BRD4-directed Super-enhancer Organization of Transcription Repression Programs Links to Chemotherapeutic Efficacy in Breast Cancer

BRD4 is well known for its role in super-enhancer organization and transcription activation of several prominent oncogenes including c-MYC and BCL2. As such, BRD4 inhibitors have being pursued as promising therapeutics for cancer treatment. However, drug resistance also occurs for BRD4-targeted therapies. Here we report that BRD4, unexpectedly, interacts with the LSD1/NuRD complex and co-localizes with this repressive complex on super-enhancers. Integrative genomic and epigenomic analyses indicate that the BRD4/LSD1/NuRD complex restricts the hyperactivation of a cluster of genes that are functionally linked to drug resistance. Intriguingly, treatment of breast cancer cells with a small molecule inhibitor of BRD4, JQ1, results in no immediate activation of the drug-resistant genes, but long-time treatment or destabilization of LSD1 by PELI1 decommissions the BRD4/LSD1/NuRD complex, leading to resistance to JQ1 as well as to a broad spectrum of therapeutic compounds. Consistently, PELI1 is up-regulated in breast carcinomas, its level is negatively correlated with that of LSD1, and the expression level of the BRD4/LSD1/NuRD complex-restricted genes is strongly correlated with a worse overall survival of breast cancer patients. Together, our study uncovers a functional duality of BRD4 in super-enhancer organization of transcription activation and repression linking to oncogenesis and chemoresistance, respectively, supporting the pursuit of a combined targeting of BRD4 and PELI1 in effective treatment of breast cancer. RNA-seq and ChIP-seq was used for the analysis of genes influenced by BRD4 and genome-wide binding signals of specific proteins.

溴结构域蛋白4（BRD4）因在超级增强子（super-enhancer）的组织调控以及包括c-MYC、BCL2在内的多个关键致癌基因的转录激活中发挥核心作用而广为人知。因此，BRD4抑制剂被开发为极具前景的癌症治疗候选药物。然而，靶向BRD4的治疗方案同样会出现耐药性问题。本研究意外发现，BRD4可与赖氨酸特异性去甲基化酶1/核小体重塑与去乙酰化酶复合物（LSD1/NuRD）发生相互作用，并与该阻遏复合物共定位于超级增强子区域。整合基因组学与表观基因组学分析显示，BRD4/LSD1/NuRD复合物可抑制一组与耐药性功能相关基因的过度激活。值得注意的是，使用BRD4小分子抑制剂JQ1处理乳腺癌细胞时，并未即刻激活耐药基因，但长期给药或PELI1（Pellino E3泛素蛋白连接酶1）介导的LSD1不稳定化会使BRD4/LSD1/NuRD复合物失活，进而导致细胞对JQ1以及多种治疗药物产生耐药性。一致的实验结果显示，PELI1在乳腺癌组织中表达上调，其表达水平与LSD1呈负相关，且BRD4/LSD1/NuRD复合物所抑制的基因的表达水平与乳腺癌患者的不良总生存率显著相关。综上，本研究揭示了BRD4在超级增强子调控中的功能双重性：分别参与转录激活与转录阻遏，并分别与肿瘤发生及化疗耐药相关，这一发现支持联合靶向BRD4与PELI1以实现乳腺癌的有效治疗。本研究采用RNA测序（RNA-seq）与染色质免疫沉淀测序（ChIP-seq）技术，分析了受BRD4调控的基因以及特定蛋白质的全基因组结合信号。