Genomic Locus Tagged by Lung Function <scp>GWAS SNV</scp> rs12477314 (2q37.3) Acts as a Regulatory Region for a Systemic Inflammatory Phenotype

SNV rs12477314 (C>T; 1000G MAF = 0.14), which maps to an intergenic region on 2q37.3, is a genome-wide significant association signal for pulmonary function in genome-wide association study meta-analyses. Bioinformatic analysis revealed that the intergenic region in proximity to the sentinel SNV is enriched for histone methylation markers suggestive of active enhancer regions modifiable by DNA methylation. The aim of this study was to investigate the functionality of putative enhancer/s and their potential interaction with CpG islands in the genomic region tagged by rs12477314 and their relevance to lung disease, in particular COPD. Two independent CRISPR/Cas9n-targeted deletions of the putative enhancer/s were performed in an airway epithelial cell line (NCI-H460). Deletion clones were subjected to RNA-Seq, and differential expression gene (DEG) datasets were generated using the Cufflinks version 2.2.1 pipeline (p-FDR < 0.05). Biological pathway analysis was performed using Qiagen's Ingenuity Pathway Analysis. Associations with the blood proteome were explored in UK Biobank. Our results suggest that the deleted regions are co-acting enhancers regulating overlapping gene expression patterns. The DEG datasets from the two genomic deletions are enriched for similar canonical pathways, which may contribute to a pro-inflammatory phenotype. Pathway-based regulatory effects analysis of the two DEG datasets resulted in identifying potential downstream biological processes. There was overlap between the pathways identified in protein association datasets and the DEG datasets. Our results suggest that the genomic region tagged by SNV rs12477314 constitutes a regulatory region responsible for regulating biological pathways conducive to a systemic inflammatory phenotype.