Mutational Profile May Impact Treatment Decisions for Smokers With Human Papillomavirus–Positive Oropharyngeal Cancer

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As opposed to arbitrarily deciding that 10 pack-years is a number that we use to define more aggressive disease, we are trying to provide a molecular basis for more aggressive disease to decide who would benefit from less aggressive vs more aggressive treatment.

Jose Zevallos, MD

Smokers whose oropharyngeal tumors are positive for the human papillomavirus (HPV) might need more aggressive treatment for their disease, according to research presented by Jose Zevallos, MD, at the 2016 Multidisciplinary Head and Neck Cancer Symposium in Scottsdale, Arizona.1

Over time, tobacco-associated mutations occur along several key cancer genes in smokers with HPV-associated oropharyngeal squamous cell carcinoma. To date, these distinct mutations and other genetic characteristics have not been well defined in the cohort, and the relationship between HPV and smoking has not been thoroughly evaluated, but new research suggests that smokers with HPV-positive throat cancer may need specifically tailored treatment, particularly in regard to intensity.

Patients with oropharyngeal squamous cell carcinoma caused by HPV generally have an excellent prognosis for disease-free survival, but patients who also smoke experience worse 5-year survival than never smokers.

Exposure to HPV and Tobacco

“HPV-positive oropharyngeal cancer, when compared to HPV-negative oropharyngeal cancer, has an excellent prognosis. If one looks at work beginning in the 1990s, we see a trend toward much improved survival in this group,” said Dr. Zevallos, Assistant Professor and Director of Oncologic Research in the Division of Head and Neck Surgical Oncology at the University of North Carolina (UNC), Chapel Hill. “We also know that these differences in survival are driven by mutational characteristics and other genomic alterations within these tumors.”

Smoking and HPV-Positive Oropharyngeal Cancer

  • There are distinct differences in the genomic characteristics of HPV-positive heavy smokers vs light smokers/nonsmokers.
  • Smokers with HPV-positive oropharyngeal cancer might need more aggressive treatment.
  • These findings suggest important implications for personalizing treatment (treatment deintensification and targeted therapies) and decision-making for patients with HPV-positive oropharyngeal squamous cell carcinoma.

“What remains unclear to date is what about patients who have exposure to both HPV and tobacco? How do these patients do, and how are the differences in outcomes between these patients manifested on a molecular level?” he stated.

HPV-positive oropharyngeal squamous cell carcinoma represents a distinct clinical entity, he added. “We know that patients with exposure to both have an intermediate outcome relative to HPV-negative tobacco-driven tumors and HPV-positive tumors and never smokers.”

Dr. Zevallos and his co-investigators sought to characterize the mutational profile of HPV-positive oropharyngeal squamous cell carcinoma by smoking status to better inform treatment.

Study Details

Targeted next-generation sequencing of more than 800 genes, including all commonly mutated genes in cancer, was performed in 66 HPV-positive oropharyngeal squamous cell carcinoma cases stratified by smoking status (< 10 pack-years vs > 10 pack-years). This metric was determined by multiplying the number of years a person has smoked by their average number of packs of cigarettes smoked per day. Of the 66 patients, 40 reported more than 10 pack-years, and 26 patients reported fewer than 10 pack-years.

Cases were identified from the Carolina Head and Neck Cancer Epidemiology (CHANCE) study, conducted from 2001 to 2006, and mutations were compared with the Catalogue of Somatic Mutations in Cancer (COSMIC), an online database of information on mutations in key cancer genes, and with The Cancer Genome Atlas (TCGA).

Mutation Rates Higher in Heavy Smokers

Patients who smoked and had a history of fewer than 10 pack-years had significantly better disease-free and overall survival rates than did heavier smokers.

Overall mutation rates were higher for HPV-positive oropharyngeal squamous cell carcinoma patients in the > 10 pack-year group, and mutations associated with tobacco exposure and worse survival were found almost exclusively within this group. They included those in TP53 (6% vs 0%, P = .428), CDKN2A (2% vs 0%, P = .758), FAT1 (14% vs 6%, P = .688), CASP8 (8% vs 0%, P = .565), NOTCH1 (18% vs 0%, P = .092), FGFR3 (10% vs 0%, P = .325), and KRAS (4% vs 0%, P = .232) genes. However, the researchers found that HLA-A mutations were more common in the < 10 pack-year cohort (73.1% vs 47.5%, P = .047).

