VictorJuiz/thesis huggingface dataset:
Genomic DNA Copy Number Variations and Cancer: Studies of Li-Fraumeni Syndrome and its Variants
Keywords: Cancer
Genomics
Copy number variations
Copy number variants
Li-Fraumeni syndrome
p53
TP53

Copy number variations (CNVs) are a major source of inter-individual genetic difference, accounting for a greater proportion of the human genome than other forms of variation. Recently, the identification of benign and pathogenic CNVs has improved due to arrays with increased coverage. Nevertheless, most CNVs have not been studied with great precision and questions persist regarding their exact breakpoint, gene content, frequency and functional impact. This is especially true in cancer, in which a role for CNVs as risk factors is under-explored. Li-Fraumeni syndrome (LFS) is a dominantly inherited disorder with an increased risk of early-onset breast cancer, sarcomas, brain tumors and other neoplasms in individuals harboring germline TP53 mutations. Known genetic determinants of LFS do not fully explain its clinical phenotype. In this thesis we describe the association between CNVs and LFS. First, by examining DNA from a healthy population and an LFS cohort using oligonucleotide arrays, we show that the number of CNVs per genome is well conserved in the healthy population, but remarkably enriched in these cancer-prone individuals. We found a significant increase in CNVs among carriers of germline TP53 mutations with a familial cancer history. Second, we find that ii specific CNVs at 17p13.1 are associated with LFS or developmental delay, depending on the exact breakpoint with respect to TP53. Using a purpose built array with 93.75% accuracy, we fine-mapped these microdeletions and find that they arise by Alu-mediated non-allelic homologous recombination, and contain common genes, whose under-expression distinguishes the two phenotypes. Third, we explore somatic CNVs in choroid plexus carcinoma tumor genomes. We show that this tumor is over-represented in LFS, and the number of somatic CNVs is associated with TP53 mutations and disease progression. These studies represent the first genomic analyses of LFS, and suggest a more generalized association between CNVs and cancer.
A Complexity Analysis of Noise-like Activity in the Nervous System and its Application to Brain State Classification and Identification in Epilepsy
Keywords: Noise-like activity
Brain
Complexity
Hippocampus
Signal analysis
Membrane potential
Electrophysiology
Network dynamics
Phase synchrony
Nonlinear dynamics
Fractal

Complexity lies halfway between stochasticity and determinism, suggesting that brain activity is neither fully random nor fully predictable but lives by the rules of nonlinear high- and low-complexity dynamics. One important aspect of brain function is noise-like activity (NLA), defined as background, electrical potential fluctuations in the nervous system distinct from spiking rhythms in the foreground. The objective of this thesis was to investigate the neurodynamical complexity of NLA recorded at the cellular and local network scales in in vitro preparations of mouse and human hippocampal tissue, under healthy and epileptiform conditions. In particular, it was found that neuronal NLA arises out of the physiological contributions of gap junctions and chemical synaptic channels and is characterized by a spectrum of complexity, ranging from high- to low-complexity, that was measured using methods from nonlinear dynamical systems theory. Importantly, the complexity of background, neuronal NLA was shown to depend on the degree of cellular interconnectivity to the surrounding local network. In addition, the complexity and multifractality of NLA was further studied at the cellular and local network scales in epileptiform transitions to seizure-like events, identifying emergent low-complexity and reduced multifractality (bordering on monofractal-type dynamics) in the pathological ictal state. Finally, dual intracellular recordings of hippocampal epileptiform activity were analyzed to measure NLA synchronicity, showing evidence for increased same- and cross-frequency correlations and increased phase synchronization in the pathological ictal state. Convergence towards increased phase synchrony manifested in lower frequency regions including theta (4-10 Hz) and beta (12-30 Hz), but also in higher frequency bands (gamma, 30-80 Hz). In summary, there is evidence to suggest that background NLA captures important neurodynamical information pertinent to the classification and identification of brain state transitions in healthy and epileptiform hippocampal dynamics, using sophisticated neuroengineering analyses of these physiological signals.
Assessment of Missense Alterations in MLH1 and their Pathogenic Significance
Keywords: Mismatch Repair
DNA repair
Cancer
Colorectal cancer
Cancer Genetics
unclassified variant
DNA alterations
Lynch syndrome

