Browsing by Author "Yang, Guang"
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- ItemOpen AccessAugmenting Genomic Applications Through Simulation and Machine Learning-based Parameter Optimization(2020-04-03) Li, Minghao; Long, Quan; Yang, Guang; De Koning, A. P. Jason; Rancourt, Derrick E.Certain methods for genomic analyses do not take advantage of the full extent of available biological context to address limited sample sizes. Another noted issue is the gulf in bioinformatics software performance between tool authors and end-users. This project explores two cases where genomic applications can be augmented: power estimations for low-prevalence condition studies and haplotype reconstruction. Power is a key statistic for predicting the success of genomic sequencing projects. Low-prevalence conditions are not amenable for usage with existing power estimation frameworks designed for common conditions and consequently will appear underpowered. SimPEL is a tool for simulation-based power estimation for sequencing studies of low-prevalence conditions. It meets an unmet need in the field and augments power estimation through the inclusion of unused genomic aspects of low-prevalence conditions. Elements of low-prevalence condition studies are input into SimPEL and a simulated cohort is applied to calculate the likelihood of identifying the true causal gene(s). SimPEL demonstrates competitive performance on single causal gene conditions and viable performance in instances of heterogeneity. PoolHapX is a haplotype reconstruction tool capable of reconstructing haplotypes and their corresponding frequencies from mixed populations. Its extensive parameter set is laborious to optimize by hand when applied toward unknown use-cases. Pattern recognition algorithms allow for the delegation of this parameter tuning process to machine learning. SLiM, an evolutionary simulation framework, provides the biological basis for the haplotype reconstruction task. Stochastic simulation of PoolHapX parameter values within a defined space generates the large-scale datasets required for supervised learning. Mapping genomic sequencing features to an optimal PoolHapX parameter set is a multi-task learning problem. A novel two-model scaffold has been designed to address this. A gradient boosted decision tree model, mapping PoolHapX parameter sets to a quantitative performance metric, is nested as the cost function of a multi-head feedforward neural network, which in turn takes an input set of summary statistics from aligned genomic data and outputs PoolHapX parameters. Hyperparameter tuning is enabled by Bayesian optimization techniques. This workflow and framework is parallely extendable toward any PoolHapX extension in the future.
- ItemOpen AccessCharacterization of the fifth member of the potassium-dependent sodium/calcium exchanger family - nckx5(2007) Yang, Guang; Lytton, Jonathan
- ItemOpen AccessCsde1, an RNA Binding Protein, Modulates Neuronal Subtype Specification(2021-09-20) Harvey, Emily M.; Yang, Guang; Huang, Peng; Kurrasch, DeborahNeuronal diversity is the root of complex function in the cerebral cortex. During cortical development, neural stem cells give rise to neurons. Neurons are a diverse cell type and can be grouped into many subtypes, each with distinct functional identities. Neurogenesis and neuronal subtype specification are carefully regulated, both temporally and spatially, by programmed gene expression. One mechanism controlling gene expression is translational regulation, which alters levels of protein synthesis. Translational regulation orchestrated by RNA binding proteins allows dynamic alterations in protein expression. Here I determine that Cold-shock domain containing E1 (Csde1), an RNA binding protein, regulates the specification of neuronal subtypes in the cerebral cortex. In the developing murine cortex, Csde1 is highly expressed in newborn neurons of the cortical plate during development. I show that reduced Csde1 expression alters neuronal subtype in the embryonic and post-natal cortex. Csde1 reduction disrupts the distribution of neuronal subtypes within the cortical plate. Additionally, reduced Csde1 expression increases mixed neuronal subtype identity. Together, this indicates that the specification of neuronal subtypes is subject to translational regulation, and that Csde1 activity is essential for specification of neurons in the cortex.
