title: 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.
authors.affiliation: Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet and University Hospital, Stockholm 171 77, Sweden.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Acevedo
authors.affiliation: Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden.
authors.forename: Lovisa E
authors.initials: LE
authors.lastname: Reinius
authors.affiliation: Systems Toxicology Team, Finnish Institute of Occupational Health, Helsinki 00250, Finland.
authors.forename: Dario
authors.initials: D
authors.lastname: Greco
authors.affiliation: Institute of Environmental Medicine.
authors.forename: Anna
authors.initials: A
authors.lastname: Gref
authors.affiliation: Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden.
authors.forename: Christina
authors.initials: C
authors.lastname: Orsmark-Pietras
authors.affiliation: Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden.
authors.forename: Helena
authors.initials: H
authors.lastname: Persson
authors.affiliation: Institute of Environmental Medicine.
authors.forename: Göran
authors.initials: G
authors.lastname: Pershagen
authors.affiliation: Department of Women's and Children's Health Centre of Allergy Research, Karolinska Institutet, Stockholm 171 77, Sweden Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm 171 64, Sweden.
authors.forename: Gunilla
authors.initials: G
authors.lastname: Hedlin
authors.affiliation: Institute of Environmental Medicine Centre of Allergy Research, Karolinska Institutet, Stockholm 171 77, Sweden Sachs' Children's Hospital, Södersjukhuset, Stockholm 118 83, Sweden and.
authors.forename: Erik
authors.initials: E
authors.lastname: Melén
authors.affiliation: Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet and University Hospital, Stockholm 171 77, Sweden.
authors.forename: Annika
authors.initials: A
authors.lastname: Scheynius
authors.affiliation: Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, University of Helsinki, Helsinki 00014, Finland.
authors.forename: Juha
authors.initials: J
authors.lastname: Kere
authors.affiliation: Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden Centre of Allergy Research, Karolinska Institutet, Stockholm 171 77, Sweden cilla.soderhall@ki.se.
authors.forename: Cilla
authors.initials: C
authors.lastname: Söderhäll
mesh_terms: D000293:Adolescent; D001249:Asthma / Q000097:blood / Q000235:genetics*; D002648:Child; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D006801:Humans; D051740:Ikaros Transcription Factor / Q000235:genetics*; D007223:Infant; D008297:Male; D008565:Membrane Proteins / Q000235:genetics*; D009363:Neoplasm Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011446:Prospective Studies; D012333:RNA, Messenger / Q000235:genetics*; D013548:Sweden; D000094524:Gasdermins
chemical_list: D051740:Ikaros Transcription Factor; D008565:Membrane Proteins; D009363:Neoplasm Proteins; D012333:RNA, Messenger; C527978:GSDMB protein, human; D000094524:Gasdermins; C106285:IKZF3 protein, human; C464399:ORMDL3 protein, human