VictorJuiz/thesis huggingface dataset:
Comparative Genomics Identifies Conserved Factors that Regulate Stemness in Adult and Cancer Stem Cells

Adult stem cells (ASCs) that self renew indefinitely and generate differentiated cell types are present in species of every phylum identified and, thus, likely share a common evolutionary origin. Cancer stem cells (CSCs), a cell type known to drive tumourigenesis and recurrence, also share these functional properties with ASCs, as well as molecular characteristics, albeit in a dysregulated manner. It is plausible that normal ASCs and CSCs utilize a common genetic circuitry to mediate their shared functional properties, and a comparative genomics strategy may uncover conserved stemness factors required for regulating stemness in normal and cancer stem cells across evolution. Here, I identified transcripts that have enriched expression and a human ortholog in planarian ASCs and cross-referenced this list to genes that are upregulated in glioblastoma stem cells (GSCs) compared to their normal stem cell counterparts. In total, I identified 76 putative stemness regulators common in both systems and I systematically knocked down expression of candidate genes in planarians by RNAi. I found 29/76 resulted in stem cell dysfunction leading to planarian death. DDX56 encodes a DEAD-box RNA helicase, and high DDX56 expression is correlated with worse clinical outcome in GBM patients. I demonstrated planarian ddx56 is required for ASC function, and ddx56(RNAi) caused impaired differentiation, reduced proliferation and ASC loss, as well as disrupted nucleolar integrity and dysregulation of ribosomal components. In patient-derived GSCs, DDX56 localized to the nucleolus, and knockout suppressed CSC growth and self-renewal in vitro. Together, I suggest a role for DDX56 in ribosomal biogenesis, where upregulation of DDX56 in a cancer context reduces nucleolar stress. Another candidate, smarcc2, encodes a core component of the BAF chromatin remodeling complex. In planarian ASCs, I determined the BAF complex regulates chromatin accessibility and therefore expression of key target genes required for differentiation to mesodermal and ectodermal lineages. Functionally, RNAi of smarcc2, or another core component brg1, caused ASC accumulation and impaired differentiation into epidermal and neural fates. Thus, the BAF complex has conserved roles in regulating differentiation across species and provides insights into mechanisms that determine fate choice in ASCs. In conclusion, I demonstrate the utility of comparative genomics and model systems to identify key stemness regulators active in stem cells across evolution, including in CSCs.

Advisor: Pearson, Bret J
Targeting Epigenetic Regulation in Clear Cell Renal Cell Carcinoma Reveals PRMT1 as a Novel Target

Clear cell renal cell carcinoma (ccRCC) is characterized by a remarkably homogenous event: biallelic inactivation of the tumour suppressor gene Von Hippel-Lindau (VHL). Loss of VHL disrupts normal oxygen sensing and causes an upregulation of hypoxia-related genetic programs. Understanding these mechanisms led to the development of targeted agents now used clinically for metastatic ccRCC. Although these therapies have improved survival outcomes, the response rates remain variable, and resistance is a persistent problem. Additionally, loss of VHL alone appears to be a necessary yet insufficient event to drive oncogenesis in the majority of ccRCC instances. Large genomics studies have revealed that co-deletions of VHL with genes involved in chromatin regulation are common and important co-drivers of tumourigenesis. Several conserved evolutionary subtypes have been described clinically and the majority implicate disruptions in epigenetic regulators. Although this molecular picture is complex, it is now clear that impairments in cellular epigenetic mechanisms are important co-drivers of disease and signal a potential vulnerability in the epigenetic network of ccRCC cells relative to their normal counterparts.In this thesis, we aim to exploit this vulnerability to identify novel therapeutic targets with potential for clinical translation. We first established a clinically relevant panel of ccRCC models and performed a screen of small molecule inhibitors targeting a spectrum of epigenetic regulators. We identified MS023, an inhibitor of type I protein arginine methyltransferases (PRMTs) as an agent with anti-tumour activity. Using orthogonal genetic technologies, we further validated PRMT1 as the specific critical dependency for cancer growth. Mechanistically, our transcriptomic and functional analyses suggest that MS023 treatment results in substantial impairments to cell cycle and DNA damage repair (DDR) pathways, while spawning an accumulation of DNA damage over time. Our PRMT1 specific proteomics analysis revealed an interactome rich in RNA binding proteins including the specific regulator of DDR mRNA metabolism: the BCLAF1/THRAP3 complex. Further mechanistic investigation suggests that MS023 treatment may result in impairments to DDR specific mRNA activities including nucleocytoplasmic transport and RNA splicing. Together, our data supports PRMT1 as a compelling target in ccRCC and informs a potential mechanism-based strategy for translational development.

