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

B M Quraishi,A Kaushal,G A Lockett,M Ray,W Karmaus,J W Holloway,F I Rezwan,S R Tetali,H Zhang,T M Everson,S H Arshad

doi:10.1186/s13148-015-0108-y

Abstract

BackgroundThe 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 (F1) of the Isle of Wight (IoW) birth cohort participants and the second generation (F2) were examined in our study. Epigenome-scale DNA methylation of F1 at age 18 years and F2 in cord blood was measured using the Illumina Infinium HumanMethylation450 Beadchip. A total of 307,357 cytosine-phosphate-guanine sites (CpGs) in the F1 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 F1 to corroborate the identified CpGs. Findings in F1 were further replicated in F2.ResultsThe 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 F2 generation, about half of the 83 CpGs identified in F1 showed the same direction of association with eczema risk as in F1, of which two CpGs were significantly associated with eczema risk, cg04850479 of the PROZ gene (risk ratio (RR) = 15.1 in F1, 95 % confidence interval (CI) 1.71, 79.5; RR = 6.82 in F2, 95 % CI 1.52, 30.62) and cg01427769 of the NEU1 gene (RR = 0.13 in F1, 95 % CI 0.03, 0.46; RR = 0.09 in F2, 95 % CI 0.03, 0.36).ConclusionsVia epigenome-scaled analyses using recursive RF followed by log-linear models, we identified 88 CpGs associated with eczema in F1, of which 41 were replicated in F2. 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).Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-015-0108-y) contains supplementary material, which is available to authorized users.

Highlights

The prevalence of eczema is increasing in industrialized nations
For the identified cytosine-phosphate-guanine sites (CpGs) via the random forest (RF)-based method, we further examined their statistical significance on their linear association with eczema risk at age 18 years using log-linear models and replicated the findings from the F1 in the second generation (F2)
Eczema frequencies in F1 (18 years) and in F2 (3, 6, and 12 months) generations stratified by sex indicated that females had higher eczema prevalence than males at 18 years of age in the F1 generation, and the prevalence switched in the newborns of the F2 generation (Table 1)

Summary

Introduction

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. Epigenome-scale DNA methylation of F1 at age 18 years and F2 in cord blood was measured using the Illumina Infinium HumanMethylation450 Beadchip. A total of 307,357 cytosine-phosphate-guanine sites (CpGs) in the F1 generation were screened via recursive random forest (RF) for their potential association with eczema at age 18. The increasing prevalence of allergic conditions including eczema is a major public health concern in industrialized nations [1]. The Illumina Infinium HumanMethylation450 Beadchip has the ability to measure DNA methylation at more than 450 K cytosine-phosphate-guanine sites (CpGs), which provides rich information for various epigenetic studies. A recent review published in 2014 by Paul et al highlighted the potential challenges in the field of epigenomics [9] such as study design, methodologies of obtaining biologic samples, high dimensionality, and highly correlated data [9, 10]

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Conclusion