Genetic variants with gene regulatory effects are associated with diisocyanate-induced asthma

• Published in: Journal of allergy and clinical immunology Vol. 142; no. 3; pp. 959 - 969
• Main Authors: Bernstein, David I., Lummus, Zana L., Kesavalu, Banu, Yao, Jianbo, Kottyan, Leah, Miller, Daniel, Cartier, André, Cruz, Maria-Jesús, Lemiere, Catherine, Muñoz, Xavier, Quirce, Santiago, Tarlo, Susan, Sastre, Joaquin, Boulet, Louis Philippe, Weirauch, Matthew T., Kaufman, Kenneth
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.09.2018; Elsevier Limited
• Subjects: Activating transcription factor 3; Alleles; Asthma; Bioinformatics; Cadherins; Cell lines; Deoxyribonucleic acid; diisocyanate; DNA; Electrophoretic mobility; electrophoretic mobility shift assay; functional genomics; Gene expression; Gene loci; Gene regulation; genetic; Genetic diversity; Genomes; histone; Histones; isocyanate; Isocyanates; luciferase assay; Mass spectroscopy; next-generation sequencing; occupational asthma; oligonucleotide; Oligonucleotides; Principal components analysis; Proteins; Single-nucleotide polymorphism; Software; Studies; Tachykinin; Tachykinin receptors; Western blotting; Workers; Zinc finger proteins; Canada; CEBPB; occupational asthma; GWAS; single nucleotide polymorphism; functional genomics; diisocyanate; electrophoretic mobility shift assay; OA; SNP; luciferase assay; EMSA; Nano-LC-MS/MS; ChIP-Seq; FAM71A; genetic; next-generation sequencing; ZBTB16; isocyanate; TACR1; SIC; Asthma; oligonucleotide; DAPA; MAF; gene regulation; bioinformatics; histone; NGS; CDH17; DA; ATF3
• ISSN: 0091-6749; 1097-6825; 1097-6825
• DOI: 10.1016/j.jaci.2018.06.022

Isocyanates are major causes of occupational asthma, but susceptibility and mechanisms of diisocyanate-induced asthma (DA) remain uncertain. The aim of this study was to identify DA-associated functional genetic variants through next-generation sequencing (NGS), bioinformatics, and functional assays. NGS was performed in 91 workers with DA. Fourteen loci with known DA-associated single nucleotide polymorphisms (SNPs) were sequenced and compared with data from 238 unexposed subjects. Ranking of DA-associated SNPs based on their likelihood to affect gene regulatory mechanisms in the lung yielded 21 prioritized SNPs. Risk and nonrisk oligonucleotides were tested for binding of nuclear extracts from A549, BEAS-2B, and IMR-90 lung cell lines by using electrophoretic mobility shift assays. DNA constructs were cloned into a pGL3 promoter vector for luciferase gene reporter assays. NGS detected 130 risk variants associated with DA (3.1 × 10−6 to 6.21 × 10−4), 129 of which were located in noncoding regions. The 21 SNPs prioritized by using functional genomic data sets were in or proximal to 5 genes: cadherin 17 (CDH17; n = 10), activating transcription factor 3 (ATF3; n = 7), family with sequence similarity, member A (FAM71A; n = 2), tachykinin receptor 1 (TACR1; n = 1), and zinc finger and BTB domain-containing protein 16 (ZBTB16; n = 1). Electrophoretic mobility shift assays detected allele-dependent nuclear protein binding in A549 cells for 8 of 21 variants. In the luciferase assay 4 of the 21 SNPs exhibited allele-dependent changes in gene expression. DNA affinity precipitation and mass spectroscopy of rs147978008 revealed allele-dependent binding of H1 histones, which was confirmed by using Western blotting. We identified 5 DA-associated potential regulatory SNPs. Four variants exhibited effects on gene regulation (ATF rs11571537, CDH17 rs2446824 and rs2513789, and TACR1 rs2287231). A fifth variant (FAM71A rs147978008) showed nonrisk allele preferential binding to H1 histones. These results demonstrate that many DA-associated genetic variants likely act by modulating gene regulation.