Targetting super enhancer associated oncogenes in esophageal squamous cell carcinoma [RNA-seq]

Esophageal squamous cell carcinoma (ESCC) is an aggressive malignancy and the major histological subtype of esophageal cancer. Although recent large-scale genomic analysis has improved the description of the genetic abnormalities of ESCC, few targetable genomic lesions were identified and no molecular-based therapy is available. To identify druggable candidates in this tumor, we performed high-throughput small-molecule inhibitor screening. The unbiased results led us to discover a highly potent anti-ESCC compound, THZ1, a newly developed covalent CDK7 inhibitor. Further in vitro and in vivo experiments showed that THZ1 has powerful anti-neoplastic properties against ESCC cells with minimal toxic effect on healthy tissues. Importantly, whole-transcriptome sequencing (RNA-Seq) revealed that low-dose THZ1 treatment led to selective inhibition of a number of oncogenic transcripts. Notably, further characterization of the genomic features of these THZ1-sensitive transcripts demonstrated that they were frequently associated with Super-Enhancer (SE). Moreover, SE analysis alone uncovered many lineage-specific master regulators in ESCC. Finally, integrative analysis of both THZ1-sensitive and SE-associated transcripts identified a number of novel oncogenes in the context of ESCC, such as PAK4, RUNX1, DNAJB1, SREBF2 and YAP1, with PAK4 being a potential druggable kinase. Together, our integrative molecular approaches identified a catalog of SE-associated lineage-specific master regulators and oncogenic transcripts in ESCC, which will significantly promote the understanding of ESCC biology. The preclinical results of THZ1 may help establish the therapeutic merit of targeting transcriptional regulation program for the treatment of this deadly malignancy. RNA-seq of esophageal cell lines treated with either DMSO or THZ1 at various time points of treatment.

食管鳞状细胞癌（Esophageal squamous cell carcinoma, ESCC）是一种侵袭性恶性肿瘤，也是食管癌的主要组织学亚型。尽管近期的大规模基因组分析已加深了对ESCC遗传异常的认知，但目前已发现的可靶向基因组病变极少，且尚无基于分子机制的治疗方案可用。为鉴定该肿瘤中的可药用靶点，我们开展了高通量小分子抑制剂筛选。无偏倚的筛选结果使我们发现了一种强效抗ESCC化合物THZ1——一种新开发的共价CDK7抑制剂。进一步的体外与体内实验表明，THZ1对ESCC细胞具有强大的抗肿瘤活性，且对健康组织的毒性极低。重要的是，全转录组测序（RNA-Seq）结果显示，低剂量THZ1处理可选择性抑制多种致癌转录本。值得注意的是，对这些THZ1敏感转录本的基因组特征进行进一步表征后发现，它们常与超级增强子（Super-Enhancer, SE）相关。此外，仅通过超级增强子分析，我们就鉴定出了ESCC中多个谱系特异性主调控因子。最后，对THZ1敏感转录本与超级增强子相关转录本的整合分析，鉴定出了ESCC背景下的多种新型致癌基因，如PAK4、RUNX1、DNAJB1、SREBF2与YAP1，其中PAK4是一种潜在的可靶向激酶。综上，我们的整合分子学方法鉴定出了ESCC中一系列与超级增强子相关的谱系特异性主调控因子及致癌转录本，这将极大推动对ESCC生物学特性的理解。THZ1的临床前研究结果或可为针对转录调控程序治疗这类致命恶性肿瘤的治疗价值提供依据。本数据集包含经二甲基亚砜（DMSO）或不同处理时间梯度的THZ1处理的食管细胞系的RNA-seq数据。