52Spatial transcriptomic mapping reveals immune-inflamed niches in sarcomatoid chromophobe renal cell carcinoma

Abstract Background Chromophobe renal cell carcinoma (ChRCC) is the second most common non-clear cell renal cell carcinoma (ncRCC). A series of 496 ChRCC from Memorial Sloan Kettering Cancer Center demonstrated that sarcomatoid features, which were present in about 1.2% of the cases, are strongly correlated with metastatic disease and reduced overall survival. Little is known about the biological and immunological characteristics of the sarcomatoid variant of ChRCC and how it differs from its classic, non-sarcomatoid form. Methods Eight ChRCC tumor samples containing both classic and sarcomatoid components were selected. Xenium Prime 5K assay (5000 curated genes related to oncoimmunology) was used for high-resolution spatial transcriptomic profiling. Data were analyzed using Seurat and custom scripts to annotate cell types and conduct detailed phenotypic analysis. Pathway enrichment and transcription factor regulatory networks were analyzed using the SENIC package. Cell-cell communication was inferred using CellChat, and spatial proximity of immune and tumor cells (“cellular neighborhoods”) was analyzed, which model spatial gene expression patterns and intercellular distances. Results Spatial transcriptomic analyses revealed a significantly more immune-inflamed tumor microenvironment in sarcomatoid regions compared to their classic counterparts. We identified distinct spatial immune “neighborhoods” in sarcomatoid areas that were enriched in CD8+ T cells, polarized macrophages, and dendritic cells. These neighborhoods exhibited organized proximity to tumor cells expressing immune evasion markers such as PD-L1. In contrast, classic regions were relatively immune-deserted. Analysis of transcription factor activity showed upregulation of IRF1 and STAT1-related programs in the immune infiltrates of sarcomatoid regions, consistent with inflammatory activation. Importantly, comparison of matched sarcomatoid and classic regions within the same tumors enabled us to define a “sarcomatoid-enriched gene signature” composed of immune-related, pro-metastatic, and epithelial-to-mesenchymal transition (EMT) genes. This signature was validated in bulk RNA-seq data from The Cancer Genome Atlas (TCGA), where it correlated with poor prognosis in ChRCC patients. Conclusions This study presents the first spatial transcriptomic atlas of sarcomatoid ChRCC in comparison to matched non-sarcomatoid (classic) from the same patient. Profound immune microenvironmental differences were identified between tumor compartments. The sarcomatoid variant exhibits hallmarks of an immune-inflamed but potentially immune-evasive phenotype, including enriched immune infiltration, pro-inflammatory signaling, and EMT-associated transcriptional programs. These findings highlight the biological differences between sarcomatoid and classic ChRCC and uncover specific immune pathways and spatial cell-cell interactions that may be targeted in future immunotherapeutic strategies. Our work also establishes a foundational spatial map for ChRCC that offers new insight into the disease heterogeneity and progression.