, Average CXCL13 expression in bystander CD8 T cell clones and qualified (clonal size > 3; left) and all (right) tumor-specific CD8 T cell clones from treatment-naïve and post-ICB non-responsive (NR) tumors; N = 19 tumors. e, Performance summary of the CXCL13-selection-based strategy in identifying tumor-reactive CD8 T cells in terms of the clone and cell numbers, corresponding to d. f-h, UMAP plots showing the expression levels of certain signature genes in the three CD8 T cell groups; N = 7 tumors. i, Gene expression heatmap for tumor-specific and bystander CD8 T cells from pre- and post-treatment responsive lung tumors (Liu et al. NSCLC data); N = 7 tumors for both left and right panels.
