Genomic Signature of Oral Squamous Cell Carcinomas from Non-Smoking Non-Drinking Patients

Abstract

Molecular alterations in 176 patients with oral squamous cell carcinomas (OSCC) were evaluated to delineate differences in non-smoking non-drinking (NSND) patients. Somatic mutations and DNA copy number variations (CNVs) in a 68-gene panel and human papilloma virus (HPV) status were interrogated using targeted next-generation sequencing. In the entire cohort, TP53 (60%) and CDKN2A (24%) were most frequently mutated, and the most common CNVs were EGFR amplifications (9%) and deletions of BRCA2 (5%) and CDKN2A (4%). Significant associations were found for TP53 mutation and nodal disease, lymphovascular invasion and extracapsular spread, CDKN2A mutation or deletion with advanced tumour stage, and EGFR amplification with perineural invasion and extracapsular spread. PIK3CA mutation, CDKN2A deletion, and EGFR amplification were associated with worse survival in univariate analyses (p < 0.05 for all comparisons). There were 59 NSND patients who tended to be female and older than patients who smoke and/or drink, and showed enrichment of CDKN2A mutations, EGFR amplifications, and BRCA2 deletions (p < 0.05 for all comparisons), with a younger subset showing higher mutation burden. HPV was detected in three OSCC patients and not associated with smoking and drinking habits. NSND OSCC exhibits distinct genomic profiles and further exploration to elucidate the molecular aetiology in these patients is warranted.

Keywords: CDKN2A; DNA copy number; EGFR; PIK3CA; TP53; alcohol; human papilloma virus; oral cancer; targeted sequencing; tobacco.

Figure 1

Summary of Squamous cell carcinomas of the head and neck (HNSCC) gene mutations reported in 15 previous studies [16,17,18,19,20,21,22,23,24,25,26,27,28,29,30], stratified by human papilloma virus (HPV) status as available. Studies dedicated to oral squamous cell carcinomas (OSCC) are shown separately. Percentage of patients with a gene mutation are shown; red indicates low percentages and yellow indicates high percentages. Grey boxes indicate that no data were available for that gene for a particular publication.

Figure 2

HPV prevalence in 176 OSCC patients for high-risk HPV subtypes 16, 18, 33, and 35 based on genomic sequencing. Tumour samples with normalised HPV read counts >1000 were considered HPV-positive. Seven oropharyngeal tumours, which are known to have a high prevalence of HPV infection, were included as control.

Figure 3

Age of diagnosis distribution for 176 OSCC patients by drinking and smoking status. NSND = non-smoker and non-drinker; SD = smokers and/or drinker.

Figure 4

Mutation map for 23 candidate genes mutated in at least 5% (9/176) of tumours from OSCC patients. Nonsense and indel mutations are indicated by red bars, missense mutations with a PolyPhen-2 score > 0.85 are indicated by purple bars, missense mutations with a PolyPhen-2 score < 0.85 indicated by grey bars. The row at the bottom indicates patients with no detected mutations in the targeted sequencing panel. The colour bar at the top denotes smokers and/or drinkers (SD, blue) and non-smokers and non-drinkers (NSND, red).

Figure 5

Kaplan–Meier survival curves for OSCC patients by TP53 mutation, PIK3CA mutation, EGFR amplification, or CDKN2A deletion status. p values are for the log rank test.

Figure 6

Distribution of mutation counts, comparing the NSND and the SD groups. NSND = non-smoker and non-drinker; SD = smokers and/or drinker.