BMC Cancer Research article BioMed Central Open Access Oral tongue cancer gene expression profiling: Identification of novel potential prognosticators by oligonucleotide microarray analysis Cherry L Estilo*†1, Pornchai O-charoenrat†2, Simon Talbot3, Nicholas D Socci4, Diane L Carlson5, Ronald Ghossein5, Tijaana Williams1, Yoshihiro Yonekawa3, Yegnanarayana Ramanathan3, Jay O Boyle6, Dennis H Kraus6, Snehal Patel6, Ashok R Shaha6, Richard J Wong6, Joseph M Huryn1, Jatin P Shah6 and Bhuvanesh Singh3,6 Address: 1Dental Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, NY, USA, 2Division of Head and Neck Surgery, Department of Surgery, Siriraj Hospital Medical School, Bangkok, Thailand, 3Laboratory of Epithelial Cancer Biology, Memorial Sloan-Kettering Cancer Center, NY, USA, 4Department of Biostatistics, Memorial Sloan-Kettering Cancer Center, NY, USA, 5Department of Pathology, Memorial Sloan-Kettering Cancer Center, NY, USA and 6Head and Neck Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, NY, USA Email: Cherry L Estilo* - estiloc@mskcc.org; Pornchai O-charoenrat - sipoc@mahidol.ac.th; Simon Talbot - sgtalbot@partners.org; Nicholas D Socci - soccin@mskcc.org; Diane L Carlson - carlsond@mskcc.org; Ronald Ghossein - ghosseir@mskcc.org; Tijaana Williams - williat3@mskcc.org; Yoshihiro Yonekawa - yoy2003@med.cornell.edu; Yegnanarayana Ramanathan - ramanaty@mskcc.org; Jay O Boyle - boylej@mskcc.org; Dennis H Kraus - krausd@mskcc.org; Snehal Patel - patels@mskcc.org; Ashok R Shaha - shahaa@mskcc.org; Richard J Wong - wongr@mskcc.org; Joseph M Huryn - hurynj@mskcc.org; Jatin P Shah - shahj@mskcc.org; Bhuvanesh Singh - singhb@mskcc.org * Corresponding author †Equal contributors Published: 12 January 2009 BMC Cancer 2009, 9:11 doi:10.1186/1471-2407-9-11 This article is available from: http://www.biomedcentral.com/1471-2407/9/11 Received: 27 February 2008 Accepted: 12 January 2009 © 2009 Estilo et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract profiling. Background: The present study is aimed at identifying potential candidate genes as prognostic markers in human oral tongue squamous cell carcinoma (SCC) by large scale gene expression Methods: The gene expression profile of patients (n=37) with oral tongue SCC were analyzed using Affymetrix HG_U95Av2 high-density oligonucleotide arrays. Patients (n=20) from which there were available tumor and matched normal mucosa were grouped into stage (early vs. late) and nodal disease (node positive vs. node negative) subgroups and genes differentially expressed in tumor vs. normal and between the subgroups were identified. Three genes, GLUT3, HSAL2, and PACE4, were selected for their potential biological significance in a larger cohort of 49 patients via quantitative real-time RT-PCR. Results: Hierarchical clustering analyses failed to show significant segregation of patients. In patients (n=20) with available tumor and matched normal mucosa, 77 genes were found to be differentially expressed (P< 0.05) in the tongue tumor samples compared to their matched normal controls. Among the 45 over-expressed genes, MMP-1 encoding interstitial collagenase showed the highest level of increase (average: 34.18 folds). Using the criterion of two-fold or greater as overexpression, 30.6%, 24.5% and 26.5% of patients showed high levels of GLUT3, HSAL2 and PACE4, respectively. Univariate analyses demonstrated that GLUT3 over-expression correlated with depth of invasion (P<0.0001), tumor size (P=0.024), pathological stage (P=0.009) and Page 1 of 13 (page number not for citation purposes)