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Characterizing Human Papillomavirus Associated Oral Epithelial Dysplasia, Damir Rosic

Electronic Thesis and Dissertation Repository

The role of high-risk human papillomavirus (HR-HPV) is well documented in oropharyngeal squamous cell carcinoma and cervical cancer. Although a subset of oral dysplastic lesions have been associated to HPV infection as well, there is currently limited data characterizing these lesions. We identified HPV-associated oral epithelial dysplasia (HPV-OED) through screening for histopathological features of HPV and p16INK4a immunoreactivity. Transcriptionally active infections were confirmed by performing RT-qPCR to identify E6 mRNA expression. We identified 82 cases of confirmed HPV-OED that showed a strong predilection for male patients and anatomical sites such as floor of mouth and ventral tongue. This group had …

The Molecular Landscape Of Early-Stage Breast Cancer With Lymph Node Metastasis, Farhad Ghasemi

Electronic Thesis and Dissertation Repository

Axillary lymph nodes (ALNs) are the primary site of metastasis in breast cancer, and their involvement has implications in disease staging, prognostication, and treatment decisions. A non-invasive modality of assessing the risk of ALN metastasis can improve care in patients with early-stage breast cancer by omitting the morbidity and costs associated with axillary surgery.

This thesis explores the molecular landscape of early-stage breast cancers with ALN metastasis and shows the potential of tumour molecular signatures in predicting ALN involvement. After a systematic review of the literature, we use data from The Cancer Genome Atlas (TCGA) to develop molecular signatures correlated …

The Role Of Reactive Oxygen Species In The Accumulation Of Driver Mutations In B Cell Acute Lymphoblastic Leukemia, Mia P. Sams

Electronic Thesis and Dissertation Repository

B cell acute lymphoblastic leukemia (B-ALL) is the most prevalent type of cancer in young children and is associated with recurrent mutations and high levels of reactive oxygen species (ROS). The antioxidant N-acetylcysteine was tested for its ability to prolong lifespan of a mouse model of B-ALL and reduce frequency of mutations. Mice treated with 1g/L of N-acetylcysteine in drinking water were found to have delayed onset of B-ALL at 11 weeks of age and changes in gene expression relating to B cell development, calcium-apoptosis signaling, and pathways in cancer, although no differences in lifespan were observed. Tumours from treated …

A Framework For Characterising Performance In Multi-Class Classification Problems With Applications In Cancer Single Cell Rna Sequencing, Erik R. Christensen

Electronic Thesis and Dissertation Repository

In many real-world scenarios, we need to use multi-class classifiers to properly identify all classes in a dataset. To evaluate performance of multi-class classifiers, we need to take various parameters into account. I created a framework that can be used to drill into the differences between algorithms in specific scenarios and better compare multiple classifiers. This allows researchers to better identify strengths and weaknesses of particular classifiers. Single-cell RNA-seq allows cancer researchers to define complex cell types (i.e. classes) in the tumour micro-environments (TME). Using eight datasets, I assessed performance of 26 methods from different perspectives, such as the ability …

Societal Preferences For Trade-Offs Between Cancer And Non-Cancer Health Outcomes: A Choice Experiment, Roxanne Garaszczuk

Electronic Thesis and Dissertation Repository

Background: Resource allocation decisions are made based on the principle of maximizing population health (efficiency). However, in practice, much higher willingness-to-pay thresholds are used for cancer therapies, with limited supportive evidence.

Objective: To quantify Canadian public preferences on trade-offs between cancer and non-cancer health outcomes.

Methods: Our systematic review identified 7 studies, but none evaluated cancer trade-offs. We conducted a survey using a sample of 300 respondents, with three resource allocation scenarios: (1) cancer versus non-cancer; (2) lung cancer versus heart failure; and (3) lung cancer prevention versus diabetes prevention.

