Extended Data Fig. 6: KLF5 facilitates enhanced SOX2 activity in squamous tumorigenesis.
From: Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence
a, SOX2-KLF5 interaction, shown by co-IP of SOX2 (top) and KLF5 (bottom), followed by immunoblotting in human ESCC cell line TE10, TT and KYSE70. b, Overlap of binding sites gained in SCPP (vs. Normal) by Sox2 and Klf5 ChIP-seq. P < 0.0001; two-sided fisher exact test with unchanged Klf5 binding sites as control. c, Percentage of gained super-enhancers in SCPP (from Fig. 3b) with Klf5 ChIP-seq occupancy. d, Immunoblots of Klf5 and Sox2 after shRNA-mediated Sox2 silencing in SCPP (representative image from 2 independent experiments). e, Overlap of downregulated genes upon shSOX2 and shKLF5 in KYSE70 (Left) and TT (Right). P < 0.0001; two-sided fisher exact test with shKLF5 unchanged genes as control. f, Genes that are significant down-regulated by shKLF5 in ESCC cell lines as a ‘Gene Set’ with GSEA to quantify their expression differences with shSOX2 in KYSE70 (Left) and TT (Right) with two-sided FDR-adjusted q-value<0.0001; nominal p < 0.0001 calculated using the GSEA package. g, Differential expression level of 95 genes regulated by SOX2 and KLF5 (genes down-regulated by shSOX2 and shKLF5 in KYSE70 and TT) in TCGA ESCC (Esophageal squamous cell carcinoma) EAC (Esophageal adenocarcinoma) and Normal esophagus samples. P < 0.0001 **** by two-sided t-tests. Boxes indicate interquartile range, and whiskers show maximum and minimum values. Horizontal line, median. h, Genes regulated by SOX2 and KLF5 in ESCC cell lines as a ‘Gene Set’ with GSEA to measure their expression differences between ESCC vs EAC (Top) and ESCC vs Normal (Bottom) with two-sided FDR-adjusted q-value<0.0001; nominal p < 0.0001 calculated using the GSEA package. i, Overlap between SOX2/KLF5 putative target genes and significantly downregulated genes upon shSOX2 (left) and shKLF5 (right) in KYSE70 (top) and TT (bottom). SOX2/KLF5 target genes are defined by intersection of 1) Significantly upregulated genes in SCPP vs Normal; 2) Genes that gain Sox2 and Klf5 binding sites in SCPP vs Normal. P-value; two-sided fisher exact test with SOX2/KLF5 unrelated genes as control.
