Identifying functional variants in COPD GWAS loci

识别 COPD GWAS 位点的功能变异

• 批准号: 9364419
• 负责人: MICHAEL H. CHO
• 金额: $ 85.37万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-15 至 2021-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9364419
• 关键词: Address; Apoptosis; Bioinformatics; Biological; Biological Assay; CRISPR/Cas technology; Candidate Disease Gene; Cell Death; Cell Line; Cell model; Cells; Chronic Obstructive Airway Disease; Complex; Computer Retrieval of Information on Scientific Projects Database; Data; Disease; Disease susceptibility; Endothelial Cells; Epithelial Cells; Fibroblasts; Functional disorder; Gene Expression; Genes; Genome; Genomic Segment; Genomics; Genotype; Goals; Hereditary Disease; Human; International; Laboratories; Linkage Disequilibrium; Lung; Methods; Minority; Molecular; Nucleic Acid Regulatory Sequences; Pathogenesis; Pathway interactions; Population; Regulatory Element; Reporter; Susceptibility Gene; T-Lymphocyte; Variant; base; cell type; chromosome conformation capture; cigarette smoke-induced; cigarette smoking; exome; gene function; genetic approach; genetic association; genetic variant; genome sequencing; genome wide association study; genome-wide; insight; interest; macrophage; monocyte; mouse model; novel; personalized medicine; promoter; response; whole genome

Project Summary The identification of novel susceptibility genes for complex diseases like COPD could transform our understanding of disease pathophysiology and provide new targets for treatment. The primary goals of this project are to identify the functional genetic variants within five well-established COPD GWAS loci; to identify the key genes influenced by these functional variants; and to assess the impact of these key genes and functional genetic variants on COPD pathogenesis. In recent collaborative GWAS through the International COPD Genetics Consortium, we found 22 genomic loci associated with COPD at genome-wide significance. We will focus our studies in this proposal on five of these COPD GWAS loci that include multiple candidate genes and for which a likely functional variant has not been identified. We hypothesize that an integrated approach that utilizes whole genome sequencing for fine mapping, gene expression data, bioinformatic approaches, and new laboratory assessments will enable the identification of the key genes and functional variants within these five COPD GWAS loci. Moreover, we hypothesize that focused cell-based studies of these key genes and their functional variants will provide novel insights into COPD pathogenesis. To address these hypotheses, we will start by identifying functional variants within these five loci using massively parallel reporter assays in multiple cell types, bioinformatic approaches with public and recently generated Omics data, and genetic association analysis. We will then determine which gene or genes are influenced by these functional variants by performing chromosome conformation capture (4C-Seq), confirming the regulatory effects of the functional variants on the endogenous promoter of the implicated gene, and demonstrating effects on gene expression of the implicated gene by gene editing the regulatory region using CRISP-Cas9 approaches. Finally, we will use cellular models to determine the effects of inactivating the key gene and its functional variants on COPD-related read-outs of cell death, apoptosis, and cell activation. To accomplish these goals, a unique and highly integrated approach combining genetic association analysis, molecular studies of regulatory elements, and functional cell-based assays has been developed that will likely provide important insights into COPD pathogenesis.

项目概要 识别慢性阻塞性肺病等复杂疾病的新易感基因可能会改变我们的认知 了解疾病的病理生理学并为治疗提供新的靶点。本次活动的主要目标 该项目旨在鉴定五个成熟的 COPD GWAS 位点内的功能性遗传变异；识别 受这些功能变异影响的关键基因；并评估这些关键基因的影响 COPD 发病机制的功能性遗传变异。最近通过国际合作 GWAS COPD 遗传学联盟，我们发现了 22 个在全基因组范围内与 COPD 相关的基因组位点。 我们将在本提案中重点研究其中五个 COPD GWAS 位点，其中包括多个候选位点 基因，并且尚未鉴定出可能的功能变异。我们假设一个集成的 利用全基因组测序进行精细绘图、基因表达数据、生物信息学的方法 方法和新的实验室评估将能够识别关键基因和功能 这五个 COPD GWAS 位点内的变异。此外，我们假设重点基于细胞的研究 这些关键基因及其功能变异将为慢性阻塞性肺病发病机制提供新的见解。致地址 这些假设，我们将首先使用大规模并行识别这五个基因座内的功能变异 多种细胞类型的报告分析、利用公共和最近生成的组学数据的生物信息方法， 和遗传关联分析。然后我们将确定哪些基因受到这些基因的影响 通过执行染色体构象捕获（4C-Seq）来识别功能变异，确认监管 功能变体对相关基因的内源启动子的影响，并证明 使用 CRISP-Cas9 基因编辑调控区域对相关基因的基因表达的影响 接近。最后，我们将使用细胞模型来确定关键基因及其失活的影响 与慢性阻塞性肺病相关的细胞死亡、细胞凋亡和细胞激活读数的功能变异。为了完成 这些目标是一种独特且高度集成的方法，结合了遗传关联分析、分子 已经开发了调节元件的研究和基于功能细胞的测定，这可能会提供 对 COPD 发病机制的重要见解。