Single-cell analysis decodes cellular dynamics in clear cell renal cell carcinoma with tumor thrombus

Venous tumor thrombus formation represents a pivotal stage in the metastatic cascade of clear cell renal cell carcinoma (ccRCC). To gain deeper insights into the cellular and molecular landscape underlying this process, we performed comprehensive single-cell RNA sequencing on primary ccRCC tumors and their matched venous tumor thrombi, aiming to systematically characterize the microenvironment of tumor thrombus formation. Our analysis reveals a distinct cellular composition within the tumor thrombus, marked by a significant enrichment of myeloid cells and a relative depletion of T/NK cells, establishing an immunosuppressive milieu at the tumor thrombus site. Notably, we identified a pro-tumorigenic tumor-associated macrophage subpopulation exhibiting M2-like polarization and pro-angiogenic/immunosuppressive characteristics that significantly expanding within the thrombus. Concomitantly, the CD8 + T cell compartment displayed transcriptional signatures indicative of functional exhaustion. Intercellular communication network analysis highlighted the upregulation of adhesion-promoting signaling pathways and context-dependent stromal-immune crosstalk within the thrombus. Furthermore, epithelial cells residing within the tumor thrombus exhibited transcriptional adaptations associated with enhanced migration and survival, alongside increased genomic instability. This study provides a valuable data resource for understanding and targeting the tumor thrombus niche.