Spatial Clustering of Immunosuppresive Macrophages in Papillary Renal Cell Carcinoma

Papillary renal cell carcinoma (pRCC) is the second most common kidney cancer, yet our understanding of its tumor immune microenvironment (TIME) remains limited. We utilized multiplex immunofluorescence (mIF) and spatial transcriptomics (ST) to evaluate immune cell architecture in pRCC contrasted with clear cell RCC (ccRCC). Localized RCC tumors (16 pRCC, 70 ccRCC) underwent mIF using immune cell markers. Spatial data in both tumor and stromal compartments of the TIME were collected. A post hoc recurrence free survival analysis (RFS) was performed using Cox proportional hazard models. Single-cell ST was performed on a subset of samples, utilizing probes against 960 transcripts. Cell abundance, cell spatial clustering, and spatially varying gene expression were analyzed. Immune cell abundance was statistically lower in pRCC amongst functional CD8 T cells, while cell clustering was higher amongst M2-like macrophages. Using ST, two genes (CCL18, GPNMB) were enriched in clustered M2-like macrophages in pRCC (FDR < 0.001). In conclusion, pRCC has greater M2-like macrophage clustering compared to ccRCC, which is associated with worse RFS in pRCC. Using ST, M2-like macrophage clustering corresponds with lipid associated TAMs (LAMs), and therapeutics against this myeloid subset are currently being tested in pRCC.