MicroRNA to microRNA Interactions and their role in Head and Neck Squamous Cell Carcinoma

Hill, Meredith Kate

MicroRNA to microRNA Interactions and their role in Head and Neck Squamous Cell Carcinoma

Hill, Meredith Kate

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Publication Type:: Thesis
Issue Date:: 2022

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Field	Value	Language
dc.contributor.author	Hill, Meredith Kate
dc.date.accessioned	2023-01-12T23:31:24Z
dc.date.available	2023-01-12T23:31:24Z
dc.date.issued	2022
dc.identifier.uri	http://hdl.handle.net/10453/164931
dc.description	University of Technology Sydney. Faculty of Engineering and Information Technology.	en_US.UTF-8
dc.description.abstract	Head and Neck Squamous Cell Carcinoma (HNSCC) is rising in incidence worldwide, hence there is an increased need to elucidate the molecular pathways responsible for this disease. MicroRNAs (miRNAs) are of great interest due to their role in the initiation and progression of several cancers, including HNSCC. These are a class of small non-coding RNAs that typically perform post-transcriptional regulation of messenger RNA (mRNA) through the recognition of complementary sequences within the 3´ untranslated region (UTR). However, several studies have demonstrated that miRNAs regulate other miRNAs, known as a miRNA-miRNA interaction. This is a relatively new area of research and no information exists pertaining to the impact of these interactions in HNSCC. This thesis focused on the discovery of miRNA-miRNA interactions in HNSCC that are initiated by the oncogenic miRNA, miR-21, and expanded upon a model for direct miRNA-miRNA regulation. To investigate miRNA-miRNA interactions in HNSCC, miR-21 was overexpressed in HNSCC cells and the changes in miRNA expression were evaluated using a TaqManTM OpenArray. Fold change analysis determined that 10 miRNAs were upregulated and 150 miRNAs were downregulated in response to miR-21. The top-most dysregulated miRNAs and their gene targets were integrated into a series of networks to determine the cellular impact of miRNA-miRNA interactions. The Cancer Genome Atlas (TCGA) HNSCC cohort was used to evaluate the changes in this set of miRNAs in patients. Of note from this analysis was miR-92a, which is a member of the miR-17~92a cluster. In vitro experimentation and miRNA sequencing confirmed that the overexpression of miR-21 resulted in the downregulation of members of the miR-17~92a cluster, as well as two other miRNAs, miR-30c and miR-375. In exploring possible mechanisms for the observed changes in the miR-17~92a cluster, its host gene, MIR17HG, was found to contain several putative miR-21 binding sites. To expand on this mode of miRNA regulation, a novel bioinformatics workflow was developed to identify predicted miRNA binding sites within pri-miRNAs. This analysis uncovered that miRNA binding sites are abundant within pri-miRNAs and were enriched compared to sites in random sequences. By using an explorative approach, this thesis collectively identified novel potential miRNA-miRNA interactions of miR-21 in HNSCC, and provided evidence that the direct binding of a miRNA to a pri-miRNA may be a widespread, albeit underexplored, mechanism for miRNA regulation. This has implications on the development of miRNA therapeutics and the use of miRNA-based biomarkers for prognostic and treatment purposes in HNSCC.	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/10453/164931/2/02whole.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	MicroRNA to microRNA Interactions and their role in Head and Neck Squamous Cell Carcinoma	en_US.UTF-8
dc.type	Thesis
utslib.copyright.status	open_access	*

Abstract:

Head and Neck Squamous Cell Carcinoma (HNSCC) is rising in incidence worldwide, hence there is an increased need to elucidate the molecular pathways responsible for this disease. MicroRNAs (miRNAs) are of great interest due to their role in the initiation and progression of several cancers, including HNSCC. These are a class of small non-coding RNAs that typically perform post-transcriptional regulation of messenger RNA (mRNA) through the recognition of complementary sequences within the 3´ untranslated region (UTR). However, several studies have demonstrated that miRNAs regulate other miRNAs, known as a miRNA-miRNA interaction. This is a relatively new area of research and no information exists pertaining to the impact of these interactions in HNSCC. This thesis focused on the discovery of miRNA-miRNA interactions in HNSCC that are initiated by the oncogenic miRNA, miR-21, and expanded upon a model for direct miRNA-miRNA regulation. To investigate miRNA-miRNA interactions in HNSCC, miR-21 was overexpressed in HNSCC cells and the changes in miRNA expression were evaluated using a TaqManTM OpenArray. Fold change analysis determined that 10 miRNAs were upregulated and 150 miRNAs were downregulated in response to miR-21. The top-most dysregulated miRNAs and their gene targets were integrated into a series of networks to determine the cellular impact of miRNA-miRNA interactions. The Cancer Genome Atlas (TCGA) HNSCC cohort was used to evaluate the changes in this set of miRNAs in patients. Of note from this analysis was miR-92a, which is a member of the miR-17~92a cluster. In vitro experimentation and miRNA sequencing confirmed that the overexpression of miR-21 resulted in the downregulation of members of the miR-17~92a cluster, as well as two other miRNAs, miR-30c and miR-375. In exploring possible mechanisms for the observed changes in the miR-17~92a cluster, its host gene, MIR17HG, was found to contain several putative miR-21 binding sites. To expand on this mode of miRNA regulation, a novel bioinformatics workflow was developed to identify predicted miRNA binding sites within pri-miRNAs. This analysis uncovered that miRNA binding sites are abundant within pri-miRNAs and were enriched compared to sites in random sequences. By using an explorative approach, this thesis collectively identified novel potential miRNA-miRNA interactions of miR-21 in HNSCC, and provided evidence that the direct binding of a miRNA to a pri-miRNA may be a widespread, albeit underexplored, mechanism for miRNA regulation. This has implications on the development of miRNA therapeutics and the use of miRNA-based biomarkers for prognostic and treatment purposes in HNSCC.

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