27 Spatial Clustering of Immunosuppressive Macrophages in Papillary Renal Cell Carcinoma

Abstract Background Papillary renal cell carcinoma (pRCC) accounts for up to 15% of all kidney cancer cases, yet our understanding of its tumor immune microenvironment (TIME) remains limited. We utilized multiplex immunofluorescence (mIF) and spatial transcriptomics (ST) to evaluate immune cell spatial architecture in pRCC and compared to that of clear cell RCC (ccRCC). Methods Surgical tumor specimens were obtained from localized RCC tumors, followed by mIF using markers for T cells, B cells, and tumor-associated macrophages (TAMs). Spatial data were derived in regions of interest (ROIs) manually selected from spatially distinct tissue compartments of the TIME. Single-cell ST was performed on a subset of patient samples, utilizing probes against 960 transcripts. Cell abundance, cell spatial clustering, and spatially varying gene expression were analyzed to identify unique features of the TIME in pRCC. Results Sixteen pRCC and 70 ccRCC patient samples underwent mIF. Compared to ccRCC, global pRCC immune cell abundance was statistically lower amongst functional CD8 T cells, while global cell spatial clustering was higher amongst M2-like macrophages as measured by mIF, including PDL1+ subsets. Using ST, seven genes were significantly associated with spatial clustering of M2-like macrophages in pRCC. Three of seven genes (CCL18, GPNMB, CD9) are known markers of lipid-associated TAMs (LAMs) (adjusted p-value < 0.1). Conclusions Compared to ccRCC, pRCC has fewer T cells but greater M2-like macrophage spatial clustering. Using ST, we found that multiple LAM-associated genes are spatially enriched in pRCC. Additional resources should be dedicated to investigating myeloid biomarkers and the impact of myeloid modulating therapeutics in pRCC.