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.

组蛋白翻译后修饰异常常与癌症密切相关。本研究采用质谱法探究乳腺癌亚型的表观遗传图谱，重点关注三阴性乳腺癌（triple-negative breast cancers, TNBCs）——这是一类缺乏明确分子靶点与有效治疗手段的异质性肿瘤群体。通过对150余例肿瘤样本的分析，本研究鉴定出可区分三阴性乳腺癌与其他乳腺癌亚型的表观遗传特征，同时可区分预后不同的三阴性乳腺癌患者。本研究采用整合表观基因组学、转录组学与蛋白质组学数据的多组学方法，探究了三阴性乳腺癌中H3K4甲基化水平升高的机制作用，证实H3K4me2可维持与三阴性乳腺癌表型相关的基因表达。通过CRISPR介导的基因编辑技术，本研究明确了多个靶点的H3K4me2水平与基因表达之间的因果关联。此外，使用H3K4甲基转移酶抑制剂处理可在体外与体内抑制三阴性乳腺癌细胞的增殖。综上，本研究揭示了一条参与三阴性乳腺癌发病机制的全新表观遗传通路，为靶向治疗提供了新的思路。实验整体设计：获取MDA-MB-231细胞系中组蛋白修饰H3K4me2的染色质免疫共沉淀测序（ChIP-seq）数据。实验分为三组：使用OICR-9429抑制剂（WDR5结构域拮抗剂）处理细胞、二甲基亚砜（DMSO）处理细胞以及未处理细胞。为实现抑制剂处理组与DMSO处理组细胞的定量比较，在抗体孵育前加入5%的果蝇掺入对照样本。