Abstract 5434: Quantitative profiling of mitochondrial DNA copy number across hereditary renal cell carcinoma subtypes

Mitochondrial DNA mutations and alterations in mitochondrial DNA copy number (mtDNA CN) have been reported in many cancer types. In hereditary renal cell carcinoma (RCC), each subtype is defined by a unique metabolic, pathologic, and clinical phenotype, and mtDNA CN can reflect the altered metabolic state of the originating tumor tissue. For example, in fumarate hydratase (FH)-deficient primary renal tumors and metastases associated with Hereditary Leiomyomatosis and Renal Cell Carcinoma (HLRCC), the loss of FH enzymatic activity leads to fumarate accumulation, loss and mutation of tumor mtDNA due to impairment of DNA Polymerase-γ, and a metabolic shift to aerobic respiration. In another RCC subtype, FLCN deficient Birt-Hogg Dubé (BHD) tumors have been characterized with high expression of PPARGC1A, a gene promoting mitochondrial biogenesis. The genotype-specific alterations in mtDNA CN, however, remain to be evaluated in many of the hereditary RCC syndromes. Here, we aim to establish a precise database of mtDNA CN alterations across the spectrum of hereditary RCC syndromes via a highly accurate droplet digital PCR (ddPCR) system. Analysis of mtDNA CN was achieved by quantifying the mitochondrial NADH-ubiquinone oxidoreductase chain 1 (MT-ND1) and mitochondrial NADH-ubiquinone oxidoreductase chain 4 (MT-ND4) genes in comparison to the nuclear reference beta-2-microglobulin (β2M) and brain-derived neurotropic factor (BDNF) genes. We employed our ddPCR protocol across multiple cohorts of RCC tumor subtypes, including Von-Hippel Lindau, BHD, FH-deficient HLRCC tumors and metastases, hereditary type 1 papillary renal carcinoma, and SDH-deficient RCC. We also studied a subset of multi-sampled tumors to assess intra-tumoral mtDNA CN heterogeneity. Our results offer a comprehensive overview of mtDNA CN quantifications across different RCC subtypes using ddPCR. Ultimately, we present a precision method to characterize mtDNA CN alterations, and we propose that tumor mtDNA CN alterations may serve as an additional biomarker to improve the clinical diagnoses of both hereditary and sporadic kidney cancers. Funded by the Intramural Research Program of the National Cancer Institute and FNLCR Contract HHSN261201500003I Citation Format: Vaishnavi S. Srirama, Christopher J. Ricketts, Cathy D. Vocke, Laura S. Schmidt, Ye Yang, Maria J. Merino, Martin Lang, Mark W. Ball, Sandeep Gurram, Daniel R. Crooks, W Marston Linehan. Quantitative profiling of mitochondrial DNA copy number across hereditary renal cell carcinoma subtypes [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 5434.