Epigenetic profiling of EMT in pancreatic cancer cells (RNA-seq)

Epithelial plasticity – reversible modulation of a cell’s epithelial and mesenchymal features – is associated with cancer metastasis and chemoresistance. This process is classically driven by a small cohort of transcription factors, several of which have been reported to functionally interact with epigenetic modifiers at the promoters of key epithelial and mesenchymal genes. However, the extent to which epigenetic changes underlie epithelial plasticity at the genomic level remains largely unknown. Here we show that genome-wide regulation of a single histone mark, H3K36me2, is critical for establishing stable epithelial-mesenchymal states in various genetic, chemical, and cellular contexts. Through targeted CRISPR-Cas9 screening, we discovered two histone-modifying enzymes involved in the writing and erasing of H3K36me2 that act reciprocally to regulate epithelial-mesenchymal identity, tumor differentiation, and metastasis. Using genetic approaches to inhibit H3K36me2, we found that modulation of the mark itself is a conserved mechanism underlying the mesenchymal state. Although H3K36me2 is distributed broadly throughout the genome, it is associated with altered enhancer activity affecting a relatively small number of genes, including those associated with master epithelial-mesenchymal regulatory factors. Our results thus outline an epigenome-scale mechanism by which a specific histone modification regulates cellular plasticity in cancer. 28 samples were sequenced with duplicates. Samples include wild type, sgNsd2, sgKdm2a, and Tgf-b treatment.