Fig. 5

ICB-resistant clones show different transcriptional signatures associated with T cell dysfunction. a PCA of RNA-seq data from parental line CT26 and ICB-resistant lines B04 and B64 suggests distinct expression profiles between the three lines. b Heatmap of relative expression of the top differentially expressed genes between the resistant lines and the parental line. c Cistrome GO enrichment of pathways up- or downregulated in line B04 compared to the parental line, integrating RNA-seq and ATAC-seq data. d Immune response-related genes Slurp1 and Tmem176b have higher RNA expression (barplot on the left) and genomic DNA accessibility (alignment plot on the right) in line B04 compared to the parental line. e Top transcription regulators in line B04 compared to the parental line, inferred from RNA-seq (by LISA) or ATAC-seq (by CistromeDB). f GR and its targets are expressed higher in line B04 compared to the parental line. Each individual value and mean ± SD are plotted for each group. g Cistrome GO enrichment of pathways up- or downregulated in line B64 compared to the parental line, integrating RNA-seq and ATAC-seq data. h Immune response-related genes Ifit1 and H2-T23 have higher RNA expression (barplot on the left) and genomic DNA accessibility (alignment plot on the right) in line B64 compared to the parental line. i GSEA shows upregulation of genes induced by long-term IFNγ induction (gene set derived from Benci et al. [15]). Each vertical black line represents a gene upregulated by long-term IFNγ induction in the Benci et al. study