VictorJuiz/thesis huggingface dataset:
Cellular Stress Induces TRB3/USP9x-dependent Notch Activation in Cancer; Therapeutic Implications

Compared to other subtypes of breast cancer (BC), triple-negative breast cancer (TNBC) has a poor prognosis and limited therapeutic options. Activation of the Notch developmental signaling pathway is a defining feature of TNBC and is an independent predictor of outcome in this malignancy. For this reason, anti-Notch agents have been explored as potential anti-cancer therapeutics. Although Notch inhibitors have demonstrated efficacy in pre-clinical studies of breast cancer, owing to the ubiquity of Notch in normal tissues, dose-limiting toxicities in humans have limited their clinical usefulness. Thus, there is a need to devise novel approaches to block Notch signaling specifically in cancer cells. We have shown that through its control of the MAPK and TGF signaling pathways, the pseudokinase Tribbles homolog 3 (TRB3), regulates the expression of the Notch ligand, JAG1. As a stress-sensor, TRB3 is markedly upregulated during hypoxia, nutrient deprivation and ER stress (ERS), prominent features of TNBC associated with tumor progression and relapse. Through its scaffolding properties, TRB3 promotes enzyme-substrate interactions, signaling pathways, and transcriptional outputs. To further understand how TRB3 is regulated in TNBC, a proteomic screen was conducted which identified the deubiquitinase USP9x as a binding partner of TRB3. USP9x activates the Notch pathway in two ways: (1) as a deubiquitinase it protects stress-generated TRB3 from ubiquitin-mediated proteasomal degradation, resulting in JAG1 up-regulation in cancer cells and (2) USP9x regulates cancer-intrinsic Notch activation by stabilizing Mind Bomb 1 (MIB1), an E3 ligase required for JAG1 ubiquitination and stabilization. Thus, in stressed TNBC cells USP9x promotes JAG1-mediated Notch activation via both the transcriptional and post-transcriptional mechanisms. Next, we used murine models of TNBC to explore TRB3/USP9x as potential therapeutic avenues to block Notch-dependent TNBC progression. While knock-out of TRB3 showed modest anti-tumor efficacy, USP9x knock-out significantly reduced Notch activation and tumor growth. This was accompanied by a switch of the tumor immune microenvironment from a “cold” immunosuppressive to a “hot” immunoreactive, tumoricidal phenotype. Consistent with these findings, pharmaceutical inhibition of USP9x occurs without appreciable toxicity in mouse models of TNBC. This work identifies a novel therapeutic approach to block cancer-intrinsic Notch activation without affecting Notch-dependent tissue homeostasis.

Advisor: Reedijk, Michael
Investigation of the TERT promoter DNA methylation status in human cancer

Telomere maintenance is a hallmark of human cancer. In the majority of human cancer, telomere maintenance is achieved by reactivation of telomerase. TERT – a reverse transcriptase component of telomerase – is a proto-oncogene that governs the telomerase activity and is transcriptionally dysregulated in cancer. While genetic alterations including mutations affecting the TERT promoter has been described, the exact mechanism of TERT reactivation in human cancer cells remains poorly understood. The focus of this Ph.D. thesis is to investigate biological and clinical implications of aberrant DNA hypermethylation within the TERT promoter observed uniquely in human cancer. I initially uncovered a cancer-specific DNA hypermethylated region within the TERT promoter – which I defined as the TERT Hypermethylated Oncological Region (THOR) – and show high prevalence of this epigenetic alteration in the context of human cancer. I then determine the biological and clinical implications of THOR hypermethylation, leading to its potency as a therapeutic target and a diagnostic biomarker. Lastly, I elucidate a new model of differential allelic THOR hypermethylation in human cancer and how it can explain differential allelic expression of TERT. Together, these studies provide an insight into the DNA methylation landscape of the TERT promoter, introduce a THOR-dependent TERT upregulatory mechanism, and propose therapeutic and diagnostic potential of THOR hypermethylation signature.

