{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T12:29:39Z","timestamp":1784291379474,"version":"3.55.0"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,12,17]],"date-time":"2019-12-17T00:00:00Z","timestamp":1576540800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,12,17]],"date-time":"2019-12-17T00:00:00Z","timestamp":1576540800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Squamous cell carcinomas of the head and neck (HNSCC) arise from mucosal keratinocytes of the upper aero-digestive tract. Despite a common cell of origin and similar driver-gene mutations which divert cell fate from differentiation to proliferation, HNSCC are considered a heterogeneous group of tumors categorized by site of origin within the aero-digestive mucosa, and the presence or absence of HPV infection. Tobacco use is a major driver of carcinogenesis in HNSCC and is a poor prognosticator that has previously been associated with poor immune cell infiltration and higher mutation numbers. Here, we study patterns of mutations in HNSCC that are derived from the specific nucleotide changes and their surrounding nucleotide context (also known as mutation signatures). We identify that mutations linked to DNA adducts associated with tobacco smoke exposure are predominantly found in the larynx. Presence of this class of mutation, termed COSMIC signature 4, is responsible for the increased burden of mutation in this anatomical sub-site. In addition, we show that another mutation pattern, COSMIC signature 5, is positively associated with age in HNSCC from non-smokers and that larynx SCC from non-smokers have a greater number of signature 5 mutations compared with other HNSCC sub-sites. Immunohistochemistry demonstrates a significantly lower Ki-67 proliferation index in size matched larynx SCC compared with oral cavity SCC and oropharynx SCC. Collectively, these observations support a model where larynx SCC are characterized by slower growth and increased susceptibility to mutations from tobacco carcinogen DNA adducts.<\/jats:p>","DOI":"10.1038\/s41598-019-55352-y","type":"journal-article","created":{"date-parts":[[2019,12,17]],"date-time":"2019-12-17T11:02:49Z","timestamp":1576580569000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Mutation signature analysis identifies increased mutation caused by tobacco smoke associated DNA adducts in larynx squamous cell carcinoma compared with oral cavity and oropharynx"],"prefix":"10.1038","volume":"9","author":[{"given":"Andrew P.","family":"South","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicoline Y.","family":"den Breems","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tony","family":"Richa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uche","family":"Nwagu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Zhan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiv","family":"Poojan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ubaldo","family":"Martinez-Outschoorn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer M.","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam J.","family":"Luginbuhl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph M.","family":"Curry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,12,17]]},"reference":[{"key":"55352_CR1","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1016\/j.celrep.2018.03.063","volume":"23","author":"JD Campbell","year":"2018","unstructured":"Campbell, J. D. et al. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep 23, 194\u2013212 e196 (2018).","journal-title":"Cell Rep"},{"key":"55352_CR2","doi-asserted-by":"publisher","first-page":"7","DOI":"10.3322\/caac.21387","volume":"67","author":"RL Siegel","year":"2017","unstructured":"Siegel, R. L., Miller, K. D. & Jemal, A. Cancer Statistics, 2017. CA Cancer J Clin 67, 7\u201330 (2017).","journal-title":"CA Cancer J Clin"},{"key":"55352_CR3","unstructured":"American Cancer Society (https:\/\/www.cancer.org\/cancer.html accessed November 2018)."