Germline mutations in mismatch repair genes predispose individuals to Lynch Syndrome, the most common colorectal cancer predisposition syndrome. MLH1 is a key mismatch repair gene that is mutated in Lynch syndrome and about a third of the genetic alterations identified in MLH1 are missense variants of unclassified clinical significance. We hypothesize that missense alterations in distinct domains of MLH1 likely affect its expression and function(s) to varying degrees. To address this we utilized several approaches to investigate the molecular basis of the pathogenicity of a panel of unclassified variants. Our results demonstrate that the MLH1 variants p.R265C and p.K618A significantly decrease the stability of the MLH1 protein, while the variant p.L749Q compromises heterodimerization of the MLH1-PMS2 complex. Given the limitations and complexity of in vitro assessment strategies, we conducted a proof-of-principle study to investigate whether missense variants in MLH1 lead to allelic imbalances at the transcriptional level. Our analysis using the PeakPicker software indicated that the missense variants c.350C>T, c.793C>T, c.1852_1853AA>GC, as well as the truncating variant c.1528C>T were associated with significantly unbalanced allelic expression. This illustrates a novel method of investigating the pathogenicity of unclassified genetic variants, which has the potential to be applied in the diagnostic setting. Previous genetic epidemiology studies from our laboratory have demonstrated that the MLH1 c.-93G>A promoter variant is strongly associated with the microsatellite instability phenotype in colorectal tumours. Additionally, this promoter variant was associated with an elevated risk of endometrial cancer in case-control studies. Results from our functional studies indicate that the c.-93G>A variant significantly alters the promoter activity of MLH1. The MLH1 promoter is bi-directional with the EPM2AIP1 gene located on the antisense strand. Interestingly, we observed that this variant significantly affected EPM2AIP1 transcription as well. Furthermore, our experiments suggest that c.-93G>A variant affects transcription by altering the affinity of nuclear factors that bind this region. Combined, these findings shed light on the possible mechanisms by which missense variants affect MLH1 expression and function, which in conjunction with results from other functional assays will help increase the accuracy and efficiency of genetic testing of inherited cancers.
Manipulating the Mechanical Microenvironment: Microdevices for High-throughput Studies in Cellular Mechanobiology
Keywords: Microdevices
Cellular Mechanobiology
Microfabrication
Mechanical stimulation
High-throughput screening
Bioreactors

Determining how biological cells respond to external factors in the environment can aid in understanding disease progression, lead to rational design strategies for tissue engineering, and contribute to understanding fundamental mechanisms of cellular function. Dynamic mechanical forces exist in vivo and are known to alter cellular response to other stimuli. However, identifying the roles multiple external factors play in regulating cell fate and function is currently impractical, as experimental techniques to mechanically stimulate cells in culture are severely limited in throughput. Hence, determining cell response to combinations of mechanical and biological factors is technically limited. In this thesis, microfabricated systems were designed, implemented and characterized to screen for the effects of mechanical stimulation in a high-throughput manner. Realizing these systems required the development of a fabrication process for precisely-aligned multilayer microstructures, and the development of a method to integrate non-traditional and clinically-relevant biomaterials into the microfabrication process. Three microfabricated platforms were developed for this application. First, an array was designed for experiments with high mechanical throughput, in which cells cultured on a surface experience a range of cyclic, uniform, equibiaxial strains. Using this array, a novel time- and strain-dependent mechanism regulating nuclear β-catenin accumulation in valve interstitial cells was identified. Second, a simpler system was designed to screen for the effects of combinatorially manipulated mechanobiological parameters on the pathological differentiation of valve interstitial cells. The results demonstrate functional heterogeneity between cells isolated from different regions of the heart valve leaflet. Last, a microfabricated platform was developed for high-throughput mechanical stimulation of cells encapsulated in a three-dimensional biomaterial, enabling the study of mechanical forces on cells in a more physiologically relevant microenvironment. Overall, these studies identified novel biological phenomena as a result of designing higher-throughput systems for the mechanical stimulation of cells.
Shiga-like Toxin 1: Molecular Mechanism of Toxicity and Discovery of Inhibitors
Keywords: ribosome inactivating protein
toxin
ribosomal stalk
proteomics

