Correlation of HPV16 gene status and gene expression in OPSCC

Introduction: Human Papillomavirus 16 (HPV16) can cause oropharyngeal squamous cell carcinoma (OPSCC). To assess the viral gene expression in primary cancer tissue we analysed the correlation of viral genomic and transcriptomic gene expression.

Material and Methods: DNA and RNA were extracted from FFPE material from 27 p16 positive OPSCC cases. We developed a qPCR assay for each of the HPV16 genes to quantitate DNA and RNA transcripts antigens. Our additional OPSCC cohort with RNA sequencing data was used to map the HPV16 genome using the ViGen pipeline.

Results: Amounts of HPV16 genes were correlated at DNA and RNA levels using the qPCR assay and could be confirmed in the RNA sequencing cohort. The RNA co-expression of all genes was detected in 37 %  and >60 %  in the qPCR and RNA seq cohort respectively.

Conclusion: We describe an HPV16 qPCR assay to quantify genomic and transcriptomic expression of HPV16 genes in OPSCC tumours and prove the findings in a separate cohort with RNA sequencing. The qPCR offers a cheap and attractive tool to diagnose HPV16 involvement in cancer. The co-expression of al HPV16 genes in a substantial number of patients is of clinical relevance as it can lead to possible virus transmission between partners.

Poster-PDF A-1148.pdf

Adrian v. Witzleben (StipendiumDFG # WI 5255/1-1:1), OW (Cancer Research UK Centre’s Network Accelerator Award Grant (A21998), SL (DFG Forschungstrainingsgruppe (GRK-2254). EC, LC and CHO (Southampton Hospitals charity donations), RNA-sequencing (Transgene).

Publication History

Article published online:
13 May 2021