Cellular and Molecular Features of Clear-Cell Renal Cell Carcinoma Tumors - Expert Commentary
Sequencing was conducted on 7 tumor samples and 2 normal adjacent tissues, yielding data from a total of 56,421 cells. The seven selected patients exhibited varying grades and stages. Cells were clustered and annotated according to established cell type markers. Immune cells represented 50% of the atlas and the total number of cancer cells was 1,763. Further clustering of cancer cells yielded 5 distinct cell types: epithelial-like, mesenchymal-like, two intermediate states, and a novel inflamed state. Researchers were able to delineate a clear molecular trajectory from epithelial to mesenchymal states. The former is characterized by oxidative phosphorylation and fatty acid metabolism pathways while the latter is characterized by epithelial-mesenchymal transition (EMT), TGF-β, and Notch pathways. The intermediate cell types did not display markers of specific cell populations. However, one of them displayed more epithelial markers and had while the other exhibited more mesenchymal markers. Cell clustering was validated in two independent datasets, yielding the same basic tumor cell types and additional cell states associated with hypoxia, apoptosis, and cell cycle.
To examine how these cancer cells were different from the cells of origin, researchers clustered 6,585 renal tubule epithelial cells into seven populations representing different nephron segments. Cells from the proximal straight tubule (PST) cluster most closely resembled the epithelial ccRCC cluster. Trajectory analysis revealed that PST cells transitioned into epithelial ccRCC cells, followed by EMT. Oncogenic transformation of PST cells is marked by expression of hypoxia genes and a switch from oxidative phosphorylation to glycolysis.
The presence of specific cell clusters was linked to distinct patient outcomes. In a univariate Cox regression analysis, whereby mesenchymal (HR = 6.07, p < 0.001), myofibroblastic cancer-associated fibroblasts (myCAFs, HR = 6.6, p < 0.001), and inflamed subtypes (HR = 9.5, p < 0.001) were strongly associated with poor survival, while the epithelial subtype was associated with better survival (HR = 0.38, p = 0.002). Spatial transcriptomics analysis revealed that myCAFs and mesenchymal cells were frequently in close proximity throughout tumor sections, particularly at the interface with normal adjacent tissue. Further analysis revealed that ligand-receptor interactions between these two cell types contributed to invasion and conversion of cells through specific signaling pathways. Interestingly, researchers also found that high myCAF signature was associated with shorter progression-free survival in patients from the BIONIKK trial (nivolumab or ipilimumab/nivolumab combination) (p = 0.005). Although mesenchymal cells were not associated with survival, 11 of 14 myCAF-high tumors also had high mesenchymal cell scores. This was particularly true in metastatic tissue samples.
Single-cell RNA-sequencing studies have been critical for the molecular characterization of different cell types and how they contribute to disease. As revealed in this study, specific tumor cell states in ccRCC are directly linked to prognosis and response to treatment. This yields valuable insight, such as the potential efficacy of treatment with tyrosine kinase inhibitors and immune checkpoint inhibitors among patients with high myCAF signatures.
Written by: Bishoy M. Faltas, MD, Director of Bladder Cancer Research, Englander Institute for Precision Medicine, Weill Cornell Medicine
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