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bioRxiv · 10.1101/2025.03.14.643063

Deciphering lung adenocarcinoma evolution and the role of LINE-1 retrotransposition

Zhang, T.·Zhao, W.·Wirth, C.·Diaz-Gay, M.·Yin, J.·Cecati, M.·Marchegiani, F.·Hoang, P. H.·Leduc, C.·Baine, M. K.·Travis, W. D.·Sholl, L. M.·Joubert, P.·Sang, J.·McElderry, J. P.·Klein, A.·Khandekar, A.·Hartman, C.·Rosenbaum, J.·Colon-Matos, F. J.·Miraftab, M.·Saha, M.·Lee, O. W.·Jones, K. M.·Caporaso, N. E.·Wong, M. P.·Leung, K. C.·Hsiung, C. A.·Chen, C.-Y.·Homer, R.·Yang, S.-R.·Pesatori, A. C.·Consonni, D.·Yang, L.·Zhu, B.·Edell, E. S.·Santamaria, J. M.·Schabath, M. B.·Yendamuri, S. S.·Manczuk, M.·Lissowska, J.·Swiatkowska, B.·Mukeria, A.·Shangina, O
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Abstract

Understanding lung cancer evolution can identify tools for intercepting its growth. In a landscape analysis of 1024 lung adenocarcinomas (LUAD) with deep whole-genome sequencing integrated with multiomic data, we identified 542 LUAD that displayed diverse clonal architecture. In this group, we observed an interplay between mobile elements, endogenous and exogenous mutational processes, distinct driver genes, and epidemiological features. Our results revealed divergent evolutionary trajectories based on tobacco smoking exposure, ancestry, and sex. LUAD from smokers showed an abundance of tobacco-related C:G>A:T driver mutations in KRAS plus short subclonal diversification. LUAD in never smokers showed early occurrence of copy number alterations and EGFR mutations associated with SBS5 and SBS40a mutational signatures. Tumors harboring EGFR mutations exhibited long latency, particularly in females of European-ancestry (EU_N). In EU_N, EGFR mutations preceded the occurrence of other driver genes, including TP53 and RBM10. Tumors from Asian never smokers showed a short clonal evolution and presented with heterogeneous repetitive patterns for the inferred mutational order. Importantly, we found that the mutational signature ID2 is a marker of a previously unrecognized mechanism for LUAD evolution. Tumors with ID2 showed short latency and high L1 retrotransposon activity linked to L1 promoter demethylation. These tumors exhibited an aggressive phenotype, characterized by increased genomic instability, elevated hypoxia scores, low burden of neoantigens, propensity to develop metastasis, and poor overall survival. Re-activated L1 retrotransposition-induced mutagenesis can contribute to the origin of the mutational signature ID2, including through the regulation of the transcriptional factor ZNF695, a member of the KZFP family. The complex nature of LUAD evolution creates both challenges and opportunities for screening and treatment plans.

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Zhang, T., Zhao, W., Wirth, C., Diaz-Gay, M., Yin, J., Cecati, M., Marchegiani, F., Hoang, P. H., Leduc, C., Baine, M. K., Travis, W. D., Sholl, L. M., Joubert, P., Sang, J., McElderry, J. P., Klein, A., Khandekar, A., Hartman, C., Rosenbaum, J., Colon-Matos, F. J., Miraftab, M., Saha, M., Lee, O. W., Jones, K. M., Caporaso, N. E., Wong, M. P., Leung, K. C., Hsiung, C. A., Chen, C.-Y., Homer, R., Yang, S.-R., Pesatori, A. C., Consonni, D., Yang, L., Zhu, B., Edell, E. S., Santamaria, J. M., Schabath, M. B., Yendamuri, S. S., Manczuk, M., Lissowska, J., Swiatkowska, B., Mukeria, A., Shangina, O. 2025-03-16. Deciphering lung adenocarcinoma evolution and the role of LINE-1 retrotransposition. https://doi.org/10.1101/2025.03.14.643063

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