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To assess the relationship of  E2  gene disruption with viral gene expression and clinical outcome in human papillomavirus (HPV) positive head and neck squamous cell carcinoma, we evaluated 31 oropharyngeal and 17 non-oropharyngeal HPV16 positive carcinomas using two PCR-based methods to test for disruption of  E2 , followed by Sanger sequencing. Expression of HPV16  E6 ,  E7  and  E2  transcripts, along with cellular  ARF  and  INK4A , were also assessed by RT-qPCR. Associations between  E2  disruption, E2/E6/E7 expression, and clinical outcome were evaluated by Kaplan-Meier analysis for loco-regional recurrence and disease-specific survival. The majority (n = 21, 68%) of HPV16 positive oropharyngeal carcinomas had an intact  E2  gene, whereas the majority of HPV16 positive non-oropharyngeal carcinomas (n = 10, 59%) had a disrupted  E2  gene. Three of the oropharyngeal tumors and two of the non-oropharyngeal tumors had deletions within  E2 . Detection of an intact  E2  gene was associated with a higher DNA viral load and increased  E2/E6/E7 ,  ARF  and  INK4A  expression in oropharyngeal tumors. Oropharyngeal carcinomas with an intact  E2  had a lower risk of loco-regional recurrence (log-rank p = 0.04) and improved disease-specific survival (p = 0.03) compared to tumors with disrupted  E2 . In addition, high E7 expression was associated with lower risk of loco-regional recurrence (p = 0.004) as was high E6 expression (p = 0.006). In summary, an intact  E2  gene is more common in HPV16 positive oropharyngeal than non-oropharyngeal carcinomas; the presence of an intact  E2  gene is associated with higher HPV viral load, higher viral oncogene expression, and improved clinical outcome compared to patients with a disrupted  E2  gene in oropharyngeal cancer.

plos one

Association of an intact E2 gene with higher HPV viral load, higher viral oncogene expression, and improved clinical outcome in HPV16 positive head and neck squamous cell carcinoma