Keywords: Cancer
DNA methylation
Epigenetics
Telomere
TERT
THOR
Advisor: Tabori, Uri
FAM46C/TENT5C Is a Tumour Suppressor in Gastric Adenocarcinoma

Despite improvements in surgical and perioperative adjuvant therapy, gastric adenocarcinoma carries a 75% case-fatality rate and approximately 40% of Western patients die of recurrent disease. As an important regulator of centriolar duplication, cell motility, and invasion, polo-like kinase 4 (PLK4) has been identified as an oncogene which affects tumourigenesis, cancer metastasis, and response to chemotherapy. Change in PLK4 expression has been identified in numerous human cancers, but Plk4’s role in gastric adenocarcinoma is not well defined; I hypothesized that Plk4 or its interactors could be intimately involved in gastric cancer metastasis and progression. The high degree of molecular heterogeneity in gastric adenocarcinoma and variability in patient outcomes highlight the importance of utilizing patient cohorts to identify novel therapeutic targets. As such, I performed a comprehensive clinical chart review of 238 consecutive gastric adenocarcinoma patients who underwent a curative-intent resection. Recurrence remained a major cause of death in this patient cohort and was only predicted by pathologic staging. Our laboratory had previously identified a number of high-confidence functional interactors of Plk4, and, for each interactor, I determined the mRNA expression in tumour vs paired normal mucosa in our patient cohort. From this interrogation, I identified low expression of FAM46C, a Plk4 inhibitor and tumour suppressor in multiple myeloma, as a novel predictor of inferior disease-specific survival and recurrence at locoregional or distant sites. In vitro experiments demonstrate that FAM46C expression is cytotoxic to gastric cancer cells and suppresses cell migration. RNA-sequencing of patients’ gastric tumour and normal mucosa further reveal that ion-channel related pathways are significantly dysregulated in low-FAM46C tumours, but not in high-FAM46C tumours, implying a novel relationship between FAM46C and ion channels. Targeted evaluation revealed a correlation between the expression of FAM46C and KCNQ1, the main potassium recycler in parietal cells, both in vitro and in patient samples. FAM46C-depleted gastric cancer cells were also better able to survive in a high KCl concentration environment. These findings provide support for FAM46C as a tumour suppressor and therapeutic target in gastric adenocarcinoma patients, and potentially reveal a new role for FAM46C in regulating KCNQ1-mediated evasion of apoptosis and epithelial-to-mesenchymal transition.

Advisor: Swallow, Carol J
What Causes Health? Revisiting the Social Determinants of Health (SDH) Through a Salutogenic Lens and Self-reported Health (SRH) as the Main Outcome: A Realist Evaluation

For centuries healthcare has been driven by a disease-oriented mindset. Built on the Enlightenment philosophers’ thoughts and insights, this mindset has separated self from body, defined health as the absence of physiological disorders, and reduced healthcare to a disease elimination campaign. Even the social determinants of health (SDH) models have been designed to reduce the prevalence of the disease and to detect and correct pathogenic mechanisms of “social production of disease.” However, studies show that people with chronic or terminal conditions identify themselves as healthy. In the late 1970s and in his theory of Salutogenesis, Antonovsky hypothesized that people with a strong sense of coherence (SOC) manage to maintain their health, facing stressors created by life challenges. Informed by the realist evaluation methodology, this study explores how a Salutogenic SDH model operates if the duality of self and body is challenged by replacing medicine-diagnosed disease with self-reported health (SRH) as the outcome of the SDH models. In the first chapter, I argued that approaching health from a pathogenic perspective is misleading and has created many unintentional harms like the medicalization of life. From synthesizing seventy-one reviews (Chapter Two), I found that SRH can replace medicine-diagnosed diseases in SDH models. The systematic review (Chapter Three) showed that SOC has a robust and positive impact on the SRH of individuals, and its impact on the relationship between SDH and SRH is similar to that between SDH and disease. However, based on the findings from two review papers, I argued that to develop a true salutogenic SDH model, merely changing the outcome and even adding SOC as another determinant to the list of SDH is not enough. In a salutogenic model, a salutogenic outcome should be supported by a salutogenic mechanism. Using a network approach to data analysis in chapter four, I created an interface between the National Population Health Survey dataset and the realist evaluation methodology. I showed how strong SOC improves the general resilience of a person’s network of determinants and protects her health when a life challenge turns a determinant in the network turns from a resource into a deficit.

