Abstract

Background: Chromophobe renal cell carcinoma (ChRCC) is the second most common non-clear cell RCC. Patients with metastatic ChRCC have a poor prognosis with a median overall survival of ~2 years. Sarcomatoid transformation occurs in ~5% of ChRCC and is associated with increased metastatic risk and reduced survival. In clear cell RCC, the sarcomatoid phenotype is associated with an immune-inflamed state and enhanced responsiveness to immunotherapy. The immune landscape of sarcomatoid ChRCC and how it differs from classic ChRCC remain poorly defined. To address this, we performed a spatial comparison of the immune microenvironment in classic versus sarcomatoid ChRCC.

Results: The 10x Genomics Xenium Prime Assay with 5k-plex target panels was performed on 10 ChRCC tumors (5 classic and 5 sarcomatoid). Hallmark pathway enrichment and differential expression analysis of pseudo-bulk data showed that sarcomatoid transformation is associated with activation of epithelial-mesenchymal transition, proliferation, and inflammatory response pathways (p < 0.05). Examining the spatial distribution of single cells, classic tumors showed an immune-excluded microenvironment, with T cells and macrophages localized to the tumor periphery. In contrast, sarcomatoid tumors exhibited an immune-infiltrated microenvironment, with T cells and macrophages present within the tumor bed. Sarcomatoid tumors showed an upregulation of CTLA4 across multiple T cell subsets, including cytotoxic CD8⁺ T cells, naïve T cells, and regulatory T cells, compared to classic tumors. Additionally, in sarcomatoid tumors, cytotoxic CD8⁺ T cells exhibited increased expression of LAG3 compared to classic tumors. Using metastasis as a proxy for sarcomatoid transformation, we compared 113 primary ChRCC tumors and 27 metastatic ChRCC tumors using bulk RNA-seq (Tempus xR). Expression profiles and immune deconvolution showed a shift from the immune-excluded, indolent primary state to an immune-modulated metastatic state marked by increased gamma delta T-cell abundance, higher LAG3 expression and decreased T cell exhaustion score (FDR < 0.05).

Conclusion: By generating the first spatially resolved immune map of ChRCC, we showed that sarcomatoid ChRCC exhibits an immune-infiltrated microenvironment with intra-tumoral T cells and macrophages, accompanied by increased expression of immune checkpoint genes including, but not limited to CTLA4 and LAG3. This higher CTLA4 is of interest given the SUNNIFORECAST trial result, where combined CTLA4 and PD1 blockade achieved a 27% objective response rate in ChRCC. We also show that metastatic progression is associated with a shift toward a gamma delta T cell-enriched immune state. Together, these findings reveal potential therapeutic vulnerabilities and support further evaluation of immune checkpoint blockade in ChRCC.

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