Dan Yang, Xinyan Wu, Xiufang Luo, Yuanyin Teng, Xiyue Duan, Tingting Kang, Wenze Wu
Stable isotope-resolved metabolomics (SIRM) has emerged as a pivotal methodology for dissecting mitochondrial metabolic reprogramming and its connection to therapeutic targets. By combining isotopically labeled substrates with metabolic flux analysis (MFA), SIRM enables dynamic, quantitative tracking of carbon flux through mitochondrial pathways. This review focuses on three disease contexts where SIRM has provided transformative insights: cancer, neurodegenerative disorders (Alzheimer's and Parkinson's diseases), and metabolic syndrome (type 2 diabetes and non-alcoholic fatty liver disease). Recent applications have delineated reprogramming signatures, identified metabolic dependencies, and elucidated drug mechanisms. SIRM also facilitates therapeutic monitoring and resistance assessment, offering quantitative biomarkers for patient stratification. We summarize recent advances, technical challenges, AI-powered innovations, and future directions, providing a foundation for optimizing metabolism-targeted therapies.