The mutagenic forces shaping the genomic landscape of lung cancer in never smokers (2024)

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Marcos Díaz-Gay, Tongwu Zhang, Phuc H. Hoang, Azhar Khandekar, Wei Zhao, Christopher D. Steele, Burçak Otlu, Shuvro P. Nandi, Raviteja Vangara, Erik N. Bergstrom, Mariya Kazachkova, Oriol Pich, Charles Swanton, Chao Agnes Hsiung, I-Shou Chang, Maria Pik Wong, Kin Chung Leung, Jian Sang, John McElderry, Lixing Yang, Martin A Nowak, Jianxin Shi, Nathaniel Rothman, David C. Wedge, Robert Homer, Soo-Ryum Yang, Qing Lan, Bin Zhu, Stephen J. Chanock, View ORCID ProfileLudmil B. Alexandrov, Maria Teresa Landi

doi: https://doi.org/10.1101/2024.05.15.24307318

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ABSTRACT

Lung cancer in never smokers (LCINS) accounts for up to 25% of all lung cancers and has been associated with exposure to secondhand tobacco smoke and air pollution in observational studies. Here, we evaluate the mutagenic exposures in LCINS by examining deep whole-genome sequencing data from a large international cohort of 871 treatment-naïve LCINS recruited from 28 geographical locations within the Sherlock-Lung study. KRAS mutations were 3.8-fold more common in adenocarcinomas of never smokers from North America and Europe, while a 1.6-fold higher prevalence of EGFR and TP53 mutations was observed in adenocarcinomas from East Asia. Signature SBS40a, with unknown cause, was found in most samples and accounted for the largest proportion of single base substitutions in adenocarcinomas, being enriched in EGFR-mutated cases. Conversely, the aristolochic acid signature SBS22a was almost exclusively observed in patients from Taipei. Even though LCINS exposed to secondhand smoke had an 8.3% higher mutational burden and 5.4% shorter telomeres, passive smoking was not associated with driver mutations in cancer driver genes or the activities of individual mutational signatures. In contrast, patients from regions with high levels of air pollution were more likely to have TP53 mutations while exhibiting shorter telomeres and an increase in most types of somatic mutations, including a 3.9-fold elevation of signature SBS4 (q-value=3.1 × 10−5), previously linked mainly to tobacco smoking, and a 76% increase of clock-like signature SBS5 (q-value=5.0 × 10−5). A positive dose-response effect was observed with air pollution levels, which correlated with both a decrease in telomere length and an elevation in somatic mutations, notably attributed to signatures SBS4 and SBS5. Our results elucidate the diversity of mutational processes shaping the genomic landscape of lung cancer in never smokers.

Competing Interest Statement

LBA is a co-founder, CSO, scientific advisory member, and consultant for io9, has equity and receives income. The terms of this arrangement have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. LBA is also a compensated member of the scientific advisory board of Inocras. LBA's spouse is an employee of Biotheranostics. ENB and LBA declare U.S. provisional patent application filed with UCSD with serial numbers 63/269,033. LBA also declares U.S. provisional applications filed with UCSD with serial numbers: 63/366,392; 63/289,601; 63/483,237; 63/412,835; and 63/492,348. LBA is also an inventor of a US Patent 10,776,718 for source identification by non-negative matrix factorization. SRY has received consulting fees from AstraZeneca, Sanofi, Amgen, AbbVie, and Sanofi; received speaking fees from AstraZeneca, Medscape, PRIME Education, and Medical Learning Institute. All other authors declare that they have no competing interests.

Funding Statement

This work was supported by the Intramural Research Program of the National Cancer Institute, US National Institute of Health (NIH) (project ZIACP101231 to MTL); by the NIH grants R01ES032547-01, R01CA269919-01, and 1U01CA290479-01 to LBA as well as by LBA's Packard Fellowship for Science and Engineering. The research performed in LBA's lab was also supported by UC San Diego Sanford Stem Cell Institute. The funders had no roles in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author Declarations

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Since the National Cancer Institute only received de-identified samples and data from collaborating centers, had no direct contact or interaction with the study participants, and did not use or generate identifiable private information, Sherlock-Lung has been determined to constitute "Not Human Subject Research (NHSR)" based on the federal Common Rule (45 CFR 46; https://www.ecfr.gov/cgi-bin/ECFR?page=browse).Non-abbreviated, full names and affiliations of all Ethics Committees / Institutional Review Boards that ruled on ethics of your study: Mary L. McMaster, Chairperson, National Cancer Institute Ethics Review Panel (ERP)Decision made: Unconditionally approved

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

Data Availability

Normal and tumor-paired CRAM files for the 871 WGS subjects of the Sherlock-Lung study have been deposited in dbGaP under the accession numbers phs001697.v1.p1.

Copyright

The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.

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PostedMay 17, 2024.

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The mutagenic forces shaping the genomic landscape of lung cancer in never smokers (2024)

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