H3K9me3, H3K27me3, H3K27ac and H3K4me3 ChIP-sequencing in SUM159PT NNMT-WT, NNMT-KOd and NNMT KOs breast cancer cells.

The cellular heterogeneity within a tumor can be determined by core genetic and epigenetic programs that operate in certain cells (tumor initiating cells – TICs), providing them with the degree of plasticity needed for induction of metastasis and resistance to therapy. Here we show that the metabolic enzyme nicotinamide N-methyl transferase (NNMT) promotes TIC plasticity in Estrogen Receptor (ER) alpha negative breast cancer. NNMT downregulation delays tumor formation and its full depletion impairs metastasis formation in mice. Mechanistically, NNMT loss increases deposition of H3K9-me2/3 and H3K27-me3 at the promoter of genes involved in stem cell regulation, shutting down their expression and upregulating luminal differentiation genes. This study reveals a major function of NNMT in maintaining core epigenetic programmes that promote TIC self-renewal and metastasis and that repress luminal differentiation. Overall design: These sequencing files include data from pulldowns of acetylated H3K27, trimethylated H3K27, H3K4 and H3K9 and the respective input samples. The cohort includes 3 biological samples derived from SUM159PT cells where NNMT expression has not been modified (WT) or it has been deleted by CRISPR-Cas9 using two different KO strategies (described in the correspondent reference and below), KOd and KOs. Each biological sample has been cultured and processed 3 independent times (1, 2 and 3): triplicates. NNMT was knocked out SUM159PT using two different strategies: one single guide (sg) RNA targeting the transcription start site (KOs) and two sgRNAs that generate a deletion of exon 1 (KOd). Several clones from each strategy were mixed to generate two oligoclonal pools of cells, KOd and KOs.