Abstract B035: Spatial multi-omic profiling of sarcomatoid and rhabdoid renal cell carcinoma reveals spatially distinct immune and tumor cell populations

Abstract Background: Rhabdoid and sarcomatoid (S/R) renal cell carcinoma (RCC) is a form of dedifferentiated RCC that can arise in the background of any RCC subtype. S/R features are associated with a more aggressive tumor phenotype and worse patient prognosis. Paradoxically, tumors with S/R differentiation demonstrate heightened sensitivity to immune checkpoint inhibitors (ICI) compared with their non-S/R counterparts. The mechanisms that drive this aggressive tumor phenotype and paradoxical ICIs sensitivity remain unclear. Prior studies have shown minimal genetic differences between S/R and non-S/R RCC, suggesting that non-genetic mechanisms drive this phenotype. Spatial multi-omic approaches are uniquely positioned to dissect the cellular and microenvironmental programs underlying S/R biology. Using a cohort of seven treatment-naïve patients with clear cell RCC (ccRCC) with S/R features, we performed spatial multi-omic characterization of tumor regions with sarcomatoid, rhabdoid, and/or ccRCC histology captured on the same tissue sections. Methods: Hematoxylin and eosin (H&E)–stained sections from seven FFPE patient samples were reviewed and annotated by a genitourinary pathologist to identify discrete regions exhibiting sarcomatoid, rhabdoid, or clear cell morphology. Following region-of-interest (ROI) annotation, the corresponding FFPE sections were processed by Singular Genomics using the G4X spatial multi-omic platform, which enables simultaneous quantification of 315 RNA transcripts, 14 protein targets, and high-resolution fluorescent H&E imaging. Results: Initial characterization of samples with sarcomatoid and clear cell features confirmed that spatial multi-omic profiling effectively captured discrete regions with canonical clear cell and sarcomatoid biology. Integrating spatial RNA and protein data, we observed marked differences in immune cell composition between these regions. Sarcomatoid regions demonstrated increased T-cell infiltration as well as higher B cell/plasma cell abundance compared with adjacent ccRCC regions. Differential gene expression (DGE) analysis of T cells isolated from sarcomatoid versus ccRCC regions revealed that sarcomatoid-associated T cells were enriched for activation markers (CD69, HLA-DRA), cytotoxic effector programs (GZMA, GZMK), and exhaustion-associated genes (LAG3). DGE analysis of tumor cells from sarcomatoid versus ccRCC regions demonstrated upregulation of antigen-presentation machinery (HLA-A, TAP1/2) along with increased expression of epithelial–mesenchymal transition–associated genes (MET, VCAM1, and CD44). Conclusions: Initial analysis of our spatial multi-omic cohort of patients with S/R ccRCC revealed distinct immune cell compositions and transcriptional programs across sarcomatoid and clear cell regions. Within annotated sarcomatoid areas, T cells exhibited a more activated and exhausted phenotype, whereas sarcomatoid tumor cells demonstrated upregulation of antigen-presentation machinery. Together, these features may explain the enhanced sensitivity of sarcomatoid RCC to ICIs. Citation Format: Zachary A. Yochum, Sayed Matar, Peter Humphrey, Adebowale Adeniran, David A. Braun. Spatial multi-omic profiling of sarcomatoid and rhabdoid renal cell carcinoma reveals spatially distinct immune and tumor cell populations [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Kidney Cancer Research: From Molecular Insights to Therapeutic Breakthroughs; 2026 Mar 13-16; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2026;86(5_Suppl_2):Abstract nr B035.