A Genome-wide Study of DNA Methylation in Nasal Epithelium and Atopy and Atopic Asthma in Children

Abstract

BACKGROUND: Up to 10-12% of U.S. children and adolescents report respiratory or skin allergies. Epigenetic mechanisms may alter the airway epithelial barrier and ultimately lead to atopic diseases. Here we aim to identify DNA methylation profiles that are associated with - and accurately classify - atopy and atopic asthma in school-aged children. METHODS: We conducted an epigenome-wide study of DNA methylation in nasal epithelium and atopy or atopic asthma in 482 Puerto Rican children. Significant methylation signals were correlated with gene expression, and top CpGs were validated by pyrosequencing. We then replicated our top methylation findings in a cohort including 72 predominantly African American children, and in another cohort including 432 children of European descent. Next, we tested nasal methylation-based classification models of atopy or atopic asthma in all cohorts. FINDINGS: DNA methylation profiles were markedly different between subjects with and without atopy. After adjustment for covariates and multiple testing, we found 8,664 differentially methylated CpGs by atopy, with P-values ranging from 9·58*e-17 to 2·18*e-22 for the top 30 CpGs. These CpGs are in or near genes relevant to epithelial barrier function, including CDHR3 (cadherin-related family member 3) and CDH26 (cadherin 26), and in other biologically plausible genes like FBXL7 (F-box and leucine-rich repeat protein 7), NTRK1 (neurotrophic receptor tyrosine kinase 1), and SLC9A3 (solute carrier family 9 member A3). Moreover, 28 of the top 30 CpGs replicated in both cohorts. Nasal methylation-based classification models of atopy and atopic asthma performed well in the Puerto Rico cohort (area under the curve=0·93-0·94 and accuracy=85%-88%) and in both replication cohorts (AUC=0·74-0·92, accuracy=68%-82%). INTERPRETATION: We have identified methylation profiles in airway epithelium that are associated with atopy and atopic asthma in children, and a nasal methylation profile that classified children by atopy or atopic asthma. This panel performed well in three independent cohorts from different ethnic/racial backgrounds. Funding: This study was supported by grants HL079966, HL117191, and MD011764 (PI: Celedon JC) from the National Heart, Lung, and Blood Institute (NHLBI) of the U.S. National Institutes of Health (NIH). Dr. Forno’s contribution was supported by NIH grant HL125666. Dr. Celedon’s contribution was additionally supported by The Heinz Endowments. Research operations at the University of Puerto Rico were additionally supported by grant U54MD007587 from the National Institute on Minority Health and Health Disparities (NIMHD) and the National Institute of Allergy and Infectious Diseases (NIAID) of the U.S. NIH. PIAMA was supported by The Netherlands Organization for Health Research and Development; The Netherlands Organization for Scientific Research; The Netherlands Lung Foundation (with methylation studies supported by AF 4.1.14.001); The Netherlands Ministry of Spatial Planning, Housing, and the Environment; and The Netherlands Ministry of Health, Welfare, and Sport. Dr. Qi is supported by a grant from the China Scholarship Council. Declaration of Interest: Dr. Celedon has received research materials from Merck, GSK and Pharmavite, to provide medications free of cost to participants in NIH-funded studies, unrelated to the current work. The other authors report no conflicts of interest. Ethical Approval: The study was approved by the institutional review boards of the University of Puerto Rico (San Juan, PR) and the University of Pittsburgh (Pittsburgh, PA).