Identification of Functional Variants in the FAM13A Chronic Obstructive Pulmonary Disease Genome-Wide Association Study Locus by Massively Parallel Reporter Assays

作者：Peter J. Castaldi, Feng Guo, Dandi Qiao, Fei Du, Zun Zar Chi Naing, Yan Li, Betty Pham, Tarjei S. Mikkelsen, Michael H. Cho, Edwin K. Silverman, Xiaobo Zhou · 发表于：American Journal of Respiratory and Critical Care Medicine · 年份：2018 · DOI：10.1164/rccm.201802-0337oc · 被引用次数：52 · 研究领域：Chronic Obstructive Pulmonary Disease (COPD) Research、Genetic Associations and Epidemiology、Genomics and Rare Diseases

RATIONALE: The identification of causal variants responsible for disease associations from genome-wide association studies (GWASs) facilitates functional understanding of the biological mechanisms by which those genetic variants influence disease susceptibility. OBJECTIVE: We aim to identify causal variants in or near the FAM13A (family with sequence similarity member 13A) GWAS locus associated with chronic obstructive pulmonary disease (COPD). METHODS: We used an integrated approach featuring conditional genetic analysis, massively parallel reporter assays (MPRAs), traditional reporter assays, chromatin conformation capture assays, and clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing to characterize COPD-associated regulatory variants in the FAM13A region in human bronchial epithelial cell lines. MEASUREMENTS AND MAIN RESULTS: Conditional genetic association suggests the presence of two independent COPD association signals in FAM13A. MPRAs identified 45 regulatory variants within FAM13A, among which six variants were prioritized for further investigation. Three COPD-associated variants demonstrated significant allele-specific activity in reporter assays. One of three variants, rs2013701, was tested in the endogenous genomic context by CRISPR-based genome editing that confirmed its allele-specific effects on FAM13A expression and on cell proliferation, providing functional characterization for this COPD-associated variant. CONCLUSIONS: The...