Tobacco smoke carcinogens exacerbate APOBEC mutagenesis and carcinogenesis

Tobacco smoke carcinogens exacerbate APOBEC mutagenesis and carcinogenesis | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Biological Sciences - Article Tobacco smoke carcinogens exacerbate APOBEC mutagenesis and carcinogenesis Reuben Harris, Erik Bergstrom, Marcos Díaz-Gay, Yufan Zhou, Nuri Temiz, and 10 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5843684/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Mutations in somatic cells are inflicted by both extrinsic and intrinsic sources and contribute over time to cancer. Tobacco smoke contains chemical carcinogens that have been causatively implicated with cancers of the lung and head & neck1,2. APOBEC family DNA cytosine deaminases have emerged as endogenous sources of mutation in cancer, with hallmark mutational signatures (SBS2/SBS13) that often co-occur in tumors of tobacco smokers with an equally diagnostic mutational signature (SBS4)3,4. Here we challenge the dogma that mutational processes are thought to occur independently and with additive impact by showing that 4-nitroquinoline 1-oxide (NQO), a model carcinogen for tobacco exposure, sensitizes cells to APOBEC3B (A3B) mutagenesis and leads to synergistic increases in both SBS2 mutation loads and oral carcinomas in vivo. NQO-exposed/A3B-expressing animals exhibit twice as many head & neck lesions as carcinogen-exposed wildtype animals. This increase in carcinogenesis is accompanied by a synergistic increase in mutations from APOBEC signature SBS2, but not from NQO signature SBS4. Interestingly, a large proportion of A3B-catalyzed SBS2 mutations occurs as strand-coordinated pairs within 32 nucleotides of each other in transcribed regions, suggesting a mechanism in which removal of NQO-DNA adducts by nucleotide excision repair exposes short single-stranded DNA tracts to enzymatic deamination. These highly enriched pairs of APOBEC signature mutations are termed didyma (Greek for twins) and are mechanistically distinct from other types of clustered mutation (omikli and kataegis). Computational analyses of lung and head & neck tumor genomes show that both APOBEC mutagenesis and didyma are elevated in cancers from smokers compared to non-smokers. APOBEC signature mutations and didyma are also elevated in normal lung tissues in smokers prior to cancer initiation. Collectively, these results indicate that DNA adducting mutagens in tobacco smoke can amplify DNA damage and mutagenesis by endogenous APOBEC enzymes and, more broadly, suggest that mutational mechanisms can interact synergistically in both cancer initiation and promotion. Biological sciences/Cancer/Cancer genomics Biological sciences/Cancer/Tumour heterogeneity Health sciences/Medical research/Genetics research Biological sciences/Evolution/Experimental evolution Biological sciences/Cancer/Lung cancer APOBEC mutagenesis bulky DNA adducts cancer development and progression nucleotide excision repair tobacco carcinogens Full Text Additional Declarations Yes there is potential Competing Interest. L.B.A. is a co-founder, CSO, scientific advisory member, and consultant for io9, has equity and receives income. E.N.B. is a consultant for io9, has equity, and receives income. The terms of these arrangements have been reviewed and approved by University of California, San Diego in accordance with its conflict of interest policies. L.B.A. is a compensated member of the scientific advisory board of Inocras. L.B.A.’s spouse is an employee of Hologic, Inc. L.B.A. and E.N.B. declare U.S. provisional applications with serial numbers: 63/289,601 and 63/269,033. L.B.A. also declares U.S. provisional applications with serial numbers: 63/366,392; 63/412,835 as well as international patent application PCT/US2023/010679. L.B.A. is also an inventor of a US Patent 10,776,718 for source identification by non-negative matrix factorization. All other authors declare that they have no competing interests. Supplementary Files TableS1v3.xlsx Supplementary Table 1 Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5843684","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Biological Sciences - Article","associatedPublications":[],"authors":[{"id":412572325,"identity":"bc0da103-ac40-460f-a155-0a5985d404ef","order_by":0,"name":"Reuben 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E.N.B. is a consultant for io9, has equity, and receives income. The terms of these arrangements have been reviewed and approved by University of California, San Diego in accordance