Master regulator transcription factors promote esophageal neoplastic evolution

项目摘要 食管腺癌是最致命的恶性肿瘤之一，其发病率有惊人的增长， 在西方国家（包括美国、英国和几个欧洲国家）， 过去的四十年尽管从最近的基因组分析中获得了新的见解， EAC的5年生存率仍然极低（~20%）。因此，我们认为， 迫切需要替代研究方法，包括先进的表观基因组研究，来了解 EAC的分子基础，用于开发新的治疗方案。Barrett食管（BE）是一种癌前病变， 条件，并被认为是专性前驱病变的EAC。在Barrett食管相关的 在肿瘤演变中，良性BE首先变为发育异常，然后进展为EAC。因此，BE作为 食管上皮癌前病变模型的建立 细胞然而，我们对促进BEAN的分子机制的理解仍然有限，关键是 问题（例如，BE恶性转化为EAC的主要驱动因素）仍未得到解决。 我们和其他人已经表明，恶性转化伴随着全基因组的获得和损失 增强子和超级增强子，它们被上游主调节子占据和调节 转录因子（MRTFs）。事实上，我们最近的研究表明，两个增强子 正常胃食管连接部（NGEJ）、BE和EAC样品之间的MRTF使用和活性。特别地， 我们已经鉴定了一组EAC特异性MRTF（ELF 3、KLF 5、GATA 6、EHF）。试点实验表明， 这4个MRTF共同占据了数百个EAC特异性增强子和超级增强子，表明它们可能 调节EAC转录组。此外，这些EAC特异性MRTF在大肠杆菌中高度且独特地表达。 EAC与正常GEJ或BE样品相比，并且在功能上是EAC细胞增殖所需的。 基于这些发现，我们假设EAC特异性MRTFs直接促进肿瘤的恶性转化。 通过在表观基因组上重新连接增强子和超级增强子来转化BE细胞， 信号通路和EAC发展所必需的细胞过程。我们将通过以下方式检验这一假设： 研究MRTF在人类BE衍生的3D类器官中的生物学功能。此外，我们会研究 肥胖和EAC之间强关联的机制基础，通过关注 MRTF和脂肪酸合成，这是我们的初步数据确定的关键下游途径。这些 研究有望建立BE相关瘤形成演变的主要驱动力，并揭示 食管转化的表观基因组机制，这将从根本上改变我们的见解， 食管癌的生物学。更重要的是，成功地执行这一建议可以确定 通过靶向脂肪酸合成途径预防和早期干预EAC的潜在途径 高风险个体（例如，难治性和/或高级别BE患者）。

PROJECT SUMMARY Esophageal adenocarcinoma (EAC) is one of the deadliest malignancies, and its incidence has strikingly increased 6-8 fold in Western countries (including the United States, UK and several European countries) over the past 4 decades. Despite new insights gained from recent genomic analyses, meaningful therapeutic improvements have not occurred and the 5-year survival of EAC has remained extremely low (~20%). Therefore, alternative research approaches, including advanced epigenomic studies, are desperately needed to understand the molecular basis of EAC for developing novel treatment regimens. Barrett’s esophagus (BE) is a premalignant condition and is considered as the obligate precursor lesion of EAC. During Barrett’s esophagus-associated neoplastic evolution, benign BE first becomes dysplastic and then progresses to EAC. Therefore, BE serves as an ideal pre-malignant model for the investigation of the step-wise neoplastic evolution of esophageal epithelial cells. However, our understanding of the molecular mechanisms promoting BEAN remains limited, with key questions (e.g., the primary drivers for the malignant transformation of BE into EAC) still unaddressed. We and others have shown that malignant transformation is accompanied by genome-wide gains and losses of enhancers and super-enhancers, which are occupied and regulated by upstream master regulator transcription factors (MRTFs). Indeed, our recent studies demonstrated profound alterations in both enhancer usage and MRTF activity between normal gastroesophageal junction (NGEJ), BE and EAC samples. Particularly, we have identified a set of EAC-specific MRTFs (ELF3, KLF5, GATA6, EHF). Pilot experiments have shown that these 4 MRTFs co-occupy hundreds of EAC-specific enhancers and super-enhancers, indicating they may regulate the EAC transcriptome. Moreover, these EAC-specific MRTFs are highly and uniquely expressed in EAC compared with normal GEJ or BE samples and are functionally required for EAC cell proliferation. Based on these findings, we hypothesize that EAC-specific MRTFs directly promote the malignant transformation of BE cells by rewiring enhancers and super-enhancers across the epigenome, activating signaling pathways and cellular processes essential for EAC development. We will test this hypothesis by investigating the biological functions of MRTFs in human BE-derived 3D organoids. In addition, we will study the mechanistic basis of the strong association between obesity and EAC by focusing on the regulatory loop of MRTF and fatty-acid synthesis, which is the key downstream pathway identified by our preliminary data. These investigations promise to establish primary driving forces of BE-associated neoplasia evolution and uncover epigenomic mechanisms underlying esophagus transformation, which will fundamentally transform our insights into the biology of esophageal cancer. More importantly, successful execution of this proposal may identify potential avenue for the prevention and early intervention of EAC by targeting fatty-acid synthesis pathway in the high-risk individuals (e.g., refractory and/or high-grade BE patients) with obese condition.