The impact of the Human papillomavirus type 16 on non-coding RNAs in Head and Neck cancer

Sais, Dayna Grace

The impact of the Human papillomavirus type 16 on non-coding RNAs in Head and Neck cancer

Sais, Dayna Grace

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Publication Type:: Thesis
Issue Date:: 2022

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Field	Value	Language
dc.contributor.author	Sais, Dayna Grace
dc.date.accessioned	2023-01-13T04:21:48Z
dc.date.available	2023-01-13T04:21:48Z
dc.date.issued	2022
dc.identifier.uri	http://hdl.handle.net/10453/164966
dc.description	University of Technology Sydney. Faculty of Engineering and Information Technology.	en_US.UTF-8
dc.description.abstract	The Human Papillomavirus is a major risk factor for Head and Neck cancers (HNC), having a strong association with the Oropharyngeal cancer (OPC) subtype. The high-risk variant, HPV type 16 (HPV16), is the cause for 90% of all HPV related OPCs. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), have been shown to have dysregulated expression in OPC. The dysregulated expression on ncRNAs can lead to tumour development. The aim of this study was to identify specific ncRNAs that HPV16 and its viral oncogenes E6 and E7 target in OPC, and the mechanisms this. To investigate HPV16s impact on miRNAs, we used an LNA array to determine the expression levels of miRNAs in OPC tissue, comparing HPV16+ and HPV16- tissues. MiR-496 and miR-33a were the most significantly deregulated. We constructed a novel HPV16-ncRNA interactome to identify mechanistic links. Interestingly, SREBF2 harbours miR-33a, and we believe there is a correlation whereby E6 and E7 regulate the expression of SREBF2/miR-33a, having a downstream impact on miR-496. TCGA analysis showed that SREBF2 was significantly higher in the HPV+ OPC. An siRNA knockout of HPV16 E6/E7 revealed that the viral oncogenes could regulate SREBF2 and miR-33a. The knockdown of SREBF2, revealed no change in miR-33a expression, suggesting that miR-33a is under its own form of regulation by HPV16. This study has identified a regulatory pathway involving HPV16 E6/E7 and specific miRNAs. We also sought to expand our research to include other regulatory RNAs such as long non-coding RNAs. The lncRNA, TRINGS (TP53-regulated induced by glucose stress), was investigated in HPV16 E6/E7 expressing cells. It was determined that TRINGS expression is decreased with the presence of the viral genes. Using a siRNA knockdown system, we demonstrated that the modulation of TRINGS expression will reduce cell viability of cervical cancer cell lines. TRINGS was also determined to be specific for HPV related cervical cancers. We believe HPV16 targets a different cohort of lncRNAs in HPV related OPC. Given this, we assessed raw RNA-sequencing data from TCGA to identify differentially expressed lncRNAs in HPV16+ OPC. In future research we aim to investigate the function of these lncRNAs in HPV related OPC. This study has identified the complexity of molecular pathways between HPV16 E6/E7 and ncRNAs and the consequences in HNC. The construction of viral interactomes combined with in vitro approaches provided novel insights for discovering mechanistic links in HPV16+ Head and Neck cancers.	en_US.UTF-8
dc.format	Thesis (PhD)
dc.language.iso	en_US	en_US.UTF-8
dc.relation	https://opus.lib.uts.edu.au/bitstream/10453/164966/2/02whole.pdf
dc.rights	The author owns the copyright in this thesis including all reproduction and reuse rights for the work. The work may not be altered without the permission of the copyright owner. Attribution is essential when quoting or paraphrasing from this thesis.
dc.rights	info:eu-repo/semantics/openAccess
dc.rights	au.edu.uts.lib/ppc
dc.title	The impact of the Human papillomavirus type 16 on non-coding RNAs in Head and Neck cancer	en_US.UTF-8
dc.type	Thesis
utslib.copyright.status	open_access	*

Abstract:

The Human Papillomavirus is a major risk factor for Head and Neck cancers (HNC), having a strong association with the Oropharyngeal cancer (OPC) subtype. The high-risk variant, HPV type 16 (HPV16), is the cause for 90% of all HPV related OPCs. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), have been shown to have dysregulated expression in OPC. The dysregulated expression on ncRNAs can lead to tumour development. The aim of this study was to identify specific ncRNAs that HPV16 and its viral oncogenes E6 and E7 target in OPC, and the mechanisms this. To investigate HPV16s impact on miRNAs, we used an LNA array to determine the expression levels of miRNAs in OPC tissue, comparing HPV16+ and HPV16- tissues. MiR-496 and miR-33a were the most significantly deregulated. We constructed a novel HPV16-ncRNA interactome to identify mechanistic links. Interestingly, SREBF2 harbours miR-33a, and we believe there is a correlation whereby E6 and E7 regulate the expression of SREBF2/miR-33a, having a downstream impact on miR-496. TCGA analysis showed that SREBF2 was significantly higher in the HPV+ OPC. An siRNA knockout of HPV16 E6/E7 revealed that the viral oncogenes could regulate SREBF2 and miR-33a. The knockdown of SREBF2, revealed no change in miR-33a expression, suggesting that miR-33a is under its own form of regulation by HPV16. This study has identified a regulatory pathway involving HPV16 E6/E7 and specific miRNAs. We also sought to expand our research to include other regulatory RNAs such as long non-coding RNAs. The lncRNA, TRINGS (TP53-regulated induced by glucose stress), was investigated in HPV16 E6/E7 expressing cells. It was determined that TRINGS expression is decreased with the presence of the viral genes. Using a siRNA knockdown system, we demonstrated that the modulation of TRINGS expression will reduce cell viability of cervical cancer cell lines. TRINGS was also determined to be specific for HPV related cervical cancers. We believe HPV16 targets a different cohort of lncRNAs in HPV related OPC. Given this, we assessed raw RNA-sequencing data from TCGA to identify differentially expressed lncRNAs in HPV16+ OPC. In future research we aim to investigate the function of these lncRNAs in HPV related OPC. This study has identified the complexity of molecular pathways between HPV16 E6/E7 and ncRNAs and the consequences in HNC. The construction of viral interactomes combined with in vitro approaches provided novel insights for discovering mechanistic links in HPV16+ Head and Neck cancers.

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http://hdl.handle.net/10453/164966