Epigenetic Heterogeneity as a Driver of Liver Disease and Cancer

肝细胞癌（HCC）是美国癌症相关死亡增长最快的原因之一， 缺乏针对这种高度异质性肿瘤的早期检测策略和治疗方法。醇 经常滥用的娱乐性药物和建立慢性感染的丙型肝炎病毒（HCV）， 肝损伤和肝硬化，并显著增加HCC的风险。虽然在这方面已经取得了很大的进展， 治疗HCV感染，大多数人不知道他们被感染。HCV治愈者或 戒酒的人仍然有患肝癌的长期风险。在筛查肝硬化患者时， HCC明显降低死亡率，>50%的HCC对一种可用的血液标记物（AFP）呈阴性， 强调了对更好屏幕的迫切需求。因此，至关重要的是要全面了解 病理过程驱动HCC，以确定那些HCC的最大风险，并开发新的 预防或逆转肝癌发生的疗法。虽然有证据表明，酒精和HCV诱导遗传 变化是有限的，我们和其他人已经表明，表观基因组的组成部分，特别是DNA， 甲基化（5 mC）和DNA羟甲基化（5 hmC）在肝脏疾病期间被严重破坏 进展然而，最大的挑战之一是确定哪些表观遗传变化是驱动因素 并且其代表了新的HCC早期检测标志物。我们全面检查了全基因组 5 mC/5 hmC分析在HCC中揭示了高频率的病因和疾病阶段特异性变化，我们 确定了一组推定的表观遗传驱动因素，我们在本提案中建立了这些驱动因素。根据这些数据，我们 我提出了三个目的来检验本申请的中心假设，即表观遗传异质性在 肝硬化是HCC发展和进展的基础。阐明这种效应背后的机制是 有望产生新的HCC驱动因素和早期检测标志物。鉴于这些都是表观遗传靶点， 它们也代表了临床上可靶向的驱动因素。在目标1中，我们定义了在 癌前肝硬化到HCC的致癌作用，并确定肿瘤演变的表观遗传驱动因素。在aim中 2，基于初步和已发表的数据，鉴定表观遗传驱动基因座并开发新的细胞 在细胞培养和PDX模型中，我们从功能上探讨了异常5 mC/5 hmC靶向的基因座在 驾驶HCC。最后，在目标3中，我们确定了循环游离DNA甲基化特征， 肝硬化患者与肝硬化合并肝癌患者之间的差异，并研究其与肿瘤的关系 异质性这些研究的结果有望极大地扩展我们对 表观遗传变化驱动HCC，为治疗提供新的可操作靶点，并建立基础 未来的研究开发5 mC作为HCC早期检测标志物。

Hepatocellular carcinoma (HCC) is among the fastest-growing causes of cancer-related death in the U.S due to a lack of early detection strategies and therapies that target this highly heterogeneous tumor. Alcohol, a frequently abused recreational drug and hepatitis C virus (HCV), which establishes chronic infection, cause liver damage and cirrhosis and dramatically enhance risk for HCC. While great strides have been made in treating HCV infection, most individuals do not know they are infected. Individuals cured of HCV or who break their alcohol addiction remain at long-term risk for HCC. While screening liver cirrhosis patients for HCC clearly reduces mortality, >50% of HCCs are negative for the one blood-based marker available (AFP), emphasizing the dire need for better screens. Thus, it is crucial to gain a complete understanding of the pathological processes driving HCC in order to define those at greatest risk for HCC and develop new therapies to prevent or reverse liver carcinogenesis. While evidence that alcohol and HCV induce genetic changes is limited, we and others have shown that components of the epigenome, particularly DNA methylation (5mC) and DNA hydroxymethylation (5hmC), are profoundly disrupted during liver disease progression. One of the greatest challenges, however, is determining which epigenetic changes are drivers and which represent novel HCC early detection markers. We comprehensively examined genome-wide 5mC/5hmC analyses in HCC to reveal high frequency etiologic- and disease-stage specific changes, and we identified a panel of putative epigenetic drivers that we build on in this proposal. Based on these data, we propose three aims to test the central hypothesis of this application that epigenetic heterogeneity in cirrhosis underpins HCC development and progression. Elucidating the mechanisms underlying this effect is expected to yield novel drivers of HCC and early detection markers. Given that these are epigenetic targets, they also represent clinically targetable drivers. In aim 1 we define epigenetic heterogeneity during carcinogenesis of premalignant liver cirrhosis to HCC and define epigenetic drivers of tumor evolution. In aim 2, building on preliminary and published data identifying epigenetic driver loci and developing novel cell culture and PDX models, we functionally interrogate the role of loci targeted by aberrant 5mC/5hmC in driving HCC. Finally, in aim 3 we identify circulating cell-free DNA methylation signatures that differentiate between patients with cirrhosis and patients with cirrhosis and HCC and study their relationships with tumor heterogeneity. Results from these studies are expected to greatly expand our understanding of how epigenetic changes drive HCC, provide new actionable targets for treatment, and establish the foundations for future studies developing 5mC as an HCC early detection marker.