Epigenome-wide association study of DNA methylation and adult asthma in the Agricultural Lung Health Study.

Epigenome-wide studies of methylation in children support a role for epigenetic mechanisms in asthma; however, studies in adults are rare and few have examined non-atopic asthma. We conducted the largest epigenome-wide association study (EWAS) of blood DNA methylation in adults in relation to non-atopic and atopic asthma.We measured DNA methylation in blood using the Illumina MethylationEPIC array among 2286 participants in a case-control study of current adult asthma nested within a United States agricultural cohort. Atopy was defined by serum specific immunoglobulin E (IgE). Participants were categorised as atopy without asthma (n=185), non-atopic asthma (n=673), atopic asthma (n=271), or a reference group of neither atopy nor asthma (n=1157). Analyses were conducted using logistic regression.No associations were observed with atopy without asthma. Numerous cytosine-phosphate-guanine (CpG) sites were differentially methylated in non-atopic asthma (eight at family-wise error rate (FWER) p<9×10 ^-8 , 524 at false discovery rate (FDR) less than 0.05) and implicated 382 novel genes. More CpG sites were identified in atopic asthma (181 at FWER, 1086 at FDR) and implicated 569 novel genes. 104 FDR CpG sites overlapped. 35% of CpG sites in non-atopic asthma and 91% in atopic asthma replicated in studies of whole blood, eosinophils, airway epithelium, or nasal epithelium. Implicated genes were enriched in pathways related to the nervous system or inflammation.We identified numerous, distinct differentially methylated CpG sites in non-atopic and atopic asthma. Many CpG sites from blood replicated in asthma-relevant tissues. These circulating biomarkers reflect risk and sequelae of disease, as well as implicate novel genes associated with non-atopic and atopic asthma.
Competing Interests: Conflict of interest: T.T. Hoang has nothing to disclose. Conflict of interest: S. Sikdar has nothing to disclose. Conflict of interest: C-J. Xu has nothing to disclose. Conflict of interest: M.K. Lee has nothing to disclose. Conflict of interest: J. Cardwell has nothing to disclose. Conflict of interest: E. Forno has nothing to disclose. Conflict of interest: M. Imboden has nothing to disclose. Conflict of interest: A. Jeong has nothing to disclose. Conflict of interest: A-M. Madore has nothing to disclose. Conflict of interest: C. Qi has nothing to disclose. Conflict of interest: T. Wang has nothing to disclose. Conflict of interest: B.D. Bennett has nothing to disclose. Conflict of interest: J.M. Ward has nothing to disclose. Conflict of interest: C.G. Parks has nothing to disclose. Conflict of interest: L.E. Beane-Freeman has nothing to disclose. Conflict of interest: D. King has nothing to disclose. Conflict of interest: A. Motsinger-Reif reports intramural research funding from the National Institute of Environmental Health Sciences, during the conduct of the study. Conflict of interest: D.M. Umbach has nothing to disclose. Conflict of interest: A.B. Wyss has nothing to disclose. Conflict of interest: D.A. Schwartz reports grants from the National Institutes of Health/National Heart, Lung, and Blood Institute (R38-HL143511, T32-HL007085, UG3/UH3-HL151865 and R01-HL149836) and the Dept of Defense Focused Program (12899593), during the conduct of the study; personal fees for consultancy from Eleven P15 Inc., outside the submitted work; and has a patent “Compositions and methods of treating or preventing fibrotic diseases” pending, a patent “Biomarkers for the diagnosis and treatment of fibrotic lung disease” pending and a patent “Methods and compositions for risk prediction, diagnosis, prognosis, and treatment of pulmonary disorders” issued. Conflict of interest: J.C. Celedón has received research materials from Pharmavite (vitamin D and placebo capsules) and GSK (inhaled steroids), in order to provide medications free of cost to participants in National Institutes of Health funded studies, unrelated to the current work. Conflict of interest: C. Laprise has nothing to disclose. Conflict of interest: C. Ober has nothing to disclose. Conflict of interest: N. Probst-Hensch has nothing to disclose. Conflict of interest: I.V. Yang is a consultant to Eleven P15 Inc., a start-up company that is focused on the early recognition and treatment of pulmonary fibrosis. Conflict of interest: G.H. Koppelman reports grants from the Lung Foundation of the Netherlands, the TETRI Foundation, TEVA the Netherlands, GSK, Vertex and the Ubbo Emmius Foundation, outside the submitted work; and has participated in advisory boards for GSK and PURE IMS, outside the submitted work. Conflict of interest: S.J. London has nothing to disclose.
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