Related Experiment Video
Updated: Apr 22, 2026
Microfluidics-based High-throughput Circulating Tumor Cell Sorting and Single-cell Sequencing Technology
Published on: November 14, 2025
Single-Cell Sequencing Plus Spatial Transcriptomics: Dissecting Tumor Heterogeneity, Immunosuppression, and Potential
Yingjing Wang1, Xia Wu1, Xiao Cheng1
1Ningbo Clinical Pathology Diagnosis Center, Ningbo, China.
Abstract:
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.
Insights
ASPSCR1::TFE3 renal cell carcinoma (RCC) exhibits high metastasis and immune suppression. Targeting MDK-LRP1 interactions and the C3 subtype may improve immunotherapy for this RCC variant.
Area of Science:
- Oncology
- Genitourinary Pathology
- Cancer Immunology
Background:
- ASPSCR1::TFE3 renal cell carcinoma (RCC) presents a unique subtype with aggressive characteristics, including frequent lymph node metastasis and poor prognosis.
- The underlying pathogenesis and immune microenvironment of ASPSCR1::TFE3 RCC remain poorly understood, limiting effective clinical interventions.
- Clear cell renal cell carcinoma (ccRCC) serves as a comparator for understanding the distinct features of ASPSCR1::TFE3 RCC.
Purpose of the Study:
- To elucidate the distinct molecular and immune profiles of ASPSCR1::TFE3 RCC compared to ccRCC.
- To identify key cellular subtypes and molecular pathways driving the aggressive phenotype of ASPSCR1::TFE3 RCC.
- To investigate the immune microenvironment and potential mechanisms of immune escape in ASPSCR1::TFE3 RCC.
Main Methods:
- Comparative analysis of formalin-fixed paraffin-embedded (FFPE) samples from ASPSCR1::TFE3 RCC and ccRCC.
- Application of single-cell sequencing to dissect cellular heterogeneity.
- Utilisation of high-resolution spatial transcriptomics to map the tumor microenvironment.
Main Results:
- Significant divergence in tumor and immune microenvironments between ASPSCR1::TFE3 RCC and ccRCC.
- ASPSCR1::TFE3 RCC is characterized by oxidative phosphorylation and epithelial-mesenchymal transition pathways, contrasting with interferon response and hypoxia in ccRCC.
- Tumor cells in ASPSCR1::TFE3 RCC segregate into C3/C4 subtypes, with the C3 subtype showing heightened expression of pro-invasive genes (MDK, MMP7, VCAN) linked to metastasis.
- An immunosuppressive phenotype in ASPSCR1::TFE3 RCC is marked by increased macrophages and exhausted T/NK cells.
- Tumor cell-macrophage interactions via MDK-LRP1 signaling contribute to immune escape.
Conclusions:
- ASPSCR1::TFE3 RCC is confirmed as a highly malignant tumor with potent immunosuppressive features and significant metastatic potential.
- The enrichment of the C3 subtype and elevated MDK expression are key molecular drivers of ASPSCR1::TFE3 RCC's aggressive behavior.
- Findings offer novel insights for targeted therapies and hold promise for expanding immunotherapy eligibility in ASPSCR1::TFE3 RCC patients.
