Rationale Genome-wide association studies (GWAS) have identified multiple genetic loci associated with chronic obstructive pulmonary disease (COPD). When integrated with GWAS results, expression quantitative trait locus (eQTL) studies can provide insight into biological mechanisms involved in disease by identifying single nucleotide polymorphisms (SNPs) that contribute to whole gene expression. However, there are multiple genetically driven regulatory and isoform-specific effects which cannot be detected in traditional eQTL analyses. Here, we identify SNPs that are associated with alternative splicing (sQTL) in addition to eQTLs to identify novel functions for COPD associated genetic variants.

Methods We performed RNA sequencing on whole blood from 3743 subjects in the COPDGene Study. RNA sequencing data from lung tissue of 1241 subjects from the Lung Tissue Research Consortium (LTRC), and whole genome sequencing data on all subjects. Associations between all SNPs within 1000 kb of a gene (cis-) and splice and gene expression quantifications were tested using tensorQTL. In COPDGene a total of 11,869,333 SNPs were tested for association with 58,318 splice clusters, and 8,792,206 SNPs were tested for association with 70,094 splice clusters in LTRC. We assessed colocalization with COPD-associated SNPs from a published GWAS[1].

Results After adjustment for multiple statistical testing, we identified 28,110 splice-sites corresponding to 3,889 unique genes that were significantly associated with genotype in COPDGene whole blood, and 58,258 splice-sites corresponding to 10,307 unique genes associated with genotype in LTRC lung tissue. We found 7,576 sQTL splice-sites corresponding to 2,110 sQTL genes were shared between whole blood and lung, while 20,534 sQTL splice-sites in 3,518 genes were unique to blood and 50,682 splice-sites in 9,677 genes were unique to lung. To determine what proportion of COPD-associated SNPs were associated with transcriptional splicing, we performed colocalization analysis between COPD GWAS and sQTL data, and found that 38 genomic windows, corresponding to 38 COPD GWAS loci had evidence of colocalization between QTLs and COPD. The top five colocalizations between COPD and lung sQTLs include NPNT, FBXO38, HHIP, NTN4 and BTC.

Conclusions A total of 38 COPD GWAS loci contain evidence of sQTLs, suggesting that analysis of sQTLs in whole blood and lung tissue can provide novel insights into disease mechanisms.

CPH has received grant funding from the Alpha-1 Foundation, Bayer, Boehringer-Ingelheim and Vertex, and consulting fees from Chiesi, Sanofi, and Takeda. MHC has received grant funding from Bayer. Edwin K. Silverman received grant support from Bayer and Northpond Laboratories. PJC has received consulting fees from Verona Pharmaceuticals and grant support from Bayer and Sanofi.

This work was funded by K01HL157613, R01HL157879, P01HL114501, X01HL139404, R01HL124233, R01HL126596, R01HL153248, R01HL149861, R01 HL111527HL135142, and NIGMS R35 GM140844. The COPDGene study (NCT00608764) is supported by grants from the NHLBI (U01HL089897 and U01HL089856), by NIH contract 75N92023D00011, and by the COPD Foundation through contributions made to an Industry Advisory Committee that has included AstraZeneca, Bayer Pharmaceuticals, Boehringer-Ingelheim, Genentech, GlaxoSmithKline, Novartis, Pfizer and Sunovion.

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IRB of Brigham and Women's Hospital gave ethical approval for this work.

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LTRC genotyping data are available on dbGaP with accession number phs001662.v1.p1 LTRC RNA-seq data are available through TOPMed, https://topmed.nhlbi.nih.gov.COPDGene data are available on dbGaP with accession numbers phs000179 and phs000765.

https://copd-moloc.bwh.harvard.edu/