VictorJuiz/thesis huggingface dataset:
Epigenetic Analysis of the Kallikrein Gene Family and Associated Pathways as a Novel Panel of Prostate Cancer Biomarkers

Aberrant epigenetic landscape is a hallmark of prostate cancer (PCa), one of the most common cancers among men worldwide. Currently, improved understanding of the molecular mechanisms driving PCa pathogenesis as well as biomarkers for improved diagnosis, prognosis and treatment of the disease are needed. Kallikrein related peptidases (KLKs) have emerged as important cancer biomarkers. However, the mechanisms leading to their deregulation in PCa are poorly understood. This thesis characterized the clinical impact of epigenetic mechanisms that regulate KLKs and associated genes contributing to PCa pathogenesis. Utilizing genome-wide DNA methylation profiling and quantitative MethyLight technology, novel tumor-specific hypermethylation of KLK6 and KLK10 was identified in PCa. KLK10 DNA methylation was associated with pathological stage and longer time to biochemical recurrence in two independent cohorts of PCa patients. KLK6 hypermethylation was observed in normal-appearing prostate tissue adjacent to PCa, which could be indicative of the epigenetic field effect. Through the use of qPCR microRNA arrays a signature of 42 upregulated microRNAs predicted to target KLKs was identified in association with Gleason score (GS)8 vs. GS6, but no signature was found in correlation with biochemical recurrence. Among these, the association of increased miR-137 with increasing GS was established in an independent cohort. Notably, expression of miR-137, predicted to target KLK10, was inversely correlated to KLK10 hypermethylation. The emerging independent clinical significance of clinicopathologic entities such as intraductal carcinoma (IDC) and carcinoma with cribriform architecture in PCa prognosis was further explored by investigating DNA hypermethylation alterations of selected candidate genes including KLK10 in association with these clinicopathologic entities. Although KLK10 methylation did not correlate with either IDC or cribriform architecture, the previously discovered methylation of APC, RASSF1A and TBX15 was significantly linked to these features in PCa. Further, the presence of large cribriform architecture or HOXD3 hypermethylation was a strong independent predictor of biochemical recurrence. Thus, this thesis presents a panel of methylated genes that demonstrated promising prognostic performance and investigated their role in the etiology of PCa. Accordingly, a novel multiplex MethyLight assay was developed for simultaneous analysis of three methylated genes with potential applications in research and clinical settings.

Keywords: Biomarkers
DNA methylation
Kallikrein-related peptidases
MicroRNA
Multiplex qPCR
Prostate cancer
Advisor: Bapat, Bharati
Infection-mediated Modulation of Drug Transporters in Pregnancy; Implications for Fetal Drug Exposure

Inflammation-mediated changes in the expression and activity of ABC drug-efflux transporters have been shown to alter disposition of their substrates. While ABC transporters play an important role in placenta by limiting transplacental transfer of xenobiotics, little is known about the impact of inflammatory stimuli on these transporters during pregnancy. Using animal models, we investigated the impact of infection-induced acute inflammation on the expression of P-GP (ABCB1), BCRP (ABCG2) and MRP1-3 (ABCC1-3) efflux transporters, as well as several OATP (SLCO) uptake transporters in livers and placentas of pregnant rats. We explored how changes in placental transporter levels impact fetal drug exposure. Our studies demonstrated that endotoxin and polyinosinic/polycytidylic acid [poly(I:C)] induce pro-inflammatory cytokine levels in plasma of pregnant rats and generally downregulate mRNA and protein expression of several important hepatic and placental drug uptake and efflux transporters. Moreover, these changes were associated with alterations in maternal and fetal drug disposition of clinically relevant substrates. Downregulation of Bcrp was associated with a pronounced increase in fetal accumulation of its substrate, glyburide in endotoxin-treated rats. Significantly increased maternal exposure to P-gp substrate, lopinavir was observed in poly(I:C)-treated rats, with evidence of altered placental transfer and fetal disposition. Additionally, bile acids, which are endogenous substrates of many affected hepatic transporters, were significantly increased in maternal plasma of poly(I:C)-treated rats. While the observed differences could also be attributed to inflammation-induced variability in drug metabolism and protein binding, our findings provide evidence that decreased expression of efflux transporters significantly contributes to modulation of materno-fetal transport and disposition. Lastly, translational studies utilizing human placenta demonstrated similar impact of infections on expression of drug transporters such as BCRP and OATP2B1, indicating the need for a closer clinical investigation of inflammation-mediated changes in transporter expression and the possible impact on maternal drug disposition and fetal drug exposure.