Results: The median respondent preferred health maximization, irrespective of the …

Incidence Of Cancer And Stage At Diagnosis Among People With Recent-Onset Psychotic Disorders, Jared C. Wootten

Electronic Thesis and Dissertation Repository

Evidence on cancer incidence in people with psychotic disorders, compared to the general population, is equivocal, although those with psychotic disorders so have more advanced stage of cancer at the time of diagnosis. The objective of this thesis was to compare cancer incidence and stage at diagnosis for people with psychotic disorders, relative to the general population. Our systematic review did not observe a significant difference in overall cancer incidence among people diagnosed with psychotic disorders (RR = 1.08, 95% CI: 1.00 to 1.16), however people with psychotic disorders were more likely to be present with advanced stage cancer at …

Differential Effects Of Kim-1 In Subcutaneous And Orthotopic Renca Models Of Kidney Cancer, Demitra M. Yotis Dy

Electronic Thesis and Dissertation Repository

Renal Cell Carcinoma (RCC) is the most common and fatal type of kidney cancer. Over 30% of patients that are diagnosed with RCC exhibit metastases. Almost 88% of patients with distant metastases succumb to the disease within 5 years of diagnosis. Kidney Injury Molecule-1 (KIM-1) is a cell surface glycoprotein that is not expressed in a healthy kidney but becomes highly expressed on proximal tubular epithelial cells (PTECs) following injury. Data from the Cancer Genome Atlas (TCGA) reveals that >90% of RCC tumours express KIM-1 mRNA and that higher expression levels correlate with increased overall survival rates of patients. The …

Characterizing The Role Of Tdg In Fxr-Dependent Signaling, Oladapo A. Onabote

Electronic Thesis and Dissertation Repository

Thymine DNA Glycosylase (TDG) plays a key role in active demethylation by excising intermediates of 5-methylcytosine. The function of TDG is required for embryonic development, as Tdg-null embryos die at E11.5. To bypass this embryonic lethality, our lab generated conditional Tdg knockout (TDG_CKO) mice. These mice develop late-onset hepatocellular carcinoma (HCC), partly due to impaired Farnesoid X Receptor (FXR) signaling. Interestingly, Fxr-knockout mice display a similar phenotype and transcriptional profile to TDG_CKO mice, prompting us to investigate a role for TDG in FXR signaling. To this end, we generated Tdg/Fxr double-knockout (DKO) mice. …

Metabolic Reprogramming By Dna Tumour Viruses, Martin Prusinkiewicz

Electronic Thesis and Dissertation Repository

Viruses are the etiological agents of approximately 12% of human cancers. However, only a subset of viral infections eventually progress to cancer. As obligate intracellular parasites, viruses create a host-cell environment that is amenable to virus replication. These changes to host-cell processes during infection are enacted by virally-encoded proteins that act as molecular hubs. When these processes intersect with pathways that encourage the development of cancer, such as the p53 tumour suppressor pathway, these virally-encoded molecular hub proteins function as viral oncoproteins. One major requirement of both virus infected cells and rapidly growing cancer cells is an altered metabolism that …

Hpv Mediated Antagonism Of The Il-18 Proinflammatory Pathway In Head And Neck Cancer, Wyatt W. Anderson

Electronic Thesis and Dissertation Repository

In this thesis, I examined the effect of human papillomavirus (HPV) on the proinflammatory IL-18 cytokine pathway in head and neck cancers. I investigated the expression and methylation of genes associated with this pathway using The Cancer Genome Atlas (TCGA) data. In HPV+ cancers, IL18, CASP1, and AIM2 were downregulated, while IL18BP was upregulated compared to HPV- cancers and adjacent non-cancerous tissues, and IL18’s promoter was significantly more methylated. I compared HPV+ and HPV- head and neck cancer cell lines for expression of RNA and protein levels of IL-18 and IL-18BP by qPCR, western blot, and ELISA. IL-18 …

Inducing Dna-Mismatch Repair Deficiency In Tumours: A Strategy To Enhance Anti-Tumour Immunity, Mikal El-Hajjar

