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

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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.