The 3D Genomic Landscape of Differential Response to EGFR/HER2 Inhibition in Endocrine-Resistant Breast Cancer [RNA-seq]. The 3D Genomic Landscape of Differential Response to EGFR/HER2 Inhibition in Endocrine-Resistant Breast Cancer [RNA-seq]

Recent studies suggested that crosstalk between ERα and EGFR/HER2 pathways plays a critical role in mediating endocrine therapy resistance. Several targeting EGFR/HER2 signaling inhibitors including FDA-approved lapatinib and gefitinib as well as a novel dual tyrosine kinase inhibitor (TKI) sapitnib showed greater inhibitory efficacies. However, how a 3D chromatin landscape of the response to the inhibition to EGFR/HER2 pathway remains to be elucidated. In this study, we conducted in situ Hi-C and RNA-seq in two ERα+ breast cancer cell systems, tamoxifen-sensitive MCF7 and T47D and tamoxifen-resistant MCF7TR and T47DTR before and after the treatment of sapitnib. We identified differential response of topologically associated domains (TADs), looping genes and expressed genes. Interestingly, we found that many differential TADs and looping genes are reversible, indicating that EGFR/HER2 signaling may play a role in reshaping and rewiring the high order genome organization. We further examined and recapitulated the reversible looping genes in 3D spheroids of breast cancer cells. Our data provides a rich resource for further evaluating chromatin structural response to anti-EGFR/HER2 targeted therapies in endocrine-resistant breast cancer. Overall design: RNA-seq experiment of 6 cell types with or without drugs, 3 biological replicates for each condition;

近期研究表明，雌激素受体α（ERα, estrogen receptor α）与表皮生长因子受体（EGFR, epidermal growth factor receptor）/人表皮生长因子受体2（HER2, human epidermal growth factor receptor 2）通路间的串扰，在介导内分泌治疗抵抗过程中发挥关键作用。多款针对EGFR/HER2信号通路的抑制剂——包括获美国食品药品监督管理局（FDA, Food and Drug Administration）批准的拉帕替尼（lapatinib）、吉非替尼（gefitinib），以及新型双靶点酪氨酸激酶抑制剂（TKI, tyrosine kinase inhibitor）萨皮替尼（sapitnib）——均展现出更优异的抑制活性。然而，针对EGFR/HER2通路抑制的应答所对应的三维染色质构象调控机制，仍有待阐明。本研究针对两类ERα阳性（ERα+）乳腺癌细胞系开展了原位Hi-C（in situ Hi-C）与转录组测序（RNA-seq）实验，两类细胞系分别为他莫昔芬敏感型MCF7、T47D，以及他莫昔芬耐药型MCF7TR、T47DTR，实验覆盖给药前与萨皮替尼给药后的两个处理阶段。本研究鉴定得到拓扑关联结构域（TADs, topologically associated domains）、环化基因与表达基因的差异应答特征。有趣的是，本研究发现大量差异TADs与环化基因的应答具有可逆性，这提示EGFR/HER2信号通路可能参与重塑并重连高阶基因组构象。本研究进一步在乳腺癌细胞三维球状体模型中，验证并重现了可逆环化基因的相关特征。本研究的数据为后续评估内分泌抵抗型乳腺癌中抗EGFR/HER2靶向治疗的染色质结构应答提供了宝贵的研究资源。整体设计：针对6种细胞系开展有无药物处理的RNA-seq实验，每种处理条件设置3次生物学重复。