Mitochondrial Genome Alterations Driving Early Lung Adenocarcinoma Evolution

Lung adenocarcinoma (LUAD) is thought to arise gradually, beginning as atypical adenomatous hyperplasia (AAH) and advancing through adenocarcinoma in situ (AIS) toward minimally invasive adenocarcinoma (MIA). Although this progression is well-described, the biological events that trigger and sustain these early transitions remain unclear Mitochondrial DNA (mtDNA) is present in many copies, lacks histone protection, and is continually exposed to oxidative stress, making it more prone to mutation than nuclear DNA. Consequently, alterations in the mitochondrial genome may provide an opportunity to identify and classify potentially aggressive preneoplastic lesions long before they reach an invasive stage. We analyzed 109 lesions from 37 non-small-cell lung cancer (NSCLC) patients, encompassing the continuum of AAH, AIS, MIA, and ACA. Whole mitochondrial genome (16.5kb) was sequenced from formalin fixed paraffin embedded (FFPE) tumor and matched normal samples using an amplicon-based Illumina NextSeq approach. Variant detection was performed with a custom pipeline (BWA, SAMtools, GATK Mutect2). We observed that somatic mtDNA alterations arise very early in the neoplastic sequence, with AAH lesions carrying numerous changes across the non-coding tRNA, rRNA, and D-loop regions, as well as repeated nonsynonymous variants in OXPHOS coding genes such as MT-ND5, MT-ATP8, and MT-CYB. Several of these mutations appeared in lesions located in different areas of the same lung, pointing to an early clonal expansion rather than isolated, random events. As lesions advanced into AIS and then MIA, the number of mitochondrial alterations increased steadily. MIA, in particular, showed the greatest accumulation of non-coding changes, and coding variants such as A8860G (ATP6) were frequent across most cases, suggesting that these alterations are not simply incidental. The expression data followed a similar trend. Specifically, in AAH and AIS, numerous mtDNA encoded OXPHOS genes showed higher expression, reflecting an early compensatory response to emerging dysfunction. By the time lesions reached the MIA stage, this pattern became less consistent, with greater variability among patient samples. Once the disease progressed to fully invasive adenocarcinoma, mitochondrial transcripts dropped broadly, fitting with at least partial metabolic shift toward glycolysis known to accompany invasion. Taken together, these patterns point toward early mtDNA instability and evolving mitochondrial transcription as features that accompany and possibly shape the stepwise development of LUAD. Acknowledgements: We extend our special thanks to patients and clinical teams at Johns Hopkins, supported by NCI EDRN grant U01CA271896 . We also acknowledge ANID for providing scholarship funding (21222011, 242230375, 752230204) and Swiss Cancer League grant (BIL KLS-3649-02-2015). Citation Format: Alvaro Gutierrez, Ido Sloma, Adrian Daniel Schubert, Karthik Suresh, Mohammad Obaidul Hoque, Carmen Gloria Ili, Evgeny Izumchenko, Santanu Dasgupta, David Sidransky. Mitochondrial genome alterations as early drivers of lung adenocarcinoma evolution [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6807.