- ItemOpen AccessDefining the Role of Proneural Genes in Neurogenesis, Specification, and Migration of Mouse VMH Neurons(2020-01) Aslan Pour Kal Bolandi, Shaghayegh; Kurrasch-Orbaugh, Deborah M.; Childs, Sarah J.; Yang, GuangThe ventromedial hypothalamus (VMH) is a hypothalamic nucleus important for controlling satiety and reproductive behaviors, among other physiologies. Despite these important roles, the genetic programs driving VMH development are just starting to be explored. Since proneural genes are one of the key drivers of neurodevelopment throughout the brain, we asked whether the proneural genes Achaete-scute homolog 1 (Ascl1) and Neurogenin 2 (Neurog2) play key roles in VMH development, given their expression in VMH progenitors. My hypothesis is that proneural genes play a role in neurogenesis, cell fate decisions and/or in the migration of VMH neurons. To start, I investigated the role of Ascl1 in the specification and fate of VMH neurons. I showed that Ascl1+ lineages give rise to a large population of VMH neurons and that Ascl1 is necessary for promoting VMHDM and VMHC neuronal specification. In addition, my results revealed that Ascl1 played an important role in the timing of neurogenesis within the tuberal hypothalamus. Next, I examined the role of Neurog2 in the neurogenesis of VMH specific neurons and showed that Neurog2 was necessary for timely cell cycle exit and birth of VMH neurons. Moreover, I showed Neurog2 was required for proper development of the VMH at both early and late embryonic developmental stages. Neurog2 is particularly important for proper differentiation of VMHVL neurons. Finally, I studied the role of Ascl1 and Neurog2 in cell sorting within the maturing VMH. My results revealed that between E15.5 to E17.5 and in the absence of either Ascl1 or Neurog2, there is a change in the final positioning of cells. Since Ascl1 and Neurog2 can act through Rnd3 and Rnd2 proteins to regulate cortical neuronal migration, I asked whether Ascl1 and Neurog2 potentially employ a similar mechanism to regulate VMH cell sorting. My results showed both Rnd2 and Rnd3 were expressed within the VMH nucleus across VMH embryonic developmental stages. In addition, at later stages such as E15.5 and E19.5, the expression of both Rnd2 and Rnd3 was significantly decreased in the absence of Neurog2 and Ascl1 respectively. Finally, using a live cell imaging technique, I assayed neuronal movement during cell sorting events within the VMH. Together, these studies provide insight into the varying roles proneural genes play in the developing tuberal hypothalamus.
- ItemEmbargoDeveloping Statistical Models For Multi-Omics Data Integration And Data Mining To Reveal Genetic Basis Underlying Diseases(2023-10-03) Li, Qing; Long, Quan; Yan, Jun; Yang, Guang; Bousman, ChadAiming to assist in the discovery of the genetic basis of complex diseases, many researchers are generating multi-scale -omics data (such as genomes, transcriptomes, and proteomes) for joint analyses. However, despite the depth of sequencing, i.e., molecular information from a single individual could be massive, the sample size (number of individuals) for a particular study is usually small. As such, many researchers organize large consortiums to aggregate data into relatively larger biobanks for worldwide researchers to reuse. In parallel to the efforts towards enhancing sample size, in this thesis work, I developed advanced models by integrating domain knowledge seamlessly with modern machine learning (ML) techniques to further biological discoveries with high-dimensional data of moderate sample sizes. The core innovation in my thesis is to improve feature selection in statistical learning by leveraging biological a priori. Centralized by the general theme of knowledge-directed feature selection, my thesis has contributed four novel developments: In my first project, I developed Interaction-integrated Linear Mixed Model (ILMM), integrating three-dimensional (3D) genomic interaction information to pre-select genetic regions for the linear mixed model. This tool avoids the astronomic number of combinations usually encountered when searching for interactions genome wide. We showed ILMM is more powerful than established models and discovered a distal regulation mechanism underlying Autism. In my second project, I developed eXplainable Autoencoder for Critical genes (XA4C), which carries out gene selection from a unique angle: the gene’s ability to interpret hidden dimensions learned by an Autoencoder using gene expression data. This work coined the term “critical gene”, which is demonstrated to be more disease-relevant than conventional terms such as differentially expressed and hub genes in expression analysis. In my third project, on top of a state-of-the-art massive machine learning model integrating 5,313 human epigenetic and transcriptomic tracks of functional-omics data, I have developed a transfer learning framework to re-task the general comprehension model towards breast cancers. This framework allows effective feature selections for improved downstream analysis, such as association mapping, as we demonstrated using the breast cancer GWAS data. In my fourth project, which is more on in-depth data analysis instead of tool building, I integrated expression and protein data in a coherent fine-mapping framework to select candidate proteins that play an important role in disease pathogenesis, discovering 176 proteins for six cancers. These discoveries are valuable for understanding cancers and drug development. In summary, the works in this thesis delivered ML tools to integrate prior knowledge for feature selections to further biological discoveries and provided additional insights into genes and proteins underlying complex diseases.
