Response and resistance to BET bromodomain inhibitors in triple negative breast cancer [ChIP-Seq]

Triple negative breast cancer (TNBC) is a heterogeneous and clinically aggressive disease for which there is no targeted therapy. Here we report the preferential and high sensitivity of TNBCs to BET bromodomain inhibitors such as JQ1 manifested by cell cycle arrest in early G1, apoptosis, and induction of markers of luminal epithelial differentiation in vitro and in vivo. The sensitivity of TNBC and other tumor types to BET inhibition establishes a rationale for clinical investigation, and a motivation to understand mechanisms of resistance. After engendering acquired resistance to BET inhibition in previously sensitive TNBCs, we utilized integrative approaches to identify a unique mechanism of epigenomic resistance to this epigenetic therapy. Resistant cells remain dependent on BRD4, confirmed by RNA interference. However, TNBC cells adapt to BET bromodomain inhibition by re-recruitment of unmutated BRD4 to super-enhancers, now in a bromodomain-independent manner. Proteomic studies of resistant TNBC identify hyper-phosphorylation of BRD4 and strong association with MED1. Together, these studies provide a rationale for BET inhibition in TNBC and argue for combination strategies to anticipate clinical drug resistance. ChIP-seq in parental and JQ1 resistant triple negative breast cancer (TNBC) in response to DMSO or JQ1 treatment

三阴性乳腺癌（Triple negative breast cancer, TNBC）是一类异质性强且临床侵袭性显著的疾病，目前尚无获批的靶向治疗方案。本研究报道了三阴性乳腺癌对BET溴结构域抑制剂（BET bromodomain inhibitors，如JQ1）具有优先且高度的敏感性，该敏感性具体体现为体外与体内实验中，细胞周期阻滞于G1早期、发生细胞凋亡，同时诱导腔上皮分化标志物的表达。三阴性乳腺癌及其他肿瘤类型对BET抑制的敏感性，为该疗法的临床研究提供了理论依据，也为解析耐药机制指明了研究方向。在使原本对BET抑制敏感的三阴性乳腺癌细胞获得性耐药后，我们采用整合组学分析方法，鉴定出了针对该表观遗传治疗的独特表观基因组耐药机制。经RNA干扰（RNA interference）验证，耐药细胞仍依赖BRD4。然而，三阴性乳腺癌细胞可通过不依赖溴结构域的方式，将未发生突变的BRD4重新招募至超级增强子（super-enhancers），从而适应BET溴结构域抑制。对耐药三阴性乳腺癌的蛋白质组学研究发现，BRD4存在高度磷酸化修饰，且与MED1存在强相互作用。综上，本研究为三阴性乳腺癌中应用BET抑制治疗提供了理论支撑，并提示需通过联合治疗策略应对临床耐药问题。本数据集包含针对亲本及JQ1耐药三阴性乳腺癌细胞，经二甲基亚砜（DMSO）或JQ1处理后的染色质免疫共沉淀测序（ChIP-seq）数据。