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 approximately 40% correlated with crotonic acid and other hub metabolites, establishing a metabolome-crotonylome axis as a novel mechanism in diabetes development.

Dr. Pratley reports support from NIH research grants (U01DK106993, R01DK138060, U01DK35131, R01DK143524, U01DK143384, U01DK127392). Investigator-initiated grant support from Abbott Laboratories, Research grants (directed to his institution): AstraZeneca AB, Biomea Fusion, Boehringer Ingelheim International GmbH, Carmot Therapeutics, Dompe, Eli Lilly and Company, Endogenex, Inc., Fractyl, Lexicon, Metavention, National Institutes of Health, Novo Nordisk, and Sanofi. Consultancy fees from: Abbott Laboratories, AbbVie Inc., Altanine Inc., Amgen Inc., AstraZeneca Pharmaceuticals LP, Bayer AG, Bayer HealthCare Pharmaceuticals, Inc., Boehringer Ingelheim Pharmaceuticals, Inc., Corcept Therapeutics Incorporated, Endogenex, Inc., F. Hoffmann-La Roche Ltd., Hanmi Pharmaceutical Co., Novo Nordisk, Pfizer, Regeneron Pharmaceuticals, Response Pharmaceuticals, Rona Therapeutics Ltd, Scholar Rock Inc., Sun Pharmaceutical Industries, Third Rock Ventures, and Verdiva Bio Dev Limited, as well as speaker fees from Abbott, Corcept, Lilly USA LLC and Novo Nordisk, and stock options from Altanine, Inc. Dr. Casu reports research funding from Enable Biosciences directed to her institution. NIH research grant U01 DK135131. All other authors declare no competing interests.

This study was funded by program funds granted to REP by the AdventHealth Translational Research Institute.

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All data produced in the present study will be available upon reasonable request to the authors after actual publication in peer-reviewed journal.