Gene expression differences associated with human papillomavirus status in head and neck squamous cell carcinoma

Robbert J C Slebos, Yajun Yi, Kim Ely, Jesse Carter, Amy Evjen, Xueqiong Zhang, Yu Shyr, Barbara M. Murphy, Anthony J. Cmelak, Brian B. Burkey, James L. Netterville, Shawn Levy, Wendell G. Yarbrough, Christine H. Chung

Research output: Contribution to journalArticle

Abstract

Human papillomavirus (HPV) is associated with a subset of head and neck squamous cell carcinoma (HNSCC). Between 15% and 35% of HNSCCs harbor HPV DNA. Demographic and exposure differences between HPV-positive (HPV+) and negative (HPV-) HNSCCs suggest that HPV+ tumors may constitute a subclass with different biology, whereas clinical differences have also been observed. Gene expression profiles of HPV+ and HPV - tumors were compared with further exploration of the biological effect of HPV in HNSCC. Thirty-six HNSCC tumors were analyzed using Affymetrix Human 133U Plus 2.0 GeneChip and for HPV by PCR and real-time PCR. Eight of 36 (22%) tumors were positive for HPV subtype 16. Statistical analysis using Significance Analysis of Microarrays based on HPV status as a supervising variable resulted in a list of 91 genes that were differentially expressed with statistical significance. Results for a subset of these genes were verified by real-time PCR. Genes highly expressed in HPV+ samples included cell cycle regulators (p16INK4A, p18, and CDC7) and transcription factors (TAF7L, RFC4, RPA2, and TFDP2). The microarray data were also investigated by mapping genes by chromosomal location (DIGMAP). A large number of genes on chromosome 3q24-qter had high levels of expression in HPV+ tumors. Further investigation of differentially expressed genes may reveal the unique pathways in HPV+ tumors that may explain the different natural history and biological properties of these tumors. These properties may be exploited as a target of novel therapeutic agents in HNSCC treatment.

Original languageEnglish (US)
Pages (from-to)701-709
Number of pages9
JournalClinical Cancer Research
Volume12
Issue number3 I
DOIs
StatePublished - Feb 1 2006
Externally publishedYes

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

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  • Cite this

    Slebos, R. J. C., Yi, Y., Ely, K., Carter, J., Evjen, A., Zhang, X., Shyr, Y., Murphy, B. M., Cmelak, A. J., Burkey, B. B., Netterville, J. L., Levy, S., Yarbrough, W. G., & Chung, C. H. (2006). Gene expression differences associated with human papillomavirus status in head and neck squamous cell carcinoma. Clinical Cancer Research, 12(3 I), 701-709. https://doi.org/10.1158/1078-0432.CCR-05-2017