Abstract 1526: An impaired ability to engage in oxidative phosphorylation as a unifying feature of renal carcinogenesis
Authors: Ziad Bakouny, Sonia Boscenco, Ruobing Cui, Keunwoo Ryu, Ritesh R. Kotecha, Maria I. Carlo, Martin H. Voss, A. Ari Hakimi, Robert J. Motzer, Payam A. Gammage, Ed Reznik, Craig B. Thompson
Journal: Cancer Research (2025)

Introduction: VHL loss is a cardinal feature of renal cell carcinoma (RCC), specifically of the clear cell RCC (ccRCC) subtype, and leads to activation of aerobic glycolysis and suppression of oxidative phosphorylation (OxPhos). In contrast, Non-VHL driven forms of RCC are a heterogeneous group of tumors with few known nuclear oncogenic drivers, none of which are shared across these tumors. Recent studies have shown that mitochondrially-encoded electron transport chain (ETC) genes, responsible for OxPhos, can be mutated in a range of cancers. Methods: Mitochondrial mutations were called using a previously published custom pipeline for variant calling (PMID: 33833465). On-target (whole genome sequencing) and off-target (whole exome and gene panel-based sequencing) reads were used. Only samples with sufficient coverage (&amp;gt;=5 reads across &amp;gt;90% of the mitochondrial genome) were included. This was performed (N with sufficient coverage) in TCGA (N= 3,265; N=324 RCC), the institutional MSK-IMPACT cohort (N= 22,252; N=568 RCC), and CCLE/Depmap (N= 377; N=11 RCC). Mutual exclusivity between each established RCC nuclear driver gene (N=16, PMID: 29617669) and the heteroplasmy of ETC truncating variants was evaluated using pairwise t-tests comparing heteroplasmy between the mutated and wild-type RCC samples for each nuclear driver gene. CERES scores from genome-wide CRISPR screens in Depmap were used to compare gene dependency between cell lines. Benjamini-Hochberg correction was used to control type I error. Results: Across all cancer types in TCGA, RCC tumors were among the most enriched in ETC truncating mutations. These mutations most commonly affected components of mitochondrial complex I and were enriched to high levels of heteroplasmy. VHL-driven ccRCC was relatively depleted in these mutations compared to other subtypes (ccRCC: 8.6%, chRCC: 20.0%, pRCC: 34.0%). Further, the heteroplasmy of truncating mutations was significantly increased in chRCC and pRCC compared to ccRCC (p&amp;lt;0.05). Among all established RCC nuclear driver genes, VHL was found to be mutually exclusive with high heteroplasmy ETC truncating mutations (q&amp;lt;0.05). These results were independently replicated in the MSK-IMPACT cohort. Using data from CCLE/Depmap, we find that while cell lines with high heteroplasmy (&amp;gt;50%; N=13) truncating mitochondrially-encoded ETC mutations have differential dependencies compared to other cell lines, ETC mutations were not synthetically lethal with VHL mutations. Conclusion: We established that mutations in VHL and in mitochondrially-encoded ETC genes are mutually exclusive in RCC and that this mutual exclusivity is not accounted for by synthetic lethality. These results suggest that mitochondrial mutations may be phenocopying the effect of VHL on OxPhos and form the basis for our planned experimental work evaluating OxPhos dysregulation as a unifying feature of renal carcinogenesis. Citation Format: Ziad Bakouny, Sonia Boscenco, Ruobing Cui, Keunwoo Ryu, Ritesh R. Kotecha, Maria I. Carlo, Martin H. Voss, A. Ari Hakimi, Robert J. Motzer, Payam A. Gammage, Ed Reznik, Craig B. Thompson. An impaired ability to engage in oxidative phosphorylation as a unifying feature of renal carcinogenesis [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 1526.