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  • Oncogenomics
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Differential expression profiling of head and neck squamous carcinoma: significance in their phenotypic and biological classification

Oncogene volume 21, pages 8206–8219 (2002)Cite this article

Abstract

The genetic events associated with the development and progression of head and neck squamous carcinoma (HNSC) are largely unknown. We analysed 12 matched pairs of histologically normal squamous mucosa and tumor specimens from six conventional and six phenotypic variants HNSC to define the differentially expressed genes in these tumors. Parallel expression analysis of 8055 unique genes was performed, and the level of the hybridization signal for each gene was measured after normalization. Hierarchical cluster analysis of the expressed genes showed distinct inter- and intra-tumoral patterns in and between conventional squamous carcinoma and squamous carcinoma variants. We also identified 26 (0.32%) differentially expressed genes that were consistently different between matched pairs of normal and tumor specimens; a selected set of the overexpressed genes was validated using real-time quantitative RT–PCR. The majority of the genes were associated with differentiation and proliferation. Our study defines a set of genes that could form the basis for the construction of limited HNSC targeted expression array and indepth studies and further highlights gene profile differences that may be useful in pathobiologic classification of HNSC.

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Acknowledgements

The authors thank Dr John G Batsakis for his constructive suggestions and Lora L Lothringer for her keen editing of the manuscript. Sue M Martinez for her secretarial assistance. This study was supported in part by funds collected pursuant to the comprehensive Tobacco Settlement agreement of 1998 and appropriated by The 76th Legislature to The University of Texas M.D. Anderson Cancer Center; the Oral Cancer Center of Excellence Grant (DE11906); and the Kenneth D Muller Professorship (A El-Naggar).

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Authors and Affiliations

  1. Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, 77030, Texas, TX, USA

    Adel K El-Naggar, Madelene M Coombes, Bao Le, Syeling Lai & Mario A Luna

  2. Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, 77030, Texas, TX, USA

    Hyung W Kim, Feng Zhan & J Jack Lee

  3. Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, 77030, Texas, TX, USA

    Gary L Clayman

  4. Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, 77030, Texas, TX, USA

    Waun Ki Hong

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  1. Adel K El-Naggar
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  2. Hyung W Kim
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Correspondence to Adel K El-Naggar.

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El-Naggar, A., Kim, H., Clayman, G. et al. Differential expression profiling of head and neck squamous carcinoma: significance in their phenotypic and biological classification. Oncogene 21, 8206–8219 (2002). https://doi.org/10.1038/sj.onc.1206021

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