Characterization of a COPD-Associated NPNT Functional Splicing Genetic Variant in Human Lung Tissue via Long-Read Sequencing
Year: 2020
Type: preprint
Abstract: Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide. Genome-wide association studies (GWAS) have identified over 80 loci that are associated with COPD and emphysema, however for most of these loci the causal variant and gene are unknown. Here, we utilize lung splice quantitative trait loci (sQTL) data from the Genotype-Tissue Expression project (GTEx) and short read sequencing data from the Lung Tissue Research Consortium (LTRC) to characterize a locus in nephronectin ( NPNT ) associated with COPD case-control status and lung function. We found that the rs34712979 variant is associated with alternative splice junction use in NPNT , specifically for the junction connecting the 2nd and 4th exons (chr4:105898001-105927336) (p=4.02×10 −38 ). This association colocalized with GWAS data for COPD and lung spirometry measures with a posterior probability of 94%, indicating that the same causal genetic variants in NPNT underlie the associations with COPD risk, spirometric measures of lung function, and splicing. Investigation of NPNT short read sequencing revealed that rs34712979 creates a cryptic splice acceptor site which results in the inclusion of a 3 nucleotide exon extension, coding for a serine residue near the N-terminus of the protein. Using Oxford Nanopore Technologies (ONT) long read sequencing we identified 13 NPNT isoforms, 6 of which are predicted to be protein coding. Two of these are full length isoforms which differ only in the 3 nucleotide exon extension whose occurrence differs by genotype. Overall, our data indicate that rs34712979 modulates COPD risk and lung function by creating a novel splice acceptor which results in the inclusion of a 3 nucelotide sequence coding for a serine in the nephronectin protein sequence. Our findings implicate NPNT splicing in contributing to COPD risk, and identify a novel serine insertion in the nephronectin protein that warrants further study.
Source: medRxiv
Language: English
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Open Access status: green
Funders: University of Minnesota, Johns Hopkins University, University of Pittsburgh, Temple University, National Jewish Health, National Institutes of Health, University of California, San Diego, National Heart, Lung, and Blood Institute, National Institute of Mental Health, National Institute on Drug Abuse, National Human Genome Research Institute, NIH Office of the Director, National Cancer Institute, National Institute of General Medical Sciences, National Institute of Neurological Disorders and Stroke, Center for Tobacco Products, Common Fund
Awards: G1052645489, G2096685756, G2168838001, G232264632, G264675175, INTEGRATIVE GENOMICS OF CLINICAL SUBTYPES IN COPDGENE, G3078883119, G3194560040, Prospective Health Outcomes and Inflammatory Biomarkers Associated with e-Cigarette Use, G4030405119, Rare variants and NHLBI traits in deeply phenotyped cohorts, G5258357286, G5326023800, (2 of 2) Genetic Epidemiology of COPD, Using Integrative Genomics To Identify and Characterize Emphysema-Associated eQTL, G631129105, G6615318374, (1 of 2) Genetic Epidemiology of COPD, SYSTEMS GENOMICS OF THE ASTHMA-COPD OVERLAP SYNDROME, Studies of Rare Genetic Variation in the Isolated Population of Sardinia, G8354759825, G9000091268, G9000228787, Realizing the potential of long-read sequencing technology, Integrative 'Omics of Transcriptome Complexity in COPD, SYSTEMS APPROACHES TO THE EPIDEMIOLOGY, GENETICS AND GENOMICS OF LUNG DISEASES, Non-coding RNA structure change in Chronic Obstructive Pulmonary Disease
OpenAlex ID: W3094035009