Epigenetic reprogramming at estrogen-receptor binding sites alters the 3D chromatin landscape in endocrine resistant breast cancer [ChIP-seq]

Endocrine therapy resistance invariably develops in estrogen receptor positive (ER+) breast cancer, but the underlying molecular mechanisms are largely unknown. Here, we show that 3-dimensional (3D) chromatin interactions both within and between topologically associating domains (TADs) frequently change in ER+ endocrine resistant breast cancer cells and that the differential interactions are enriched for genetic variants at CTCF-bound anchors. Ectopic chromatin interactions are preferentially enriched at active enhancers and promoters and ER binding sites and are associated with altered expression of ER-regulated genes, consistent with dynamic remodelling of ER pathways accompanying the development of endocrine resistance. Importantly, new 3D chromatin interactions often occur coincidently with hypermethylation and loss of ER binding. Additionally, alterations in active (A-type) and inactive (B-type) chromosomal compartments are also associated with decreased ER binding and atypical interactions and gene expression. Together, our results suggest that 3D epigenome remodelling is a key mechanism underlying endocrine resistance in ER+ breast cancer. Hi-C, WGS, WGBS, ChIP-seq and RNA-seq were conducted in endocrine-sensitive breast cancer cells (MCF7) and its two endocrine-resistant derivatives - tamoxifen-resistant (TAMR) cells and fulvestrant-resistant (FASR) cells.

雌激素受体阳性（ER+）乳腺癌总会发展出内分泌治疗耐药性，但其潜在分子机制在很大程度上仍未明确。本研究发现，在ER+内分泌耐药乳腺癌细胞中，拓扑关联结构域（TADs）内部及之间的三维（3D）染色质相互作用频繁发生改变，且此类差异相互作用在CTCF结合锚点处的遗传变异中显著富集。异位染色质相互作用优先富集于活性增强子、启动子及ER结合位点，并与ER调控基因的表达改变相关，这与内分泌耐药发生过程中ER通路的动态重塑相一致。值得注意的是，新型3D染色质相互作用往往与高甲基化及ER结合丧失同时发生。此外，活性（A型）与非活性（B型）染色体区室的改变也与ER结合减少、异常染色质相互作用及基因表达变化相关。综上，本研究结果表明，三维表观基因组重塑是ER+乳腺癌内分泌耐药的关键机制。本研究在内分泌敏感型乳腺癌细胞（MCF7）及其两种内分泌耐药衍生细胞——他莫昔芬耐药（TAMR）细胞与氟维司群耐药（FASR）细胞中，开展了Hi-C测序、全基因组测序（WGS）、全基因组亚硫酸氢盐测序（WGBS）、染色质免疫共沉淀测序（ChIP-seq）及RNA测序（RNA-seq）。