Epigenetic therapy suppresses tumour growth by rewiring ER-mediated long-range chromatin interactions in ER+ endocrine-resistant breast cancer [RNA-seq]

Here we investigate the impact of epigenetic therapy with Decitabine in endocrine-resistant ER+ breast cancer by using patient-derived xenograft (PDX) models. Decitabine treatment restrained tumour growth, inhibited cell proliferation and resulted in significant loss of DNA methylation, particularly at enhancers and repetitive elements. Systematic integration of matched in situ Hi-C / PCHi-C, EPIC, RNA-seq and ChIP–seq datasets revealed widespread differences in epigenome regulation and enhancer-promoter communication with Decitabine. We find that loss of DNA methylation with Decitabine strongly affects the open (A) and closed (B) compartment structure and TAD boundary insulation. Our study identified and focused on key DNA methylation-dependent, enhancer ER binding sites that are activated in Decitabine-treated PDX tumours, enabling direct interactions between promoters and multiple distal enhancers, inducing expression of ER target genes and pathways. Overall, we demonstrate that epigenetic therapy inhibits tumour progression through to rewiring of ER-mediated 3D chromatin interactions and transcriptome programs. Our findings suggest that targeting the 3D epigenome with epigenetic therapies represents a promising strategy for anti-cancer treatment in ER+ endocrine resistant breast cancer patients. To understand the Decitabine-induced molecular changes driving tumour regression on a global scale, we used in situ Hi-C to generate genome-wide 3D genome maps of PDX breast tumours treated with Decitabine. At the same time, we examined the genome-wide DNA methylation (EPIC Microarrays), promoter-anchored interactome (Promoter Capture Hi-C (PCHi-C)), transcription factor binding (ER and FOXA1 ChIP-seq) and gene expression (RNA-seq) in the same tumours.

本研究采用患者来源异种移植模型（patient-derived xenograft, PDX），探究地西他滨（Decitabine）表观遗传疗法在内分泌抵抗型雌激素受体阳性（ER+）乳腺癌中的作用效果。地西他滨处理可抑制肿瘤生长与细胞增殖，并显著降低DNA甲基化水平，尤其在增强子与重复序列区域。通过系统整合匹配的原位Hi-C、启动子捕获Hi-C（PCHi-C）、EPIC甲基化微阵列、RNA测序（RNA-seq）及染色质免疫沉淀测序（ChIP–seq）数据集，本研究揭示了地西他滨处理后表观基因组调控与增强子-启动子互作的广泛改变。研究发现，地西他滨引发的DNA甲基化丢失会显著影响开放（A）与闭合（B）区室结构，以及拓扑关联域（Topologically Associating Domain, TAD）边界的绝缘性。本研究鉴定并聚焦于地西他滨处理的PDX肿瘤中激活的、依赖DNA甲基化的关键增强子结合雌激素受体（ER）位点，这些位点可介导启动子与多个远端增强子之间的直接相互作用，进而诱导雌激素受体靶基因及相关通路的表达。综上，本研究证实表观遗传疗法可通过重塑雌激素受体介导的三维染色质相互作用网络与转录组程序，抑制肿瘤进展。本研究结果表明，采用表观遗传疗法靶向三维表观基因组，有望成为内分泌抵抗型ER+乳腺癌患者的抗肿瘤治疗策略。为在全基因组层面解析地西他滨诱导的、驱动肿瘤消退的分子改变，本研究采用原位Hi-C技术，构建了地西他滨处理的PDX乳腺癌肿瘤的全基因组三维基因组图谱。与此同时，本研究对同一批肿瘤开展了全基因组DNA甲基化检测（EPIC微阵列）、启动子锚定相互作用组分析（启动子捕获Hi-C, PCHi-C）、转录因子结合检测（ER与叉头框蛋白A1（FOXA1）染色质免疫沉淀测序）以及基因表达分析（RNA测序）。