Molecular Consequences of Pathogenic SDHA Variants: From Defective Flavinylation and Assembly to Lipid Remodeling

Background Succinate dehydrogenase (SDH), also known as complex II, connects the tricarboxylic acid cycle with oxidative phosphorylation, and mutations in its subunits are linked to mitochondrial disease and cancer. However, the molecular consequences of SDHA pathogenic variants remain poorly understood. Here, we generated a panel of patient-derived SDHA variants in an SDHA knockout HEK293 cell model and examined their effects on SDH assembly, function, and cellular metabolism. Results We found that SDHA mutations differentially affect SDH assembly and stability, yet most variants display severely impaired catalytic activity, despite partial or complete enzyme assembly. Loss of SDH function reduced succinate-driven respiration, altered the content of complexes I and IV, and shifted respiration toward NADH-supported pathways. Metabolomic and lipidomic analyses revealed extensive metabolic remodeling, including reorganization of the tricarboxylic acid cycle, succinate accumulation, and adaptive regulation of polyunsaturated fatty acid metabolism. Variants retaining partial SDH activity exhibited intermediate structural, functional, and metabolic phenotypes. Conclusions These findings define how different pathogenic variants of SDHA disrupt SDH structure and function, drive divergent metabolic adaptations, and provide mechanistic insight into the heterogeneous disease manifestations associated with SDHA deficiency.