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ABSTRACT

Background Papillary renal cell carcinoma (pRCC) is the second most common kidney cancer subtype, yet our understanding of its tumor immune microenvironment (TIME) remains limited. Objective We utilized multiplex immunofluorescence (mIF) and spatial transcriptomics (ST) to evaluate immune cell architecture in pRCC contrasted with clear cell RCC (ccRCC). Methods Localized RCC tumors (16 pRCC, 70 ccRCC) underwent mIF using markers for T cells, B cells, and tumor-associated macrophages (TAMs). 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 density, cell spatial clustering, and spatially varying gene expression were analyzed. Results Immune cell density was statistically lower in pRCC amongst functional CD8T 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) and are known markers of lipid-associated TAMs (LAMs). Conclusion Compared to ccRCC, pRCC has greater M2-like macrophage clustering. Using ST, M2-like macrophage clustering corresponds with lipid associated TAMs (LAMs), and therapeutics against this myeloid subset are currently being tested in pRCC.

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