Integrative metabolomics and genomics reveal molecular signatures for type 2 diabetes and its cardiovascular complications

Background: Metabolites are pivotal in the biological process underlying type 2 diabetes (T2D) and its cardiovascular complications. Nevertheless, their contributions to these diseases have not been comprehensively evaluated, particularly in East Asian ancestry. This study aims to elucidate the metabolic underpinnings of T2D and its cardiovascular complications and leverage multi-omics integration to uncover the molecular pathways involved. Method: This study included 1180 Chinese participants from the Zhejiang Metabolic Syndrome Cohort (ZMSC). A total of 1912 metabolites were profiled using high-coverage widely targeted and non-targeted metabolic techniques. Multivariable logistic regression models and orthogonal partial least squares discriminant analysis were used to identify T2D-related metabolites. A metabolome-wide genome-wide association study (GWAS) in ZMSC, followed by two-sample Mendelian randomization (MR) analyses, was conducted to explore potential causal metabolite-T2D associations. To enhance cross-ancestry generalizability, MR analyses were conducted in European ancestry to explore the potential causal effects of serum metabolites on T2D and its cardiovascular complications. Furthermore, multi-omics evidence was integrated to explore the underlying molecular mechanisms. Results: We identified six metabolites associated with T2D in Chinese, supported by metabolome analysis and genetic-informed causal inference. These included two potential protective factors (PC [O-16:0/0:0] and its derivative LPC [O-16:0]) and four potential risk factors ([R]-2-hydroxybutyric acid, 2-methyllactic acid, eplerenone, and rauwolscine). Cross-ancestry metabolome-wide analysis further revealed four shared potential causal metabolites, highlighting the potential protective role of creatine for T2D. Through multi-omics integration, we revealed a potential regulatory path initialized by a genetic variant near CPS1 (coding for a urea cycle-related mitochondrial enzyme) influencing serum creatine levels and subsequently modulating the risk of T2D. MR analyses further demonstrated that nine urea cycle-related metabolites significantly influence cardiovascular complications of T2D. Conclusion: Our study provides novel insights into the metabolic underpinnings of T2D and its cardiovascular complications, emphasizing the role of urea cycle-related metabolites in disease risk and progression. These findings advance our understanding of circulating metabolites in the etiology of T2D, offering potential biomarkers and therapeutic targets for future research. What is currently known about this topic?: Research insights: Metabolites are crucial for understanding diabetes biology.Multi-omics integration aids in revealing complex mechanisms. What is the key research question?: How do serum metabolites affect diabetes and its cardiovascular outcomes? What is new?: Novel diabetes-related metabolites identified in Chinese populations.Consistent metabolites associated with diabetes and glycemic traits in East Asians and Europeans.Emphasizing the role of urea cycle pathway in cardiometabolic disease. How might this study influence clinical practice?: Findings could guide diabetes prevention and personalized management strategies. © The Author(s) 2025.