Global Hypomethylation in Childhood Asthma Identified by Genome-Wide DNA-Methylation Sequencing Preferentially Affects Enhancer Regions

To assess the impact of epigenetic regulation in the development of asthma through whole genome bisulfite sequencing used to characterize global DNA-methylation profiles of asthmatic children compared with healthy controls.Data and samples were derived from 3 different birth cohorts: LINA, LISA, and PASTURE (defined in Fig 1 legend). Forty asthmatic and 42 age- and sex-matched control children ages 5 to 15 years old were included in this study.For 48 children examined at the time of an established asthma phenotype, peripheral blood was obtained to analyze with paired cord blood DNA samples that were available (n = 23 asthma, n = 25 controls) and run through WGBS. Differentially methylated regions (DMRs) were categorized in groups as genotype-associated, cell-type-dependent, or prenatally primed. Identification of genes in networks previously associated with asthma-related outcomes was performed using natural language processing via search filters in PubMed and PubMed Central open access literature databases. In addition, cluster analysis of DMR-associated genes, including all enhancer DMR target genes and genes closest to the next transcription start site, was performed. Targeted analysis of functional translation of epigenetic regulation was examined at the transcriptional and protein levels.In all, 158 DMRs were identified in asthmatic children compared with controls, of which 37% were related to the proportion of blood eosinophils. A global hypomethylation (all except 2 DMRs) was discovered affecting mainly enhancer regions and regulating key immune genes, such as IL-4, IL5-RA, and EPX (eosinophil peroxidase). The DMRs were found in 267 samples and could be linked to aberrant gene expression. Within the group of 158 DMRs, 56 were perturbed already at birth and linked to some extent to prenatal exposures, such as to tobacco smoke or phthalates. DMRs showed enrichment for 20 binding motifs related to different transcription factors previously associated with asthma, including the Th2 master regulator GATA3. Two-thirds of the DMRs were in genomic regulatory elements, with 74% intersecting with enhancers versus 1% with promoters. Cord blood DNA-hypomethylation of several regions involved in the LFA-1 signaling cascade was observed and may contribute to a higher risk for asthma development.This is a novel epigenetic study based on whole genome sequencing that has shown that marked dysregulation of enhancer regions occurs in childhood asthma.As whole genomic sequencing becomes more readily available and affordable, identification of genetic and epigenetic risk factors for the development of asthma may be used for preventative interventions. This study illustrates how children at high risk may be identified using several complementary analyses of asthma-related DMRs.