Transcriptomic signatures of neuronal differentiation and their association with risk genes for autism spectrum and related neuropsychiatric disorders.

Genes for autism spectrum disorders (ASDs) are also implicated in fragile X syndrome (FXS), intellectual disabilities (ID) or schizophrenia (SCZ), and converge on neuronal function and differentiation. The SH-SY5Y neuroblastoma cell line, the most widely used system to study neurodevelopment, is currently discussed for its applicability to model cortical development. We implemented an optimal neuronal differentiation protocol of this system and evaluated neurodevelopment at the transcriptomic level using the CoNTeXT framework, a machine-learning algorithm based on human post-mortem brain data estimating developmental stage and regional identity of transcriptomic signatures. Our improved model in contrast to currently used SH-SY5Y models does capture early neurodevelopmental processes with high fidelity. We applied regression modelling, dynamic time warping analysis, parallel independent component analysis and weighted gene co-expression network analysis to identify activated gene sets and networks. Finally, we tested and compared these sets for enrichment of risk genes for neuropsychiatric disorders. We confirm a significant overlap of genes implicated in ASD with FXS, ID and SCZ. However, counterintuitive to this observation, we report that risk genes affect pathways specific for each disorder during early neurodevelopment. Genes implicated in ASD, ID, FXS and SCZ were enriched among the positive regulators, but only ID-implicated genes were also negative regulators of neuronal differentiation. ASD and ID genes were involved in dendritic branching modules, but only ASD risk genes were implicated in histone modification or axonal guidance. Only ID genes were over-represented among cell cycle modules. We conclude that the underlying signatures are disorder-specific and that the shared genetic architecture results in overlaps across disorders such as ID in ASD. Thus, adding developmental network context to genetic analyses will aid differentiating the pathophysiology of neuropsychiatric disorders

Prenatal Neurogenesis in Autism Spectrum Disorders.

An ever-increasing body of literature describes compelling evidence that a subset of young children on the autism spectrum show abnormal cerebral growth trajectories. In these cases, normal cerebral size at birth is followed by a period of abnormal growth and starting in late childhood often by regression compared to unaffected controls. Recent work has demonstrated an abnormal increase in the number of neurons of the prefrontal cortex suggesting that cerebral size increase in autism is driven by excess neuronal production. In addition, some affected children display patches of abnormal laminar positioning of cortical projection neurons. As both cortical projection neuron numbers and their correct layering within the developing cortex requires the undisturbed proliferation of neural progenitors, it appears that neural progenitors lie in the center of the autism pathology associated with early brain overgrowth. Consequently, autism spectrum disorders associated with cerebral enlargement should be viewed as birth defects of an early embryonic origin with profound implications for their early diagnosis, preventive strategies, and therapeutic intervention

Astrocytes and Microglia and Their Potential Link with Autism Spectrum Disorders.

The cellular mechanism(s) underlying autism spectrum disorders (ASDs) are not fully understood although it has been shown that various genetic and environmental factors contribute to their etiology. As increasing evidence indicates that astrocytes and microglial cells play a major role in synapse maturation and function, and there is evidence of deficits in glial cell functions in ASDs, one current hypothesis is that glial dysfunctions directly contribute to their pathophysiology. The aim of this review is to summarize microglia and astrocyte functions in synapse development and their contributions to ASDs

Sex differences in brain plasticity: a new hypothesis for sex ratio bias in autism.

Several observations support the hypothesis that differences in synaptic and regional cerebral plasticity between the sexes account for the high ratio of males to females in autism. First, males are more susceptible than females to perturbations in genes involved in synaptic plasticity. Second, sex-related differences in non-autistic brain structure and function are observed in highly variable regions, namely, the heteromodal associative cortices, and overlap with structural particularities and enhanced activity of perceptual associative regions in autistic individuals. Finally, functional cortical reallocations following brain lesions in non-autistic adults (for example, traumatic brain injury, multiple sclerosis) are sex-dependent. Interactions between genetic sex and hormones may therefore result in higher synaptic and consecutively regional plasticity in perceptual brain areas in males than in females. The onset of autism may largely involve mutations altering synaptic plasticity that create a plastic reaction affecting the most variable and sexually dimorphic brain regions. The sex ratio bias in autism may arise because males have a lower threshold than females for the development of this plastic reaction following a genetic or environmental event

