Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers [ChIP-seq]. Homo sapiens

Chromatin regulators have become highly attractive targets for cancer therapy, yet many of these regulators are expressed in a broad range of healthy cells and contribute generally to gene expression. An important conundrum has thus emerged: how can inhibition of a general regulator of gene expression produce selective effects at specific oncogenes? Here we investigate how inhibition of the transcriptional coactivator BRD4 (Bromodomain containing 4) leads to selective inhibition of disease-critical oncogenes in a highly malignant blood cancer, multiple myeloma (MM). We found that BRD4 generally occupies the promoter elements of active genes together with the Mediator coactivator, but remarkably high levels of these two coactivator proteins were associated with a small set of exceptionally large enhancers. These super-enhancers are associated with genes that feature prominently in MM biology, including the MYC oncogene. Treatment of MM tumor cells with the BET-bromodomain inhibitor JQ1 led to preferential loss of BRD4 at super-enhancers and consequent transcription elongation defects that preferentially impact genes with super-enhancers, including the c-MYC oncogene. Super-enhancers were found at key oncogenic drivers in many other tumor cells. Thus, super-enhancers can regulate oncogenic drivers in tumor cells, which in some cells can be preferentially disrupted by BRD4 inhibition, which in turn contributes to the selective transcriptional effects observed at these oncogenes. These observations have implications for the discovery of novel cancer therapeutics directed at components of super-enhancers in diverse tumor types. Overall design: ChIP-Seq for chromatin regulators and RNA Polymerase II in multiple myeloma, glioblastoma multiforme, and small cell lung cancer

染色质调控因子已成为癌症治疗领域极具吸引力的靶点，但其中多数调控因子可在多种健康细胞中广泛表达，并普遍参与基因表达调控。由此催生了一个关键科学难题：如何通过抑制这类普遍存在的基因表达调控因子，实现对特定癌基因的选择性作用？本研究针对转录辅激活因子BRD4（Bromodomain containing 4）的抑制效应展开探究，解析其在恶性血液癌症多发性骨髓瘤（multiple myeloma, MM）中选择性抑制致病关键癌基因的分子机制。
研究发现，BRD4通常与中介体辅激活因子共同结合于活跃基因的启动子区域；值得注意的是，这两种辅激活蛋白的高丰度富集，仅与一小簇异常庞大的增强子区域相关。这类超级增强子（super-enhancers）与多发性骨髓瘤生物学功能中的核心基因密切相关，其中包括MYC癌基因。
使用BET溴结构域抑制剂JQ1处理MM肿瘤细胞后，BRD4在超级增强子区域的结合出现优先丢失，进而引发转录延伸缺陷，该缺陷会优先影响携带超级增强子的基因，包括c-MYC癌基因。
在多种其他肿瘤细胞的关键致癌驱动基因区域中，均检测到超级增强子的存在。综上，超级增强子可调控肿瘤细胞中的致癌驱动基因；在部分细胞中，这类基因可通过BRD4抑制被优先阻断，这也解释了在上述癌基因中观察到的选择性转录效应。上述研究结果为针对多种肿瘤类型中超级增强子组分开发新型癌症治疗药物提供了理论依据。
本研究整体实验设计：对多发性骨髓瘤、多形性胶质母细胞瘤及小细胞肺癌样本，开展染色质调控因子与RNA聚合酶II（RNA Polymerase II）的染色质免疫共沉淀测序（ChIP-Seq）分析。