Abstract 159: Spatial multimodal understanding of disease heterogeneity and aggressiveness in renal cell carcinoma

Abstract Renal cell carcinomas (RCC) are highly heterogeneous and aggressive cancers with diverse histological subtypes, molecular profiles, tumor microenvironments (TMEs), and clinical behaviors. Intratumoral heterogeneity (ITH), a hallmark of RCC, arises from distinct subclones within the same tumor that vary histopathologically and molecularly. To elucidate the biological mechanisms underlying RCC tumorigenesis at single-cell resolution, we examined 155 tumor specimens from 78 cases, encompassing clear cell RCC (ccRCC), papillary RCC (pRCC), chromophobe RCC (chRCC), and rare subtypes. We utilized 80 single-nucleus RNA sequencing (snRNA-seq) and 55 single-nucleus ATAC sequencing (snATAC-seq) datasets alongside advanced spatial biology techniques, including 27 Xenium In Situ, 12 Visium spatial transcriptomics (ST), and 7 co-detection by indexing (CODEX) samples. The connection of matched bulk proteogenomic data, clinical annotations, and histopathological evaluations from H&E staining further enhanced our spatial multimodal investigation. From single-nucleus sequencing of over half a million nuclei, we identified specific transcriptional programs and chromatin accessibility patterns among RCC subtypes, including HIF pathway dysregulation in ccRCC and MET pathway activation in pRCC. We also identified markers and constructed signature scores for rare but high-grade phenotypes, such as the aggressive rhabdoid and sarcomatoid features in ccRCC. Spatial analyses confirmed the utility of these feature-associated signatures for detection, quantification, and potential therapeutic targeting. Furthermore, we characterized the spatial organization and tumor-TME interactions, providing critical insights into spatially diverse ITH in RCC. Notably, a Grade-4 ccRCC sample exhibited three distinct tumor subclones and regions of necrosis characterized by Xenium, CODEX, and Visium profiling. Among these, a rhabdoid-associated subclone showed tumor-intrinsic signatures of elevated cell cycle activity and epithelial-mesenchymal transition (EMT), distinguishing it from conventional ccRCC subclones and indicating higher metastatic potential. We further revealed a unique macrophage subpopulation closely interacting with the rhabdoid subclone, forming an immunosuppressive niche that likely contributes to immune evasion, resistance to immunotherapies, and disease recurrence. Collectively, our spatial multimodal findings delineate the molecular signatures and mechanisms underlying RCC heterogeneity and aggressive features. By linking spatially distinct subclones to tumor progression and therapeutic resistance, this study provides valuable insights for developing personalized and effective therapeutic strategies to improve outcomes for RCC patients. Citation Format: Yize Li, Wagma Caravan, Yuwei Zhang, Andrew Houston, Siqi Chen, Chia-Kuei Mo, Preet Lal, Xiangwei Fang, Xiyi Wei, Ruiyang Liu, Ilya Strunilin, Yizhe Song, Song Cao, Cody Weimholt, Hui Zhang, Feng Chen, Li Ding Spatial multimodal understanding of disease heterogeneity and aggressiveness in renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 159.