Dec 7, 2015

Integrated analysis links TP53, NOTCH, SLC38A and 11p with survival in patients with oral tongue squamous cell carcinoma

BioRxiv : the Preprint Server for Biology
Neeraja M KrishnanBinay Panda

Abstract

Head and neck squamous cell carcinoma (HNSCC) are a heterogeneous group of cancers affecting multiple subsites, including oral cavity. Oral or anterior tongue tumors (OTSCC) are an aggressive group of squamous cell carcinomas, characterized by their early spread to lymph nodes and higher rate of regional failure compared to other oral cavity cancers. There is a rise in the incidence of oral tongue cancer among younger population (<50yrs); many of who lack the typical associated risk factors of alcohol and/or tobacco exposure. In order to carry out an ensemble learning and prediction method with multiple parameters classifying survival, we generated data, on somatic mutations in genes from exome sequencing, immediate upstream and downstream flanking nucleotides of the somatic mutations, DNA methylation, loss of heterozygosity (LOH), copy number variations (CNV), gene expression, significant pathways altered and Human Papilloma Virus (HPV) infection, from 50 OTSCC patients. Results of our analysis identified somatic mutations in NOTCH2 and/or TP53, and/or LOH in 11p to associate with better disease free survival in HPV positive patients (P = 0.0254) and not in HPV negative patients (P = 0.414). We validated the latter in patients...Continue Reading

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Mentioned in this Paper

TP53 gene
Entire Oral Cavity
Biochemical Pathway
DNA Methylation [PE]
Human Papillomavirus
Malignant Neoplasm of Tongue
Classification
Tobacco
Protein Methylation
Notch

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