Keywords: Critical Realism
Network Analysis
Salutogenesis
Self-Reported Health
Sense of Coherence
Social Determinants of Health
Advisor: Poland, Blake
Topology and Magnetism in Quantum Materials

In this thesis, we study various electron systems with nontrivial topological characters emerging in real space, in reciprocal space, or driven by electron-electron interactions, from which a variety of extraordinary properties in thermodynamics, transport, and optics are uncovered. We begin with systems hosting real-space skyrmion spin texture known to induce an emergent magnetic field for conduction electrons in metallic magnets, resulting in observable anomalies in transport phenomena such as Hall effect and Nernst effect. We examine how the topological charge density of skyrmions can be tuned by the Zeeman field coupled to the spin texture, which in turn tunes the emergent magnetic field. Conduction electrons sensing such a tuneable emergent magnetic field are shown to exhibit anomalous quantum oscillations in physical quantities in addition to the conventional quantum oscillations from Landau quantization due to an orbital magnetic field. We then turn to study the impact of skyrmions on the optical Hall conductivity of the conduction electrons, from which a high-frequency resonant feature is found. A sum rule is discovered, which relates properties of the Hall resonance to the density of skyrmions in the system. The second part of the thesis is inspired by a remarkable oxide ferromagnet SrRuO3 where both momentum-space and real-space topology have been reported. Earlier works suggested the presence of topological Weyl nodes in the band structure, while Hall-effect experiments on its thin films detected anomalies reminiscent of the Hall-effect signature of skyrmions. In fact, there is a debate on the skyrmion origin versus the momentum space Berry curvature origin of these anomalies. Intriguingly, similar anomalies are observed in magneto-optical Kerr effect in thin films. We provide theoretical evidence suggesting a common origin from magnetic domains for the observed anomalies: (1) Kerr anomalies arise from magnetic domains and an unusual non-monotonic relation between Kerr angle and magnetization, whereas (2) Hall anomalies may be linked to highly skew domain-wall scatterings, occurring when there are Weyl nodes near the Fermi level. Finally, we study a bilayer Haldane model where Hubbard interactions can drive a topologically trivial band insulator into a strongly correlated topological phase. A slave-rotor mean-field approach is used to study its phase diagram and its properties, including its edge electron spectral function.

Keywords: anomalous Hall effect
chiral spin liquid
Kerr effect
optical Hall effect
skyrmion
Weyl semimetal
Advisor: Paramekanti, Arun
Substance Use Recovery and Stigma in Rural Contexts

BackgroundThe concept of recovery holds international legitimacy as a client-centered, strengths-based approach to mental health and substance use. How dominant recovery discourses shape the identities and affect the lives of people with substance use issues in rural areas have received little attention. The purpose of this three-paper dissertation is to better understand power operating within recovery discourses and trace the sociocultural processes by which stigmatized identities are constructed and resisted. Foucauldian and intersectionality theories are used to address the questions: 1) How do recovery discourses shape the identities of people with substance use issues in rural Ontario? 2) How do recovery discourses affect the daily lives of people with substance use issues in rural Ontario? 3) What strategies for resistance are employed to challenge substance use stigma? Methods Paper 1 presents a critical discourse analysis (CDA) of two federal documents to examine how recovery is understood in Canada. Paper 2 applies a CDA to 40 semi-structured interviews with people with substance use issues in two rural communities to explore how they adopt and contest recovery discourses. Paper 3 presents a thematic analysis of the same 40 interviews to consider how people with substance use issues experience recovery, stigma, and resistance. Findings Findings from Paper 1 illustrate that dominant recovery discourses are enmeshed in complex networks of neoliberal, biomedical, legal, and moral discourses that (re)produce stigmatized identities at macro and micro levels, complicating the recovery literature and challenging normative assumptions related to substance use. Papers 2 and 3 present the voices of people with substance use issues in rural areas. Their experiences and perspectives align with and contest dominant recovery discourses and provide numerous strategies of resistance to counter substance use stigma. Conclusion This thesis complicates the growing body of substance use recovery literature in rural communities. The analyses of federal documents and personal narratives not only expose underlying power relations and ideological values that construct a reductionist model of recovery and perpetuate stigmatized identities, but encourage researchers, educators, policymakers, practitioners, and marginalized groups to advocate for more equitable approaches to recovery that eradicate stigma related to rural substance use.

