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

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

卷:142

Article

Bernstein, David I.¹  Lummus, Zana L.¹  Kesavalu, Banu¹  Yao, Jianbo³  Kottyan, Leah²  Miller, Daniel⁴  Cartier, Andre^6,7  Cruz, Maria-Jesus⁸  Lemiere, Catherine^6,7  Munoz, Xavier⁸  Quirce, Santiago^10,9  Tarlo, Susan¹¹  Sastre, Joaquin^9,12  Boulet, Louis Philippe¹³  Weirauch, Matthew T.^2,4,5  Kaufman, Kenneth^2,4,14 

[1] Univ Cincinnati, Coll Med, Div Immunol Allergy & Rheumatol, Cincinnati, OH USA

[2] Univ Cincinnati, Coll Med, Dept Pediat, Cincinnati, OH USA

[3] West Virginia Univ, Div Anim & Nutr Sci, Morgantown, WV USA

[4] Cincinnati Childrens Hosp Med Ctr, Ctr Autoimmune Genom & Etiol, Cincinnati, OH 45229 USA

[5] Cincinnati Childrens Hosp Med Ctr, Div Biomed Informat & Dev Biol, Cincinnati, OH 45229 USA

[6] Univ Montreal, Dept Med, Montreal, PQ, Canada

[7] Hop Sacre Coeur Montreal, Div Resp, Montreal, PQ, Canada

[8] Hosp Valle De Hebron, Resp Dept, Barcelona, Spain

[9] CIBER Enfermedades Resp CIBERES, Madrid, Spain

[10] Hosp La Paz, IdiPAZ, Dept Allergy, Madrid, Spain

[11] Univ Toronto, Dept Med, Toronto, ON, Canada

[12] Fdn Jimenez Diaz, Dept Allergy, Madrid, Spain

[13] Univ Laval, Hop Laval, Inst Univ Cardiol & Pneumol Quebec, Ste Foy, PQ, Canada

[14] Cincinnati VA Med Ctr, Cincinnati, OH USA

关键词: Asthma;    bioinformatics;    diisocyanate;    electrophoretic mobility shift assay;    functional genomics;    gene regulation;    genetic;    his tone;    isocyanate;    luciferase assay;    next-generation sequencing;    occupational asthma;    oligonucleotide;    single nucleotide polymorphism;   

DOI  :  10.1016/j.jaci.2018.06.022

来源: Elsevier

【 摘 要 】

Background: Isocyanates are major causes of occupational asthma, but susceptibility and mechanisms of diisocyanate-induced asthma (DA) remain uncertain. Objective: The aim of this study was to identify DA-associated functional genetic variants through next-generation sequencing (NGS), bioinformatics, and functional assays. Methods: 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. Results: NGS detected 130 risk variants associated with DA (3.1 x 10-6 to 6.21 X 10-i), 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. Conclusions: 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.

【 授权许可】

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