HPV16-A1 Genotype is Associated with Poor Recurrence-Free Survival in HPV16 Associated Squamous Cell Carcinoma of the Oropharynx

Purpose/Objective(s)

HPV-positive squamous cell carcinoma of the oropharynx (HPV+ OPSCC) is the most prevalent HPV-associated malignancy in the United States and is primarily caused by HPV16. Favorable treatment outcomes have led to increasing interest in treatment de-escalation to reduce treatment-related morbidity. Prognostic biomarkers are needed to identify appropriately low-risk patients for reduced treatment intensity. Large series of complete HPV16 genome sequencing from HPV+ OPSCC tumors are lacking in the literature. Therefore, we sought to test the hypothesis that HPV16 genotype is prognostic of recurrence-free survival (RFS) in HPV16+ OPSCC.

Materials/Methods

Targeted sequencing of 104 patients with HPV16+ OPSCC tumors was performed, providing complete coverage of all HPV16 open reading frames. Clinical features were retrospectively extracted from the medical record. A second cohort of OPSCC patients was sequenced using total RNA sequencing, which identified 89 patients with HPV16+ OPSCC for analysis.

Results

A high degree of coding diversity in the HPV16 was identified, with 93 distinct protein-coding HPV16 genotypes amongst the 104 patients subject to HPV (DNA) sequencing. As found in uterine cervical carcinoma, E7 was the most conserved amongst HPV16 viral genes. Sub-clonal variants were more likely to be non-synonymous and were enhanced for APOBEC-related mutagenesis. The HPV16-A1 sub-lineage was the most prevalent (approximately 70%). Genotypes closely related to HPV16-A1 were associated with increased numbers of copy-number variants in the human genome. Genotypes divergent from HPV16-A1 were strongly associated with favorable RFS as compared to HPV16-A1 (or similar genotypes); this finding was independent of tobacco smoke exposure. HPV16 genotypes divergent from HPV16-A1 were subsequently validated in an independent cohort (subject to RNA sequencing), to be associated with improved RFS in patients with moderate (less than 30 pack-years) and low (no more than 10 pack-years) of tobacco smoke exposure.

Conclusion

HPV16 viral genotype is highly diverse in HPV associated OPSCC. Sequence divergence from the HPV16-A1 reference sequence is strongly associated with improved RFS in patients with moderate to no tobacco smoke exposure. This finding was confirmed in two independent cohorts. HPV16 genotype is a promising potential biomarker that could be easily adopted to guide therapeutic decision-making related to de-escalation therapy. Prognostic genotypic information can be obtained from clinical samples stored in FFPE applying either DNA or RNA sequencing technology.