Abstract 4739: The immunogenomic landscape of HPV-associated oropharyngeal squamous cell carcinoma by smoking and treatment response
Authors: Zolkind Paul , Wahle Ben , Skidmore Zachary , Mazul Angela , Griffith Obi , Griffith Malachi , Zevallos Jose P. 
Published: September 2020

Abstract
Background: Human papilloma virus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC) is an increasingly common malignancy and public health epidemic. Overall, outcomes in HPV-associated OPSCC are very good but treatment failure is associated with a devastating prognosis. Although tobacco use is one of the few clinical biomarkers associated with worse prognosis, the mechanisms underlying this disparity are not well understood. The goal of this study was to investigate the genomic and immune related alterations associated with tobacco use in HPV-associated OPSCC.
Methods: We prospectively identified a cohort of 53 patients with HPV-associated OPSCC with corresponding clinical and demographic data. Tumor DNA and RNA were extracted from FFPE samples along with whole blood as a control for variant calling. We performed whole exome sequencing, mutational signature analysis and a 770 gene RNA-based NanoString immuno-oncology assay to further interrogate these tumors.
Results: We identified that smokers and non-smokers had remarkably well conserved copy number alterations and mutational alterations. Mutational alterations in tumors across the cohort including in heavy smokers had frequent mutations in PIK3CA, FGFR3, ZNF750 that largely reflect the known alterations common in HPV-associated OPSCC. Regardless of smoking status, we rarely observed mutations typical of non-HPV associated head and neck cancers such as TP53, CDKN2A, and FAT1. COSMIC mutational signature analysis revealed that a majority of the tumors expressed an APOBEC signature (#2 and #13) consistent with viral etiology of tumorigenesis. Strikingly, none of the tumors expressed mutational signatures associated with tobacco use (#4 and #29). We then performed an RNA-based NanoString immuno-oncology assay to investigate differences within the immune microenvironment. We identified significantly upregulated expression of genes associated with myeloid derived suppressor cell (MDSC) recruitment and activity including S100A8/A9, S100A12, CXCR2, CXCL1, and ARG2, suggesting a potential association between tobacco use, MDSC-driven immunosuppression and poorer prognosis.
Conclusion: In this genomic analysis of HPV-associated OPSCC, we demonstrate that tobacco use does not clearly induce structural or mutational differences within the tumor cells. Even in heavy tobacco users, the mutational signatures reflect a tumor driven by its viral etiology and more closely aligns to non-tobacco using HPV-associated OPSCC than it does HPV-negative OPSCC. The poorer prognosis in smokers may be related to alterations in the immune microenvironment including the recruitment and activity of MDSCs. This provides further evidence that strategies to target MDSC activity in the immune microenvironment may be effective in high-risk HPV-OPSCC smokers.
Citation Format: Paul Zolkind, Ben Wahle, Zachary Skidmore, Angela Mazul, Obi Griffith, Malachi Griffith, Jose P. Zevallos. The immunogenomic landscape of HPV-associated oropharyngeal squamous cell carcinoma by smoking and treatment response [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4739.