Electronic Thesis and Dissertation Repository

Immunotherapy has improved patient outcomes in advanced or metastatic settings across a number of cancers. Patients with tumours deficient in the DNA mismatch repair (DNA-MMR) pathway often show high response rates to immune checkpoint inhibitors (ICIs) with a rise in immune surveillance. However, little is known about the immune sensitization effects of inducing DNA- MMR-deficiency in low tumour mutational burden (TMB) cancers, such as ICI refractory neuroblastoma. In addition, the dynamic T-cell profile that results from such a DNA-MMR inactivation, and whether this may confer a therapeutic benefit, is poorly understood. Here we used CRISPR/CAS9 genome editing technology to knock …

Exploiting The Immunomodulatory Potentials Of Inkt Cells In Sepsis And Cancer., Joshua Choi

Electronic Thesis and Dissertation Repository

Invariant natural killer T (iNKT) cells are a unique unconventional T cell subset that recognize glycolipids presented by CD1d expressing cells. The prototypical glycolipid agonist of iNKT cells, α-Galactosylceramide (α-GalCer), can induce the rapid release of an arsenal of cytotoxic effector molecules and enormous amounts of immunomodulatory cytokines as early as two hours after activation. In addition to α-GalCer, various glycolipid agonists are available that allow for specific, in vivo targeting of iNKT cells, and can exert divergent T-helper (T_H)1 and/or T_H2 immune responses. Therefore, the type of response instigated by iNKT cells can profoundly influence …

B Cell Acute Lymphoblastic Leukemia Is Driven By Activating Janus Kinase Mutations Cooperating With Spi1 And Spib Deletions In A Murine Model, Michelle Lim

Electronic Thesis and Dissertation Repository

B cell acute lymphoblastic leukemia (B-ALL) is caused by genetic lesions in developing B cells that function as drivers for accumulation of additional mutations in an evolutionary selection process. We investigated secondary drivers of leukemogenesis and their mechanism(s) of arising in a mouse model of B-ALL driven by PU.1/Spi-B deletion (Mb1-CreDPB). Whole exome sequencing revealed recurrent mutations in Jak3 (encoding Janus Kinase 3) and Jak1. Mutations with high variant allele frequency (VAF) were dominated by C->T transition mutations that were compatible with AID, whereas the majority of mutations, with low VAF, were dominated by C->A transversions associated with …

Practical Applications And Future Directions Of Genetic Code Expansion: Validation Of Novel Akt1 Substrates And The Design Of A Synthetic Auxotroph Strain Of B. Subtilis, Mcshane M. Mckenna

Electronic Thesis and Dissertation Repository

In Chapter 1, site-specifically phosphorylated variants of the oncogene Akt1 were made in Escherichia coli using the orthogonal translation system that enable genetic code expansion with phosphoserine. The differentially phosphorylated variants of Akt1 were used to validate newly predicted Akt1 substrates. The predicted target sites of the peptide substrates were synthesized and subjected to in vitro kinase assays to quantify the activity of each Akt1 phosphorylated variant towards the predicted peptide. A previously uncharacterized kinase-substrate interaction between Akt1 and a peptide derived from RAB11 Family Interacting Protein 2 (RAB11FIP2) was validated in vitro. Chapter 2 describes the preliminary development of …

Evaluating The Utility Of Protein Biomarker, S100a7, And Diagnostic Test, Straticyte, In Predicting The Progression Of Oral Dysplasia, Lachlan Mclean

Electronic Thesis and Dissertation Repository

Five-year survival of oral cancer has remained relatively unchanged despite advancements in treatment, mostly because diagnosis is often made at an advanced stage of disease. The progression of dysplasia to oral cancer often follows a stepwise progression. Histopathology is considered the ‘gold standard’ for diagnosing dysplasia and lesions at a high risk of progression to oral cancer, but lends itself to subjectivity. The protein biomarker, S100A7, in oral dysplasia and squamous cell carcinoma has shown some predictive value for the transformation of dysplasia to cancer. Straticyte, a diagnostic test utilizing S100A7 to predict the probability of progression of oral dysplasia …

