College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea.
College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea.
EBioMedicine. 2019 Feb;40:488-503. doi: 10.1016/j.ebiom.2018.12.056. Epub 2019 Jan 9.
The injured liver loses normal function, with concomitant decrease of key identity genes. Super-enhancers contribute to mammalian cell identity. Here, we identified core transcription factors (TFs) that are active in hepatocytes, using genome-wide analysis and hierarchical ordering of super-enhancer distribution.
Expression of core TFs was assessed in a cohort of patients with hepatitis or cirrhosis and animal models. Quantitative PCR, chromatin immunoprecipitation assays, and hydrodynamic gene delivery methods were used to assess gene regulation and hepatocyte viability. RNA-sequencing data were generated to investigate the role of LRH1 in hepatocyte protection from injury.
Network analysis of super-enhancer-associated gene interactions and expression arrays for cohorts of patients with hepatitis and cirrhosis enabled us to identify a super-enhancer-associated network, and LRH1, HNF4α, PPARα, and RXRα as core TFs. In mouse models, expression of core TFs was robustly inhibited by single and multiple challenge(s) with liver toxicant. RNA-seq analysis revealed changes in expression in the super-enhancer-associated genes sensitively biased toward repression by intoxication. LRH1 gene delivery prevented the loss of hepatic super-enhancer-associated signaling circuitry in toxicant-challenged mice, and protected the liver from injury, indicating the role of LRH1 in hepatocyte identity and viability. In hepatocytes, overexpression of each core TF promoted induction of other TFs.
Overall, this study identified LRH1-driven pathway as a circuitry responsible for hepatocyte identity by using cistromic analysis, improving our understanding of liver pathophysiology and identifying novel therapeutic targets.
受损的肝脏会失去正常功能，同时关键的身份基因也会减少。超级增强子有助于哺乳动物细胞的身份识别。在这里，我们使用全基因组分析和超级增强子分布的层次排序，鉴定了在肝细胞中活跃的核心转录因子（TF）。
在一组患有肝炎或肝硬化的患者和动物模型中评估核心 TF 的表达。使用定量 PCR、染色质免疫沉淀测定和水力基因传递方法来评估基因调控和肝细胞活力。生成 RNA-seq 数据以研究 LRH1 在保护肝细胞免受损伤中的作用。
超级增强子相关基因相互作用的网络分析和肝炎及肝硬化患者队列的表达谱阵列分析使我们能够识别出一个超级增强子相关网络，以及 LRH1、HNF4α、PPARα 和 RXRα 作为核心 TF。在小鼠模型中，核心 TF 的表达被单次和多次肝毒物挑战强烈抑制。RNA-seq 分析显示，超级增强子相关基因的表达变化在中毒时敏感地偏向于抑制。LRH1 基因传递可防止毒物挑战小鼠中肝超级增强子相关信号通路的丢失，并保护肝脏免受损伤，表明 LRH1 在肝细胞身份和活力中的作用。在肝细胞中，每个核心 TF 的过表达均促进了其他 TF 的诱导。
总的来说，这项研究通过顺式作用分析鉴定了 LRH1 驱动的途径作为负责肝细胞身份的电路，从而提高了我们对肝脏病理生理学的理解，并确定了新的治疗靶点。