},{"key":"55352_CR4","doi-asserted-by":"publisher","first-page":"2013","DOI":"10.1002\/ijc.28112","volume":"133","author":"P Bose","year":"2013","unstructured":"Bose, P., Brockton, N. T. & Dort, J. C. Head and neck cancer: from anatomy to biology. Int J Cancer 133, 2013\u20132023 (2013).","journal-title":"Int J Cancer"},{"key":"55352_CR5","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1038\/nrc.2018.11","volume":"18","author":"CR Leemans","year":"2018","unstructured":"Leemans, C. R., Snijders, P. J. F. & Brakenhoff, R. H. The molecular landscape of head and neck cancer. Nat Rev Cancer 18, 269\u2013282 (2018).","journal-title":"Nat Rev Cancer"},{"key":"55352_CR6","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1002\/ijc.31294","volume":"143","author":"R Abrahao","year":"2018","unstructured":"Abrahao, R. et al. The influence of smoking, age and stage at diagnosis on the survival after larynx, hypopharynx and oral cavity cancers in Europe: The ARCAGE study. Int J Cancer 143, 32\u201344 (2018).","journal-title":"Int J Cancer"},{"key":"55352_CR7","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1016\/j.canep.2015.02.004","volume":"39","author":"E Leoncini","year":"2015","unstructured":"Leoncini, E. et al. Clinical features and prognostic factors in patients with head and neck cancer: Results from a multicentric study. Cancer Epidemiol 39, 367\u2013374 (2015).","journal-title":"Cancer Epidemiol"},{"key":"55352_CR8","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1056\/NEJMoa0912217","volume":"363","author":"KK Ang","year":"2010","unstructured":"Ang, K. K. et al. Human papillomavirus and survival of patients with oropharyngeal cancer. N Engl J Med 363, 24\u201335 (2010).","journal-title":"N Engl J Med"},{"key":"55352_CR9","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/j.oraloncology.2019.09.008","volume":"98","author":"RT Hughes","year":"2019","unstructured":"Hughes, R. T. et al. Human papillomavirus-associated squamous cell carcinoma of the larynx or hypopharynx: Clinical outcomes and implications for laryngeal preservation. Oral Oncol. 98, 20\u201327 (2019).","journal-title":"Oral Oncol."},{"key":"55352_CR10","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1016\/j.oraloncology.2019.03.001","volume":"91","author":"BY Hernandez","year":"2019","unstructured":"Hernandez, B. Y. et al. Human papillomavirus DNA detection, p16INK4a, and oral cavity cancer in a U.S. population. Oral Oncol. 91, 92\u201396 (2019).","journal-title":"Oral Oncol."},{"key":"55352_CR11","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-01877-7","volume":"8","author":"S Peri","year":"2017","unstructured":"Peri, S. et al. NSD1- and NSD2-damaging mutations define a subset of laryngeal tumors with favorable prognosis. Nat Commun 8, 1772 (2017).","journal-title":"Nat Commun"},{"key":"55352_CR12","doi-asserted-by":"crossref","unstructured":"Ghasemi, F. et al. Mutational analysis of head and neck squamous cell carcinoma stratified by smoking status. JCI Insight 4 (2019).","DOI":"10.1172\/jci.insight.123443"},{"key":"55352_CR13","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/ng.3757","volume":"49","author":"S Papillon-Cavanagh","year":"2017","unstructured":"Papillon-Cavanagh, S. et al. Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas. Nat Genet 49, 180\u2013185 (2017).","journal-title":"Nat Genet"},{"key":"55352_CR14","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1038\/nature14129","volume":"517","author":"Cancer Genome Atlas, N","year":"2015","unstructured":"Cancer Genome Atlas, N. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 517, 576\u2013582 (2015).","journal-title":"Nature"},{"key":"55352_CR15","doi-asserted-by":"publisher","first-page":"1969","DOI":"10.1200\/JCO.2008.18.2188","volume":"27","author":"SA Duffy","year":"2009","unstructured":"Duffy, S. A. et al. Pretreatment health behaviors predict survival among patients with head and neck squamous cell carcinoma. J Clin Oncol 27, 1969\u20131975 (2009).","journal-title":"J Clin Oncol"},{"key":"55352_CR16","doi-asserted-by":"publisher","first-page":"2733","DOI":"10.1002\/lary.26083","volume":"126","author":"AJ Platek","year":"2016","unstructured":"Platek, A. J. et al. Smoking cessation is associated with improved survival in oropharynx cancer treated by chemoradiation. Laryngoscope 126, 2733\u20132738 (2016).","journal-title":"Laryngoscope"},{"key":"55352_CR17","doi-asserted-by":"publisher","first-page":"2185","DOI":"10.1007\/s00432-016-2203-7","volume":"142","author":"G Descamps","year":"2016","unstructured":"Descamps, G. et al. Classical risk factors, but not HPV status, predict survival after chemoradiotherapy in advanced head and neck cancer patients. J Cancer Res Clin Oncol 142, 2185\u20132196 (2016).","journal-title":"J Cancer Res Clin Oncol"},{"key":"55352_CR18","doi-asserted-by":"publisher","first-page":"2102","DOI":"10.1200\/JCO.2011.38.4099","volume":"30","author":"ML Gillison","year":"2012","unstructured":"Gillison, M. L. et al. Tobacco smoking and increased risk of death and progression