Keywords: Drug transporters
Fetal drug exposure
Infection
Inflammation
Placenta
Pregnancy
Advisor: Piquette-Miller, Micheline
Characterization of the Myc-JPO2 Transformation Axis in Medulloblastoma

MYCC over-expression and amplification is a hallmark of the most aggressive subtype of medulloblastoma, yet mechanisms by which Myc drives group 3 medulloblastoma pathogenesis remain unclear. Previously our lab discovered JPO2 as a novel Myc co-transforming protein that acts as a Myc transcriptional co-repressor of the potent tumour suppressor TSP-1. My thesis project investigated the hypothesis that the Myc-JPO2 signalling axis regulates cellular and molecular pathways important in medulloblastoma transformation. My thesis studies have demonstrated that TSP-1 has potent anti-metastatic effects in Myc-induced MB xenograft models, and also mediates chemo- and radio-sensitivity via down-regulation of PI3K signalling in MB cells. Significantly, treatment with pharmacologic TSP-1 peptidomimetic, ABT-898, induces apoptosis in two murine models of Myc-driven group 3 MB. My studies demonstrated that ectopic expression of JPO2 also directly induces formation of metastatic and infiltrative MB phenotype in part by augmenting PI3K/AKT signalling via interaction with LEDGF/p75, a pro-survival and pro-migratory oncoprotein in MB. My aggregate findings identify JPO2 as an important modulator of the pro-metastatic Myc-P13K/AKT signalling pathway in MB and indicate TSP-1 mediated suppression of the Myc-JPO2-PI3K signalling axis as an attractive therapeutic approach to target metastatic MB.

Keywords: brain tumour
JPO2
medulloblastoma
metastasis
Myc
Advisor: Huang, Annie
Conjugated Polymer Nanostructures and Supercapacitors

Controlling the nanostructure of conjugated polymers is essential for their application to functional materials. In Part 1 of this work, I present two novel methods for controlling conjugated polymer nanostructure using electrochemical polymerization in hard templates. First, we report the synthesis and characterization of a series of nanostructures and propose a mechanism whereby morphology changes as a function of building block. We show how side-chain hydrophobicity can be used to prepare nanostructures with a geometry that is different from the shape of the template. Hydrophobic side-chains result in collapsed, nonlinear, and nonrigid shapes, while hydrophilic side-chains lead to linear nanostructures. Second, I present a study of the morphology of polythiophene nanostructures synthesized in different solvent/electrolyte systems. We find that the wall thickness of such nanostructures is greatly influenced by the choice of solvent/electrolyte, which affects the rate of polymerization. Solvent/electrolyte systems that increase the rate of thiophene polymerization yield solid nanowires, whereas systems that decrease the rate of polymerization yield thin-wall nanotubes. A solvent/electrolyte system that leads to an intermediate polymerization rate yields thick wall nanotubes. The results in Part 1 open new opportunities for preparing nanostructures with greater complexity, functionality, and distinct optical properties. Conjugated polymers that can store both a positive and negative charge can function as both the positive and negative charge storage material in a supercapacitor device, however few have been explored for this application. In part 2, I describe the synthesis of several monomers and their electrodeposited polymer electrodes. First, using different donor-acceptor molecular structures we examine the effect of electron acceptor concentration and show that device stability is improved significantly by increasing the acceptor concentration. Supercapacitors with specific energy and power of 11 Wh/kg (at 0.5 A/g) and 20 kW/kg (at 50 A/g with an energy of 3.6 Wh/kg) are reported. Further, we provide computational insight into the important chemical requirements for achieving even better performing supercapacitors. Working from these experimental and computational results, we selected thieno[3,4-b]pyrazines as a class of molecule to explore. Thieno[3,4-b]pyrazines form narrow band gap homopolymers, storing both positive and negative charge. Initial investigations into four poly(thieno[3,4-b]pyrazine)s as charge storage electrodes is presented.

