Integrated Omic Analysis of Oropharyngeal Carcinomas Reveals Human Papillomavirus (HPV)–dependent Regulation of the Activator Protein 1 (AP-1) Pathway

Abstract

a HPV-positive oropharyngeal carcinoma (OPC) patients have superior outcomes relative to HPV-negative patients, but the underlying mechanisms remain poorly understood. We conducted a proteomic investigation of HPV-positive (n ‫؍‬ 27) and HPV-negative (n ‫؍‬ 26) formalinfixed paraffin-embedded OPC biopsies to acquire insights into the biological pathways that correlate with clinical behavior. Among the 2,633 proteins identified, 174 were differentially abundant. These were enriched for proteins related to cell cycle, DNA replication, apoptosis, and immune response. The differential abundances of cortactin and methylthioadenosine phosphorylase were validated by immunohistochemistry in an independent cohort of 29 OPC samples (p ‫؍‬ 0.023 and p ‫؍‬ 0.009, respectively). An additional 1,124 proteins were independently corroborated through comparison to a published proteomic dataset of OPC. Furthermore, utilizing the Cancer Genome Atlas, we conducted an integrated investigation of OPC, attributing mechanisms underlying differential protein abundances to alterations in mutation, copy number, methylation, and mRNA profiles. A key finding of this integration was the identification of elevated cortactin oncoprotein levels in HPV-negative OPCs. These proteins might contribute to reduced survival in these patients via their established role in radiation resistance. Through interrogation of Cancer Genome Atlas data, we demonstrated that activation of the ␤1-integrin/FAK/cortactin/

Novel Insights into Head and Neck Cancer using Next-Generation “Omic” Technologies

“…Nonetheless, consistent with gene expression studies, HPV-dependent upregulation of proteins involved in cell cycle, DNA replication processes, and downregulation of epidermal development/cell differentiation pathways was corroborated, and downregulation of keratinization and extracellular matrix proteins was newly observed (50)(51)(52) …”

“…To address these issues, much work is underway to develop patient-derived xenograft models (58). Proteomics studies have been underrepresented in characterization of oropharyngeal cancer; however, as proteins represent cumulative effects of all upstream genomic aberrations and can provide indication of protein function, signaling, and cellular localization, their further application is warranted in the elucidation of clinical phenotypes (52). Finally, it is important to bear in mind that the molecular spectrum of HNSCC reflects strong influences by what appear to be significantly different tumor microenvironments in HPV þ versus HPV À tumors, which likely also play a critical role in therapeutic response, and undoubtedly require further interrogation.…”

Salvage surgery for locally recurrent oropharyngeal cancer

“…Their tumors may share some biological features similar to the tobacco-driven HPV-unrelated tumors, which could also account for the nondifferential outcomes after salvage surgery by HPV status. 31,32 In addition, the nonsignificant difference in outcomes based on p16 status in our study may also be a function of the small sample size, and therefore limited study power to detect any potential difference. Fakhry et al 33 recently reported on disease progression of HPV-related and HPV-unrelated oropharyngeal SCC after definitive chemoradiation in the cohort of patients from the Radiation Therapy Oncology Group trials 0129 and 0522.…”

“…Thirteen of 19 patients (68%) with p16‐positive oropharyngeal SCC in the present study had more than 10 pack‐years of tobacco exposure. Their tumors may share some biological features similar to the tobacco‐driven HPV‐unrelated tumors, which could also account for the nondifferential outcomes after salvage surgery by HPV status . In addition, the nonsignificant difference in outcomes based on p16 status in our study may also be a function of the small sample size, and therefore limited study power to detect any potential difference.…”

Cytokeratin 7 in Oropharyngeal Squamous Cell Carcinoma: A Junctional Biomarker for Human Papillomavirus–Related Tumors

“…It is possible that HPV-related carcinogenesis may occur in infected surface rather than reticulated epithelial cells, without a potential selective advantage from CK7 expression. This may explain the lack of any significant difference in previous proteome analysis of oropharyngeal SCC (45)(46)(47), and it may in future be worthwhile comparing protein expression between the oropharynx and other sites, especially given the known specificity of HPV to the oropharynx. It is also possible that non-HPV-related carcinogenesis may occur in CK7-expressing crypt epithelial cells (29), which could explain those cases with raised CK7 H-score, but HPV-and p16-negative oropharyngeal SCCs (24 cases).…”