for patients with p16-positive and p16-negative oropharyngeal cancer. J Clin Oncol 30, 2102\u20132111 (2012).","journal-title":"J Clin Oncol"},{"key":"55352_CR19","doi-asserted-by":"crossref","unstructured":"Ma, B., Stepanov, I. & Hecht, S. S. Recent Studies on DNA Adducts Resulting from Human Exposure to Tobacco Smoke. Toxics 7 (2019).","DOI":"10.3390\/toxics7010016"},{"key":"55352_CR20","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nature12477","volume":"500","author":"LB Alexandrov","year":"2013","unstructured":"Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415\u2013421 (2013).","journal-title":"Nature"},{"key":"55352_CR21","first-page":"763","volume":"30","author":"S Nik-Zainal","year":"2015","unstructured":"Nik-Zainal, S. et al. The genome as a record of environmental exposure. Mutagenesis 30, 763\u2013770 (2015).","journal-title":"Mutagenesis"},{"key":"55352_CR22","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1126\/science.aag0299","volume":"354","author":"LB Alexandrov","year":"2016","unstructured":"Alexandrov, L. B. et al. Mutational signatures associated with tobacco smoking in human cancer. Science 354, 618\u2013622 (2016).","journal-title":"Science"},{"key":"55352_CR23","doi-asserted-by":"publisher","first-page":"1402","DOI":"10.1038\/ng.3441","volume":"47","author":"LB Alexandrov","year":"2015","unstructured":"Alexandrov, L. B. et al. Clock-like mutational processes in human somatic cells. Nat Genet 47, 1402\u20131407 (2015).","journal-title":"Nat Genet"},{"key":"55352_CR24","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1038\/nature21703","volume":"543","author":"YS Ju","year":"2017","unstructured":"Ju, Y. S. et al. Somatic mutations reveal asymmetric cellular dynamics in the early human embryo. Nature 543, 714\u2013718 (2017).","journal-title":"Nature"},{"key":"55352_CR25","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1038\/nature19768","volume":"538","author":"F Blokzijl","year":"2016","unstructured":"Blokzijl, F. et al. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 538, 260\u2013264 (2016).","journal-title":"Nature"},{"key":"55352_CR26","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1016\/j.oraloncology.2017.09.002","volume":"74","author":"DL Faden","year":"2017","unstructured":"Faden, D. L. et al. Multi-modality analysis supports APOBEC as a major source of mutations in head and neck squamous cell carcinoma. Oral Oncol 74, 8\u201314 (2017).","journal-title":"Oral Oncol"},{"key":"55352_CR27","doi-asserted-by":"crossref","unstructured":"Cho, R. J. et al. APOBEC mutation drives early-onset squamous cell carcinomas in recessive dystrophic epidermolysis bullosa. Sci Transl Med 10 (2018).","DOI":"10.1016\/j.jid.2017.07.734"},{"key":"55352_CR28","doi-asserted-by":"publisher","first-page":"1282","DOI":"10.1016\/j.cell.2019.02.012","volume":"176","author":"M Petljak","year":"2019","unstructured":"Petljak, M. et al. Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis. Cell. 176, 1282\u20131294 (2019).","journal-title":"Cell."},{"key":"55352_CR29","doi-asserted-by":"publisher","first-page":"3842","DOI":"10.1158\/1078-0432.CCR-14-0565","volume":"20","author":"CR Pickering","year":"2014","unstructured":"Pickering, C. R. et al. Squamous cell carcinoma of the oral tongue in young non-smokers is genomically similar to tumors in older smokers. Clin Cancer Res. 20, 3842\u20138 (2014).","journal-title":"Clin Cancer Res."},{"key":"55352_CR30","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.oraloncology.2018.04.006","volume":"81","author":"DM Vossen","year":"2018","unstructured":"Vossen, D. M. et al. Comparative genomic analysis of oral versus laryngeal and pharyngeal cancer. Oral Oncol. 81, 35\u201344 (2018).","journal-title":"Oral Oncol."},{"key":"55352_CR31","doi-asserted-by":"crossref","unstructured":"Chen, J., Jacox, L. A., Saldanha, F. & Sive, H. Mouth development. Wiley Interdiscip Rev Dev Biol 6 (2017).","DOI":"10.1002\/wdev.275"},{"key":"55352_CR32","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1016\/j.ydbio.2014.12.037","volume":"399","author":"V Lungova","year":"2015","unstructured":"Lungova, V., Verheyden, J. M., Herriges, J., Sun, X. & Thibeault, S. L. Ontogeny of the mouse vocal fold epithelium. Dev Biol 399, 263\u2013282 (2015).","journal-title":"Dev Biol"},{"key":"55352_CR33","doi-asserted-by":"publisher","first-page":"3243","DOI":"10.1200\/JCO.2015.61.2358","volume":"33","author":"A Bhatia","year":"2015","unstructured":"Bhatia, A. & Burtness, B. Human Papillomavirus-Associated