The Role Of Kidney Injury Molecule-1 In The Metastasis Of Renal Cell Carcinoma, Jasper Lee

Electronic Thesis and Dissertation Repository

Over 30% of patients with renal cell carcinoma (RCC) present with metastases, with median survival of 2 years. Kidney injury molecule 1 (KIM-1) is a cell-surface glycoprotein expressed by >90% of RCC tumours. Preliminary data mined from The Cancer Genome Atlas RNA-sequencing database indicates that KIM-1 overexpression predicts overall survival in patients. Here we sought to determine if tumour KIM-1 plays a role in RCC cell extravasation and metastasis to the lungs. In vitro invasion and in vivo metastasis assays were performed to investigate the metastatic potential of KIM-1-expressing cells, and RNA-seq was conducted to identify differentially expressed genes between …

Functional Investigation Of The Role Of The Retinoblastoma Protein In Genome Stability, Aren E. Marshall

Electronic Thesis and Dissertation Repository

Genome instability is an enabling characteristic of cancerous cells. It has recently been discovered that the retinoblastoma protein (pRB), typically known for its role in cell cycle regulation, also aids in the maintenance of genome stability. Intriguingly, mutations to the pRB gene, RB1, can arise late in tumorigenesis in cancer cells whose cell cycle regulation is already compromised by another mutation. This suggests that pRB’s functions in genome stability could underlie cancer relevant characteristics that are independent of its ability to negatively regulate proliferation. The overall aim of this thesis is to characterize the different means through which pRB …

Applications Of Phosphotyrosine Superbinding Sh2 Domain Variants, Xuguang Liu

Electronic Thesis and Dissertation Repository

Protein tyrosine kinases (PTKs, or TKs) have emerged as one of the most intensively pursued targets in the development of anti-cancer therapeutics, due to their critical roles in the phosphotyrosine (pTyr)-mediated signaling network that regulates many cancer-related cellular activities. The TKs, tyrosine phosphorylation phosphatases (PTPs) and pTyr recognition SH2 proteins are intensively tyrosine phosphorylated, which play a pivotal role in determining the signaling outcome of this network. More than 50% of all human proteins are tyrosine phosphorylated and many of these TK substrates have been proven functional in TK regulated cellular activities. Therefore, proteomics studies of tyrosine phosphorylation are of …

Characterization Of Genomic Copy Number Variation In Mus Musculus Associated With The Germline Of Inbred And Wild Mouse Populations, Normal Development, And Cancer, Maja Milojevic

Electronic Thesis and Dissertation Repository

Mus musculus is a human commensal species and an important model of human development and disease with a need for approaches to determine the contribution of copy number variants (CNVs) to genetic variation in laboratory and wild mice, and arising with normal mouse development and disease. Here, the Mouse Diversity Genotyping array (MDGA)-approach to CNV detection is developed to characterize CNV differences between laboratory and wild mice, between multiple normal tissues of the same mouse, and between primary mammary gland tumours and metastatic lung tissue.

A CNV detection pipeline was used in conjunction with evaluated probe sets, targeting 925,378 loci …

The Role Of Thymine-Dna Glycosylase In Transcriptional Regulation, Bart Kolendowski

Electronic Thesis and Dissertation Repository

Precise control over transcriptional regulation is required for normal cell function. Errors in transcriptional regulation underpin many diseases including cancer. Thymine DNA Glycosylase (TDG) is a base excision repair protein and a coregulator that has been implicated in a diverse set of fundamental biological processes including embryonic development, nuclear receptor signaling and Wnt signaling. Importantly, TDG has been shown to play an important role in transcriptional regulation in a wide variety of systems. Details surrounding the mechanism through which TDG acts remain unclear. In this thesis we explore the role of TDG in Estrogen Receptor (ER)-dependent signaling and in cellular …

