Molecular classification of head and neck squamous cell carcinoma using cDNA microarrays

Belbin, Thomas J.; Singh, Bhuvanesh; Barber, Ilana; Wenig, Bruce M.; Smith, Richard V.; Prystowsky, M. B.; Childs, Geoffrey

doi:10.1038/87004

Cited by 75 publications

(89 citation statements)

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“…A direct comparison between that study and ours is difficult, because 1) the sample sizes were significantly different; 2) the sample processing procedures used in the two studies were significantly different; 3) the GeneChip analysis software and self-organizing maps algorithms used in that study to determine differential gene expression differed significantly from the regression-based algorithm used in our study; and 4) our statistical approach accounted for the potential false positive findings from making comparisons between a large number of genes in a small number of samples. Another study 52 -a retrospective analysis of 17 patients with head and neck carcinoma-identified 375 genes with expression that distinguished patients into two groups with distinct clinical outcomes. Given the prospective nature of our study, as we follow our patients for their disease outcome, we will be able to assess whether the 314 differentially expressed genes between OSCC tissues and normal tissues are the same genes that differentiate patients according to their disease outcome.…”

Section: Discussionmentioning

confidence: 99%

Transcriptional expression profiles of oral squamous cell carcinomas

Méndez

Cheng

Farwell

et al. 2002

Cancer

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BACKGROUNDCurrently, the classification of oral squamous cell carcinoma (OSCC) depends heavily on the clinical and pathologic examination of tissue. This system can lead to the classification of potentially heterogeneous tumors into single groups when they may have different degrees of aggressiveness. No system to date has incorporated genetic changes as a factor by which to classify OSCC tumors.METHODSTo test the hypothesis that OSCC has a genome‐wide genetic expression profile that differs from normal oral tissue and that transcriptional expression profiling can be used to characterize the heterogeneity among tumors, the authors examined the genetic expression profiles of 26 invasive squamous cell carcinomas of the oral cavity and oropharynx, 2 premalignant lesions, and 18 normal oral tissue samples using oligonucleotide arrays that contained probes representing approximately 7000 full‐length human genes.RESULTSUsing hierarchical clustering analysis, the data show that oral carcinomas are distinguishable from normal oral tissue based on genome‐wide transcriptional expression patterns. However, there is genetic expression profile heterogeneity among tumors of a particular histopathologic grade and stage. In addition, using a statistical approach that integrated normalization and regression analysis, the authors found 314 genes that were expressed differentially in the OSCC samples with statistical significance (P ≤ 0.05). Of these, 239 genes were overexpressed in the OSCC samples, whereas 75 genes were down‐regulated.CONCLUSIONSNo statistically significant differences in gene expression were found between early‐stage disease and late‐stage disease or between metastatic tumors and nonmetastatic tumors. The implications of these findings for the prediction of clinical outcome and for the discovery of new OSCC tumor markers are discussed. Cancer 2002;95:1482–94. © 2002 American Cancer Society.DOI 10.1002/cncr.10875

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Section: Discussionmentioning

confidence: 99%

Transcriptional expression profiles of oral squamous cell carcinomas

Méndez

Cheng

Farwell

et al. 2002

Cancer

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“…To date, functional genomic analysis on HNSCC has been limited (126). Potential use of functional genomics with HNSCC may be in diagnosis, prognosis, and response to therapy.…”

Section: Functional Genomicsmentioning

confidence: 99%

Squamous Cell Carcinoma of the Upper Aerodigestive Tract: Precursors and Problematic Variants

Wenig

2002

Modern Pathology

120

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“…HNSCC may be a useful system for studying lymphatic metastasis because of the high probability of lymphatic spread and low probability of hematogenous spread. A recent study has identified a gene signature for recurrent disease in HNSCC and several studies have investigated the changes in gene expression from normal tissue to carcinoma, but studies involving lymphatic metastasis have been limited by the small number of genes assessed and/or lack of a rigorous efficacy test of the metastatic signature (Alevizos et al, 2001;Belbin et al, 2002;Mendez et al, 2002;Hwang et al, 2003;Gonzalez et al, 2003;Leethanakul et al, 2003;Nagata et al, 2003;Chung et al, 2004;Ginos et al, 2004;Schmalbach et al, 2004;Warner et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Gene expression signature predicts lymphatic metastasis in squamous cell carcinoma of the oral cavity

et al. 2004

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Metastasis via the lymphatics is a major risk factor in squamous cell carcinoma of the oral cavity (OSCC). We sought to determine whether the presence of metastasis in the regional lymph node could be predicted by a gene expression signature of the primary tumor. A total of 18 OSCCs were characterized for gene expression by hybridizing RNA to Affymetrix U133A gene chips. Genes with differential expression were identified using a permutation technique and verified by quantitative RT-PCR and immunohistochemistry. A predictive rule was built using a support vector machine, and the accuracy of the rule was evaluated using crossvalidation on the original data set and prediction of an independent set of four patients. Metastatic primary tumors could be differentiated from nonmetastatic primary tumors by a signature gene set of 116 genes. This signature gene set correctly predicted the four independent patients as well as associating five lymph node metastases from the original patient set with the metastatic primary tumor group. We concluded that lymph node metastasis could be predicted by gene expression profiles of primary oral cavity squamous cell carcinomas. The presence of a gene expression signature for lymph node metastasis indicates that clinical testing to assess risk for lymph node metastasis should be possible.

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Molecular classification of head and neck squamous cell carcinoma using cDNA microarrays

Abstract: Head and neck squamous cell carcinoma (HNSCC) is the fifth most common cancer worldwide and accounts for 95% of the head and neck cancer cases in the Western world. Over the past three decades advancements in management have

Cited by 75 publications

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Transcriptional expression profiles of oral squamous cell carcinomas

Transcriptional expression profiles of oral squamous cell carcinomas

Squamous Cell Carcinoma of the Upper Aerodigestive Tract: Precursors and Problematic Variants

Gene expression signature predicts lymphatic metastasis in squamous cell carcinoma of the oral cavity

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