Datasheet1_Reorganization of 3D chromatin architecture in doxorubicin-resistant breast cancer cells.docx

Background: Doxorubicin resistance remains a major therapeutic challenge leading to poor survival prognosis and treatment failure in breast cancer. Although doxorubicin induces massive changes in the transcriptional landscape are well known, potential diagnostic or therapeutic targets associated with the reorganization of three-dimensional (3D) chromatin architecture have not yet been systematically investigated.
Methods: Here we performed in situ high-throughput chromosome conformation capture (Hi-C) on parental and doxorubicin-resistant MCF7 (MCF7-DR) human breast cancer cells, followed by integrative analysis of HiC, ATAC-seq, RNA-seq and TCGA data.
Results: It revealed that A/B compartment switching was positively correlated to genome-wide differential gene expression. The genome of MCF7-DR cells was spatially reorganized into smaller topologically associating domains (TADs) and chromatin loops. We also revealed the contribution of increased chromatin accessibility and potential transcription factor families, including CTCF, AP-1 and bHLH, to gained TADs or loops. Intriguingly, we observed two condensed genomic regions (∼20 kb) with decreased chromatin accessibility flanking TAD boundaries, which might play a critical role in the formation or maintenance of TADs. Finally, combining data from TCGA, we identified a number of gained and lost enhancer-promoter interactions and their corresponding differentially expressed genes involved in chromatin organization and breast cancer signaling pathways, including FA2H, FOXA1 and JRKL, which might serve as potential treatment targets for breast cancer.
Conclusion: These data uncovered a close connection between 3D genome reorganization, chromatin accessibility as well as gene transcription and provide novel insights into the epigenomic mechanisms involving doxorubicin resistance in breast cancer.

背景：多柔比星（Doxorubicin）耐药仍是乳腺癌治疗的重大挑战，可导致患者生存预后不良及治疗失败。尽管多柔比星引发转录组全景的广泛改变已广为人知，但与三维（3D）染色质构象重排相关的潜在诊断或治疗靶点，迄今尚未得到系统研究。
方法：本研究对亲本及多柔比星耐药人乳腺癌MCF7（MCF7-DR）细胞开展原位高通量染色体构象捕获（Hi-C）实验，随后对Hi-C、ATAC-seq、RNA-seq及癌症基因组图谱（TCGA）数据进行整合分析。
结果：研究发现，A/B区室转换与全基因组差异基因表达呈正相关。MCF7-DR细胞的基因组在空间上重排为更小的拓扑关联结构域（TAD）及染色质环。本研究还揭示了染色质可及性升高及包括CCCTC结合因子（CTCF）、激活蛋白1（AP-1）与碱性螺旋-环-螺旋（basic helix-loop-helix, bHLH）在内的潜在转录因子家族，对新增TAD及染色质环形成的贡献。值得注意的是，我们在TAD边界侧翼观察到两个约20 kb的浓缩基因组区域，其染色质可及性降低，该区域可能在TAD的形成或维持中发挥关键作用。最后，结合TCGA数据，我们鉴定出多个新增及丢失的增强子-启动子相互作用，及其对应的参与染色质组织与乳腺癌信号通路的差异表达基因，包括FA2H、FOXA1与JRKL，这些基因或可作为乳腺癌潜在治疗靶点。
结论：本研究数据揭示了3D基因组重排、染色质可及性与基因转录之间的紧密关联，为阐明乳腺癌多柔比星耐药的表观基因组机制提供了全新视角。