- ItemOpen AccessThe Glyoxalase 1 – Methylglyoxal Pathway Regulates Neurite Development of Cerebral Cortical Neurons in the Mammalian Brain(2020-05) Mohammad, Lamees; Yang, Guang; Guo, Jiami; McFarlane, Sarah; Huang, Carol T.L.Newborn neurons of the mammalian cerebral cortex undergo substantial morphological changes during development. Neurite elongation and branching are crucial morphological changes in early neuronal development that are necessary for the formation of dendrites and axons – structural elements that allow neurons to communicate with each other and form circuits. One factor that has received little attention as a possible regulator of neurite development is metabolism. In this thesis, I show that methylglyoxal, an intermediate metabolite of glycolysis, and its metabolizing enzyme, glyoxalase 1 (Glo1) regulate the elongation and branching of neurites. Knockdown of Glo1 expression using short-hairpin RNA or inhibiting the enzymatic activity of Glo1 in cultured mouse cortical neurons reduces neurite length and impairs branching organization. Furthermore, I found that knockdown or inhibition of Glo1 activity perturbs development of both excitatory projection neurons and inhibitory interneurons. When neurons are treated with excessive methylglyoxal, morphological perturbation is recapitulated. These results suggest a link between methylglyoxal metabolism and neuronal development and provide the foundation for future studies of the molecular mechanisms that mediate this metabolic regulation.
- ItemOpen AccessHypoxia-induced Suppression of EGF/MAPK Signaling Delays Steroid-Dependent Maturation in Drosophila(2022-08) Turingan, Michael Jacobi; Grewal, Savraj; Childs, Sarah; Yang, Guang; Cobb, JohnFor proper animal development, tissues and organs require sufficient oxygen; defects in oxygen supply (hypoxia) can cause developmental disorders(1). In humans, disrupted oxygen supply underlies many diseases(2). Although tissue-culture studies have revealed much about adaptation to hypoxia at the cellular level(3 4), less is known of what mediates whole-body responses. My research employs Drosophila to study how hypoxia affects development at the organismal level. Drosophila larvae have evolved to grow on decaying food – an environment of low ambient oxygen(5–8). Hence, they provide a good genetic model to study how hypoxia influences physiology and development. In the lab, larvae exposed to hypoxia (5% O2) adapt by reducing their growth and delaying development to the pupal stage. However, the molecular bases for these adaptations remain unclear. The larval-pupal developmental transition is controlled by a neuroendocrine pathway involving the prothoracic gland (PG), an endocrine organ that produces the maturation steroid hormone ecdysone (9,10). At the end of the larval period, neuronal input to the PG triggers autocrine signaling through the conserved Epidermal Growth Factor Receptor (Egfr)/MAP kinase (ERK) pathway, which induces the PG to synthesize and release ecdysone(11). This ecdysone acts on all tissues to initiate maturation(11). My data suggest this autocrine Egf/ERK signaling is blunted in hypoxia, thus delaying the developmental transition. Since signaling and key aspects of steroid hormone regulation are conserved between Drosophila and humans (9,10,12), my work provides insights into how the program of development can adapt to fluctuating environmental conditions.
