Mutations and copy number (CN) variants are associated with distinct Mes-like and Epi-like TF activation in GC. (A) Nonsynonymous CDH1 mutation status separates TFs with differential expression between Mes-like and Epi-like cell lines. Shown is TCGA-STAD expression in tumors with and without a CDH1 nonsynonymous mutation (t-test P < 0.05 and |log2FC| > 0.25). (B) Human TFs ranked in order of DNA CN alteration rate in TCGA-STAD primary tumors. (C) Chromatin accessibility landscape and TF binding of ZEB1 and SMAD4 in the GATA6 locus. GATA6_E1 and GATA6_E2 are putative Epi-like and normal stomach enhancers, where GATA6 binds in GATA6 ChIP-seq in AGS GC cell line. (D) GATA4 has reduced CN in non-Epi cell lines, and MAPK9 has amplified CN in non-Epi cell lines. Average CN differences between Epi GC cell lines and non-Epi (Mes and Intermediate) GC cell lines are shown for protein-coding genes whose expression and CN correlate. CN values are obtained by DNA sequencing, in which “−2” marks deep DNA deletion, “0” shows a normal diploid genome, and “+2” is for deep DNA amplification in the gene locus. Mann–Whitney U test P < 0.05. (E) CN variation is consistent with altered GATA4 and MAPK9 expression across samples. r is the Pearson's correlation between CN scores and gene expression.
