A child's spit epigenome can reveal its respiratory allergy risk

Abstract

Environmental exposures like parental lifestyle and diet, smoking, obesity and exposure to toxin can modulate disease risk. Epigenetic DNA methylation changes can be part of the underlying molecular mechanisms. Early life exposures can alter DNA methylation patterns, and thereby predispose the child to develop respiratory allergy (RA) later in life. Longitudinal birth cohorts are instrumental to study disease development, but DNA biomarker research is hampered because blood sampling is kept to a minimum for practical and ethical reasons. Saliva is a non-invasive and convenient source of DNA that can be used for biomarker research. In this study, we aimed at discovery and confirmation of differential methylation regions (DMR) in saliva of children with RA when comparing to controls. Saliva samples collected in two independent longitudinal birth cohorts in Belgium were analyzed using Illumina Methylation 450K BeadChips.A statistical analysis pipeline was developed in R to identify genome-wide differential methylation. The Illumina Methylation 450K BeadChips revealed 13 DMR in saliva from 11y old allergic children (N=26) vs. controls (N=20). 5 DMR were located in genes involved in IL4 signalling and Th2-response, showing a link with wheezing and other RA phenotypes. The 13 DMR were selected for further biological and technical validation by iPLEX MassArray analysis in the same birth cohort as well as in a second cohort (N=78). This project is providing novel insights in the molecular mechanisms that may predispose children to RA development. We are among the first to show the utility of saliva to identify DNA methylation marks in children that are relevant for RA.