Single cell atlas of kidney cancer endothelial cells reveals distinct expression profiles and phenotypes

Abstract Background Tumor endothelial cells (TECs) represent the primary interface between the tumor microenvironment and circulating immune cells, however their phenotypes are incompletely understood in highly vascularized clear cell renal cell carcinoma (ccRCC). Methods We purified tumor and matched normal endothelial cells (NECs) from ccRCC specimens and performed single-cell RNA-sequencing to create a reference-quality atlas available as a searchable web resource for gene expression patterns. We established paired primary TECs and NECs cultures for ex vivo functional testing. Results TECs from multiple donors shared a common phenotype with increased expression of pathways related to extracellular matrix regulation, cell-cell communication, and insulin-like growth factor signaling. This phenotype was shared with hepatocellular carcinoma associated TECs, suggesting convergent TEC phenotypes between unrelated tumors. Cultured TECs stably maintained a core program of differentially regulated genes which promoted resistance to apoptosis after vascular endothelial growth factor removal and increased adhesiveness to subsets of immune cells including regulatory T-cells. Conclusions Our studies demonstrate that TECs have a distinct phenotype that is shared by TECs from different tumor types and stable in ex vivo culture. The distinct adhesive interaction of TECs with immune cells raises the possibility of their modulation to improve immune cell-based therapies for RCC.