A novel genomic signature reclassifies an oral cancer subtype

M Samman, HM, Wood, C. Conway, L Stead, C Daly, R Chalkley, S Berri, B Senguven, L Ross, P Egan, P Chengot, TK Ong, M Pentenero, S Gandolfo, A Cassenti, P Cassoni, A Al Ajlan, A Samkari, W Barrett, K MacLennanA High, P Rabbitts

    Research output: Contribution to journalArticle

    5 Citations (Scopus)

    Abstract

    Verrucous carcinoma of the oral cavity (OVC) is considered a subtype of classical oral squamous cell carcinoma (OSCC). Diagnosis is problematic, and additional biomarkers are needed to better stratify patients. To investigate their molecular signature, we performed low‐coverage copy number (CN) sequencing on 57 OVC and exome and RNA sequencing on a subset of these and compared the data to the same OSCC parameters. CN results showed that OVC lacked any of the classical OSCC patterns such as gain of 3q and loss of 3p and demonstrated considerably fewer genomic rearrangements compared to the OSCC cohort. OVC and OSCC samples could be clearly differentiated. Exome sequencing showed that OVC samples lacked mutations in genes commonly associated with OSCC (TP53, NOTCH1, NOTCH2, CDKN2A and FAT1 ). RNA sequencing identified genes that were differentially expressed between the groups. In silico functional analysis showed that the mutated and differentially expressed genes in OVC samples were involved in cell adhesion and keratinocyte proliferation, while those in the OSCC cohort were enriched for cell death and apoptosis pathways. This is the largest and most detailed genomic and transcriptomic analysis yet performed on this tumour type, which, as an example of non‐metastatic cancer, may shed light on the nature of metastases. These three independent investigations consistently show substantial differences between the cohorts. Taken together, they lead to the conclusion that OVC is not a subtype of OSCC, but should be classified as a distinct entity.
    Original languageEnglish
    Pages (from-to)2364-2373
    Number of pages9
    JournalInternational Journal of Cancer
    Volume137
    Issue number10
    Early online date9 Jun 2015
    DOIs
    Publication statusPublished - 15 Nov 2015

    Keywords

    • Oral
    • Cancer
    • HNSCC
    • Verrucous
    • NGS

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  • Cite this

    Samman, M., Wood, HM., Conway, C., Stead, L., Daly, C., Chalkley, R., Berri, S., Senguven, B., Ross, L., Egan, P., Chengot, P., Ong, TK., Pentenero, M., Gandolfo, S., Cassenti, A., Cassoni, P., Al Ajlan, A., Samkari, A., Barrett, W., ... Rabbitts, P. (2015). A novel genomic signature reclassifies an oral cancer subtype. International Journal of Cancer, 137(10), 2364-2373. https://doi.org/10.1002/ijc.29615