The incidence of human papillomavirus (HPV) associated oropharyngeal cancers (OPC) has been rising, making it one of the most common HPV-related malignancies. The high-risk variant HPV16 accounts for up to 90% of HPV-related OPC. The molecular pathways underpinning this disease still require further elucidation and given the expanding universe of non-coding RNA (ncRNA) families, it is paramount we begin to understand their contribution.
In this study, we aimed to uncover the interaction between two major ncRNA families towards carcinogenesis, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). LncRNAs and miRNAs are described as independent regulators; however, increasing evidence suggests the two families can interact with each other, with lncRNAs acting as “sponges” for miRNAs. We analysed the RNA-sequencing data from The Cancer Genome Atlas of 49 OPC patient samples to identify differentially expressed (DE) lncRNAs, miRNAs and mRNAs between HPV16+ and HPV- tissues. Using a 5-fold cut-off, we found 37 DE-lncRNAs in HPV16-positive OPC. With this dataset, we built an RNA axis interactome to visualize the interactions between lncRNA/miRNA/mRNA. A large majority of the DE lncRNAs had the potential to bind to one or more DE-miRNA, impacting multiple miRNA targets. The DE-lncRNAs were linked to cellular pathways including cell cycle and proliferation, signal receptor binding and the PI3K-Akt signalling pathway, highlighting the critical role they play in HPV16-related OPC.
One of the most significantly downregulated lncRNAs, Linc00911 was validated in cell lines and in a second OPC patient cohort. The results showed that Linc00911 expression was decreased in the presence of HPV16. Next, we overexpressed the HPV16 major viral oncogenes E6 and E7 in iHFKS and this resulted in the decreased expression of Linc00911. Linc00911 has not previously been reported in OPC or HPV16-related cancers and is unique to this study.
Overall, these results have demonstrated that HPV16 can alter the expression of lncRNAs in OPC and that specific oncogenes, E6 and E7, may induce these changes, as observed for Linc00911. Through an interactome analysis, we also identify possible lncRNA-miRNA sponging interactions in HPV16+ OPC. In summary, the lncRNA/miRNA/mRNA axis is impacted by HPV16 and these. molecular interactions may play an important role in HPV virally driven cancers.