Role Of High Molecular Weight Hyaluronan In Ultraviolet B Light-Induced Transformation, Katelyn Cousteils

Electronic Thesis and Dissertation Repository

Keratinocyte carcinomas (KCs) are the most common cancers globally. Ultraviolet light is the key risk factor for these cancers but sunscreen has proven ineffective in their prevention, indicating a need for new prophylactic agents. Chronic elevation of high molecular weight (HMW) tissue hyaluronan (HA) in skin is linked to tumor resistance in the naked mole rat. To directly assess the role of this polysaccharide in resistance to keratinocyte tumors, a HMW HA phosphatidylethanolamine (HA-PE) formulation that penetrates skin and accumulates as coats around keratinocytes was prepared. The tumor resistance properties of the HA-PE formulation were tested in a mouse model …

Design And Synthesis Of Hyaluronan:Rhamm Interaction Inhibitors, Emily Rodrigues

Electronic Thesis and Dissertation Repository

A major component of the extracellular matrix is hyaluronan, a regulator of cell migration/survival and differentiation during response-to-injury processes. The receptor for hyaluronan-mediated motility (RHAMM) binds to HA and has limited constitutive expression but is upregulated during tissue injury. Blocking HA fragment:RHAMM interactions has therapeutic potential for treating cancer but truncation of RHAMM into peptides mimicking only the HA binding domains is predicted to lose their natural α-helical structure. The goal of this project is to explore the effects cyclizing each binding domain has on helicity and its biological effect. Eighteen peptides were synthesized and cyclized using lactam bridges. The …

Angiogenesis And Neo-Microcirculatory Function In Diseased Tissue Revealed By Intravital Microscopy, Giovanni-Michele Arpino

Electronic Thesis and Dissertation Repository

Angiogenesis is the process of generating new blood microvessels. In adults, angiogenesis is fundamental to tumor biology and also to tissues rendered ischemic from vascular occlusion. Despite a promising appeal, strategies designed to simulate or otherwise modify the angiogenic process in adult tissues have yet to realize significant therapeutic potential. Importantly, understanding the structure and function of new microvascular networks formed in adult, diseased tissues is limited. In fact, it remains unknown if a new or regenerated microcirculation can effectively deliver oxygen to the tissue. The purpose of this thesis was to seek out novel determinants of functional angiogenesis and …

Investigating E2f Independent Cell Cycle Control And Tumor Suppression By Prb, Michael J. Thwaites

Electronic Thesis and Dissertation Repository

Cellular division is primarily controlled at the G1 to S-phase transition of the cell cycle by the retinoblastoma tumor-suppressor protein (pRB). The ability of pRB to restrict S-phase entry is primarily attributed to the repression of E2F transcription factors required to upregulate cell cycle target genes necessary for cellular division. Interestingly, while pRB is disrupted in the vast majority of human cancers, mutations typically target upstream regulators of pRB leading to inactivation through hyperphosphorylation. The rarity of direct pRB mutations suggests that the regulation of the cell cycle by pRB may involve additional mechanisms outside of E2F repression, as this …

Using Machine Learning To Predict Chemotherapy Response In Cell Lines And Patients Based On Genetic Expression, Dimo Angelov

Electronic Thesis and Dissertation Repository

The goal of this thesis was to examine different machine learning techniques for predicting chemotherapy response in cell lines and patients based on genetic expression. After trying regression, multi-class classification techniques and binary classification it was concluded that binary classification was the best method for training models due to the limited size of available cell line data. We found support vector machine classifiers trained on cell line data were easier to use and produced better results compared to neural networks. Sequential backward feature selection was able to select genes for the models that produced good results, however the greedy algorithm …