Keywords: Cancer
Epigenetics
Protein Arginine Methyltransferases
Renal Cell Carcinoma
Advisor: Ailles, Laurie
Effects of Back Pain and Mental Health Conditions on Health Care Utilization and Costs: A Population-based Perspective using a Novel Data Platform in Back Pain Research

Back pain is the leading cause of disability globally, and a driver of health care utilization across health systems. Back pain is a complex condition with multiple contributors to disability, including biopsychosocial factors and comorbidities. Notably, this includes mental health conditions as common comorbidities that can negatively impact back pain outcomes. Given the growing burden of back pain and its relationship with mental health, this dissertation aims to comprehensively examine the effects of back pain and mental health conditions at the population level. The first objective assessed the effects of back pain on health care utilization and costs among Ontario adults in a single-payer health system. In this population-based cohort study, adults with back pain had substantially higher rates of health care utilization and costs than those without back pain. Incremental costs corresponded to an annual burden of $759 million in Ontario. The second objective assessed the association between depressive symptoms/depression and outcomes in persons with back pain. This systematic review and meta-analysis found that depressive symptoms may be associated with disability and worse recovery for acute and chronic back pain, and greater primary health care utilization for acute back pain. The third objective assessed the joint effects of back pain and mental health conditions on health care utilization and costs among Ontario adults in a single-payer health system. In this population-based cohort study, the joint effects of back pain and mental health conditions on back pain-specific utilization and opioid prescription were greater than expected, with evidence of synergism. Study findings quantify the substantial burden of back pain on the Ontario health system, and highlight adults with back pain and mental health conditions as a priority group with worse outcomes and greater health care needs. This dissertation offers unique contributions to musculoskeletal epidemiologic research through several methodological approaches, including novel linkages between survey and administrative data for Ontario, propensity-score matching, prognostic review methodology, and analyses of joint effects. Overall, this dissertation provides the evidentiary basis to inform health programs and resources planning tailored to back pain and mental health conditions, to improve population health and health care sustainability in Ontario.

Keywords: back pain
costs
health care utilization
mental health
population-based
Advisor: Rosella, Laura C
New Nurses’ Perceptions of Work Environments and Work Outcomes in Mental Health Practice Settings: A Multi-method Study

Background: New graduate nurses (NGNs) are a vital resource to the nursing workforce given the forecasted staffing trends. NGNs face complex work environments in addition to the challenges inherent in transitioning to practice that shape their initial work experiences. The mental health (MH) practice setting, in particular, has been under-examined with respect to NGNs’ perceptions of the work environment (WE), as have work outcomes. Objectives: This study: 1) identified the perceptions of NGNs working in a MH WE; 2) explored their perceptions of MH nursing culture; 3) determined the extent to which NGNs in MH settings experience job satisfaction (JS), burnout (BO) and turnover intention (TI), and 4) examined whether relationships exist between the MH WE and work outcomes. Methods: A multi-method research design was undertaken with NGNs practicing in MH settings in Ontario, Canada and included the use of a survey of 165 NGNs and interviews with a sample of 15 participants. Nurses working in MH settings with three-years or less of experience were recruited from the College of Nurses of Ontario (CNO) registry. Results: Quantitative and qualitative data were considered independently and also triangulated. Survey data found that NGN working in MH settings perceive the quality of the WE to be favourable, except their participation in the internal governance. JS was insignificant as an explanatory variable relating to TI. Levels of JS, BO and TI were all deemed to be of concern for NGNs. Moreover, nursing WE was found to contribute significantly to said outcomes. Qualitative findings offered further context with themes emerging addressing the rewards/challenges related to caring for patients, such as patient aggression, along with factors in the WE that impact the development of nurse outcomes. Significance: This study resulted in an improved understanding of the WE in MH settings from the lens of NGNs, providing important context regarding what shapes their experience of undesirable work outcomes. These insights and NGN views on MHN facilitates nurse leaders’ understanding of what is needed for NGNs to survive and thrive in a MH practice setting. Strengthening this knowledge will help to support and sustain the MH nursing workforce.