Ribosome-inactivating proteins (RIPs) such as Shiga-like toxin 1 (SLT-1) halt protein synthesis in eukaryotic cells by depurinating a single adenine base in the sarcin-ricin loop of 28S rRNA. The molecular details involved in the ER lumenal escape and subsequent site-specific depurination are lacking, despite a general understanding of the biochemical basis of SLT-1 toxicity. Using a combination of yeast-2-hybrid and HeLa lysate pull-down followed by LC-MS/MS we have discovered yeast and human proteins that interact with the catalytic A1 chain of SLT-1. Yeast-2-hybrid library screens followed by the expression of full-length protein candidates and pull-down experiments yielded Cue2 as the only yeast cellular component that binds to the SLT-1 A1 chain. Further truncational analysis revealed that the known protein domains (two Cue domains and a Smr domain) within the primary sequence of Cue 2 were not essential for the interaction. Cue2 is a yeast monoubiquitin binding protein of no known function that is structurally homologous to the human ubiquitin-associated domain which has been implicated in intracellular routing and ER-associated degradation. Pull-down experiments indicated that the mechanism by which the catalytic domain of RIPs cleaves its substrate involves initial docking interactions with the ribosomal stalk by virtue of a conserved acidic C-terminal peptide domain common to all three stalk proteins P0, P1, and P2. The A1 chain of SLT-1 transiently binds to this peptide with a modest binding constant and rapid on and off rates. Mutagenesis of charged residues within the A1 chain identified a cationic surface that interacts with the peptide motif. In addition, phage-display was used to rapidly probe the importance of each residue within this C-terminal ribosomal peptide. The analysis revealed a complementary acidic surface and an additional hydrophobic motif involved in the interaction. Moreover, deletion mutagenesis performed on the ribosomal protein P0 revealed that the A1 chain binds to an alternate site on P0 in proximity to the contact sites for P1/P2 heterodimers. These results demonstrate that the catalytic chain of RIPs such as SLT-1 dock on ribosomes using two classes of binding sites located within the ribosomal stalk which may aid in orienting their catalytic domain in close proximity to the depurination site.
The Role of PIDD in Apoptosis and Innate Antiviral Immunity
Keywords: PIDD
apoptosis
Innate antiviral immunity
caspase-2
death domain
leucine-rich repeats

PIDD has previously been described as a death domain (DD)-containing protein that is inducible upon p53 activation and plays a role in programmed cell death. It has previously been shown that PIDD interacts with RAIDD (RIP-associated ICE/CED3 homologous protein with a death domain) in a cytoplasmic complex known as the PIDDosome, which results in the activation of capsase-2 and ultimately in cell death in response to DNA damage. Despite earlier studies on PIDD, however, the physiological role of PIDD has not been elucidated. Thus, we have generated PIDD-deficient mice and examined its in vivo functions particularly in cell death and in antiviral innate immunity. The first major aim of the thesis is to determine whether or not PIDD is required in cell death. PIDD mice are developmentally normal and do not display a pronounced phenotype. Surprisingly, PIDD deficiency perturbed neither DNA damage-induced nor stress-induced cell death in a variety of cell types, suggesting that PIDD may not play a critical role in cell death. In addition, caspase-2 processing occurred normally in the absence of PIDD in response to ionizing irradiation or etoposide treatment, indicating that PIDD is dispensable in the cleavage of caspase-2. The second major aim is to examine the role of PIDD and RAIDD in LCMV-induced innate immunity. To study the role of PIDD and RAIDD in antiviral immune responses, I have generated PIDD/RAIDD double-deficient mice and challenged them with lymphocytic choriomeningitis virus (LCMV). Interestingly, I observed that ablation of both PIDD and RAIDD together resulted in defective viral clearance in the spleen, but not in other organs including the lung, liver, and kidney. In addition, the production of type I IFN was also decreased in the mice deficient in both PIDD and RAIDD. However, the cytotoxicity of the T lymphocytes was largely intact in the absence of both PIDD and RAIDD. Collectively, our results suggest that PIDD is dispensable in cell death, yet PIDD and RAIDD together have a synergistic effect in LCMV-induced antiviral innate immunity. The findings presented in this thesis provide a better understanding of the physiological role of PIDD and may ultimately contribute to the novel therapeutic strategies for the proper control of viral infection.
Machine Learning Algorithms for Geometry Processing by Example
Keywords: geometry processing
learning
segmentation
labeling
illustration
hatching
line drawing
curvature
machine learning
geometry processing by example
non-photorealistic rendering
artistic rendering

