Mutation signature analysis identifies increased mutation caused by tobacco smoke associated DNA adducts in larynx squamous cell carcinoma compared with oral cavity and oropharynx

Andrew P South,Adam J Luginbuhl,Uche Nwagu,Tingting Zhan,Jennifer M Johnson,Nicoline Y Den Breems,Joseph M Curry,Shiv Poojan,Tony Richa,Ubaldo Martinez-Outschoorn

doi:10.1038/s41598-019-55352-y

Andrew P South, Adam J Luginbuhl + Show 8 more

Open Access

https://doi.org/10.1038/s41598-019-55352-y

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Abstract

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.

Highlights

Squamous cell carcinomas of the head and neck (HNSCC) arise from mucosal keratinocytes of the upper aero-digestive tract
In our recent examination of mutation signatures in head and neck are SCC (HNSCC) arising in non-sun exposed sites, we observed striking sub-site specificity to the presence of tobacco smoke-associated mutations (COSMIC signature 4, the signature associated with tobacco exposure[27], Fig. 1A and Supplementary Fig. S1A)
Larynx SCC have a significantly greater proportion of COSMIC signatures 4 and 5 compared with oral cavity and oropharynx SCC, as well as a concomitant significant reduction in signature 1 compared with oral cavity and oropharynx SCC, and a significant reduction in COSMIC signature 2 compared with oropharynx (Fig. 1A)

Summary

Introduction

Squamous cell carcinomas of the head and neck (HNSCC) arise from mucosal keratinocytes of the upper aero-digestive tract. Overall survival figures differ by major anatomical sub-site and a number of studies demonstrate larynx SCC have overall improved 5 year survival compared with oral cavity tumors[6,7], suggesting that SCC arising at different locations within the upper aero-digestive tract are distinct entities with respect to incidence and outcome. For HPV negative tumors further sub-classification can be based on copy number alterations (CNA) or presence of specific mutations and epigenetic variation[11,12,13,14] Often these differences are not exclusive to anatomical location where, for example, identification of NSD1 and NSD2 mutations define a sub-class of both oral cavity and larynx SCC11,12. If repair processes are overwhelmed or are deficient, the DNA adducts can persist and cause mutations during DNA replication[19]

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