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Updated: May 15, 2026
RNAscope for In situ Detection of Transcriptionally Active Human Papillomavirus in Head and Neck Squamous Cell Carcinoma
Published on: March 11, 2014
A Pilot Study Comparing HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas by Whole Exome
Anthony C Nichols1, Michelle Chan-Seng-Yue, John Yoo
1Department of Otolaryngology-Head and Neck Surgery, Western University, Victoria Hospital, London Health Science Centre, Room B3-431A, 800 Commissioners Road East, London, ON, Canada N6A 5W9 ; London Regional Cancer Program, London, ON, Canada N6A 4L6 ; Lawson Health Research Institute, London, ON, Canada N6C 2R5 ; Department of Oncology, Western University, London, ON, Canada N6A 4L6 ; Department of Pathology, Western University, London, ON, Canada N6A 5C1.
Abstract:
Background. Next-generation sequencing of cancers has identified important therapeutic targets and biomarkers. The goal of this pilot study was to compare the genetic changes in a human papillomavirus- (HPV-)positive and an HPV-negative head and neck tumor. Methods. DNA was extracted from the blood and primary tumor of a patient with an HPV-positive tonsillar cancer and those of a patient with an HPV-negative oral tongue tumor. Exome enrichment was performed using the Agilent SureSelect All Exon Kit, followed by sequencing on the ABI SOLiD platform. Results. Exome sequencing revealed slightly more mutations in the HPV-negative tumor (73) in contrast to the HPV-positive tumor (58). Multiple mutations were noted in zinc finger genes (ZNF3, 10, 229, 470, 543, 616, 664, 638, 716, and 799) and mucin genes (MUC4, 6, 12, and 16). Mutations were noted in MUC12 in both tumors. Conclusions. HPV-positive HNSCC is distinct from HPV-negative disease in terms of evidence of viral infection, p16 status, and frequency of mutations. Next-generation sequencing has the potential to identify novel therapeutic targets and biomarkers in HNSCC.
Insights
Next-generation sequencing reveals distinct genetic profiles in human papillomavirus- (HPV-)positive and HPV-negative head and neck cancers. This pilot study identified specific gene mutations, highlighting potential new therapeutic targets and biomarkers for HPV-positive HNSCC.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Next-generation sequencing (NGS) is crucial for identifying therapeutic targets and biomarkers in cancer.
- Head and neck squamous cell carcinoma (HNSCC) can be classified based on human papillomavirus (HPV) status.
- Understanding genetic differences between HPV-positive and HPV-negative HNSCC is vital for targeted therapies.
Purpose of the Study:
- To compare genetic alterations between an HPV-positive tonsillar cancer and an HPV-negative oral tongue cancer using whole-exome sequencing.
- To identify potential novel therapeutic targets and biomarkers in HPV-positive HNSCC.
Main Methods:
- DNA extraction from blood and tumor tissue of two patients (one HPV-positive, one HPV-negative).
- Whole-exome enrichment using the Agilent SureSelect All Exon Kit.
- Sequencing performed on the ABI SOLiD platform.
Main Results:
- The HPV-negative tumor exhibited slightly more mutations (73) compared to the HPV-positive tumor (58).
- Mutations were frequently observed in zinc finger genes (ZNF family) and mucin genes (MUC family).
- MUC12 gene mutations were present in both HPV-positive and HPV-negative tumors.
Conclusions:
- HPV-positive HNSCC is genetically distinct from HPV-negative HNSCC, differing in viral presence, p16 status, and mutation frequency.
- NGS analysis holds significant potential for discovering new therapeutic targets and biomarkers in HNSCC.
- The findings underscore the importance of HPV status in stratifying HNSCC for personalized treatment approaches.
