Lipidomic Profiling Reveals Distinct Molecular Signatures Across Clinical Subtypes of Myasthenia Gravis

Background/Objectives: Myasthenia gravis (MG) is an immune-mediated neuromuscular disorder for which antibody-based assays have limited sensitivity, particularly in double-seronegative MG (dsNMG), highlighting the need for complementary biomarkers. Given their roles in immune regulation, membrane integrity, and metabolic stress responses, lipids represent promising candidates for biomarker discovery. Methods: We designed a prospective case–control study and systematically stratified 68 patients with myasthenia gravis (MG) according to clinical classification and autoantibody status. Using LC–MS/MS, we quantified 824 lipids in 136 serum samples collected from these patients and 68 healthy controls. The analyzed subtypes included ocular MG (OMG), generalized MG (GMG), acetylcholine receptor antibody-positive MG (AChR-MG), and dsNMG. Differential lipid analysis, correlation network construction, KEGG pathway enrichment, and multivariable logistic regression were performed. Diagnostic and subtype prediction models were developed using LASSO with 10 × 10 repeated cross-validation and interpreted using Shapley Additive exPlanations (SHAP) analysis. A longitudinal follow-up analysis was conducted to assess dynamic associations between lipid signatures and disease activity. Results: In total, 240 lipids were significantly altered in MG compared with controls. Lipids distinguishing GMG from OMG were enriched in ether lipid metabolism, necroptosis, and sphingolipid signaling pathways. AChR-MG and dsNMG shared lipid networks related to membrane remodeling and signaling regulation, whereas dsNMG exhibited marked elevations in acylcarnitines and bile acid-related metabolites, potentially reflecting a distinct phenotype characterized by altered energy metabolism. The lipid-based model achieved an AUC of 0.917 for distinguishing MG from controls, and AUCs of 0.77 and 0.71 for differentiating AChR-MG from dsNMG and GMG from OMG, respectively. Longitudinal analyses showed that SM(d18:1/23:0) and Cer(d24:1/18:0(2OH)) displayed dynamic changes consistent with disease activity. Conclusions: Serum lipidomics revealed subtype-specific metabolic features of MG, with stable disease-associated remodeling and dynamic sphingolipid changes potentially reflecting disease activity. By integrating systematic clinical and antibody-based subtype stratification with longitudinal follow-up, this study supports lipidomics as a complementary tool for precision diagnosis and disease stratification, particularly in antibody-negative dsNMG.