Keywords: conducting polymer
conjugated polymer
energy storage
nanomaterial
nanotube
supercapacitor
Advisor: Seferos, Dwight S
Metal-chelating Polymers for Auger Electron Radioimmunotherapy

Radioimmunotherapy is a promising strategy for cancer treatment. The incorporation of metal-chelating polymers (MCPs) into radioimmunoconjugates (RICs) can increase the specific activities of RICs due to the multiple radioactive isotope binding sites provided by MCPs. This thesis describes the synthesis and characterization of a library of biotin end-capped MCPs (Bi-MCP). These Bi-MCP are designed to conjugate with the Fab fragment of trastuzumab modified with streptavidin (tmFab-SAv) and labeled with 111In, to form RICs. Trastuzumab has specific targeting ability towards human epidermal growth factor receptor-2 (HER2), which is overexpressed on certain types of breast cancer cells. 111In can generate Auger electrons which are able to induce the lethal cleavage of nuclear DNA. The strategy of labeling tmFab-SAv with Bi-MCP should enhance the number of 111In delivered per HER2 targeting event, and thereby increase the radiotoxicity delivered to the HER2+ cancer cells. Auger electrons have ultrashort tissue penetration ranges (

Keywords: Antibody
Antibody-Polymer conjugates
Metal-Chelating Polymers
Radioimmunotherapy
RAFT polymerization
Advisor: Winnik, Mitchell A
Polo-Like Kinase 4 (PLK4) Function in Cancer Progression

Invasion and metastasis are responsible for the majority of deaths from cancer, but the molecular mechanisms that facilitate execution of the metastatic cascade remain incompletely understood. One strategy is to identify genes that drive the metastatic process, and then target these drivers with biologic therapies in either the adjuvant or the metastatic setting. The polo family member polo-like kinase 4 (Plk4), is a serine-threonine kinase that is most highly expressed at the centrosome, where it is a master regulator of centriole duplication. Emerging evidence suggests that increased Plk4 levels in established malignancy may promote tumour progression; high levels of Plk4 expression have been reported in many tumour types, including breast, colorectal and pancreas, and its overexpression has been linked with resistance to therapy and death from cancer. While the critical role played by Plk4 in centriolar biogenesis is well-acknowledged, we recently discovered a novel and unexpected localization of Plk4 to the edges of lamellipodia and filopodia of motile cells, and identified a gene expression pattern predictive of reduced motility in Plk4+/- murine embryonic fibroblasts. I functionally validated this prediction in cancer cells, showing enhancement by Plk4 of cancer cell migration and invasion in vitro, and of MDA-MB-231 human breast cancer xenograft progression. Furthermore, this Plk4-driven invasive phenotype correlates with acquisition of an epithelial-to-mesenchymal transition (EMT) profile, cell polarity, spreading and enhanced directional protrusion formation. Investigation of pathways upstream of actin polymerization revealed that Plk4 regulates activation of the motility-related RhoGTPase Cdc42, and others have demonstrated that Plk4 promotes Rac1 activation, however this was insufficient for Plk4-induced motility in our system. In a BioID screen for Plk4 interactors, members of the Arp2/3 complex were identified, and I confirmed a novel physical and functional interaction between Plk4 and Arp2 in mediating Plk4-driven cancer cell movement. The interaction is mediated through the Plk4 PB1-PB2 domain, and results in phosphorylation of Arp2 at the T237/T238 activation site. These results provide a further rationale for application of targeted anti-Plk4 therapy in the clinical treatment of cancer patients, and reveal a new role for Plk4 in regulating Arp2/3-mediated actin cytoskeletal rearrangement.

