Extended Data Fig. 3: Activated enhancers in ICB-resistant cancer cells.
A. Spearman pairwise correlation of RNA and ATAC libraries. Heatmap is hierarchically clustered. B. PCA of H3K4me3, H3K27ac, and H3K4me1 signals for B16 and Res 499 cells with or without Stat1 knockout (SKO) sorted from in vivo tumors (n = 2 mice per group). C. Strategy for integrated annotation of putative regulatory elements. D. Summary profiles of H3K4me3, H3K27ac, and ATAC signal intensity over activated or deactivated promoters and enhancers (n = 2 mice per condition for H3K4me3 and H3K27ac assays; n = 5 mice per condition for ATAC assay). E. Genomic regions where Res 499 activated or deactivated regulatory elements reside. Only regulatory elements with significant differences in H3K27ac, H3K4me3, or ATAC signal intensity are included (FDR < 0.05). F. Example tracks for activated enhancers in Res 499 that are either pre-existing (left) or de novo activated (right). G. Enriched PANTHER pathways for genes located within a 50 Kb cis-regulatory window of Res 499 activated enhancers. P-values determined by Fisher’s exact test and FDR calculated by the Benjamini-Hochberg procedure. All pathways shown are significant with FDR < 0.01. H. Chromatin accessibility of the subset of Res 499 activated enhancers induced by chronic IFNG signaling (900 out of 3,738 enhancers) in cancer cells sorted from the indicated in vivo tumors (n = 3 mice per condition), where each row represents a chronic IFNG-induced enhancer. Summary enrichment scores for these loci are shown in Fig. 2i. B16 tumors were treated with IFNG in vitro for 6 hours (acute) or 3.5 weeks (chronic) prior to implantation into syngeneic mice. I. Enrichment of archetype motifs in Res 499 activated enhancers that are chronic IFNG-induced or not. P-values are color-coded and larger circle sizes indicate greater significance. TF motifs highlighted in red are associated with IFN signaling, TF motifs highlighted in blue are associated with inflammatory memory. J. Normalized ATAC-seq insertion counts at DNA footprints with ISRE motifs in B16 or Res 499 cells.
