Genetic and Functional Dissection of a Cluster of COPD GWAS Signals on Chromosome 4q

项目摘要 与慢性阻塞性肺疾病(COPD)易感性相关的20多个基因组区域 是通过全基因组关联研究(GWAS)发现的；然而，功能变体和 他们在这些COPD基因座中影响的基因已经在一小部分基因组区域被发现。 慢性阻塞性肺病的全球遗传研究中心已经确定了几个遗传关联信号的区域集群，最显著的是在 染色体4Q，其中HHIP、FAM13A、GSTCD、TET2和BTC附近的全基因组显著基因座 被发现了。这些聚类区可以代表：1)独立的遗传决定因素 分离的基因；2)调控同一基因的多个GWAS基因座；或3)协调的区域网络 受调控的基因。如果多个COPD基因座调控同一基因，那么该基因在 COPD的发病机制会加重。这个项目的主要目标是识别功能基因 染色体4Q上COPD基因座簇内的变异；以确定受这些变异影响的关键基因 功能变异；并评估这些关键基因和功能遗传变异对COPD的影响 发病机制。我们假设染色体4q上的区域基因网络是由功能基因调控的 将影响COPD相关细胞表型(包括细胞)的COPD基因座内的遗传变异 死亡、细胞衰老和/或炎症。为了解决这一假设，我们将首先确定 肺上皮和肺组织中4Q染色体功能变异的大规模平行报告分析 单核/巨噬细胞系以及公共和新近产生的OMIC的生物信息学方法 和遗传学数据。然后我们将确定哪些基因或哪些基因受到这些功能变异的影响 进行环化染色质构象捕捉(4C-Seq)并演示功能性 用CRISPR-CAS9方法研究区域基因表达的变异。最后，我们将使用手机 确定功能变异体及其调控基因失活对COPD相关影响的模型 细胞死亡、细胞衰老和炎症的读数。为了实现这些目标，一个独特而高度 结合调控元件的分子研究和基于功能细胞的分析的综合方法 可能会为COPD的发病机制提供重要的见解。

Project Summary More than 20 genomic regions related to chronic obstructive pulmonary disease (COPD) susceptibility have been discovered using genome-wide association studies (GWAS); however, the functional variants and the genes that they influence within those COPD GWAS loci have been found in a small minority of genomic regions. GWAS in COPD have identified several regional clusters of genetic association signals, most notably on chromosome 4q, where genome-wide significant loci near HHIP, FAM13A, GSTCD, TET2, and BTC have been discovered. These clustered GWAS regions could represent: 1) Independent genetic determinants influencing separate genes; 2) Multiple GWAS loci regulating the same gene; or 3) A regional network of coordinately regulated genes. If multiple COPD GWAS loci regulate the same gene, the biological impact of that gene in COPD pathogenesis would be increased. The primary goals of this project are to identify the functional genetic variants within the cluster of COPD GWAS loci on chromosome 4q; 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. We hypothesize that a regional network of genes on chromosome 4q is regulated by functional genetic variants within COPD GWAS loci that will influence COPD-related cellular phenotypes including cell death, cellular senescence, and/or inflammation. To address this hypothesis, we will start by identifying functional variants on chromosome 4q using massively parallel reporter assays in lung epithelial and monocyte/macrophage cell lines along with bioinformatic approaches with public and recently generated Omics and genetics data. We will then determine which gene or genes are influenced by these functional variants by performing circularized chromatin conformation capture (4C-Seq) and demonstrating effects of functional variants on gene expression of regional genes using CRISPR-Cas9 approaches. Finally, we will use cellular models to determine the effects of inactivating the functional variants and their regulated genes on COPD-related read-outs of cell death, cellular senescence, and inflammation. To accomplish these goals, a unique and highly integrated approach combining molecular studies of regulatory elements and functional cell-based assays has been developed that will likely provide important insights into COPD pathogenesis.