Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum

Abstract

The rapidly evolving field of metabolomics aims at a comprehensive measurement of ideally all endogenous metabolites in a cell or body fluid. It thereby provides a functional readout of the physiological state of the human body. Genetic variants that associate with changes in the homeostasis of key lipids, carbohydrates, or amino acids are not only expected to display much larger effect sizes due to their direct involvement in metabolite conversion modification, but should also provide access to the biochemical context of such variations, in particular when enzyme coding genes are concerned. To test this hypothesis, we conducted what is, to the best of our knowledge, the first GWA study with metabolomics based on the quantitative measurement of 363 metabolites in serum of 284 male participants of the KORA study. We found associations of frequent single nucleotide polymorphisms (SNPs) with considerable differences in the metabolic homeostasis of the human body, explaining up to 12% of the observed variance. Using ratios of certain metabolite concentrations as a proxy for enzymatic activity, up to 28% of the variance can be explained (p-values 10⁻¹⁶ to 10⁻²¹). We identified four genetic variants in genes coding for enzymes (FADS1, LIPC, SCAD, MCAD) where the corresponding metabolic phenotype (metabotype) clearly matches the biochemical pathways in which these enzymes are active. Our results suggest that common genetic polymorphisms induce major differentiations in the metabolic make-up of the human population. This may lead to a novel approach to personalized health care based on a combination of genotyping and metabolic characterization. These genetically determined metabotypes may subscribe the risk for a certain medical phenotype, the response to a given drug treatment, or the reaction to a nutritional intervention or environmental challenge. This paper reports what is, to the best of our knowledge, the first genome-wide association (GWA) study with metabolic traits as phenotypic traits. By simultaneous measurements of single nucleotide polymorphisms (SNPs) and serum concentrations of endogenous organic compounds in a human population, we identify genetically determined variants in metabolic phenotype (metabotype) that exhibit large effect sizes. Four of these polymorphisms are located in genes coding for well-characterized enzymes of the lipid metabolism. We find that individuals with different genotypes in these genes have significantly different metabolic capacities with respect to the synthesis of some polyunsaturated fatty acids, the beta-oxidation of short- and medium-chain fatty acids, and the breakdown of triglycerides. In this approach, the concept of the “genetically determined metabotype” as an intermediate phenotype is central, as it becomes a measurable quantity in the framework of GWA studies with metabolomics. The investigation of the genetically determined metabotypes in their biochemical context might help to better understand the pathogenesis of common diseases and gene–environment interactions. These findings could result in a step towards personalized health care and nutrition based on a combination of genotyping and metabolic characterization.