HPV16 transcriptional patterns in oropharyngeal squamous cell carcinoma with different clinical outcomes

Abstract Human papillomavirus (HPV) 16 is the leading cause of oropharyngeal squamous cell carcinoma (OPSCC) in many Western countries. Although patients with HPV16-positive OPSCC generally have better outcomes than those with HPV-negative disease, significant heterogeneity exists, and a subset of these patients still experience poor prognosis. The contribution of viral gene expression patterns to this heterogeneity remains unclear. In this study, deep RNA sequencing was performed on laser-capture microdissected archival tumor samples from 50 HPV-positive OPSCC patients with known clinical outcomes (29 good prognosis, 21 poor prognosis). RNA sequencing confirmed HPV16 in 40 cases (22 good prognosis, 18 poor prognosis), which were included in the HPV16-specific transcriptional analyses. Residual microbial reads were additionally assessed as a quality-control measure. Higher relative E6 expression and more frequent absence of L1 and E5 transcripts were observed in the poor-prognosis group. These associations were nominally significant in the primary analyses but did not remain statistically significant after false discovery rate correction. In exploratory regression analyses adjusted for advanced nodal stage, higher relative E6 expression and absence of E5 and L1 remained nominally associated with poor prognosis. Sensitivity analysis excluding the 25% of HPV16-positive samples with the lowest total HPV read counts strengthened the observed E6 difference but attenuated the associations for E5 and L1 transcript absence. Overall, this exploratory study identifies HPV16 transcriptional differences between OPSCC tumors from patients with different clinical outcomes. These findings are hypothesis-generating and require validation in larger, independent cohorts before prognostic or clinical relevance can be inferred.