Abstract 3971: Single-cell transcriptomic insights into tumor and immune dynamics driving resistance to sitravatinib, nivolumab, and ipilimumab in advanced clear cell renal cell carcinoma
Authors: Kai Yu, Ying Yuan, Jianfeng Chen, Xinmiao Yan, Menuka Karki, Fei Duan, Rahul Annil Sheth, Priya Rao, Kanishka Sircar, Amishi Yogesh Shah, Amado Zurita-Saavedra, Giannincola Genovesa, Min Li, Chih-Chen Yeh, Minghao Dang, Guangchun Han, Yanshuo Chu, Max Hallin, Peter Olson, Rui Yang, Daniela Slavin, Hirak Der-Torossian, Curtis Chin, Nizar M Tannir, Linghua Wang, Jianjun Gao, Pavlos Msaouel
Journal: Cancer Research (2025)

Abstract The combination of sitravatinib, nivolumab, and ipilimumab offers a novel approach to enhance immunotherapy outcomes in advanced clear cell renal cell carcinoma (ccRCC). To explore the immunomodulatory and resistance mechanisms underlying this triplet therapy, we performed single-cell RNA sequencing (scRNA-seq) on tumor samples collected longitudinally from 12 patients across treatment timepoints. Transcriptomic data from 70,526 cells, including 58,331 tumor microenvironment (TME) cells, revealed dynamic shifts in cellular composition and transcriptional states during therapy. Analysis of TME cells identified eight major cell types, with notable increases in T cells and reductions in myeloid and endothelial cells post-treatment. Baseline T cell abundance correlated with improved clinical response, while fibroblast enrichment predicted resistance. Tumor cells were classified into ten transcriptionally distinct clusters, including a treatment-resistant population (C8) enriched in epithelial-mesenchymal transition (EMT), hypoxia, and glycolysis signatures. These signatures correlated with shorter progression-free survival in the trial cohort and worse survival outcomes in an external TCGA ccRCC dataset. T cell states showed a transition from cytotoxic to exhausted phenotypes in non-responders and end-of-treatment samples, suggesting a role for T cell dysfunction in resistance. Similarly, myeloid cells exhibited a shift toward immunosuppressive phenotypes, characterized by M2-like macrophages and inhibitory signaling pathways. These findings elucidate resistance mechanisms to the triplet therapy, highlighting EMT-driven tumor cell states and immunosuppressive TME dynamics as key contributors. The identification of a tumor-specific C8 signature provides a potential biomarker for predicting poor responses and tailoring therapeutic strategies. Further validation in larger cohorts is needed to optimize patient selection and therapeutic outcomes. Citation Format: Kai Yu, Ying Yuan, Jianfeng Chen, Xinmiao Yan, Menuka Karki, Fei Duan, Rahul Annil Sheth, Priya Rao, Kanishka Sircar, Amishi Yogesh Shah, Amado Zurita-Saavedra, Giannincola Genovesa, Min Li, Chih-Chen Yeh, Minghao Dang, Guangchun Han, Yanshuo Chu, Max Hallin, Peter Olson, Rui Yang, Daniela Slavin, Hirak Der-Torossian, Curtis Chin, Nizar M Tannir, Linghua Wang, Jianjun Gao, Pavlos Msaouel. Single-cell transcriptomic insights into tumor and immune dynamics driving resistance to sitravatinib, nivolumab, and ipilimumab in advanced clear cell 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 3971.