Genomewide gene expression profiles of HPV-positive and HPV-negative oropharyngeal cancer potential implications for treatment choices

Pawadee Lohavanichbutr, John Houck, Wenhong Fan, Bevan Yueh, Eduardo Mendez, Neal Futran, David R. Doody, Melissa P. Upton, D Gregory Farwell, Stephen M. Schwartz, Lue Ping Zhao, Chu Chen

Research output: Contribution to journalArticle

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Abstract

Objective: To study the difference in gene expression between human papillomavirus (HPV)-positive and HPV-negative oral cavity and oropharyngeal squamous cell carcinoma (OSCC).Design: We used Affymetrix U133 plus 2.0 arrays to examine gene expression profiles of OSCC and normal oral tissue. The HPV DNA was detected using polymerase chain reaction followed by the Roche LINEAR ARRAY HPV Genotyping Test, and the differentially expressed genes were analyzed to examine their potential biological roles using the Ingenuity Pathway Analysis Software, version 5.0. Setting: Three medical centers affiliated with the University of Washington.Patients: A total of 119 patients with primary OSCC and 35 patients without cancer, all of whom were treated at the setting institutions, provided tissues samples for the study.Results: Human papillomavirus DNA was found in 41 of 119 tumors (34.5%) and 2 of 35 normal tissue samples (5.7%); 39 of the 43 HPV specimens were HPV-16. A higher prevalence of HPV DNA was found in oropharyngeal cancer (23 of 31) than in oral cavity cancer (18 of 88). We found no significant difference in gene expression between HPV-positive and HPV-negative oral cavity cancer but found 446 probe sets (347 known genes) differentially expressed in HPV-positive oropharyngeal cancer than in HPV-negative oropharyngeal cancer. The most prominent functions of these genes are DNA replication, DNA repair, and cell cycling. Some genes differentially expressed between HPV-positive and HPV-negative oropharyngeal cancer (eg, TYMS, STMN1, CCND1, and RBBP4) are involved in chemotherapy or radiation sensitivity. Conclusion: These results suggest that differences in the biology of HPV-positive and HPV-negative oropharyn-geal cancer may have implications for the management of patients with these different tumors.

Original languageEnglish (US)
Pages (from-to)180-188
Number of pages9
JournalArchives of Otolaryngology - Head and Neck Surgery
Volume135
Issue number2
DOIs
StatePublished - Feb 2009

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Oropharyngeal Neoplasms
Transcriptome
Therapeutics
Mouth
Squamous Cell Carcinoma
Mouth Neoplasms
Genes
DNA
Neoplasms
Gene Expression
Human papillomavirus 16
Radiation Tolerance

ASJC Scopus subject areas

  • Otorhinolaryngology
  • Surgery

Cite this

Genomewide gene expression profiles of HPV-positive and HPV-negative oropharyngeal cancer potential implications for treatment choices. / Lohavanichbutr, Pawadee; Houck, John; Fan, Wenhong; Yueh, Bevan; Mendez, Eduardo; Futran, Neal; Doody, David R.; Upton, Melissa P.; Farwell, D Gregory; Schwartz, Stephen M.; Zhao, Lue Ping; Chen, Chu.

In: Archives of Otolaryngology - Head and Neck Surgery, Vol. 135, No. 2, 02.2009, p. 180-188.

Research output: Contribution to journalArticle

Lohavanichbutr, P, Houck, J, Fan, W, Yueh, B, Mendez, E, Futran, N, Doody, DR, Upton, MP, Farwell, DG, Schwartz, SM, Zhao, LP & Chen, C 2009, 'Genomewide gene expression profiles of HPV-positive and HPV-negative oropharyngeal cancer potential implications for treatment choices', Archives of Otolaryngology - Head and Neck Surgery, vol. 135, no. 2, pp. 180-188. https://doi.org/10.1001/archoto.2008.540
Lohavanichbutr, Pawadee ; Houck, John ; Fan, Wenhong ; Yueh, Bevan ; Mendez, Eduardo ; Futran, Neal ; Doody, David R. ; Upton, Melissa P. ; Farwell, D Gregory ; Schwartz, Stephen M. ; Zhao, Lue Ping ; Chen, Chu. / Genomewide gene expression profiles of HPV-positive and HPV-negative oropharyngeal cancer potential implications for treatment choices. In: Archives of Otolaryngology - Head and Neck Surgery. 2009 ; Vol. 135, No. 2. pp. 180-188.
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abstract = "Objective: To study the difference in gene expression between human papillomavirus (HPV)-positive and HPV-negative oral cavity and oropharyngeal squamous cell carcinoma (OSCC).Design: We used Affymetrix U133 plus 2.0 arrays to examine gene expression profiles of OSCC and normal oral tissue. The HPV DNA was detected using polymerase chain reaction followed by the Roche LINEAR ARRAY HPV Genotyping Test, and the differentially expressed genes were analyzed to examine their potential biological roles using the Ingenuity Pathway Analysis Software, version 5.0. Setting: Three medical centers affiliated with the University of Washington.Patients: A total of 119 patients with primary OSCC and 35 patients without cancer, all of whom were treated at the setting institutions, provided tissues samples for the study.Results: Human papillomavirus DNA was found in 41 of 119 tumors (34.5{\%}) and 2 of 35 normal tissue samples (5.7{\%}); 39 of the 43 HPV specimens were HPV-16. A higher prevalence of HPV DNA was found in oropharyngeal cancer (23 of 31) than in oral cavity cancer (18 of 88). We found no significant difference in gene expression between HPV-positive and HPV-negative oral cavity cancer but found 446 probe sets (347 known genes) differentially expressed in HPV-positive oropharyngeal cancer than in HPV-negative oropharyngeal cancer. The most prominent functions of these genes are DNA replication, DNA repair, and cell cycling. Some genes differentially expressed between HPV-positive and HPV-negative oropharyngeal cancer (eg, TYMS, STMN1, CCND1, and RBBP4) are involved in chemotherapy or radiation sensitivity. Conclusion: These results suggest that differences in the biology of HPV-positive and HPV-negative oropharyn-geal cancer may have implications for the management of patients with these different tumors.",
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AU - Yueh, Bevan

AU - Mendez, Eduardo

AU - Futran, Neal

AU - Doody, David R.

AU - Upton, Melissa P.

AU - Farwell, D Gregory

AU - Schwartz, Stephen M.

AU - Zhao, Lue Ping

AU - Chen, Chu

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