Keywords: critical discourse analysis
identity
recovery
rural
stigma
substance use
Advisor: Fang, Lin
Smart Thermostat Use in Multi-unit Residential Buildings: Impacts on Occupant Behaviour, Thermal Comfort, and Energy Performance

As the proportion of the population who resides in urban centers grows, the number of dwellings in high-rise residential buildings is also increasing. Heating, ventilation, and air conditioning (HVAC) typically accounts for over half of all energy use in this building type and, as such, consideration of these loads is key to effective energy demand-side management. Connected, smart thermostats provide new opportunities for energy management in high-rise residential buildings by facilitating access to suite-level data for building operators and researchers, improving occupant interfaces, and enabling the implementation of new in-suite HVAC control strategies (e.g., occupancy-based and load shifting control, as explored here). In this thesis, the impacts of smart thermostat use on occupant behaviour, thermal comfort, and energy performance were investigated through a field study in two contemporary high-rise residential buildings in Toronto, Canada. The key findings for each of these areas are summarized below.1. Occupant Thermal Comfort and Behaviours: Over-conditioning of suites occurred frequently in both buildings, despite the presence of in-suite temperature controls, resulting in thermal discomfort for occupants. As compared to conventional, programmable thermostats, higher schedule programming rates were observed amongst the study population, who has smart thermostats installed in their suites. 2. Thermostat Control Strategies:Occupancy-based thermostat control was estimated to reduce suite-level HVAC use by 5.9% ± 46% on average in the studied suites, however the energy impacts were limited by pre-existing short terminal HVAC unit runtimes (average runtime of 5 minutes/hour in the heating season and 12 minutes/hour in the cooling season). Overall, the load shifting strategy was ineffective, however, substantial shifting of suite HVAC load from on-peak to off-peak periods was observed in a subset of suites. 3. Chiller Plant Operation and Performance: Based on chiller plant operation data, modelling showed that reductions in building space cooling demand had diminishing returns in terms of reducing electricity use –the first 10% to 20% of space cooling demand reductions had the most impact on chiller plant electricity use. Further, using weather-based regression models and typical meteorological year forecasts for the 2040s, space cooling electricity use was forecasted to increase by 21% over 2020 levels.

Keywords: energy management
HVAC
multi-unit residential buildings
occupant comfort
residential buildings
smart thermostats
Advisor: Touchie, Marianne F
Additive Material and Device Engineering for Stable Perovskite Solar Cells

