Coregulated metabolite networks associated with global protein crotonylation are central pathophysiological processes in prediabetes and diabetes

Type 2 diabetes and prediabetes affect hundreds of millions of people globally, yet the metabolic networks underlying disease development remain poorly understood. Using untargeted liquid chromatography-mass spectrometry (LC-MS/MS), we profiled a total of 15,470 (900 known) serum metabolite features across the human diabetes spectrum (the most comprehensive coverage reported to date). Weighted coexpression network analysis of samples from people with normal glucose tolerance, prediabetes, and type 2 diabetes, collected at baseline and 2 hours after an oral glucose tolerance test, revealed tightly coregulated modules strongly associated with glycemic dysregulation, insulin resistance, and islet dysfunction. Notably, short-chain organic acids, particularly crotonic acid, emerged as hubs of the diabetes-associated networks, accumulating progressively with disease severity. Reanalysis of extracellular vesicle proteomics from the same cohort showed that 16.5% of circulating proteins were crotonylated, with 47.6% correlated with crotonic acid and other hub metabolites, establishing a metabolome-crotonylome axis as a novel mechanism in diabetes development.