Fig. 4. Differential transcription factor binding after PD-1 pathway block-ade contributes to an altered transcriptional network during TEX reinvigoration.
(A) Enrichment of TF binding motifs in OCRs lost or gained after anti-PD-L1 treatment. (B) Wellington bootstrap analysis of TF binding in pairwise comparisons for each cell type; the top 10 TFs (in boxes) enriched in all OCRs are shown. Full list in table S10. (C) TF footprint for NFATc1 in TEX and NFκB-p65 in anti-PD-L1–treated TEX. (D) Integrated network analysis of the transcriptional and epigenetic changes after anti-PD-L1 treatment. Lines connect TFs predicted to have altered activity to corresponding genes regulated. Details in table S11. (E) LFC of genes significantly changed by anti-PD-L1 treatment compared to genes significantly induced by the “partnerless” NFAT construct CA-RIT-NFAT1 (30). (F) Venn diagram showing genes near OCRs containing given TF motifs in TEFF, TEX, or both (overlap) (top left). Percentage difference in TF target genes changed (P < 0.05, LFC ≥ 0.3) with anti-PD-L1 in overlap compared to TEX only (bottom left). Sum of the absolute value of the LFC in expression in TF target genes after anti-PD-L1 treatment (right). ATAC-seq data shown are combined replicates for each condition.