Abstract 4845: Ultra-deep sequencing of mitochondrial genome to explore the dynamic mutational changes associated with oral cavity squamous cell carcinoma progression
Authors: Singh Alka , Koppayi Ashwin Lakshman , Wu Ping , Lingen Mark , Mishra Vasudha , Pearson Alexander , Rosenberg Ari , Agrawal Nishant , Suresh Karthik , Izumchenko Evgeny 
Published: April 2023

Abstract
Oral cavity squamous cell carcinoma (OCSCC) is a devastating disease, causing substantial morbidity and mortality. While many OCSCCs arise from an existing dysplastic lesion, not all oral premalignant lesions progress to OCSCC. Current methods for oral premalignancy and OCSCC diagnosis (visual and tactile exam followed by tissue biopsy and histologic evaluation) cannot discriminate between benign inflammatory changes and high-risk premalignant lesions that require interventions, underscoring the need for molecular-based biomarkers. The multi-step cancer progression from normal epithelium to premalignant lesion and invasive SCC is driven by the accumulation of genetic alterations, including changes in mitochondrial DNA (mtDNA). Due to the lack of protective histones and limited repair mechanisms, mtDNA is susceptible to damage by environmental carcinogens and reactive oxygen species, a byproduct of the oxidative phosphorylation system. As a result, mutation rate in mtDNA is ~10 times higher than in nuclear DNA, and may greatly facilitate the risk of mitochondrial dysfunction. Previous studies underscore that acquisition of somatic mtDNA mutations directly involved in tumorigenesis, and not merely epiphenomena. However, the impact of these studies is limited by an incomplete understanding of mitochondrial genomic alterations in the transition of preneoplastic lesions to invasive disease. In this study we used a unique cohort of 27 patients with matched longitudinally collected samples (histologically normal mucosa, dysplastic lesion, and SCC) coupled with novel ultra-deep mitochondrial sequencing (mtDNA-Seq) method to assess the mtDNA mutational landscape throughout the continuum of OCSCC progression. Using a custom bioinformatics workflow, somatic mutations were detected in a subset of the premalignant lesions, with overall higher mutational load observed in OCSCC specimens. While sequencing revealed a large degree of inter-patient heterogeneity, a panel of non-synonymous aberrations were present in both premalignant and invasive neoplasms. The majority of shared mutations showed an increase in fractional abundance in tumors, compared to the precursor lesions (suggesting a spatial expansion of these clones as they progressed histologically), and were enriched for coding mutations in complex-I subunits (critical region for ATP production), which is associated with an oncogenic phenotype. Additionally, mtDNA content increased in OCSCC tumor in a subset of patients, suggesting a cell compensation for defective oxidative phosphorylation and lower ATP production per mitochondria. Here we report the first comprehensive characterization of mitochondrial mutational landscape in dysplastic and invasive SCC lesions, and reveal key molecular events associated with the transition from non-invasive to invasive state.
Citation Format: Alka Singh, Ashwin Lakshman Koppayi, Ping Wu, Mark Lingen, Vasudha Mishra, Alexander Pearson, Ari Rosenberg, Nishant Agrawal, Karthik Suresh, Evgeny Izumchenko. Ultra-deep sequencing of mitochondrial genome to explore the dynamic mutational changes associated with oral cavity squamous cell carcinoma progression. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4845.