Keywords: mental health settings
new graduate nurse
novice nurse
psychiatric hospitals
work environment
Advisor: McGillis Hall, Linda
Act to Control: The Grand General Indian Council, The Department of Indian Affairs, and the Struggle over the Indian Act in Ontario, 1850-1906.

This dissertation examines the development of the Indian Act in nineteenth-century Ontario within the context of Indigenous political response to the law. The Grand General Indian Council of Ontario was a cross-reserve political organization that met every two years after 1870 to review legislation affecting their communities and to urge the government to act on their recommendations. Representing various communities, nations, and legal frameworks, the Council was built on historic alliances between the Anishinaabe and the Haudenosaunee. Over the years, they drew on multiple forms of Indigenous law, as well as put forward a plethora of political strategies including engagement with and accommodation of some parts of the law itself. Understanding the plurality of legal frameworks and political thought put forward by the Council makes clear the diversity in how Indigenous leaders negotiated the shifting tactics of the government in their efforts to entrench control over reserve communities, as well as demonstrates how their political vision never neatly aligned with government goals. This dissertation also examines the changing legal mechanisms developed by the Department of Indian Affairs and the expansion of the Indian Agent system¬–often in relation to resistance– that ultimately undermined even the most accommodationist alternatives put forward by the Council. Each chapter traces one aspect of the Indian Act (or related legislation) that was of particular concern to both the Council and the Department of Indian Affairs: resource regulation, enfranchisement, reserve governance, inheritance, and the role of Indian Agents. I argue that the application of the Indian Act in Ontario can be understood as a series of contestations over local jurisdiction on reserves. These contestations make clear that while the development of the Indian Act has conventionally been understood as a top-down process, with law being passed in Ottawa being directly applied to reserves, this framing overlooks Indigenous political leaders who opposed the law or sought to have it altered to suit their needs, the difficulties that Indian Agents had in imposing the law, and how the law changed in response to these various struggles over local jurisdiction.

Keywords: Canadian History
Colonialism
Indian Act
Indigenous History
Law
Ontario History
Advisor: Bohaker, Heidi
An Investigation on Advanced Functional Carbonaceous Materials for High Performance Composites in Fuel Cell Applications

Hydrogen fuel cell, one of the main power sources in environmentally benign hydrogen economy, has its own cost and performance limitations which is a large drawback for moving forward with this demanding technology to reduce GHG emissions particularly in the transportation sector from mid-to-heavy duty vehicles. Research on the bipolar plates, a vital component, can be a solution to address this on-going issue which needs improvement in electrical and mechanical attributes. In this dissertation, investigation was carried out on anisotropically distributed advanced functional carbonaceous materials along with the introduction of novel biocarbons which can facilitate to improve the performance of carbon polymer composites by increasing the movement of charged particles through decoupling of repulsion, increased conjugated carbon-carbon aromatic structure and through the spin non-conservation in the crystal lattice structure. The highest electrical conductivity was achieved 221 S/cm and flexural strength 64 MPa, well above the US DOE target of 100 S/cm and 25 MPa respectively. It was observed that the non-destructive porous structure measurement can determine the extent of electrical conductivity. A novel continuous carbon fiber process showed crucial potential in improved mechanical properties with excellent electrical conductivity. The use of multi-fillers and intercalated carbonaceous materials can help to reduce the density, thickness and weight to a large extent which is important for the fabrication of a highly conductive, mechanically flexible and light-weight composite. In this research, a holistic approach of effective intrinsic properties, optimized process parameters and novel functional materials proved to facilitate achieving a high-performance composite for bipolar plates.