The over-pruning hypothesis of autism

This article outlines the over-pruning hypothesis of autism. The hypothesis originates in a neurocomputational model of the regressive sub-type (Thomas, Knowland & Karmiloff-Smith, 2011a,b). Here we develop a more general version of the over-pruning hypothesis to address heterogeneity in the timing of manifestation of ASD, including new computer simulations which can reconcile the different observed developmental trajectories (early onset, late onset, regression) via a single underlying atypical mechanism; and which show how unaffected siblings of individuals with ASD may differ from controls either by inheriting a milder version of the pathological mechanism or by co-inheriting the risk factors without the pathological mechanism. The proposed atypical mechanism involves overly aggressive synaptic pruning in infancy and early childhood, an exaggeration of a normal phase of brain development. We show how the hypothesis generates novel predictions that differ from existing theories, including that (1) the first few months of development in ASD will be indistinguishable from typical, and (2) the earliest atypicalities in ASD will be sensory and motor rather than social. Both predictions gain cautious support from emerging longitudinal studies of infants at risk of ASD. We review evidence consistent with the over-pruning hypothesis, its relation to other current theories (including C. Frith’s under-pruning proposal; C. Frith, 2003, 2004), as well as inconsistent data and current limitations. The hypothesis situates causal accounts of ASD within a framework of protective and risk factors (Newschaffer et al., 2012); clarifies different versions of the broader autism phenotype (i.e., the implication of observed similarities between individuals with autism and their family members); and integrates data from multiple disciplines, including behavioural studies, neuroscience studies, genetics, and intervention studies

FMRP and CYFIP1 at the synapse and their role in psychiatric vulnerability

There is increasing awareness of the role genetic risk variants have in mediating vulnerability to psychiatric disorders such as schizophrenia and autism. Many of these risk variants encode synaptic proteins, influencing biological pathways of the postsynaptic density and, ultimately, synaptic plasticity. Fragile X Mental Retardation 1 (FMR1) and Cytoplasmic FRMP-Interacting Protein (CYFIP1) contain two such examples of highly penetrant risk variants and encode synaptic proteins with shared functional significance. In this Review, we will discuss the biological actions of FMRP and CYFIP1, including their regulation of i) protein translation and specifically FMRP targets, ii) dendritic and spine morphology and iii) forms of synaptic plasticity such as long-term depression. We draw upon a range of preclinical studies that have used genetic dosage models of FMR1 and CYFIP1 to determine their biological function. In parallel, we discuss how clinical studies of Fragile X Syndrome or 15q11.2 deletion patients have informed our understanding of FMRP and CYFIP1 proteins, and highlight the latest psychiatric genomic findings that continue to implicate FMRP and CYFIP1. Lastly, we assess the current limitations in our understanding of FMRP and CYFIP1 biology and how they must be addressed before mechanism-led therapeutic strategies can be developed for psychiatric disorders

Transcriptomics of Gabra4 knockout mice reveals common NMDAR pathways underlying autism, memory, and epilepsy

Autism spectrum disorder (ASD) is a neuronal developmental disorder with impaired social interaction and communication, often with abnormal intelligence and comorbidity with epilepsy. Disturbances in synaptic transmission, including the GABAergic, glutamatergic, and serotonergic systems, are known to be involved in the pathogenesis of this disorder, yet we do not know if there is a common molecular mechanism. As mutations in the GABAergic receptor subunit gene GABRA4 are reported in patients with ASD, we eliminated the Gabra4 gene in mice and found that the Gabra4 knockout mice showed autistic-like behavior, enhanced spatial memory, and attenuated susceptibility to pentylenetetrazol-induced seizures, a constellation of symptoms resembling human high-functioning autism. To search for potential molecular pathways involved in these phenotypes, we performed a hippocampal transcriptome profiling, constructed a hippocampal interactome network, and revealed an upregulation of the NMDAR system at the center of the converged pathways underlying high-functioning autism-like and anti-epilepsy phenotypes

