GeneWeaver: a web-based system for integrative functional genomics

High-throughput genome technologies have produced a wealth of data on the association of genes and gene products to biological functions. Investigators have discovered value in combining their experimental results with published genome-wide association studies, quantitative trait locus, microarray, RNA-sequencing and mutant phenotyping studies to identify gene-function associations across diverse experiments, species, conditions, behaviors or biological processes. These experimental results are typically derived from disparate data repositories, publication supplements or reconstructions from primary data stores. This leaves bench biologists with the complex and unscalable task of integrating data by identifying and gathering relevant studies, reanalyzing primary data, unifying gene identifiers and applying ad hoc computational analysis to the integrated set. The freely available GeneWeaver (http://www.GeneWeaver.org) powered by the Ontological Discovery Environment is a curated repository of genomic experimental results with an accompanying tool set for dynamic integration of these data sets, enabling users to interactively address questions about sets of biological functions and their relations to sets of genes. Thus, large numbers of independently published genomic results can be organized into new conceptual frameworks driven by the underlying, inferred biological relationships rather than a pre-existing semantic framework. An empirical ‘ontology’ is discovered from the aggregate of experimental knowledge around user-defined areas of biological inquiry

Accelerating Discovery for Complex Neurological and Behavioral Disorders Through Systems Genetics and Integrative Genomics in the Laboratory Mouse

Recent advances in systems genetics and integrative functional genomics have greatly improved the study of complex neurological and behavioral traits. The methods developed for the integrated characterization of new, high-resolution mouse genetic reference populations and systems genetics enable behavioral geneticists an unprecedented opportunity to address questions of the molecular basis of neurological and psychiatric disorders and their comorbidities. Integrative genomics augment these strategies by enabling rapid informatics-assisted candidate gene prioritization, cross-species translation, and mechanistic comparison across related disorders from a wealth of existing data in mouse and other model organisms. Ultimately, through these complementary approaches, finding the mechanisms and sources of genetic variation underlying complex neurobehavioral disease related traits is becoming tractable. Furthermore, these methods enable categorization of neurobehavioral disorders through their underlying biological basis. Together, these model organism-based approaches can lead to a refinement of diagnostic categories and targeted treatment of neurological and psychiatric disease

Contextual Analysis of Large-Scale Biomedical Associations for the Elucidation and Prioritization of Genes and their Roles in Complex Disease

Vast amounts of biomedical associations are easily accessible in public resources, spanning gene-disease associations, tissue-specific gene expression, gene function and pathway annotations, and many other data types. Despite this mass of data, information most relevant to the study of a particular disease remains loosely coupled and difficult to incorporate into ongoing research. Current public databases are difficult to navigate and do not interoperate well due to the plethora of interfaces and varying biomedical concept identifiers used. Because no coherent display of data within a specific problem domain is available, finding the latent relationships associated with a disease of interest is impractical. This research describes a method for extracting the contextual relationships embedded within associations relevant to a disease of interest. After applying the method to a small test data set, a large-scale integrated association network is constructed for application of a network propagation technique that helps uncover more distant latent relationships. Together these methods are adept at uncovering highly relevant relationships without any a priori knowledge of the disease of interest. The combined contextual search and relevance methods power a tool which makes pertinent biomedical associations easier to find, easier to assimilate into ongoing work, and more prominent than currently available databases. Increasing the accessibility of current information is an important component to understanding high-throughput experimental results and surviving the data deluge

Abnormal COX2/PGE2 Signalling in the Developing Cerebellum - A Link to Autism Spectrum Disorders

Autism spectrum disorders (ASDs) include a group of neurodevelopmental conditions that are characterized by deficits in social interaction and communication, increases in repetitive/restricted often stereotyped behaviour, and increases in anxiety. The heterogeneous nature of ASDs with regards to symptoms but also genetic profiles of ASD individuals, make understanding factors contributing to the disorder complex. However, literature suggests that ASDs arise from a combination of genetic and environmental factors. Clinical studies have suggested that abnormal lipid signalling, as a result of environmental insults can contribute to the etiology of ASDs. The phospholipid membrane of cells within the can be metabolized into lipid signalling molecules, including prostaglandins. Prostaglandin E2 (PGE2) is one of the most utilized lipid signalling molecules in the brain, involved in developmental processes such as synaptogenesis, migration, and differentiation of neuronal stem cells. Abnormal levels of PGE2, as well as COX-1 and COX-2, the rate-limiting enzymes in PGE2 synthesis have been linked to ASD. Furthermore, various environmental risk factors including exposure to heavy metals, infection/inflammation in pregnancy, exposure to pesticides, fragrances, and the use of over-the-counter medications such as aspirin and acetaminophen can affect PGE2 levels and are linked to ASD. The exact mechanisms that link abnormal COX2/PGE2 signalling to ASD are still unclear. To help address the lack of information, in this dissertation we first examine the effect of exposure to PGE2 on differentiated neuroectodermal (NE-4C) stem cells. Further, Studies have demonstrated that the cerebellum may be important in the etiology of ASDs. Interestingly there is evidence that PGE2 can affect postnatal development of the cerebellum. We examine the effect of increases (in a maternal PGE2 injection model) and decreases (in a COX-2--KI model) in PGE2 levels on prenatal neurodevelopment. We specifically examine the effects of these increases and decreases on cytoskeletal-dependent morphology through dendritic morphology within the cerebellum. Additionally, we examine the effect of prenatal PGE2-exposure on cerebellar-dependent motor function postnatally. Given the importance of sex as a factor in examining neurodevelopmental disorders such as ASD that have a large sex bias towards males, all of our in vivo studies address the modulation of the PGE2 effect by sex. These studies demonstrate that abnormal COX2/PGE2 signalling can affect important neurodevelopmental processes in vitro and development of the cerebellum in vivo. We observed disruptions in cytoskeletal dynamics, and changes in the expression of cytoskeletal proteins corresponding to abnormal COX2/PGE2 signalling. In PGE2-exposed mice, the changes in dendritic morphology in the cerebellum, corresponded to deficits in cerebellar motor function. Further, we found that the disruption of COX2/PGE2 affected development in a sex-dependent manner. The findings strengthen the involvement of COX2/PGE2 signalling in normal development of the brain and further suggest that abnormal COX2/PGE2 signalling as a result of exposure to environmental factors can result in neuropathologies including those found in ASD