with its conflict of interest policies. L.B.A. is a compensated member of the scientific advisory board of Inocras. L.B.A.’s spouse is an employee of Hologic, Inc. L.B.A. and E.N.B. declare U.S. provisional applications with serial numbers: 63/289,601 and 63/269,033. L.B.A. also declares U.S. provisional applications with serial numbers: 63/366,392; 63/412,835 as well as international patent application PCT/US2023/010679. L.B.A. is also an inventor of a US Patent 10,776,718 for source identification by non-negative matrix factorization. All other authors declare that they have no competing interests.","formattedTitle":"Tobacco smoke carcinogens exacerbate APOBEC mutagenesis and carcinogenesis","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"APOBEC mutagenesis, bulky DNA adducts, cancer development and progression, nucleotide excision repair, tobacco carcinogens ","lastPublishedDoi":"10.21203/rs.3.rs-5843684/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5843684/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Mutations in somatic cells are inflicted by both extrinsic and intrinsic sources and contribute over time to cancer. Tobacco smoke contains chemical carcinogens that have been causatively implicated with cancers of the lung and head \u0026 neck1,2. APOBEC family DNA cytosine deaminases have emerged as endogenous sources of mutation in cancer, with hallmark mutational signatures (SBS2/SBS13) that often co-occur in tumors of tobacco smokers with an equally diagnostic mutational signature (SBS4)3,4. Here we challenge the dogma that mutational processes are thought to occur independently and with additive impact by showing that 4-nitroquinoline 1-oxide (NQO), a model carcinogen for tobacco exposure, sensitizes cells to APOBEC3B (A3B) mutagenesis and leads to synergistic increases in both SBS2 mutation loads and oral carcinomas in vivo. NQO-exposed/A3B-expressing animals exhibit twice as many head \u0026 neck lesions as carcinogen-exposed wildtype animals. This increase in carcinogenesis is accompanied by a synergistic increase in mutations from APOBEC signature SBS2, but not from NQO signature SBS4. Interestingly, a large proportion of A3B-catalyzed SBS2 mutations occurs as strand-coordinated pairs within 32 nucleotides of each other in transcribed regions, suggesting a mechanism in which removal of NQO-DNA adducts by nucleotide excision repair exposes short single-stranded DNA tracts to enzymatic deamination. These highly enriched pairs of APOBEC signature mutations are termed didyma (Greek for twins) and are mechanistically distinct from other types of clustered mutation (omikli and kataegis). Computational analyses of lung and head \u0026 neck tumor genomes show that both APOBEC mutagenesis and didyma are elevated in cancers from smokers compared to non-smokers. APOBEC signature mutations and didyma are also elevated in normal lung tissues in smokers prior to cancer initiation. Collectively, these results indicate that DNA adducting mutagens in tobacco smoke can amplify DNA damage and mutagenesis by endogenous APOBEC enzymes and, more broadly, suggest that mutational mechanisms can interact synergistically in both cancer initiation and promotion.","manuscriptTitle":"Tobacco smoke carcinogens exacerbate APOBEC mutagenesis and carcinogenesis","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-06-03 12:55:59","doi":"10.21203/rs.3.rs-5843684/v1","editorialEvents":[],"status":"published","journal":{"display":false,"email":"[email protected]","identity":"nature","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"nature","sideBox":"Learn more about [Nature](http://www.nature.com/nature/)","snPcode":"","submissionUrl":"","title":"Nature","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"a6e36b69-ceef-460e-9345-03b2d1d3507e","owner":[],"postedDate":"June 3rd, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":43997367,"name":"Biological sciences/Cancer/Cancer genomics"},{"id":43997368,"name":"Biological sciences/Cancer/Tumour heterogeneity"},{"id":43997369,"name":"Health sciences/Medical research/Genetics research"},{"id":43997370,"name":"Biological sciences/Evolution/Experimental evolution"},{"id":43997371,"name":"Biological sciences/Cancer/Lung cancer"}],"tags":[],"updatedAt":"2025-06-03T12:55:59+00:00","versionOfRecord":[],"versionCreatedAt":"2025-06-03 12:55:59","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-5843684","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5843684","identity":"rs-5843684","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}