A Potential Role For Sap97 In Psychiatric Disorders

The goal of this dissertation is to further understand the genetic architecture of neuropsychiatric disorders, such as autism spectrum disorder (ASD) and schizophrenia (SCZ). We attempt to understand the functional significance of the gene synapse associated protein of 97KDa (SAP97) and identify a novel role for SAP97 in the etiology of neuropsychiatric disorders. SAP97 belongs to a family of scaffolding proteins, the membrane-associated guanylate kinases (MAGUKs), that are highly enriched in the postsynaptic density of synapses and play an important role in organizing protein complexes necessary for synaptic development and plasticity. Large-scale genetic studies have implicated MAGUKs in neuropsychiatric disorders such as intellectual disability, ASD, and SCZ, but knock-out mice have been impossible to study because the Sap97 null mice die soon after birth due to a craniofacial defect. In Chapter 2, we studied the transcriptomic and behavioral consequences of a viable, brain-specific conditional knockout of Sap97 (SAP97-cKO). RNA sequencing (RNAseq) from hippocampi from control and SAP97-cKO male animals identified 67 differentially expressed transcripts, which were specifically enriched for SCZ-related genes. Subjecting SAP97-cKO mice to a battery of behavioral tests revealed a subtle anxiety-like phenotype present in both male and female SAP97-cKO animals, as well as a mild male-specific cognitive deficit and female-specific motor learning deficit. Collectively, this work suggests that loss of Sap97 alters behavior, and may contribute to some of the endophenotypes present in SCZ. In Chapter 3, we discuss how the SAP97-cKO mouse may serve as a novel model system for interrogating aspects of the cellular and molecular defects underlying SCZ and other related neuropsychiatric disorders

Genetic implications of individual intervention and neuronal dysfunction in neurodevelopmental disorders

Neurodevelopmental disorders (NDDs) are a group of conditions appearing in childhood, with developmental deficits that produce impairments of functioning. Autism spectrum disorder (ASD) is a common NDD with a high heritability affected by complex genetic factors, including both common and rare variants. Behavior interventions such as social skills group training (SSGT) have been widely used in school-aged autistic individuals to relieve social communication difficulties in a group setting. Studies have confirmed that intervention outcomes can be influenced by sex and age, but how the genetic risk contributes to the outcome variability remains elusive. Furthermore, although large population cohorts have been well studied and have found numerous genes associated with ASD and NDDs, the molecular and neuronal outcomes of risk variants and genes are unclear. Therefore, this thesis included four studies in which the effects of genetic factors on intervention outcomes and cellular level neuronal functions were investigated. Results from this thesis may provide a genetic perspective for further studies to explore potential individualized treatments for ASD and other NDDs. Specifically, In STUDY 1-3, exome sequencing and microarray were performed on individuals from a randomized controlled trial of SSGT (KONTAKT®). Common and rare variants, including copy number variations (CNVs) and exome variants, were tested for association effects with SSGT and standard care intervention outcomes. Polygenic risk scores (PRSs) were calculated from common variants, and clinically significant rare CNVs and rare exome variants were prioritized. Molecular diagnoses were identified in 12.6% of the autistic participants. PRSs and carrier status of clinically significant rare variants were associated with intervention outcomes, although with varied effects on both SSGT and standard care. In addition, genetic scores representing variant loads in specific gene sets were obtained from rare and common variants in ASD-related pathways. Outcomes of interventions were differentially associated with genetic scores for ASD-related gene sets including synaptic transmission and transcription regulation from RNA polymerase II. After combining genetic information and behavior measures, a machine learning model was able to select important features and confirm that the intervention outcomes were predictable. In STUDY 4, genetic variants affecting Calcium/Calmodulin Dependent Serine Protein Kinase (CASK) gene, a risk gene for NDDs, were examined using human induced pluripotent stem cell-derived neuronal models to identify the cellular effects of these mutation consequences. CASK protein was reduced in maturing neurons from mutation carriers. Bulk RNA sequencing results revealed that the global expression of genes from presynaptic development and CASK network were downregulated in CASK-deficient neurons compared to controls. Neuronal cells influenced by CASK mutations showed a decrease of inhibitory presynapse size and changed excitatory-inhibitory (E/I) balance in developing neural circuitries. In summary, this is the first study to investigate the association of genome-wide rare and common variants with ASD intervention outcomes. Differential variant effects were found for individuals receiving SSGT or standard care. Future studies should include genetic information at different levels to improve molecular genetic testing for diagnoses and intervention plans. Presynapses and E/I imbalance could be an option to be developed for the treatment of CASK-related disorders