Multi-omics profiling reveals intrathymic triggers and novel biomarkers in thymoma-associated myasthenia gravis

BACKGROUND: The pathogenic mechanisms through which thymoma induces myasthenia gravis (MG) remain incompletely understood. While MG pathogenesis involves neuromuscular junction defects and peripheral immune dysregulation, the specific contribution of thymoma microenvironment is poorly defined. METHODS: We conducted the first comparative multi-omics analysis of MG-associated thymomas (MGTH) versus non-MG thymomas, integrating single-cell transcriptomics, proteomics, and TCR/BCR repertoire sequencing. Key findings were validated across species using TCGA transcriptomic data, tissue microarrays, co-culture and antigen presentation assays, a Cd4CreSocs3fl/fl murine model and flow cytometry to delineate the underlying microenvironmental and molecular drivers. RESULTS: We observed broad expression of synaptic genes in MGTH, including elevated acetylcholine receptor (AChR)-encoding gene CHRNA1, in the absence of detectable intratumoral anti-AChR antibodies. Our analysis revealed a pathogenic JUND-SOCS3 axis governing T cell differentiation, wherein pan-T cell JUND overexpression transcriptionally repressed SOCS3, driving proinflammatory Th1/Th17 polarization in both Cd4CreSocs3fl/fl mice and MGTH patients. We further identified a novel neuro-synaptic thymic epithelial cell (nsTEC) subset characterized by markedly reduced HLA-I/II expression and aberrant synaptic gene expression. Functional co-culture assays confirmed that these nsTECs exhibited impaired antigen presentation and failed to efficiently activate T cells. Clonally expanded TTN+ memory B cells were identified in both MGTH stroma and peripheral blood, and their abundance correlated positively with anti-titin antibody titers. Analysis of cellular interactomes revealed rewired stromal-immune crosstalk in MGTH, wherein nsTECs existed as immunologically inert compartments, lacking detectable cytokine responsiveness or cellular interactions. TCR/BCR profiling demonstrated antigen-driven clonal expansion and repertoire restriction in MGTH. Furthermore, we identified the CDR sequences of antigen-specific clones. CONCLUSIONS: We demonstrate that thymoma-associated MG arises from three convergent mechanisms: disordered T-cell differentiation, defective thymic antigen presentation, and autoantigen-specific B-cell expansion. This model identifies previously unappreciated, synergistic therapeutic targets for intervention.