Keywords: Biocarbon
Biocomposite
Bipolar plate
Carbon polymer composite
Hydrogen Fuel Cell
Renewable Energy
Advisor: Sain, Mohini MS
Swallowing Physiology and Impairment in Individuals with Parkinson Disease

Parkinson Disease (PD) is a common neurological disorder that is expected to affect 9 million people worldwide by 2030. Dysphagia is highly prevalent in PD, and can result in aspiration pneumonia, malnutrition, and dehydration. The purpose of this doctoral dissertation is to provide a comprehensive overview of swallowing physiology in PD, elucidate potential relationships between swallowing physiology and swallowing function, and to examine the effectiveness of an exercise-based intervention protocol for improving impaired swallowing physiology in PD. The first chapter of this dissertation provides an overview of normal swallowing, dysphagia, and PD pathology. Chapter 2 synthesizes and compares existing evidence on the effectiveness of interventions for dysphagia in PD patients, in the form of a systematic review. Our review highlighted a situation of clinical equipoise and a low certainty evidence base, precluding our ability to make strong recommendations to guide practice. Furthermore, it demonstrated that to manage PD-related dysphagia, it is imperative for clinicians to have an understanding of the physiological mechanisms that contribute to impairment. Building on this discussion, Chapter 3 involved a cross-sectional study of swallowing physiology in PD, using quantitative videofluoroscopic analysis. Measures of swallowing safety, efficiency, timing and kinematics were obtained and compared against healthy reference data. In addition, we explored the effects of liquid thickness on swallowing physiology. Through this analysis we were able to delineate mechanisms of swallowing impairment related to PD from those due to aging, revealing potential targets for intervention and rehabilitation. Given the prominent role that the tongue plays in bolus formation, control, and propulsion in swallowing, interventions to improve tongue strength may positively impact swallowing. To evaluate the utility of including a tongue pressure training component in dysphagia intervention for people with PD, we compared tongue pressure generation capacity in PD and other neurodegenerative populations to healthy controls, presented in Chapter 4. Putting together these findings, Chapter 5 describes an exercise-based rehabilitation protocol, using a tongue pressure measurement device for biofeedback, designed to target the identified physiological mechanisms of swallowing impairment in PD. Finally, we outline limitations and suggest priorities for future research in Chapter 6.

Keywords: Intervention
Neurodegenerative
Parkinson Disease
Rehabilitation
Speech-Language Pathology
Swallowing
Advisor: Steele, Catriona M
Development and Validation of the Juvenile Idiopathic Arthritis Magnetic Resonance Imaging - Sacroiliac Joint Scoring System (JAMRIS-SIJ)

