Gene Signature Predicts Outcomes in HPV-Related Oropharyngeal Cancers

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HPV gene signature was associated with outcomes in patients with HPV-related oropharyngeal cancers and could become a prognostic biomarker.
HPV gene signature was associated with outcomes in patients with HPV-related oropharyngeal cancers and could become a prognostic biomarker.

Study researchers identified a human papillomavirus (HPV) gene signature associated with outcomes among patients with HPV-related oropharyngeal cancers. The findings were published online January 10, 2019, in JCI Insight.1

“Patients with HPV-positive oropharyngeal tumors are living a long time after radiation treatment, but often are left with significant long-term morbidity, including problems with speech or swallowing,” said corresponding author on the study Curtis Pickering, PhD, in a press release.2 He is assistant professor of head and neck surgery, The University of Texas MD Anderson Cancer Center, Houston. “Therefore, there's a desire among clinicians to reduce, or de-escalate, therapy to lessen severe side effects. However, we currently don't have good biomarkers to safely determine which patients are candidates for de-escalation.”

To identify a possible gene signature, researchers retrospectively evaluated the level of HPV gene expression in 80 oropharyngeal squamous cell carcinoma tumor tissues from The Cancer Genome Atlas.

Using a panel of 582 genes, 3 subgroups were identified: HPV-negative tumors and 2 different HPV-positive tumor subgroups. One HPV-positive subgroup had similar survival to that of HPV-negative tumors and suggested a distinctly different subgroup within HPV-positive tumors. Statistically significant differences in survival were found among all 3 groups (P <.001).

Further investigation revealed a 38-gene panel that could differentiate between the 2 HPV-positive tumor groups and was associated with a difference in survival (P <.001). 

Study researchers then developed a biomarker signature and evaluated it in 2 independent cohorts of HPV-positive squamous cell carcinomas from the oropharynx and cervix and found it to be prognostic for survival.

“These findings could translate to improved patient stratification for treatment deintensification and new therapeutic approaches for treatment-resistant HPV-related cancer,” the study authors wrote.1


  1. Gleber-Netto FO, Rao X, Guo T, et al. Variations in HPV function are associated with survival in squamous cell carcinoma [published online January 10, 2019]. JCI Insight. doi: 10.1172/jci.insight.124762
  2. The University of Texas MD Anderson Cancer Center. Novel biomarker appears predictive of outcome in patients with HPV-related head and neck cancers [press release]. Published January 10, 2019. Accessed January 31, 2018.

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