Oropharyngeal Cancer: Defining Risk Groups and Clinical Trials. J Clin Oncol 33, 3243\u20133250 (2015).","journal-title":"J Clin Oncol"},{"key":"55352_CR34","doi-asserted-by":"publisher","first-page":"1893","DOI":"10.1245\/s10434-014-4237-x","volume":"22","author":"J Liu","year":"2015","unstructured":"Liu, J. et al. Ki67 Expression has Prognostic Significance in Relation to Human Papillomavirus Status in Oropharyngeal Squamous Cell Carcinoma. Ann Surg Oncol 22, 1893\u20131900 (2015).","journal-title":"Ann Surg Oncol"},{"key":"55352_CR35","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1002\/hed.20977","volume":"31","author":"M Ritta","year":"2009","unstructured":"Ritta, M. et al. Cell cycle and viral and immunologic profiles of head and neck squamous cell carcinoma as predictable variables of tumor progression. Head Neck. 31, 318\u2013327 (2009).","journal-title":"Head Neck."},{"key":"55352_CR36","doi-asserted-by":"publisher","first-page":"27185","DOI":"10.18632\/oncotarget.8448","volume":"7","author":"LG Ledgerwood","year":"2016","unstructured":"Ledgerwood, L. G. et al. The degree of intratumor mutational heterogeneity varies by primary tumor sub-site. Oncotarget 7, 27185\u201327198 (2016).","journal-title":"Oncotarget"},{"key":"55352_CR37","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.ccell.2014.12.001","volume":"27","author":"N McGranahan","year":"2015","unstructured":"McGranahan, N. & Swanton, C. Biological and therapeutic impact of intratumor heterogeneity in cancer evolution. Cancer Cell 27, 15\u201326 (2015).","journal-title":"Cancer Cell"},{"key":"55352_CR38","doi-asserted-by":"publisher","first-page":"1519","DOI":"10.1136\/bmj.38142.554479.AE","volume":"328","author":"R Doll","year":"2004","unstructured":"Doll, R., Peto, R., Boreham, J. & Sutherland, I. Mortality in relation to smoking: 50 years\u2019 observations on male British doctors. BMJ 328, 1519 (2004).","journal-title":"BMJ"},{"key":"55352_CR39","doi-asserted-by":"publisher","first-page":"7307","DOI":"10.1038\/sj.onc.1205807","volume":"21","author":"MJ Thun","year":"2002","unstructured":"Thun, M. J., Henley, S. J. & Calle, E. E. Tobacco use and cancer: an epidemiologic perspective for geneticists. Oncogene 21, 7307\u20137325 (2002).","journal-title":"Oncogene"},{"key":"55352_CR40","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1016\/j.celrep.2012.12.008","volume":"3","author":"LB Alexandrov","year":"2013","unstructured":"Alexandrov, L. B., Nik-Zainal, S., Wedge, D. C., Campbell, P. J. & Stratton, M. R. Deciphering signatures of mutational processes operative in human cancer. Cell Rep. 3, 246\u2013259 (2013).","journal-title":"Cell Rep."},{"key":"55352_CR41","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0893-4","volume":"17","author":"R Rosenthal","year":"2016","unstructured":"Rosenthal, R., McGranahan, N., Herrero, J., Taylor, B. S. & Swanton, C. deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution. Genome Biol 17, 31 (2016).","journal-title":"Genome Biol"},{"key":"55352_CR42","doi-asserted-by":"publisher","unstructured":"Alexandrov, L. B. et al. The Repertoire of Mutational Signatures in Human Cancer BioRxiv, https:\/\/doi.org\/10.1101\/322859 (2019).","DOI":"10.1101\/322859"},{"key":"55352_CR43","doi-asserted-by":"crossref","unstructured":"Yee, T. W. Vector Generalized Linear and Additive Models, in Springer Series in Statistics, Editors Diggle, P., Gather, U. & Zeger, S. ISSN: 0172\u20137397 (2015).","DOI":"10.1007\/978-1-4939-2818-7"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-55352-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-55352-y","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-55352-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,17]],"date-time":"2022-12-17T17:29:18Z","timestamp":1671298158000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-55352-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,12,17]]},"references-count":43,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,12]]}},"alternative-id":["55352"],"URL":"https:\/\/doi.org\/10.1038\/s41598-019-55352-y","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,12,17]]},"assertion":[{"value":"15 July 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 November 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 December 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"A.P.S. is an Editorial Board Member of Scientific Reports. The authors declare no other relevant competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"19256"}}