Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels

Saliva, as a biofluid, is inexpensive and non-invasive to obtain, and provides a vital tool to investigate oral health and its interaction with systemic health conditions. There is growing interest in salivary biomarkers for systemic diseases, notably cardiovascular disease. Whereas hundreds of genetic loci have been shown to be involved in the regulation of blood metabolites leading to unprecedented insights into the pathogenesis of complex human diseases, little is known about the impact of host genetics on salivary metabolites. Here we report the first genome-wide association study exploring 476 salivary metabolites in 1,419 subjects of European ancestry from the TwinsUK cohort (discovery phase). A total of 14 salivary metabolites were significantly associated (p<10-10) with genetic variants that mapped to 11 distinct loci, most of which replicated in the Study of Health in Pomerania (SHIP-2) cohort. Interestingly, while only a limited number of the loci that are known to regulate blood metabolites were also associated with salivary metabolites in our study, we identified several novel saliva-specific locus-metabolite associations, including associations for the AGMAT (with the metabolites 4-guanidinobutanoate and beta-guanidinopropanoate), ATP13A5 (with the metabolite creatinine) and DPYS (with the metabolites 3-ureidopropionate and 3-ureidoisobutyrate) loci. Our study suggests that there are biological pathways which are specific to the regulation of the salivary metabolome. In addition, some of our findings may have clinical relevance, such as the utility of the pyrimidine (uracil) degradation metabolites in predicting 5-fluorouracil toxicity and the role of the agmatine pathway metabolites as biomarkers of oral health.