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

项目摘要 超过20个与慢性阻塞性肺疾病（COPD）易感性相关的基因组区域， 使用全基因组关联研究（GWAS）发现;然而，功能变体和 在这些COPD GWAS基因座内，它们影响的基因已经在少数基因组区域中发现。 COPD中的GWAS已经确定了几个遗传关联信号的区域集群，最值得注意的是 染色体4 q，其中HHIP、FAM 13 A、GSTCD、TET 2和BTC附近的全基因组显著位点已被发现。 发现了这些聚集的GWAS区域可以代表：1）独立的遗传决定因素影响 2）多个GWAS基因座调控同一基因;或3）一个区域性的协调网络， 调控基因如果多个COPD GWAS基因座调节相同的基因，则该基因在 COPD的发病率会增加。该项目的主要目标是确定功能性遗传 染色体4 q上COPD GWAS基因座簇内的变异;以鉴定受这些变异影响的关键基因。 功能性变异;并评估这些关键基因和功能性遗传变异对COPD的影响 发病机制我们假设染色体4 q上的区域基因网络是由功能性的 COPD GWAS基因座内的遗传变异将影响COPD相关的细胞表型，包括细胞 死亡、细胞衰老和/或炎症。为了解决这个假设，我们将首先确定 在肺上皮细胞中使用大规模平行报告基因测定染色体4 q上的功能变体， 单核细胞/巨噬细胞系沿着生物信息学方法与公共和最近生成的组学 和遗传学数据。然后，我们将确定哪些基因或基因受到这些功能变体的影响， 进行环化染色质构象捕获（4C-Seq）并证明功能性 使用CRISPR-Cas9方法对区域基因的基因表达进行变异。最后，我们将使用蜂窝 模型，以确定失活功能变体及其调节基因对COPD相关性的影响。 细胞死亡、细胞衰老和炎症的读数。为了实现这些目标，一个独特的，高度 结合调控元件的分子研究和基于功能细胞的测定的综合方法， 这将可能为COPD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.