Abstract PR01: HPV structure and functional alterations impact prognosis in HPV (+) oropharyngeal squamous cell carcinoma
Authors: Zevallos Jose P. , Mazul Angela L. , Zhao Xiaobei , Jo Heejoon , Nathan Cherie-Ann , Olshan Andrew F. , Chera Bhishamjit S. , Hayes D. Neil 
Published: September 2020

Abstract
Background: Over the last two decades, there has been a sharp increase in the incidence of oropharyngeal squamous cell carcinoma (OPSCC) linked to human papillomavirus (HPV). Compared to tobacco-associated, HPV (-) cancers, HPV (+) tumors are generally less aggressive and more likely to respond to new deintensified treatment regimens. However, there is a subset of HPV (+) OPSCC patients with poor oncologic outcomes, and an understanding of underlying molecular characteristics of HPV (+) OPSCC with poor prognosis is lacking. In this study, we sought to determine the impact of HPV-tumor genomic interactions and their impact on prognosis. We define novel, quantifiable, sequencing-based metrics of HPV structure and function with prognostic significance.
Methods: We performed targeted DNA sequencing of 770 cancer-associated genes and the full-length HPV genome on 259 HPV (+) OPSCC cases derived from four cohorts. Sequencing data were routed through automated pipelines for DNA, including 1) somatic variant detection, 2) structural variations, and 3) quantitative and qualitative characterization of full-length HPV sequencing. Patients were assigned as either “high” or “low” based on the inherent binomial distribution of E6 and E7 normalized sequenced read counts across the cohort. Patient outcomes were assessed using the hazard ratio from the Cox proportional hazards regression adjusting for known and suspected confounders of outcome including stage, age, and smoking status defined as greater than 10 pack years.
Results: We demonstrate that both HPV viral read count and HPV structure significantly impact prognosis in HPV (+) OPSCC. In addition to integrated and episomal structure, we define a novel viral structural subtype in 15% of cases characterized by simple or complex rearrangement composed of single or multiple breakpoints within the viral genome. Furthermore, we demonstrate that patients with the lowest HPV viral loads had a 30% greater hazard of death compared to patients with high viral loads. When we considered the impact of HPV counts and HPV structure taken together, we note that Integrated cases with low viral load were associated with outcomes much lower than expected for HPV-positive oropharyngeal cancer (5-year overall survival: 56.8%). These results were unaffected by smoking status measured by ever/never smoking or pack-year status.
Conclusions: In the largest sequenced HPV (+) OPSCC cohort to date, we identify a quantifiable measure of HPV structure and function with prognostic significance. We define a novel rearranged viral structure and define integrated low viral count cases as associated with dismal survival. These findings highlight the molecular heterogeneity of HPV (+) OPSCC and provide a framework for future clinical trials based on molecular viral characterization.
Citation Format: Jose P. Zevallos, Angela L. Mazul, Xiaobei Zhao, Heejoon Jo, Cherie-Ann Nathan, Andrew F. Olshan, Bhishamjit S. Chera, D. Neil Hayes. HPV structure and functional alterations impact prognosis in HPV (+) oropharyngeal squamous cell carcinoma [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; 2019 Apr 29-30; Austin, TX. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_2):Abstract nr PR01.