Single-Cell Sequencing Plus Spatial Transcriptomics: Dissecting Tumor Heterogeneity, Immunosuppression, and Potential Targets for ASPSCR1::TFE3 Renal Cell Carcinoma.

ASPSCR1::TFE3 renal cell carcinoma (RCC) is a rare subtype with frequent lymph node metastasis and poor prognosis. Its obscure pathogenesis and immune microenvironment greatly limit clinical management. Here, this study integrated single-cell sequencing and high-resolution spatial transcriptomics to profile formalin-fixed paraffin-embedded specimens of ASPSCR1::TFE3 RCC and clear cell RCC. Marked distinctions in tumor and immune landscapes were identified between the two subtypes. Clear cell RCC was enriched in interferon response and hypoxia pathways, while ASPSCR1::TFE3 RCC favored oxidative phosphorylation and epithelial-mesenchymal transition. Tumor cells were classified into C3/C4 clusters; the metastasis-related C3 subtype highly expressed pro-invasive genes including MDK, MMP7, and VCAN. ASPSCR1::TFE3 RCC displayed an immunosuppressive microenvironment with abundant macrophages and exhausted T/natural killer cells. MDK-LRP1 crosstalk between tumor cells and macrophages facilitated immune escape. These findings define ASPSCR1::TFE3 RCC as a highly metastatic, immunosuppressive malignancy driven by C3 enrichment and elevated MDK, offering novel targets for targeted and immunotherapeutic strategies.