A Histone-Centric Multi-Omics Study Shows that Increased H3K4 Methylation Sustains Triple Negative Breast Cancer Phenotypes
Altered histone post-translational modifications are frequently associated with cancer. Here, we applied mass-spectrometry to study the epigenetic landscapes of breast cancer subtypes, with a particular focus on triple-negative breast cancers (TNBCs), a heterogeneous group lacking welldefined molecular targets and effective therapies. The analysis of over 150 tumors revealed epigenetic signatures that discriminate TNBCs from the other BC subtypes, and that distinguish TNBC patients with different prognoses. Employing a multi-OMICs approach integrating epigenomics, transcriptomics, and proteomics data, we investigated the mechanistic role of increased H3K4 methylation in TNBCs, demonstrating that H3K4me2 sustains the expression of genes associated with the TNBC phenotype. Through CRISPR-mediated editing, we established a causal relationship between H3K4me2 and gene expression for several targets. Furthermore, treatment with H3K4 methyltransferase inhibitors reduced TNBC cell growth in vitro and in vivo. Collectively, our result unraveled a novel epigenetic pathway implicated in TNBC pathogenesis and suggests new opportunities for targeted therapy. Overall design: ChIP-seq data of the histone modification H3K4me2 in MDA-MB-231 cell line. Cells were treated with the OICR-9429 inhibitor (antagonist of the WDR5 domain), with DMSO or untreated. For the quantitative comparison between cells treated with the inhibitor and cells treated with DMSO, 5% Drosophila spike-in was added before the incubation with antibodies.