This thesis proposes machine learning algorithms for processing geometry by example. Each algorithm takes as input a collection of shapes along with exemplar values of target properties related to shape processing tasks. The goal of the algorithms is to output a function that maps from the shape data to the target properties. The learned functions can be applied to novel input shape data in order to synthesize the target properties with style similar to the training examples. Learning such functions is particularly useful for two different types of geometry processing problems. The first type of problems involves learning functions that map to target properties required for shape interpretation and understanding. The second type of problems involves learning functions that map to geometric attributes of animated shapes required for real-time rendering of dynamic scenes. With respect to the first type of problems involving shape interpretation and understanding, I demonstrate learning for shape segmentation and line illustration. For shape segmentation, the algorithms learn functions of shape data in order to perform segmentation and recognition of parts in 3D meshes simultaneously. This is in contrast to existing mesh segmentation methods that attempt segmentation without recognition based only on low-level geometric cues. The proposed method does not require any manual parameter tuning and achieves significant improvements in results over the state-of-the-art. For line illustration, the algorithms learn functions from shape and shading data to hatching properties, given a single exemplar line illustration of a shape. Learning models of such artistic-based properties is extremely challenging, since hatching exhibits significant complexity as a network of overlapping curves of varying orientation, thickness, density, as well as considerable stylistic variation. In contrast to existing algorithms that are hand-tuned or hand-designed from insight and intuition, the proposed technique offers a largely automated and potentially natural workflow for artists. With respect to the second type of problems involving fast computations of geometric attributes in dynamic scenes, I demonstrate algorithms for learning functions of shape animation parameters that specifically aim at taking advantage of the spatial and temporal coherence in the attribute data. As a result, the learned mappings can be evaluated very efficiently during runtime. This is especially useful when traditional geometric computations are too expensive to re-estimate the shape attributes at each frame. I apply such algorithms to efficiently compute curvature and high-order derivatives of animated surfaces. As a result, curvature-dependent tasks, such as line drawing, which could be previously performed only offline for animated scenes, can now be executed in real-time on modern CPU hardware.
High-Throughput Screening for Novel Anti-cancer Radiosensitizers for Head and Neck Cancer
Keywords: Head and neck cancer
Radiation therapy
High-throughput screens
Experimental therapeutics

