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

染色体 4q 上 COPD GWAS 信号簇的遗传和功能剖析

基本信息

批准号：
10403423
负责人：
MICHAEL H. CHO
金额：
$ 88.26万
依托单位：
BRIGHAM AND WOMEN'S HOSPITAL
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-05-01 至 2024-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10403423
关键词：
Address Affect Bioinformatics Biological Biological Assay Biological Process CRISPR/Cas technology Cell Aging Cell Death Cell Line Cell model Cells Chromatin Chromatin Conformation Capture and Sequencing Chromosome 4 Chromosomes Chronic Obstructive Pulmonary Disease Complex Data Disease Disease susceptibility Dissection Distant Epigenetic Process Epithelial Gene Expression Genes Genetic Genetic Determinism Genetic Diseases Genetic Predisposition to Disease Genomic Segment Goals Individual Inflammation Laboratories Link Lung Mediating Minority Molecular Pathogenesis Phenotype Public Health Regulatory Element Reporter Research Signal Transduction Source Structure of parenchyma of lung Trans-Omics for Precision Medicine U937 Cells Variant Work base cell type chromosome conformation capture cigarette smoking disorder risk gene network genetic association genetic variant genome sequencing genome wide association study genome-wide genomic locus insight macrophage monocyte transcriptome sequencing transcriptomics whole genome

项目摘要

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.

项目概要超过 20 个与慢性阻塞性肺疾病 (COPD) 易感性相关的基因组区域通过全基因组关联研究 (GWAS) 发现；然而，功能变体和在少数基因组区域中发现了它们在 COPD GWAS 位点内影响的基因。慢性阻塞性肺疾病 (COPD) 中的 GWAS 已确定了几个区域性遗传关联信号簇，最显着的是染色体 4q，其中 HHIP、FAM13A、GSTCD、TET2 和 BTC 附近的全基因组重要位点已被发现了。这些聚集的 GWAS 区域可以代表： 1) 影响的独立遗传决定因素分离的基因； 2）多个GWAS位点调控同一基因；或 3) 协调的区域网络调控基因。如果多个 COPD GWAS 位点调节同一基因，则该基因的生物学影响 COPD的发病机制将会增加。该项目的主要目标是确定功能遗传染色体 4q 上 COPD GWAS 基因座簇内的变异；以确定受这些影响的关键基因功能变体；并评估这些关键基因和功能性遗传变异对慢性阻塞性肺病的影响发病。我们假设 4q 染色体上的基因区域网络受到功能性调控 COPD GWAS 位点内的遗传变异将影响 COPD 相关细胞表型，包括细胞死亡、细胞衰老和/或炎症。为了解决这个假设，我们首先要确定使用肺上皮和肺上皮细胞中的大规模平行报告基因检测来确定染色体 4q 上的功能变异单核细胞/巨噬细胞系以及公共和最近生成的组学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受到这些功能变异的影响执行环状染色质构象捕获 (4C-Seq) 并展示功能性的影响使用 CRISPR-Cas9 方法改变区域基因的基因表达。最后，我们将使用蜂窝确定功能变异及其调控基因失活对 COPD 相关疾病的影响的模型读取细胞死亡、细胞衰老和炎症。为了实现这些目标，一个独特且高度结合调节元件的分子研究和基于功能细胞的测定的综合方法的开发可能将为 COPD 发病机制提供重要的见解。