Neurobiology of Lipid Signalling in the Developing Brain: Link to Autism Spectrum Disorders

Autism spectrum disorders (ASDs) are neurodevelopmental conditions diagnosed by atypical behaviours in social interaction and communication, along with stereotyped, restricted and repetitive behaviours. The exact cause of ASDs is unclear but is likely from a combination of genetic and environmental influences. Various clinical studies have identified an association between irregular lipid signalling and ASDs. Lipids are major components of brain cells and serve as a supply for signalling molecules such as prostaglandin E2 (PGE2). Cyclooxygenase-2 (COX-2) is the key enzyme responsible for PGE2 production in the brain. The COX-2/PGE2 signalling pathway is essential for development and maintenance of healthy neural functions. Genetic defects or exposure to various environmental agentssuch as infections or drugscan disrupt the levels of PGE2. However, investigation into the molecular mechanisms by which disrupted COX-2/PGE2 signalling or irregular PGE2 levels might affect the development of the nervous system and contribute to the pathogenesis of ASDs is sparse. Addressing this gap in knowledge was the main purpose of this dissertation. We found that PGE2 interacts with the key developmental Wnt signalling pathway in vitro by affecting neuroectodermal stem cell motility and proliferation (Study 1) and by promoting their differentiation into neurons (Study 2). In addition, prenatal PGE2 exposure disrupted cell density and increased migration in ASD-implicated areas of the mouse brain (Study 3). Decreased PGE2 (via COX-2-deficiency) or increased PGE2 in mice also led to abnormal microglial density and morphology (Study 4). Lastly, behavioural outcomes related to ASDs were quantified in COX-2-deficient and PGE2-exposed mice (Study 5 and 6). Our findings support epidemiological and clinical reports implicating the COX-2/PGE2 pathway in ASDs. We provide novel evidence that disturbances in the COX-2/PGE2 pathway results in aberrant neurodevelopment, including molecular, cellular, and behavioural differences analogous to those described in ASDs. Importantly, this array of research studies is one of the first to investigate mechanisms related to ASDs in both males and females and at various developmental stages, which is greatly underrepresented in the current literature. Altogether, this dissertation exposes the COX-2/PGE2 pathway as an autism candidate pathway and offers important insight into the complex, unknown etiology of ASDs

Autism candidate genes via mouse phenomics.

Autism spectrum disorders (ASD) represent a group of developmental disabilities with a strong genetic basis. The laboratory mouse is increasingly used as a model organism for ASD, and MGI, the Mouse Genome Informatics resource, is the primary model organism database for the laboratory mouse. MGI uses the Mammalian Phenotype (MP) ontology to describe mouse models of human diseases. Using bioinformatics tools including Phenologs, MouseNET, and the Ontological Discovery Environment, we tested data associated with MP terms to characterize new gene-phenotype associations related to ASD. Our integrative analysis using these tools identified numerous mouse genotypes that are likely to have previously uncharacterized autistic-like phenotypes. The genes implicated in these mouse models had considerable overlap with a set of over 300 genes recently associated with ASD due to small, rare copy number variation (Pinto et al., 2010). Prediction and characterization of autistic mutant mouse alleles assists researchers in studying the complex nature of ASD and provides a generalizable approach to candidate gene prioritization

CYFIP1-dependent regulatory networks during cortical differentiation of human pluripotent stem cells: Implications in neuropsychiatric diseases

Copy number variants affecting the chromosomic locus ch15q11.2 are associated with an increased risk for the development of neuropsychiatric disorders. CYFIP1 is one of the four genes within the 15q11.2 region and is the most studied thus far. While multiple studies have demonstrated a role for CYFIP1 in the physiology and morphology of neuronal cells, how altered expression of CYFIP1 and the other 15q11.2 genes confer risk to neuropsychiatric disorders remain largely unknown. Increased levels of CYFIP1 caused a delayed in neurogenesis while decreased levels caused the progenitor cells to prematurely differentiate into neural cells.This thesis investigates the transcriptional changes associated with altered levels of CYFIP1 in order to elucidate the mechanisms behind the observed cellular phenotypes. RNAseq analysis revealed altered overlapping pathways in these cells that could explain the observed phenotype. This also revealed new functions associated with CYFIP1-regulated genes involving mitochondrial and cholesterol metabolism. Common variant analysis indicated that amongst the CYFIP1-regulated genes, those that are targets of FMRP show a significant enrichment for genetic variants conferring increased risk for schizophrenia. In-depth analysis indicated that AKT3 was one of the top candidate genes involved in the development of the abnormal phenotype observed in cells with altered CYFIP1 expression. Genetic manipulation of ATK3 using a lentiviral CRISPR/Cas9 system showed evidence that AKT3 is involved, in part, in the maintenance of the neural progenitor cells in CYFIP1tg cultures. This thesis demonstrates that the defects caused by altered CYFIP1 expression can be explained partly by changes in AKT3 activity elucidating a potential mechanism behind the neuropsychiatric phenotype associated with 15q11.2 CNVs