DNA methylation in childhood asthma: an epigenome-wide meta-analysis

Summary Background DNA methylation profiles associated with childhood asthma might provide novel insights into disease pathogenesis. We did an epigenome-wide association study to assess methylation profiles associated with childhood asthma. Methods We did a large-scale epigenome-wide association study (EWAS) within the Mechanisms of the Development of ALLergy ( MeDALL) project. We examined epigenome-wide methylation using Illumina Infinium Human Methylation450 BeadChips (450K) in whole bloodin 207 children with asthma and 610 controls at age 4–5 years, and 185 children with asthma and 546 controls at age 8 years using a cross-sectional case-control design. After identification of differentially methylated CpG sitesin the discovery analysis, we did a validation study in children (4–16 years; 247 cases and 2949 controls) from six additional European cohorts and meta-analysed the results. We next investigated whether replicated CpG sitesin cord blood predict later asthma in 1316 children. We subsequently investigated cell-type-specific methylation of the identified CpG sitesin eosinophils and respiratory epithelial cells and their related gene-expression signatures. We studied cell-type specificity of the asthma association of the replicated CpG sitesin 455 respiratory epithelial cell samples, collected by nasal brushing of 16-year-old children as well as in DNA isolated from blood eosinophils (16 with asthma, eight controls [age 2–56 years]) and compared this with whole-bloodDNA samples of 74 individuals with asthma and 93 controls (age 1–79 years). Whole-bloodtranscriptional profiles associated with replicated CpG siteswere annotated using RNA-seq data of subsets of peripheral blood mononuclear cells sortedby fluorescence-activated cell sorting. Findings 27 methylated CpG siteswere identified in the discovery analysis. 14 of these CpG siteswere replicated and passed genome-wide significance (p −7 ) after meta-analysis. Consistently lower methylation levels were observed at all associated loci across childhood from age 4 to 16 years in participants with asthma, but not in cord blood at birth. All 14 CpG siteswere significantly associated with asthma in the second replication study using whole-bloodDNA, and were strongly associated with asthma in purified eosinophils. Whole-bloodtranscriptional signatures associated with these CpG sitesindicated increased activation of eosinophils, effector and memory CD8 T cells and natural killer cells, and reduced number of naive T cells. Five of the 14 CpG siteswere associated with asthma in respiratory epithelial cells, indicating cross-tissue epigenetic effects. Interpretation Reduced whole-bloodDNA methylation at 14 CpG sitesacquired after birth was strongly associated with childhood asthma. These CpG sitesand their associated transcriptional profiles indicate activation of eosinophils and cytotoxic T cellsin childhood asthma. Our findings merit further investigations of the role of epigenetics in a clinical context. Funding EU and the Seventh Framework Programme (the MeDALLproject).