Identifying CpG sites associated with eczema via random forest screening of epigenome-scale DNA methylation

Abstract

Background: The prevalence of eczema is increasing in industrialized nations. Limited evidence has shown the association of DNA methylation (DNA-M) with eczema. We explored this association at the epigenome-scale to better understand the role of DNA-M. Data from the first generation (F 1) of the Isle of Wight (IoW) birth cohort participants and the second generation (F 2) were examined in our study. Epigenome-scale DNA methylation of F 1 at age 18 years and F 2 in cord blood was measured using the Illumina Infinium HumanMethylation450 Beadchip. A total of 307,357 cytosine-phosphate-guanine sites (CpGs) in the F 1 generation were screened via recursive random forest (RF) for their potential association with eczema at age 18. Functional enrichment and pathway analysis of resulting genes were carried out using DAVID gene functional classification tool. Log-linear models were performed in F 1 to corroborate the identified CpGs. Findings in F 1 were further replicated in F 2. Results: The recursive RF yielded 140 CpGs, 88 of which showed statistically significant associations with eczema at age 18, corroborated by log-linear models after controlling for false discovery rate (FDR) of 0.05. These CpGs were enriched among many biological pathways, including pathways related to creating transcriptional variety and pathways mechanistically linked to eczema such as cadherins, cell adhesion, gap junctions, tight junctions, melanogenesis, and apoptosis. In the F 2 generation, about half of the 83 CpGs identified in F 1 showed the same direction of association with eczema risk as in F 1, of which two CpGs were significantly associated with eczema risk, cg04850479 of the PROZ gene (risk ratio (RR) = 15.1 in F 1, 95 % confidence interval (CI) 1.71, 79.5; RR = 6.82 in F 2, 95 % CI 1.52, 30.62) and cg01427769 of the NEU1 gene (RR = 0.13 in F 1, 95 % CI 0.03, 0.46; RR = 0.09 in F 2, 95 % CI 0.03, 0.36). Conclusions: Via epigenome-scaled analyses using recursive RF followed by log-linear models, we identified 88 CpGs associated with eczema in F 1, of which 41 were replicated in F 2. Several identified CpGs are located within genes in biological pathways relating to skin barrier integrity, which is central to the pathogenesis of eczema. Novel genes associated with eczema risk were identified (e.g., the PROZ and NEU1 genes).