Urologic Oncology Fellow Moffitt Cancer Center Tampa, FL, United States
Background: Immunotherapy (IO) has improved response rates for patients with advanced clear cell renal cell carcinoma (ccRCC), but most will develop resistance. We sought to utilize cellular-level spatial transcriptomics in the pre- and post-IO treatment settings to better understand IO resistance in ccRCC.
Methods: Tissue was obtained from primary ccRCC kidney tumors. Matched tumor and stromal regions of interest (ROI) were included for analysis. Spatial molecular imaging (SMI) was obtained for each region using Nanostring’s CosMx platform. Cell abundance and clustering were then analyzed by treatment status. Colocalization of phenotyped cells was quantified using univariate and bivariate Ripley’s K. Radii between 9 and 90um were visually compared to identify an appropriate search distance; a final radius of 27um was selected. Spatial gene set enrichment (GSE) analysis followed by a posthoc spatial analysis of associated transcripts from select enriched gene sets were performed. Moran’s I test was used to quantify colocalization of receptor-ligand pairs. Analysis was performed in R using the spatialTIME package.
Results: 15 treatment naïve and 6 IO treated patients were evaluated. Compared to treatment naive tumors, IO treated tumors harbored more CD8+ T cells and neutrophils in the stromal ROI (p < 0.001 for both), and more non-classical monocytes in the tumor ROI (p=0.002). Greater univariate clustering was observed for principal cells in the stroma (p=0.011) and regulatory T cells in the tumor (p < 0.001) following IO. On spatial GSE, the endothelial to mesenchymal (EMT) pathway was enriched and two associated ligand-receptor transcript pairs were significantly colocalized; COL4A1 and ITGAV in the stroma (p=0.024). Expression of these genes was highest amongst fibroblasts and tumor cells (Figure).
Conclusions: We found a shift in the abundance and clustering of immune cells in the tumor immune microenvironment of ccRCC following IO treatment. Additionally, we saw significant colocalization of transcripts associated with the EMT pathway.
