Abstract 6684: Spatial multi-omics profiling of clear cell renal cell carcinoma (ccRCC) pre-and post-immunotherapy identifies new druggable targets

Abstract Introduction: Immunotherapy (IO) and VEGF targeting TKIs have transformed outcomes of patients with advanced ccRCC. However, much less is known about treatment resistance mechanisms after IO therapy. Methods: 15 patients (pts) with advanced ccRCC who had tumor samples pre- and post-treatment (Tx, IO-IO or IO-TKI) were included in this study. Tumors were profiled using the Nanostring GeoMx spatial profiling platform. 4 to 12 regions of interest (ROIs) were selected for each patient, and the ROIs were further segmented into tumor (PanCK+), immune (CD45+), and stroma (PanCk-, CD45-) compartments. Differentially expressed genes and proteins were assessed with Gene Set Enrichment Analysis (GSEA). Bulk gene expression was further deconvoluted to profile immune cell subsets using CIBERSORT. Deep learning algorithms analyzed H0.01) post-Tx but not after IO-TKI (Log2FC -0.070, p0.01). Some patients who received IO/TKIs had decreased tumor angiogenic expression post-Tx. NMF clustering classified post-Tx as NMF4 in 6/15 patients (4 of 10 in IO-TKI cohort and 2 of 5 in IO-IO cohort). NMF cluster 3 remained post-IO in most patients.While most pre-IO samples had moderate to high immune infiltration, post-IO samples had even higher levels. Notably, CIBERSORT profiling revealed post-IO proportion of immune suppressive regulatory T cells were decreased (IO-TKI, p 0.01), while cytotoxic CD8+ T cells were increased (IO-TKI, p 0.01) with both Tx cohorts. However, resting NK cells were increased (p=0.29), while activated NK cells were decreased (p 0.01) significantly only in IO-IO treated subsets. Conclusion: Molecular gene expression changes in RCC after IO-based therapy identified clinical targets in residual tumors. NMF cluster 4 persistence, CD8+ infiltration, and reduction in Treg proportion suggests an expansion or persistence of immune cells post-IO. NMF cluster 3 and increased proportion of resting NK cells may explain the resistance of residual tumor post-IO. Given the heterogeneity in RCC, it is imperative to profile individual tumors to improve IO therapy outcomes. Ongoing analyses include IHC target validation. Citation Format: Navneet Kaur, Wadih Issa, Ze Yu, Hua Zhong, Aleksandra Weronika Nielsen, Jay Jasti, Shahed Abdullah, Libin Yan, Damla Gunenc, Qinhan Zhou, Andrew DeVilbiss, Satwik Rajaram, Payal Kapur, Chao Xing, Liwei Jia, Andrew Z. Wang, Tian Zhang. Spatial multi-omics profiling of clear cell renal cell carcinoma (ccRCC) pre-and post-immunotherapy identifies new druggable targets abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6684.