ABSTRACTIntroduction: This thesis utilized a mixed method approach in the development and validation of the Juvenile Arthritis Magnetic Resonance Imaging Sacroiliac Joint Scoring System (JAMRIS-SIJ) in Juvenile Idiopathic Arthritis (JIA). JIA is a chronic inflammatory disease that affects joint function, resulting in a significant effect on the quality of life. MRI is the best diagnostic modality for SIJ imaging in JIA due to its ability to detect early signs of inflammation before radiography, providing for the direct visualization of osteochondral changes to guide treatment. The objective of this research thesis project was to develop a reliable and valid imaging outcome measure that can detect change during JIA interventions. This dissertation describes a series of studies reporting the development and validation process of the JAMRIS-SIJ. Methods: JAMRIS-SIJ development was conducted using a combination of the synthesis of existing related scoring systems in the literature and a multi-iteration nominal group process among over 30 multidisciplinary international imaging and clinical experts to arrive at consensus on the measurement domain and items for the assessment of SIJ inflammation and damage. Thereafter, using data-driven methodology, cases of patients with JIA were selected to test the reliability and validity of the JAMRIS-SIJ. Results: An all-inclusive definition of the SIJ MRI lesions for the inflammation in the order of their relative importance weights in the JAMRIS-SIJ are osteitis (25.7%), bone marrow edema (24.3%), inflammation in erosion cavity (16.9%), joint space enhancement (13.1%), joint space fluid (9.1%), capsulitis (7.3%) and enthesitis (4.6%). Likewise, for damage domain are ankylosis (41.3%), erosion (25.1%), backfill (13.9%), sclerosis (10.7%), and fat metaplasia lesion (9.1%). The intraclass correlation coefficient for inter-rater reliability was 0.77 and 0.60 for inflammation and damage domain respectively. Conclusion: This project reports the novel JAMRIS-SIJ scoring system and initial stages of validation of this scoring system. To our knowledge, this is a pioneer initiative towards the development of a sacroiliac joint MRI outcome measurement tool targeted on the pediatric population considering the unique imaging characteristics of growing bones, cartilage, and bone marrow. The understanding gained from this research may lead to the development of future guidelines for MR imaging outcomes in rheumatology clinical trials.

Keywords: JAMRIS-SIJ
Juvenile Idiopathic Arthritis
Magnetic Resonance Imaging
Outcome Measurement Tool
Sacroiliac Joint
Sacroiliitis
Advisor: Doria, Andrea S
Stretch-Induced Regulation of Hippo Signaling in Lung Microvascular Endothelial Cells – A Novel Mechanism of Overventilation-Induced Pulmonary Fibrosis

Mechanical ventilation is a mainstay of current therapy for patients with acute respiratory distress syndrome (ARDS). However, mechanical ventilation can also cause ventilator-induced lung injury (VILI) that may ultimately progress to pulmonary fibrosis. This can contribute to high dependency on ventilator support and escalate ARDS mortality. The current study focused on the role of the mechanosensitive transcriptional co-factor TAZ, a key player in the Hippo-signaling pathway, as it has been found to be translocated into the nucleus of fibrotic lung tissue but not in healthy tissue. Here, we used Human Pulmonary Microvascular Endothelial cells (HPMECs) to explore the crucial role of TAZ, its upstream regulators, and downstream effects in the pathogenesis of mechanical overventilation-associated lung fibrosis. We have defined upstream mechanotransduction pathways, whereby TAZ localization is regulated in the context of mechanical stretch through Aurora A kinase (AURKA) and FAK, which act by promoting RhoA activation. By examining high-stretched HPMECs, we found that mechanical stretch increased the translocation of TAZ from the cytosol to the nucleus in a dose- and time-dependent manner. Particularly, the nuclear to cytoplasmic ratio of TAZ increased after 3h of stretch at 18% compared to the static controls. Stretch-induced TAZ translocation was blocked by the inhibition of AURKA iii and FAK. Consistently, pharmacological inhibition of Aurora kinase and FAK prevented RhoA activation. In vivo, acid instillation and overventilation induced histological alterations typical of fibrotic remodeling, in particular, the loss of aerated airspace volume in alveoli and alveolar ducts together with alveolar septal wall thickening. These alterations were far less pronounced in endothelial TAZ-deficient mice which, despite a discrete alveolar septal wall thickening, showed an overall preserved acinar architecture with aerated alveoli. Collectively, these findings i) demonstrate that stretch increases TAZ nuclear localization in HPMECs in a time and stretch - dependent manner, ii) define that AURKA and FAK regulate the endothelial response to stretch upstream of TAZ, and iii) highlight that endothelial TAZ is an important driver of overventilation induced lung fibrosis. Together these findings raise the possibility that pharmacological targeting of TAZ or its upstream signaling cascade may attenuate the pathogenesis of mechanical overventilation-associated lung fibrosis.

Advisor: Kuebler, Wolfgang