- ItemOpen AccessMITOCHONDRIAL SKELETAL DISORDERS PROVIDE INSIGHT INTO THE EFFECT OF MITOCHONDRIAL PROTEOSTATIC STRESS ON STEROIDOGENESIS(2023-09-22) Zhao, Tian Rui; Shutt, Timothy; Khan, Aneal; Innes, Micheil; Yang, Guang; Bech-Hansen, TorbenMitochondria are best known for their role in energy production, and impairments in this essential function are generally thought to cause mitochondrial disease, which typically affects organs and tissues with high energy demand. However, increasing evidence shows that impairments to other critical mitochondrial functions such as lipid metabolism, and steroidogenesis can also contribute to mitochondrial diseases. In this thesis, we identified a group of mitochondrial diseases where mitochondrial protein homeostasis is disrupted, which we termed mitochondrial skeletal disorders, as the patients exhibited phenotypes such as skeletal dysplasia, short stature, and cataracts. In addition, further investigation identified a potential mechanism by which altered mitochondrial protein homeostasis and increased steroidogenesis may contribute to these patient phenotypes. First, we identified novel pathogenic variants in phosphatidylserine decarboxylase (PISD) gene from patients with short stature, neurodevelopmental issues, and cataracts. We demonstrated that the variants impair function and stability of PISD and are likely causative of their disease. We also identified evidence for impaired activity of inner mitochondrial membrane (IMM) proteases, suggesting dysfunctions in mitochondrial protein homeostasis. To further investigate the mechanism by which impaired mitochondrial proteostasis may lead to these phenotypes, we tested the hypothesis that impaired mitochondrial proteostasis can lead to overproduction of the stress hormone cortisol, as this could potentially explain the patients’ phenotypes described above. Using both pharmacological and genetic stresses to impair mitochondrial proteostasis, we showed impaired mitochondrial protein import activates STARD1, a mitochondrial protein crucial in steroidogenesis. We then showed that increased cortisol production is STARD1 dependent and follows a biphasic response to mitochondrial stress. Overall, these findings expand our current understanding of mitochondrial disease and link mitochondrial quality control and steroidogenesis as potential disease mechanisms.
- ItemOpen AccessThe Role of Ciliopathy Genes in Axonal Development(2022-01-26) Catalano, Christy Nicole; Guo, Jiami; Mains, Paul; McFarlane, Sarah; Yang, GuangPrimary cilia are tiny, microtubule-based organelles that project from the body of all mammalian cells and function as the cellular signalling hub. Genetic mutation of ciliary genes leads to multi-organ system dysfunction causing a group of diseases called ciliopathies. Notably, ciliopathy patients present with severe neurological phenotypes, including intellectual disability and prominent axon tract defects, suggesting a role for primary cilia in axonal development. However, the mechanisms behind axonal phenotypes in ciliopathies are not well understood. The formation of axons requires the assembly of very long microtubules, which are nucleated by the centrosome. As the cell’s microtubule organizing centre and the organelle that forms the base of the primary cilium, the centrosome is a common link between the axonal cytoskeleton and the cilium. Therefore, I hypothesized that the loss of ciliary proteins could impact the microtubule cytoskeleton, which in turn could influence axonal morphology and microtubule-based trafficking. This thesis investigates the role of two proteins that localize to the centrosome and base of the cilium, Ahi1 and Bbs7, in axonal development. Using targeted shRNA gene knockdown in cortical mouse neurons, I first investigated the roles of Ahi1 and Bbs7 in axonal morphology. Then, I further analyzed the role of Ahi1 in axons, using live cell imaging to examine axonal trafficking along microtubules. This thesis provides evidence that initial axonal outgrowth and axonal branching are inhibited by ciliary gene knockdown. I also present evidence that the trafficking of early endosomes and synaptic vesicles along axonal microtubules is altered by Ahi1 deficiency, which could impact axon growth, health, and synaptic function. Further research will be necessary to understand the exact cause and consequences of these changes in axonal morphology and trafficking; however, this thesis substantiates a role for primary cilia in regulating the developing axon.