Pathways, HPV Type, and Read Depth

According to the researchers, the molecular profile of HPV-positive smokers is similar to that of patients with HPV-negative head and neck cancer, but with important distinguishing characteristics. “When we look at our data in terms of pathways, like HPV-negative cancers, we see receptor tyrosine kinase mutations and amplifications in this group of patients. We also see amplifications of the PIK3CA gene and deletions of PTEN,” said Dr. Zevallos. “Other important distinguishers between this group and typical HPV-negative never smokers was the presence of NFE2L2 and KEAP1. They are key components of oxidative stress response.”

After investigation of HPV type (eg, HPV-16, HPV-18) and read depth (ie, the number of times a particular nucleotide is detected during DNA sequencing), the researchers noted the accumulation of tobacco-associated mutations over time and concluded that the number of HPV reads (ie, the number of nucleotide sequences uniquely aligning to the HPV genome) was inversely related to smoking and survival status. They suggested that these mutations may lead to less dependency on HPV-mediated oncogenesis.

“Patients who smoke and patients who were deceased from their cancer had lower numbers of HPV viral reads, which means that potentially, these tumors began as HPV-driven but over time developed subclones that were driven by tobacco-associated gene mutations as a result of exposure to smoking,” said Dr. Zevallos.

More Tailored Treatment on the Horizon

Christine Gourin, MD

Christine Gourin, MD

“This study is so important because we know that the molecular fingerprint of HPV-related oropharyngeal cancer is different from anything that we’ve seen before. It’s a different patient population with different outcomes than the population I treated when I was in training, and we don’t yet understand fully why this fingerprint is so different and why tobacco affects the fingerprint,” said Christine Gourin, MD, Associate Professor of Otolaryngology at Johns Hopkins.

“These findings of differences in the molecular phenotypes of light smokers vs heavy smokers are something we all appreciate clinically, and we need to understand better to tailor treatment,” said Dr. Gourin.

The findings on the distinct differences in genomic characteristics of HPV-positive heavy smokers vs light smokers/nonsmokers “could have important implications for personalizing treatment and influencing decision-making on HPV-positive oropharyngeal squamous cell carcinoma treatment deintensification and targeted therapies, particularly in regard to less aggressive treatment for HPV-positive tumors, because of their excellent prognosis,” added Dr. Zevallos.

“As opposed to arbitrarily deciding that 10 pack-years is a number that we use to define more aggressive disease, we are trying to provide a molecular basis for more aggressive disease to decide who would benefit from less aggressive vs more aggressive treatment,” he said.

Larger studies focused on defining high-risk HPV-positive oropharyngeal squamous cell carcinoma through DNA and RNA sequencing are currently underway at UNC.

“This work is going to lead to a better understanding of the disease,” said Brian Nussenbaum, MD, Director of Head and Neck Surgical Oncology at Washington University School of Medicine, St. Louis. “I do wonder if there’s some synergy going on with the HPV-associated mutations that are occurring related to the viral integration with the mutations and gene alterations caused by the tobacco exposure, particularly since the dose of tobacco is relatively low (10 pack-years) to define a distinctly different population of patients with worse survival. I think that this work will lead to different ideas in terms of improving survival for these patients.”

“This may also help with stratification in terms of clinical trials, and you could potentially imagine a day where we would be stratifying enrollment in a deintensification or intensification clinical trial based on the mutational profile of their tumors,” added Dr. ­Nussenbaum. ■

Disclosure: Drs. Zevallos, Gourin, and Nussenbaum reported no potential conflicts of interest.


1. Zevallos JP, Yim E, Brennan P, et al: Molecular profile of HPV-positive oropharyngeal squamous cell carcinoma stratified by smoking status. 2016 Multidisciplinary Head and Neck Cancer Symposium. Abstract 1. Presented February 18, 2016.