Keywords: Arp2/3
BioID
Cancer Progression
Invasion and Metastasis
Plk4
Plk4 inhibitor
Advisor: Swallow, Carol J.
First Hospitality for Educability: An Ethical, Epistemological, and Political Symbiotic Relationship

The major aim of the thesis is to inquire into the human problem of the exclusion and marginalization of 'the other' from a philosophical and historical perspective. The problem arises from a modern conceptual paradigm in which 'the other' is not engaged with. The modern paradigm was influenced by the rise of nationalism, imperialism and colonialism, as well as neo-Cartesian philosophy in which the self constructs his or her thinking on a non-relational process with the other since the emphasis is on the self. Traditionally in philosophy, the notion of 'first philosophy' was based on metaphysics (as in the case of Aristotle), or epistemology (as in the case of Descartes). The thesis argues that the problem of exclusion is intrinsically linked to the lack of a first philosophy that is based on a symbiotic relationship between ethics, epistemology and politics. Utilizing and building on the work of Hannah Arendt, Emanuel Levinas, Jacques Derrida, and Zygmunt Bauman the thesis develops an original argument for the centrality of the engagement with 'the other', a conception of 'first philosophy' based on ethics, epistemology and politics, and the formulation of 'first hospitality' for educability. To concretize the development of the philosophical argument developed in the thesis, the historical happening of the Holocaust is utilized as a hermeneutic for modernity through which the construct of 'first hospitality' emerges as an educable response to the problem of exclusion. The thesis ends with concrete and practical implications for education based on the argument of the thesis as well as the critique of the popular discourse in education on inclusion. From a practical perspective, the thesis offers the notion of 'welcoming education' that is based on 'the other' as agent, as a democratic alternative to inclusion.

Keywords: Democracy
Diversity
Education
Hospitality
Inclusion
Leadership
Advisor: Portelli, John P
Informal Learning with Technology: A Narrative of Self-determined Learning

Much education is formalized and revolves around satisfying an externally mandated curriculum. Informal, self-determined learning allows individuals to select a more democratic learner-centered approach to education; one that may matter more to the learner than to any other external person or institution. The underlying premise of this research is that informal, self-determined learning through technology is capable of opening up different avenues of learning. Through a narrative methodology and a conceptual framework identified as Full Access Learning (FUAL), learning â and education in general â is opened up and personalized in different ways, informally and often with technology. Examples of self-determined learning with technology are explored, including the author's own lived experience of constructing learning through digital and informal means. Such self-determined and informal learning, through FUAL, can prove to be a space where diverse and personal educational initiatives are encouraged and modernized in an effort to synchronize with the current societal technological norms of the 21st century. A broader goal of this research, however, is to provide further evidence for learners who may not connect well with more formal and traditional learning approaches, such as schooling, and to add to the argument that different ways of learning can help individuals thrive. Learning that is personal and meaningful can create individual growth opportunities. What transpires from personal growth can have multiple ripple effects. As technology continues to evolve and becomes more ubiquitous, different ways of learning can occur. The challenge is to discover and engage in multiple ways of self-determined learning, as each learner determines appropriate.

Keywords: educational technology
informal learning
internal curriculum
self-determined learning
self-directed learning
self-paced
Advisor: Cooper, Karyn
B Cell Dynamics within the Bone Marrow Microenvironment: Comparisons of Inflammation and Steady State

For adult mice and humans the bone marrow is of critical importance in the generation and function of B lymphocytes. It is here that B cells are born from early hematopoietic progenitors; and where the first selection checkpoints occur to enforce central tolerance. Moreover, the bone marrow exhibits characteristics reminiscent of a secondary lymphoid organ, providing a home for a large population of recirculating mature B cells; these cells are capable of mounting rapid immune responses against blood borne pathogens, in situ. The bone marrowâ s ability to support these diverse functions is highly dependent on its organized structure and complex microenvironment. Multiple cell types and soluble cytokines are involved in regulating hematopoietic and immunological activities and the characterization of these factors remains an active area of research. However, peripheral signals, such as inflammation, are capable of modulating the bone marrow microenvironment with a dramatic effect on B cells. Herein, data is presented detailing how acute peritoneal inflammation and breast cancer can each alter the bone marrow environment to shape the B cell compartment. Further, experiments are described that suggest a role for basophils in aiding immature B cell survival and maturation in steady state and inflammation. Together these findings characterize novel environmental components important in B cell development and highlight the exquisite sensitivity of the bone marrow organ to peripheral cues.