Metal-halide perovskite solar cells (PSCs) have risen rapidly in solar power conversion efficiency over the past decade. However, practical impact for PSCs will require stable materials and device architectures. The thesis focuses on strategies to improve the stability of PSCs and to realize devices that achieve high efficiency combined with good stability. In particular, the use of chemical additives – those that transform 3D lattices into quantum wells, additives that stabilize desired 3D crystal structures, and dopants that help shape the electric field profile in devices – adds a degree of freedom that I exploit in perovskite engineering with the goal of uniting performance and stability.I begin by analyzing ion-migration-induced degradation in PSCs operating at maximum power point (MPP). I find that using quasi-2D perovskites suppresses this undesired ion migration process. Compared to 3D devices that operate reliably for less than 10 hours, optimized quasi-2D perovskites show negligible performance degradation over 80 hours of operation while providing efficiency comparable to that of 3D perovskite devices. Next, I investigate the structural stability of CsPbI3 perovskite. I propose a method to create stable tetragonal Cs-based perovskites with a bandgap near 1.7 eV by adding small amounts of large A-site cations into the crystal lattice. Using mixed Cs and large organic cations, I stabilized Cs-based perovskites and achieve a power conversion efficiency (PCE) of 15.2% and MPP stability of 230 hours. Finally, I investigate the stability and efficiency of devices that exploit perovskites with a p-i-n structure that is thermally stable at 85°C. CsFA perovskite is known to be thermally stable but has previously yielded low performance due to a low charge carrier diffusion length. I propose a band-engineering method to enhance the extraction of photocharges. Compared to the original p-i-n CsFA solar cells with a PCE of 18%, band-engineered solar cells achieved 20.3% stabilized power output and survive an 85°C heating test. This work presents a suite of strategies to improve the stability of PSCs, an important step toward economic and environmental impact. The understanding of PSC degradation and the countermeasures provided in this work contribute to further development of perovskite-based devices.

Keywords: additive
perovskite
solar cell
stability
Advisor: Sargent, Edward H
Molecular Biology of Childhood Brain Tumours

Malignancies of the central nervous system are the leading cause of cancer-related death in children. These cancers pose a significant clinical burden due to limited treatment options and substantial morbidity from chemotherapy and radiation sequelae during childhood. Two of the most common pediatric brain tumours are medulloblastoma and ependymoma. Over the past decade, advances in genomics have allowed for these tumours to be classified into molecularly and clinically distinct subgroups. These studies have enabled researchers to identify drivers of tumorigenesis, uncover novel vulnerabilities, and propose putative targeted treatments. In this thesis, I continue to build upon these findings. First, examining the genetic landscape of non-coding mutations in medulloblastoma we identify a highly recurrent mutation in the U1 small nuclear RNA. These mutations are prognostically relevant, represent a novel type of splicing-related mutation, and provide a new avenue to develop targeted immunotherapies. Next, we establish primary patient derived models of the lethal PFA ependymoma subgroup. Through a series of experiments, we characterize a metabolic-epigenetic axis that drives PFA growth and propose a “Goldilocks Model” of PFA tumorigenesis. Finally, we establish that the metabolic phenotype of PFA mirrors that of normal cerebellar development. Thus, characterizing the molecular biology of medulloblastoma and ependymoma has revealed novel drivers of disease, advancing our capacity to develop targeted treatments for these dismal cancers.

Advisor: Taylor, Michael D
Recognition of the Pseudomonas syringae type III effector HopF1r by the Arabidopsis NLR ZAR1

The plant pathogen Pseudomonas syringae uses the needle-like type III secretion system (T3SS) to inject virulence factors known as type III secreted effector proteins (T3SEs) directly into the plant cell. T3SEs disrupt plant immune pathways, allowing for successful colonization. However, plants have evolved resistance (R) genes that encode for nucleotide-binding leucine-rich repeat (NLR) proteins that detect the presence of some effectors, and subsequently trigger an immune response that suppresses pathogen growth. Recognition of effectors by NLRs often involves monitoring another host protein for effector-induced molecular perturbations; upon detection of these modifications, an immune response is triggered. For example, the NLR ZAR1 senses effector-mediated perturbations of associated kinases to detect at least 6 families of T3SEs. The effector HopF2a/HopF1r from P. syringae pv. aceris M302273PT has been found to trigger immunity in Arabidopsis. The objective of my research was 1) to identify other potential genetic requirements for HopF2a/HopF1r recognition in Arabidopsis, and 2) to understand how these components are involved in the HopF2a/HopF1r recognition mechanism. In this thesis, I demonstrate that recognition of HopF2a/HopF1r requires the R gene ZAR1, as well as the kinases ZRK3 and PBL27. The results of this project provide insight into how a single NLR is able to recognize several unrelated effectors by associating with different members of a diverse family of kinases, providing plants with the potential to defend themselves against a wide variety of pathogens.

Advisor: Desveaux, Darrell