Metabolome-Wide Mendelian Randomization and Observational Study Reveal Causal Links Between Circulating Metabolites and Youth-Onset Type 2 Diabetes

Despite the increasing prevalence of type 2 diabetes in youth, its causal associations with circulating biomarkers remain elusive. We first aimed to identify circulating metabolites causally linked to youth-onset type 2 diabetes using Mendelian randomization (MR). By analyzing 675 metabolites from large metabolomic European genome-wide association studies (GWAS) and data on youth type 2 diabetes from the multiancestry Progress in Diabetes Genetics in Youth (ProDiGY) consortium, we identified 34 candidate metabolites. Among these, phosphatidylcholine (pc) ae C42:3 and propionylcarnitine provided the strongest evidence of association with youth-onset type 2 diabetes, based also on positive genetic colocalization and sensitivity analyses accounting for adiposity. Among the 34 candidate metabolites, 23 were retained following colocalization and a replication MR using independent metabolomic GWAS and testing effects on adult type 2 diabetes. Furthermore, we validated associations of six of these metabolites with glucose metabolism–related traits in an observational study in the Avon Longitudinal Study of Parents and Children (ALSPAC). Notably, pc ae C42:3 levels at age 7 years were linked to dysglycemia and insulin resistance in adolescence. These findings underscore the dynamic role of metabolites in glucose metabolism in childhood, offering insights for future screening and treatment strategies. Article Highlights Metabolism is key in the pathogenesis of type 2 diabetes in both children and adults, and large-scale metabolomic studies offer a unique source for discovery of biomarkers for these conditions. Leveraging human genetics, we explored whether altered levels of circulating metabolites in the blood are causally linked to type 2 diabetes in youth across different ancestries. Our Mendelian randomization analysis identified causal associations for 34 metabolites, and, among these, Mendelian randomization replication and colocalization prioritized 23 metabolites. Observational evidence from the Avon Longitudinal Study of Parents and Children (ALSPAC) study validated effects on glucose homeostasis for six of these metabolites, among which phosphatidylcholine ae C42:3 emerged as the most promising biomarker. These findings highlight the role of metabolism in glucose homeostasis pathophysiology in youth.