HPV16 is implicated in around 30% of oropharyngeal cancers (OPCs). HPV-associated OPCs generally show a better prognosis, but 20% deviate from this trend, indicating a need for better molecular profiling. HPV16-E5 is an oncoprotein encoded by an mRNA that undergoes extensive splicing, with only one specific transcript being translatable. The prognostic significance of this E5-productive transcript in HPV-related OPCs is not well-studied.

We retrospectively analysed 74 HPV16-positive OPC cases diagnosed between 2011 and 2021. FFPE tissue samples were used for p16, EGFR, and HLA-I analysis by immunohistochemistry while E5, productive E5, E6 and E7 transcripts were detected by qPCR. Survival analysis was conducted using Kaplan-Meier curves and log-rank tests.

Productive HPV16-E5 transcripts were detected in 11.3% of OPCs. There was no significant association between HPV16-E5 transcripts and EGFR or HLA-I expression. However, the presence of the productive E5 transcript was associated with worse progression-free survival (PFS) (p = 0.0024). EGFR or HLA-I expression was not significantly associated with PFS (p = 0.17 and p = 0.93, respectively).

This study demonstrates for the first time the presence of E5-productive transcripts in HPV16-positive OPCs and its association with poorer PFS, highlighting its potential as a prognostic marker. Further research with larger cohorts is needed to validate these findings.