Fig. 3. Greater tumor cell-intrinsic immune program induction and MAPK pathway inhibition in patients with better outcome.

a, t-distributed stochastic neighbor embedding plot of 419,551 cells color coded for the indicated cell type. ILC, innate lymphoid cell; NK, natural killer cell; Tgd, gamma-delta T cell; Tprolif, proliferating T cell. b, Percentage of indicated cell types (on- versus pretreatment biopsies) in patients with PFS > 6 months (n = 11) and patients with PFS < 6 months (n = 12; two-tailed Wilcoxon rank sum tests). c, Volcano plots showing upregulated and downregulated DEGs (on treatment versus pretreatment) in tumor epithelial cells of patients with PFS > 6 months and PFS < 6 months. Black dots on the volcano plots indicate adjusted P < 0.05 (two-tailed Wilcoxon rank sum test) and log₂FC ≥ 1. Significant DEGs involved in antigen processing and presentation (gold), the IFN pathway (red) and chemokine activity (blue) are labeled. d, log₂FC (on treatment versus pretreatment) of expression of ISGs involved in indicated immune pathways in tumor epithelial cells of patients with PFS > 6 months and PFS < 6 months. e, Enriched immune-related Gene Ontology terms in tumor epithelial cells of patients with PFS > 6 months and PFS < 6 months. Dotted line indicates false discovery rate (FDR) = 0.05. ‘Ag’ denotes antigen. f–h, Changes of epithelial ISG score (on treatment versus pretreatment) (f), pEpiTd19 ISG score (on treatment versus pretreatment) (g) and MAPK score (on treatment versus pretreatment) (h) in tumor epithelial cells of patients with PFS > 6 months (n = 9) and PFS < 6 months (n = 10; Wilcoxon signed rank test).