Risk of childhood asthma is associated with CpG-site polymorphisms, regional DNA methylation and mRNA levels at the GSDMB/ORMDL3 locus

Abstract

Single-nucleotide polymorphisms (SNPs) in GSDMB (Gasdermin B) and ORMDL3 (ORMDL sphingolipid biosynthesis regulator 3) are strongly associated with childhood asthma, but the molecular alterations contributing to disease remain unknown. We investigated the effects of asthma-associated SNPs on DNA methylation and mRNA levels of GSDMB and ORMDL3. Genetic association between GSDMB/ORMDL3 and physician-diagnosed childhood asthma was confirmed in the Swedish birth-cohort BAMSE. CpG-site SNPs (rs7216389 and rs4065275) showed differences in DNA methylation depending on carrier status of the risk alleles, and were significantly associated with methylation levels in two CpG sites in the 5′ UTR (untranslated region) of ORMDL3. In the Swedish Search study, we found significant differences in DNA methylation between asthmatics and controls in five CpG sites; after adjusting for lymphocyte and neutrophil cell counts, three remained significant: one in IKZF3 [IKAROS family zinc finger 3 (Aiolos); cg16293631] and two in the CpG island (CGI) of ORMDL3 (cg02305874 and cg16638648). Also, cg16293631 and cg02305874 correlated with mRNA levels of ORMDL3. The association between methylation and asthma was independent of the genotype in rs7216389, rs4065275 and rs12603332. Both SNPs and CpG sites showed significant associations with ORMDL3 mRNA levels. SNPs influenced expression independently of methylation, and the residual association between methylation and expression was not mediated by these SNPs. We found a differentially methylated region in the CGI shore of ORMDL3 with six CpG sites less methylated in CD8+ T-cells. In summary, this study supports that there are differences in DNA methylation at this locus between asthmatics and controls; and both SNPs and CpG sites are independently associated with ORMDL3 expression.

Differential DNA methylation identified in the blood and retina of AMD patients

“…These methylation differences are on the order of changes observed in other recent studies. For example, significant methylation differences of »5% were seen in the brains of multiple sclerosis patients, 35 and the blood of patients with schizophrenia 36 and asthma, 37 suggesting that very small differences could have important functional implications in disease pathology. Likewise, relatively small methylation differences have be linked to changes in gene expression, which hint at potential functional effects of our observed methylation differences.…”

“…meQTL analysis in Illumina 450K samples Observed high-quality genotypes on 290 subjects with Illumina 450k data (out of 298, 97.3%) were obtained from dbGaP (accession: phs000182.v2.p1). SNPs on chromosome 10 were phased using ShapeIT, 37 and the 6 megabase area flanking the AMD risk SNP (chr10:121214448-127214448) was imputed up to the latest 1000 Genomes Phase 3 reference panel using Impute2 38 to obtain genotype calls for rs10490924 and rs72631113. Using the previously calculated surrogate variables (SVs, see above), we performed meQTL analyses separately within AMD patients (NV and GA together) and controls, at both SNPs, using the linear model of the form: Meth j D a C bSNP j C zSV j C e j for person j.…”

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“…TSLP is expressed primarily by epithelial cells at barrier surfaces such as the skin, gut and lung in response to danger signals. TSLP genetic variants strongly support the role of both genetic and epigenetic factors contributing to asthma susceptibility in the 17q21 locus [9,10].…”

The role of ORMDL proteins, guardians of cellular sphingolipids, in asthma

“…childhood-onset asthma (48). Thus, regulation of ORMDL3 expression in patients with asthma is affected by histone modifications and binding of transcription factors.…”