Integrative genomics analysis identifies ACVR1B as a candidate causal gene of emphysema distribution in non-alpha 1-antitrypsin deficient smokers

For the COPDGene Investigators

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Several genetic risk loci associated with emphysema apico-basal distribution (EABD) have been identified through genome-wide association studies (GWAS), but the biological functions of these variants are unknown. To characterize gene regulatory functions of EABD-associated variants, we integrated EABD GWAS results with 1) a multi-tissue panel of expression quantitative trait loci (eQTL) from subjects with COPD and the GTEx project and 2) epigenomic marks from 127 cell types in the Roadmap Epigenomics project. Functional validation was performed for a variant near ACVR1B. Results: SNPs from 168 loci with P-values < 5× 10-5in the largest GWAS meta-analysis of EABD (Boueiz A. et al, AJRCCM 2017) were analyzed. 54 loci overlapped eQTL regions from our multi-tissue panel, and 7 of these loci showed a high probability of harboring a single, shared GWAS and eQTL causal variant (colocalization posterior probability≥0.9). 17 cell types exhibited greater than expected overlap between EABD loci and DNase-I hypersensitive peaks, DNaseI hotspots, enhancer marks, or digital DNaseI footprints (permutation P-value < 0.05), with the strongest enrichment observed in CD4+, CD8+, and regulatory T cells. A region near ACVR1B demonstrated significant colocalization with a lung eQTL and overlapped DNase-I hypersensitive regions in multiple cell types, and reporter assays in human bronchial epithelial cells confirmed allele-specific regulatory activity for the lead variant, rs7962469. Conclusions: Integrative analysis highlights candidate causal genes, regulatory variants, and cell types that may contribute to the pathogenesis of emphysema distribution. These findings will enable more accurate functional validation studies and better understanding of emphysema distribution biology.

Original languageEnglish (US)
JournalUnknown Journal
DOIs
StatePublished - Sep 22 2017

Keywords

  • Chronic obstructive pulmonary disease
  • Emphysema
  • Emphysema distribution
  • Integrative genomics

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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