title: Whole-Genome Saliva and Blood DNA Methylation Profiling in Individuals with a Respiratory Allergy.
abstract: The etiology of respiratory allergies (RA) can be partly explained by DNA methylation changes caused by adverse environmental and lifestyle factors experienced early in life. Longitudinal, prospective studies can aid in the unravelment of the epigenetic mechanisms involved in the disease development. High compliance rates can be expected in these studies when data is collected using non-invasive and convenient procedures. Saliva is an attractive biofluid to analyze changes in DNA methylation patterns. We investigated in a pilot study the differential methylation in saliva of RA (n = 5) compared to healthy controls (n = 5) using the Illumina Methylation 450K BeadChip platform. We evaluated the results against the results obtained in mononuclear blood cells from the same individuals. Differences in methylation patterns from saliva and mononuclear blood cells were clearly distinguishable (PAdj<0.001 and |Δβ|>0.2), though the methylation status of about 96% of the cg-sites was comparable between peripheral blood mononuclear cells and saliva. When comparing RA cases with healthy controls, the number of differentially methylated sites (DMS) in saliva and blood were 485 and 437 (P<0.05 and |Δβ|>0.1), respectively, of which 216 were in common. The methylation levels of these sites were significantly correlated between blood and saliva. The absolute levels of methylation in blood and saliva were confirmed for 3 selected DMS in the PM20D1, STK32C, and FGFR2 genes using pyrosequencing analysis. The differential methylation could only be confirmed for DMS in PM20D1 and STK32C genes in saliva. We show that saliva can be used for genome-wide methylation analysis and that it is possible to identify DMS when comparing RA cases and healthy controls. The results were replicated in blood cells of the same individuals and confirmed by pyrosequencing analysis. This study provides proof-of-concept for the applicability of saliva-based whole-genome methylation analysis in the field of respiratory allergy.
authors.affiliation: Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium.
authors.forename: Sabine A S
authors.initials: SA
authors.lastname: Langie
authors.affiliation: Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium.|Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Wilrijk, Belgium.|Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Szarc Vel Szic
authors.affiliation: Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Wilrijk, Belgium.|Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.
authors.forename: Ken
authors.initials: K
authors.lastname: Declerck
authors.affiliation: Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium.
authors.forename: Sophie
authors.initials: S
authors.lastname: Traen
authors.affiliation: Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium.
authors.forename: Gudrun
authors.initials: G
authors.lastname: Koppen
authors.affiliation: Laboratory of Cancer Research and Clinical Oncology, Center for Medical Genetics, University of Antwerp, Edegem, Belgium.
authors.forename: Guy
authors.initials: G
authors.lastname: Van Camp
authors.affiliation: Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium.|Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.|University of Southern Denmark, Institute of Public Health, Department of Environmental Medicine, Odense, Denmark.
authors.forename: Greet
authors.initials: G
authors.lastname: Schoeters
authors.affiliation: Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Wilrijk, Belgium.|Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.
authors.forename: Wim
authors.initials: W
authors.lastname: Vanden Berghe
authors.affiliation: Environmental Risk and Health unit, Flemish Institute for Technological Research (VITO), Mol, Belgium.|Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.
authors.forename: Patrick
authors.initials: P
authors.lastname: De Boever
mesh_terms: D000328:Adult; D016022:Case-Control Studies; D016000:Cluster Analysis; D019175:DNA Methylation / Q000235:genetics*; D053263:Gene Regulatory Networks; D015894:Genome, Human; D006801:Humans; D006967:Hypersensitivity / Q000097:blood* / Q000235:genetics*; D007249:Inflammation / Q000235:genetics / Q000473:pathology; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D008168:Lung / Q000473:pathology*; D015203:Reproducibility of Results; D012463:Saliva / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D015398:Signal Transduction / Q000235:genetics