Interaction between Genome and Heavy Metals in Nonalcoholic Fatty Liver Disease

摘要 本项目的最终目的是发现和验证基因与重金属（GXM）的相互作用， 人类肝脏，并了解其在非酒精性脂肪肝（NAFLD）中的作用。NAFLD是最 常见的慢性肝病影响超过30%的美国人口，造成沉重的社会负担。 NAFLD的特征在于涉及多个细胞的一系列组织学变化。当前没有任何 批准的药物治疗可用于NAFLD。因此，迫切需要鉴定基因和 环境风险因素，以促进新的诊断，预防和治疗的发展 战略布局NAFLD是一种典型的基因-环境（GXE）相互作用的复杂疾病。过去 十年来，虽然NAFLD的GWAS已经确定了许多遗传风险等位基因，但越来越多的研究 表明暴露于重金属（Pb、Cd、Hg、As等）与NAFLD风险增加有关。 然而，到目前为止，还没有令人信服的研究来评估各种自然因素之间的相关性。 在人类肝脏和NAFLD组织学中积累的金属，特别是在临床定义的患者队列中。 更重要的是，缺乏关于自然和长期积累金属的关键知识， 与肝脏基因组相互作用，共同带来NAFLD的风险。我们对人类肝脏的初步研究 组织已经成功地证明多种金属确实与NAFLD相关。通过利用 我们先前收集的多组学数据，我们已经初步确定了许多金属反应基因， 基因（MR-基因）、表达数量性状基因座（eQTL）和等位基因特异性表达基因座（ASE），这些基因是 进一步富集NAFLD及其相关途径。我们的目的是在这项研究中，进一步扩大我们的研究， 大规模，高度详细和综合的分析，以彻底了解GXM相互作用的作用， 人类的NAFLD为此，我们的团队一直在合作建立人类肝脏组织的收集， 细胞和NAFLD患者群组。我们还开发了各种技术平台，例如散装/单电池（Sc） RNAseq和ATAC-seq，以及用于GXE数据分析的多种生物信息学和统计学工具。与 这些制剂，我们的具体目标是：1）分析冷冻人肝组织中的重金属（n=560）， 鉴定MR基因、eQTLs/ASEs，并检测它们与NAFLD的相关性; 2）处理原代肝细胞 人群与各种金属，并阐明如何不同的肝细胞的基因组响应金属与 Sc-RNAseq和ATAC-seq，以及3）验证GXM相互作用与NAFLD之间的关联 在一个大型临床定义的NAFLD患者队列（n=1313）中观察组织学严重程度。我们的研究将首次 评估GXM相互作用在NAFLD中的作用和机制，并为科学界提供 重要的数据，为NAFLD研究，药物发现和超越开辟新的途径。

ABSTRACT The ultimate goal of this project is to discover and validate the gene Х heavy metal (GXM) interactions in human livers and to understand their role in nonalcoholic fatty liver disease (NAFLD). NAFLD is the most common chronic liver disease affecting over 30% of the U.S population, resulting in a heavy social burden. NAFLD is characterized by a spectrum of histological changes with multiple cells involved. Currently, no approved drug treatment is available for NAFLD. Therefore, it is an urgent need to identify both genetic and environmental risk factors to facilitate the development of new diagnostic, preventive, and therapeutic strategies. NAFLD is a typical complex disease involving gene-environment (GXE) interactions. Over the past decade, while GWAS for NAFLD have identified numerous genetic risk alleles, a growing body of research has demonstrated that exposure to heavy metals (Pb, Cd, Hg, As, etc.) are associated with increased NAFLD risk. However, there is no compelling study thus far to assess the correlation between various naturally accumulated metals in human livers and the NAFLD histology, especially in clinically defined patient cohorts. More importantly, there lacks critical knowledge about how naturally and chronically accumulated metals interact with the liver genome and together confer risks for NAFLD. Our preliminary studies in human liver tissues have successfully demonstrated that multiple metals are indeed correlated with NAFLD. By leveraging our previously collected multi-omics data, we have preliminarily identified numerous metal-response genes (MR-genes), expression quantitative traits loci (eQTLs), and allele-specific expression loci (ASEs), which are further enriched to NAFLD and its related pathways. We aim in this study to further expand our study to a large-scale, highly detailed, and integrated analysis to thoroughly understand the role of GXM interactions in NAFLD in humans. To this end, our team has been collaborating to establish collections for human liver tissue, cells and NAFLD patient cohorts. We have also developed various technical platforms e.g. bulk/single cell (Sc) RNAseq and ATAC-seq, as well as multiple bioinformatics and statistical tools for GXE data analyses. With these preparations, we specifically aim: 1) To profile heavy metals in frozen human liver tissues (n=560), identify MR-genes, eQTLs/ASEs, and test their associations with NAFLD; 2) To treat the primary liver cell populations with various metals and to elucidate how the genome of different liver cells respond to metals with Sc-RNAseq and ATAC-seq, and 3) To validate the association between GXM interactions and NAFLD histology severity in a large clinically defined NAFLD patient cohort (n=1313). Our study will for the first time evaluate the role and mechanism of GXM interactions in NAFLD and will provide the scientific community important data to open new avenues to NAFLD research, drug discovery, and beyond.