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.
The identification of novel susceptibility genes for chronic obstructive pulmonary disease (COPD) could transform our understanding of this disease and provide new targets for personalized treatments. We will identify the functional genetic variants located within five regions of the genome that have been implicated in COPD pathogenesis by genome-wide association studies. We will also determine the genes that these functional variants influence and the biological mechanisms by which these genes and their functional variants impact COPD susceptibility.
|Sakornsakolpat, Phuwanat; Morrow, Jarrett D; Castaldi, Peter J et al. (2018) Integrative genomics identifies new genes associated with severe COPD and emphysema. Respir Res 19:46|
|Prokopenko, Dmitry; Sakornsakolpat, Phuwanat; Fier, Heide Loehlein et al. (2018) Whole-Genome Sequencing in Severe Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 59:614-622|