Comprehensive Molecular Characterization Of Human Nodal, Scott D. Findlay

Electronic Thesis and Dissertation Repository

Nodal and related ligands are highly conserved members of the TGF-beta superfamily with well-established and essential roles in the early embryonic development of vertebrates, and in cell fate decisions in human embryonic stem (hES) cells. Aberrant NODAL signaling also generally promotes pro-tumourigenic phenotypes and the progression of a wide array of human cancers. Despite being pursued as a potential therapeutic target, many aspects of NODAL’s molecular biology remain poorly understood. This thesis provides a comprehensive characterization of gene expression from the human NODAL locus at multiple levels. First, an intronic NODAL SNP known as rs2231947 was found to be functional …

Dose-Related Sex Differences In The Establishment Of Conditioned Disgust (Anticipatory Nausea), And The Effect Of Peripubertal And Adult Immune System Stimulation With The Endotoxin Lipopolysaccharide (Lps) On Learning And Memory In The Rat, Caylen J. Cloutier

Electronic Thesis and Dissertation Repository

This thesis examined sex differences in the establishment of lithium chloride (LiCl) – induced conditioned disgust behavior (anticipatory nausea) to a distinct context, as well as, the establishment of conditioned place avoidance (CPA) using rodent models. Also examined were potential sex differences in response to treatment with the bacterial endotoxin, lipopolysaccharide (LPS), and its effect on learning and memory. In Chapter 2, male and female naïve Long-Evans rats were injected (intraperitoneally; i.p.) with either 200 µg/kg LPS or 0.9% (NaCl), 90 minutes prior to i.p. injections of either 128 mg/kg LiCl or 0.9% NaCl, and immediately placed into a distinctive …

Characterization Of The Catalytic Ck2 Subunits With Substitutions At Residues Involved In Inhibitor Binding, Paul Desormeaux

Electronic Thesis and Dissertation Repository

CK2 is a constitutively active, ubiquitously expressed and pleiotropic serine/threonine protein kinase that is implicated in many cellular functions including tumorigenesis. CK2 has two catalytic subunits, CK2a and CK2a’, that carry out its function in the cell. Previous studies have indicated that inhibitor-refractory mutants have been effective in recovering residual CK2 activity, in the presence of inhibitors, when compared to wild type CK2. Based on these observations, inhibitor-refractory mutants were created for both CK2a and CK2a’ and tested with various concentrations with two CK2-specific inhibitors, CX-4945 and inhibitor VIII. The CK2a triple mutant (V66A/I174A/H160D) was tested in inducible U2OS Flp-In …

Longitudinal Evaluation Of Patient Concerns After Surgery For Head And Neck Cancer, Isabel Wozniczka

Electronic Thesis and Dissertation Repository

The primary purpose of this study was to investigate and describe the longitudinal effects of shoulder and neck mobility, strength, and quality of life (QOL) following neck dissection (ND) surgery and identify the concerns of head and neck cancer (HNC) patients. ND is one of the standard procedures for treating HNC, which results in many complications and dysfunctions that can have an effect on a patient’s QOL.

The study had 27 eligible HNC participants who underwent ND, of which eight participated in the shoulder range of motion (ROM) and strength and 12 participated in the QOL patient-reported outcomes analysis. The …

Characterization Of Numb As A Regulator Of Anaplastic Lymphoma Kinase, Ran Wei

Electronic Thesis and Dissertation Repository

Cellular events rely on protein-protein interactions that are often mediated by modular domains which recognize particular sequence motifs in binding partners. The NUMB protein is the first described cell fate determinant and multifaceted adaptor that is involved in a wide variety of cellular events. NUMB mainly mediates protein interactions via its modular PTB domain. Here we present a systematic investigation of the NUMB-PTB interactome by employing an integrative strategy combining both protein and peptide arrays. We profiled NUMB-PTB binding specificity and interacting proteins genome-wide. The receptor tyrosine kinases (RTKs) are found highly enriched in the interactome, raising the possibility that …