Despite advances in therapeutic options for head and neck cancer (HNC), treatment-associated toxicities and overall clinical outcomes have remained disappointing. Even with radiation therapy (RT), which remains the primary curative modality for HNC, the most effective regimens achieve local control rates of 45-55%, with disease-free survival rates of only 30-40%. Thus, the development of novel strategies to enhance tumor cell killing, while minimizing damage to the surrounding normal tissues, is critical for improving cure rates with RT. Accordingly, we sought to identify novel radiosensitizing therapies for HNC, exploiting a high-throughput screening (HTS) approach. Initially, a cell-based phenotype-driven HTS of ~2,000 commercially available natural products was conducted, utilizing the short-term MTS cell viability assay. Cetrimonium bromide (CTAB) was identified as a novel anti-cancer agent, exhibiting in vitro and in vivo efficacy against several HNC models, with minimal effects on normal fibroblasts. Two major limitations of our findings, however, were that CTAB did not synergize with radiation, nor was its precise cellular target(s) elucidated. Consequently, an alternative strategy was proposed involving a target-driven RNAi-based HTS. Since the colony formation assay (CFA) is the gold standard for measuring cellular effects of radiation in vitro, an automated high-throughput colony-formation read-out was developed as a more appropriate end-point for radiosensitivity. Although successful as a tool for the discovery of potent anti-cancer cytotoxics, a technical drawback was its limited dynamic range. Thus, the BrdU incorporation assay, which measures replicative DNA synthesis and is a viable CFA alternative, was employed. From an RNAi-based screen of ~7000 human genes, uroporphyrinogen decarboxylase (UROD), a key regulator of heme biosynthesis, was identified as a novel tumor-selective radiosensitizing target against HNC in vitro and in vivo. Radiosensitization appeared to be mediated via tumor-selective enhancement of oxidative stress from perturbation of iron homeostasis and increased ROS production. UROD was significantly over-expressed in HNC patient biopsies, wherein lower pre-RT UROD levels correlated with improved disease-free survival, suggesting that UROD expression could also be a potential predictor for radiation response. Thus, employing a HTS approach, this thesis identified two novel therapeutic strategies with clinical potential in the management of HNC.
Molecular Mechanisms Involved in the Regulation of Circadian Clock Gene and Neuropeptide Transcription: Influence of Palmitate
Keywords: neuroendocrinology
circadian rhythms
hypothalamus
neuropeptides

Canadians live in a society where the sun does not dictate the workday. Our lifestyles must shift to cater to the 24-hour demands of a fast paced global community. As a result our circadian rhythms are altered, leading to dysregulation of key physiological processes responsible for the maintenance of essential functions like energy homeostasis. Energy homeostasis is controlled by neuropeptide-expressing neurons within the hypothalamus. These neurons are affected by circulating hormone and nutrient levels in addition to their endogenous molecular clock machinery that controls cellular processes. Therefore, hypotheses were generated that non-SCN hypothalamic neurons express orexigenic neuropeptides in a rhythmic fashion without external influence from the SCN as a result of internal rhythmicity; and that elevated concentrations of palmitate, a ubiquitous saturated FFA common in a high fat diet, have direct influence on the mRNA levels of circadian clock components Bmal1, Clock, Per2, Rev-erbα and the potent orexigenic neuropeptides NPY, AgRP and ppGhrelin through mechanisms related to HAT, SIRT1 and AMPK. Using the mHypoE-44 neurons, a well characterized cell line that expresses the molecular clock and specific neuropeptides these hypotheses were explored in four studies. Neuropeptide expression within the mHypoE-44 neurons was determined to be rhythmic. NPY and NT demonstrate significant 24-hour rhythms. CRH and ppGhrelin mRNA cycled significantly in an ultradian fashion, oscillating approximately every 18 h. AgRP mRNA did not show a significant rhythm. We identified rhythmic binding of BMAL1 to the NPY promoter, suggesting clock-mediated control of neuropeptide expression. Bmal1 and Clock mRNA levels were elevated with palmitate, whereas Per2 and Rev-erbα mRNA showed significant decreases following palmitate treatment. Palmitate increased the acetylation of both BMAL1 and PER2 proteins. Alteration of AMPK activity altered the mRNA levels of all clock genes assayed and AMPK activation diminished the palmitate-induced changes in Bmal1 mRNA. Palmitate significantly elevated both NPY and ppGhrelin mRNA levels. Chemical modifiers that decrease acetylation altered these systems. AMPK activation reduced the palmitate-induced changes in NPY mRNA levels. These findings demonstrate that non-SCN neurons have rhythmic neuropeptide transcript levels. This thesis elucidates a direct effect of palmitate on the molecular clock and neuropeptide expression at the level of the hypothalamic neuron; and these findings highlight a role for HAT/SIRT1 activation and AMPK in these important processes, which ultimately contribute to the understanding of circadian dysregulation and energy balance.