Keywords: B cells
Bone Marrow
Breast Cancer
Cancer
Lymphopoiesis
PyMT
Advisor: Paige, Christopher J
Functional Linear Regression in High Dimensions

Functional linear regression has occupied a central position in the area of functional data analysis, and attracted substantial research attention in the past decade. With increasingly complex data of this type collected in modern experiments, we conduct further investigations in response to the great need of statistical tools that are capable of handling functional objects in high-dimensional spaces. In the first project, we deal with the situation that functional and non-functional data are encountered simultaneously when observations are sampled from random processes and a potentially large number of scalar covariates. It is difficult to apply existing methods for model selection and estimation. We propose a new class of partially functional linear models to characterize the regression between a scalar response and those covariates, including both functional and scalar types. The new approach provides a unified and flexible framework to simultaneously take into account multiple functional and ultra-high dimensional scalar predictors, identify important features and improve interpretability of the estimators. The underlying processes of the functional predictors are considered to be infinite-dimensional, and one of our contributions is to characterize the impact of regularization on the resulting estimators. We establish consistency and oracle properties under mild conditions, illustrate the performance of the proposed method with simulation studies, and apply it to air pollution data. In the second project, we further explore the linear regression by focusing on the large-scale scenario that the scalar response is related to potentially an ultra-large number of functional predictors, leading to a more challenging model framework. The emphasis of our investigation is to establish valid testing procedures for general hypothesis on an arbitrary subset of regression coefficient functions. Specifically, we exploit the techniques developed for post-regularization inference, and propose a score test for the large-scale functional linear regression based on the so-called de-correlated score function that separates the primary and nuisance parameters in functional spaces. The proposed score test is shown uniformly convergent to the prescribed significance, and its finite sample performance is illustrated via simulation studies.

Keywords: decorrelated score function
estimation consistency
FPCA
multiplier bootstrap
nonconvex penalty
oracle property
Advisor: Yao, Fang
Vexatio Falsorum Fratrum: The Medieval Laybrother in the Order of Sempringham in Context

This dissertation examines the laybrothers and laysisters of the Order of Sempringham, otherwise known as the Gilbertines, after their founder, Gilbert of Sempringham, and with a particular emphasis on their revolt that took place in the middle of the twelfth century. The view of the revolt is entirely one-sided in historiography, and in this dissertation I ask how it should be perceived and suggest a very different take on the matter. In order to provide context to the revolt and its aftermath, it is necessary to examine both the institution of laybrotherhood and the Order of Sempringham in closer detail. In the first chapter I study the historiography concerning when and how laybrothers arose (and eventually declined to much reduced numbers) as an institution and the various ways in which the laybrothers in general have been defined. In the second chapter I introduce the Gilbertine primary sources and discuss the history of the Order of Sempringham. My third chapter concentrates on the Gilbertine laybrothers' revolt itself in context and fourth on the reputation incurred by laybrothers both generally as as institution in the Middle Ages and more specifically, those involved in the Gilbertine revolt. My fifth chapter considers the daily life of Gilbertine laybrothers and laysisters as a consequence of the revolt and suggests why no laysisters were involved in the revolt. Overall, this dissertation shows that the Gilbertine laybrothers had good reasons for their revolt, and that rather than being rebuked and reviled, they ought to be listened to for attempting to deal with what they perceived as problems within the order. More generally, it is my opinion that medieval laybrothers have been unfairly portrayed, and this dissertation is in part an attempt to rectify that situation.

Keywords: Gilbertine
Laybrothers
Laysisters
Sempringham
Advisor: Cochelin, Isabelle