Clear and non-clear cell renal cell carcinomas and the ability to engage in oxidative phosphorylation.

Abstract

4542 Background: The impairment of oxidative phosphorylation (OxPhos) and upregulation of aerobic glycolysis, mediated by the loss of VHL , are key features of clear cell renal cell carcinoma (ccRCC). In contrast, non-clear cell renal cell carcinoma (RCC) denotes a heterogeneous group of tumors with few known nuclear oncogenic drivers. 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 ( > = 5 reads across > 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 frequently 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 < 0.05). Among all established RCC nuclear driver genes, VHL was found to be mutually exclusive with high heteroplasmy ETC truncating mutations (q < 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 ( > 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. Further, knockout of nuclear ETC components of complex I in Depmap was associated with little to no effect on cell survival. Conclusions: 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.