Comparing DNA methylation profiles in saliva and intestinal mucosa

Abstract

Background Altered epigenetic profiles are a feature of intestinal diseases, including ulcerative colitis and Crohn’s disease. DNA methylation studies in these diseases have utilised intestinal mucosal tissue or blood which can be difficult to collect, particularly for large-scale research studies. Saliva is an attractive alternative for epigenetic studies as it is easy to collect and provides high quality methylation profiles. The aim of the study was to determine the utility of saliva as an alternative for DNA methylation studies of intestinal disorders. Results DNA methylation in saliva and intestinal mucosa samples were compared in individuals ( n = 10) undergoing endoscopies using the Illumina Infinium Methylation 450 K Beadchip array. We found that DNA methylation was correlated between tissue types within an individual (Pearson correlation co-efficient r = 0.92 to 0.95, p < 0.001). Of the 48,541 probes (approximately 11% of CpG sites) that were differentially methylated between saliva and intestinal mucosa (adjusted p < 0.001, |Δβ| ≥ 20%), these mapped to genes involved in tissue-specific pathways, including the apelin signalling and oxytocin pathways which are important in gastrointestinal cytoprotection and motility. Conclusions This study suggests that saliva has the potential to be used as an alternate DNA source to invasive intestinal mucosa for DNA methylation research into intestinal conditions. Electronic supplementary material The online version of this article (10.1186/s12864-019-5553-0) contains supplementary material, which is available to authorized users.

Comparison of DNA methylation profiles from saliva in Coeliac disease and non-coeliac disease individuals

“…It is unknown whether the differences in DNA methylation profiles are unique to intestinal mucosal tissue or are also present in other tissues. We have previously shown that DNA methylation profiles in saliva correlated well with DNA methylation profiles from intestinal mucosal tissue [17]. The current study compared DNA methylation profiles in saliva from individuals with and without CD, to identify DNA methylation profiles unique to GFD managed CD.…”

Genome-Wide DNA Methylation Changes Associated With High-Altitude Acclimatization During an Everest Base Camp Trek

“…By focusing on a singular tissue type, our results may be restricted to salivary tissue alone. However, salivary DNA methylation patterns have been shown to correlate with DNA methylation from blood ( Thompson et al, 2013 ; Langie et al, 2016 ), intestinal mucosa ( Hearn et al, 2019 ), and the brain ( Smith et al, 2015 ). Furthermore, saliva panels have shown proteomic changes upon hypoxic exposure in cell cultures ( Jain et al, 2020 ), suggesting the relevance of this tissue for analyzing the overall hypoxic response.…”

Methylation Status of <i>GLP2R, LEP</i> and <i>IRS2</i> in Small for Gestational Age Children with and without Catch-up Growth

“…Saliva is composed of more than 99% water, and also contains white blood cells and epithelial cells, which represent the cell types of the oral mucosa. Previous DNA methylation studies comparing profiles between tissue types within individuals have shown that regions of tissue-specific differential methylation mainly map to CpG poor regions and demonstrated that methylation profiles correlating positively between saliva and diverse tissue in question ( 22 , 23 ). The viability of saliva as an alternative for less accessible tissues, including brain, lung/bronchial epithelium, and peripheral blood mononuclear cells, and in a recent study, intestinal mucosa, has been demonstrated ( 23 ).…”

“…Previous DNA methylation studies comparing profiles between tissue types within individuals have shown that regions of tissue-specific differential methylation mainly map to CpG poor regions and demonstrated that methylation profiles correlating positively between saliva and diverse tissue in question ( 22 , 23 ). The viability of saliva as an alternative for less accessible tissues, including brain, lung/bronchial epithelium, and peripheral blood mononuclear cells, and in a recent study, intestinal mucosa, has been demonstrated ( 23 ). The similar composition and function of mucosa between the oral mucosa and intestinal mucosa suggests that comparable methylation profiles between saliva and intestinal tissue might exist, and strengthens the idea that saliva has the potential to be used as an alternative for more difficult to sample tissues ( 22 ).…”