- ItemOpen AccessUbiquitin Signaling Regulates P-Body Assembly(2021-06-21) Kedia, Shreeya; Yang, Guang; Huang, Peng; Mains, Paul Elliott; Corcoran, JenniferDuring the development of the central nervous system, neural stem cells give rise to different cell populations including neurons and glia. To en¬sure the genesis of the correct cell populations in the developing brain, there exists and intricate system of gene expression regulation. One such mechanism of gene expression regulation is the presence of membrane-less ribonucleoprotein (RNP) granules in the cell such as Processing bodies (PBs). These dynamic organelles are sites of RNA metabolism that can temporarily sequester mRNAs resulting in translational repression and/or decay. Therefore, to understand the molecular mechanism by which PBs regulate stem cell homeostasis, it is critical to delineate the signaling regulating PB dynamics. To this end, my thesis explores a novel non-proteolytic monoubiquitination-based signaling mechanism, where monoubiquitination of a core PB protein called 4E-T drives PB assembly. Mechanistically, PB dynamics are fine-tuned by a deubiquitinase called Otud4, which deubiquitinates 4E-T to disassemble PBs. This dynamic ubiquitination signaling therefore, functions as an essential molecular switch to coordinate PB dynamics in neural stem cells.
- ItemOpen AccessUnderstanding the roles for CELF2 in post-transcriptional regulation for the fate of neural stem cells.(2021-09) Kopp, Drayden; Long, Quan; Yang, Guang; Bousman, Chad; Nguyen, Minh DangThe development of the mammalian brain is built by neural stem cells (NSCs) which differentiate into neurons, glial cells and will self-renew to grow the NSC population. The balancing of self-renewal and differentiation is precisely orchestrated as the brain develops. The fate of NSCs are achieved by intrinsic gene regulation along with extrinsic environmental factors. As gene regulation is an essential process for all cells, understanding its coordination is important to understand how the fate of cells are determined. Gene regulation can occur at three main levels: transcriptional, post-transcriptional and post-translational. Regarding NSCs, transcriptional and post-translational regulation have been studied extensively, while post-transcriptional regulation has had limited research. An understudied post-transcriptional regulator, CELF2, has been found to be associated with neural developmental disorders. Further studies from our lab found that CELF2 is essential for NSC fate decisions. My thesis aims to understand what transcripts are targeted by CELF2 using bioinformatics analysis. With this data, the targeted genes can be categorized into groups based on their functionality. Using this data, I aim to determine what genes and what cellular functions are most impacted by CELF2. Furthermore, as the CELF family is not well studied evolutionarily, I wish to construct a phylogenetic tree to understand how the family may have evolved in association with complex animals. With these findings, I am to expand the field of post-transcriptional regulation and its impact on the developing brain.
- ItemOpen AccessUsing CRISPR-Cas9 to Generate Isogenic Controls from DCMA Patient-Derived Induced Pluripotent Stem Cells(2022-03-29) Degtiarev, Vladislav; Greenway, Steven; Yang, Guang; Bousman, ChadDilated cardiomyopathy with ataxia syndrome (DCMA) is an autosomal recessive disease frequently characterized by heart failure in early childhood. Although globally rare, DCMA is common in the Hutterites of southern Alberta who represent the largest collection of patients in the world. Alberta Children’s Hospital investigators previously identified a single intronic G>C mutation in the poorly characterized gene DNAJC19 as being responsible for DCMA. In collaboration with Stanford University, we have generated induced pluripotent stem cell (iPSCs) from DCMA patient peripheral blood mononuclear cells. Differentiating iPSCs into beating cardiomyocytes (iPSC-CMs) creates a disease-, patient-, and tissue-specific in vitro model of DCMA. However, our current model system has limitations due to lack of appropriately matched controls. This thesis aimed to create isogenic controls from our patient-derived iPSCs using the clusters of regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated endonuclease 9 (Cas9) system. We hypothesized that repairing the G>C mutation in DNAJC19 of our patient iPSCs will produce iPSC-CMs with a phenotype comparable to healthy controls and introducing the G>C mutation into DNAJC19 of healthy iPSCs will produce iPSC-CMs with a DCMA phenotype. Although isogenic controls have yet to be derived, this thesis outlines a potential workflow for the genomic editing of DCMA iPSCs. Our approach utilizes the use of an RNP-complex system that is delivered to iPSCs via lipofection using Lipofectamine Stem.