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 approximately two years. Sarcomatoid transformation occurs in around 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 the classic form remains poorly defined. To address this, we performed a spatial comparison of the immune microenvironment in classic versus sarcomatoid ChRCC.

Method – The 10x Genomics Xenium Prime Assay with 5k-plex target panels was performed on 10 ChRCC tumors (6 classic, 3 sarcomatoid, and 1 mixed). Bulk RNA-seq (Tempus xR) analysis was performed on 113 primary and 27 metastatic ChRCC tumors.

Results – Examining the spatial distribution of single cells on 10 ChRCC tumors, we found that 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. Sarcomatoid tumors showed 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. Hallmark pathway enrichment and differential expression analysis of pseudo-bulk data showed that sarcomatoid transformation is associated with significant activation of epithelial-mesenchymal transition, proliferation, and inflammation pathways. Using metastasis as a proxy for sarcomatoid transformation, we compared 113 primary and 27 metastatic ChRCC tumors using bulk RNA-seq. Expression profiles and immune deconvolution showed a shift from the immune-excluded, indolent primary state to an immune-modulated metastatic state marked by increased γδ 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 displays 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 CTLA-4 and PD-1 blockade (Ipilimumab + Nivolumab) achieved a 27% objective response rate in ChRCC. These findings reveal potential therapeutic vulnerabilities and support further evaluation of immune checkpoint blockade in sarcomatoid ChRCC.

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