Super-resolution microscopy and deep learning methods: what can they bring to neuroscience: from neuron to 3D spine segmentation

Kalirin-7 Controls Activity-Dependent Structural and Functional Plasticity of Dendritic Spines

Formation of dendritic spine and synapse is an essential final step of brain wiring to establish functional communication in the developing brain. Recent findings have displayed altered dendritic spine and synapse morphogenesis, plasticity, and related molecular mechanisms in animal models and post-mortem human brains of autism spectrum disorders (ASD) and intellectual disability (ID). Many genes and proteins are shown to be associated with spines and synapse development, and therefore neurodevelopmental disorders. In this review, however, particular attention will be given to chromatin modifiers such as AT-Rich Interactive Domain 1B (ARID1B), KAT8 regulatory non-specific lethal (NSL) complex subunit 1 (KANSL1), and WD Repeat Domain 5 (WDR5) which are among strong susceptibility factors for ASD and ID. Emerging evidence highlights the critical status of these chromatin remodeling molecules in dendritic spine morphogenesis and synaptic functions. Molecular and cellular insights of ARID1B, KANSL1, and WDR5 will integrate into our current knowledge in understanding and interpreting the pathogenesis of ASD and ID. Modulation of their activities or levels may be an option for potential therapeutic treatment strategies for these neurodevelopmental conditions.

Managing insomnia in children with autism spectrum disorder

A shifting view of neurodevelopmental disability

Neurodevelopmental disorders (NDDs) are a complex grouping of conditions arising in childhood relating to altered development and function of the brain. The primary conditions classified as NDDs include autism spectrum disorder (ASD), intellectual disability, attention deficit hyperactivity disorder, as well as motor, communication, and specific learning disorders. Many NDDs are known to have significant genetic risk, but the particular genes and molecular pathways controlling this genetic risk are still poorly understood. In addition to the genetic etiology of NDDs themselves, understanding the role of genetics in commonly associated comorbidities, such as sleep dysfunction or epilepsy in ASD, and how these insights might be leveraged to develop new therapeutics, remains a central goal of NDD genetic research. In ASD in particular, mutations in more than 100 genes have been significantly linked to increased risk for ASD. However, projections based on the frequency of mutations in these known risk genes has suggested that over 1000 genes may significantly increase risk for ASD when mutated. In response to this prediction, several machine learning approaches have been developed to use genome-wide data sources to predict which genes are the best candidates for ASD risk gene discovery. However, with different sources of data and training strategies used for each of these scores, there is not a clear consensus in the community on the most important predictors of genetic risk. My work develops a new ASD risk gene score that combines the benefits of all prior scores through a machine learning approach called ”ensemble learning”, unifying the previous scores while providing additional genome-wide data sources for model training. By comparing the previous scores with my work, I demonstrate the effectiveness of ensemble learning in this setting, and provide an ASD risk gene score that is enriched across a variety of ASD genetic data domains, such as common variant risk and gene expression data. While ASD as a whole has many known genetic associations, differences in medical issues experienced by those with ASD are highly variable, and the genetic factors underlying these comorbidities remain unclear. For instance, more than 70% of individuals with ASD have issues with sleep, but it is unknown whether genetic changes explain this difference seen between individuals with of ASD. Simply put, we know that genetics plays a large role in ASD, but we do not know the specifics of how genes map to subtypes of ASD. My work bridges this gap by studying the genetics of sleep dysfunction within individuals with ASD. To my knowledge, I am the first to be able to demonstrate and report that sleep dysfunction in ASD has a significant genetic component. Further, I find that genetic risk for ADHD, BMI, and several other conditions heightens an autistic individual’s risk for having issues with sleep. This work also uncovers associations between the type of sleep issue an individual has and the drugs that may be most effective for restoring normal sleep. Another major medical issue faced by individuals with ASD is epilepsy, with over 20% of individuals diagnosed with ASD having or going on to develop epilepsy later in life. Similar to sleep issues in ASD, treatment options in epilepsy are often effective but fall short in approximately 30% of cases. Finding treatments for these individuals who fail to find relief from the standard of care options is of critical importance. My work uses a bioinformatic technique called drug repositioning to computationally prioritize drugs that may be capable of reversing the transcriptional state induced by epilepsy. This approach yielded 184 potential therapeutic compounds, of which 4 were selected and tested in a zebrafish model of epilepsy. Three of the four compounds showed significant seizure suppression activity, including one with no previous literature surrounding its use in epilepsy (pyrantel tartrate). While a diverse set of work, the common thread is leveraging computational genetic techniques to better understand the causes, symptoms, and treatments of neurodevelopmental and associated disorders. By using ensemble learning, this work establishes a unified autism risk gene score that effectively summarizes a gene’s level of association with autism. Through studying sleep issues in ASD, I find a significant role for common variant risk and establish several genetic associations for poor sleep in ASD, such as ADHD and BMI genetic risk factors. Lastly, by using gene expression to model an effective therapeutic for epilepsy, this work reports on the first possible use of pyrantel tartrate in the treatment of epilepsy. Taken together, these findings demonstrate the power of leveraging big genetic datasets and innovative techniques in order to understand complex disease.

Activity-Dependent Dendritic Spine Structural Plasticity Is Regulated by Small GTPase Rap1 and Its Target AF-6

SNX26, a brain-enriched RhoGAP, plays a key role in dendritic arborization during early neuronal development in the neocortex. In mature neurons, it is localized to dendritic spines, but little is known about its role in later stages of development. Our results show that SNX26 interacts with PSD-95 in dendritic spines of cultured hippocampal neurons, and as a GTPase-activating protein for Cdc42, it decreased the F-actin content in COS-7 cells and in dendritic spines of neurons. Overexpression of SNX26 resulted in a GTPase-activating protein activity-dependent decrease in total protrusions and spine density together with dramatic inhibition of filopodia-to-spine transformations. Such effects of SNX26 were largely rescued by a constitutively active mutant of Cdc42. Consistently, an shRNA-mediated knockdown of SNX26 significantly increased total protrusions and spine density, resulting in an increase in thin or stubby type spines at the expense of the mushroom spine type. Moreover, endogenous expression of SNX26 was shown to be bi-directionally modulated by neuronal activity. Therefore, we propose that in addition to its key role in neuronal development, SNX26 also has a role in the activity-dependent structural change of dendritic spines in mature neurons.

The promise of precision medicine in autism

A better understanding of the endocannabinoid system and a relaxation in regulatory control of cannabis globally has increased interest in the medicinal use of cannabinoid-based products (CBP). We provide a systematic review of the rationale and current clinical trial evidence for CBP in the treatment of neuropsychiatric and neurodevelopmental disorders in children and adolescents. A systematic search of MEDLINE, Embase, PsycINFO, and the Cochrane Central Register of Trials was performed to identify articles published after 1980 about CBP for medical purposes in individuals aged 18 years or younger with selected neuropsychiatric or neurodevelopmental conditions. Risk of bias and quality of evidence was assessed for each article. Of 4466 articles screened, 18 were eligible for inclusion, addressing eight conditions (anxiety disorders (n = 1); autism spectrum disorder (n = 5); foetal alcohol spectrum disorder (n = 1); fragile X syndrome (n = 2); intellectual disability (n = 1); mood disorders (n = 2); post-traumatic stress disorder (n = 3); and Tourette syndrome (n = 3)). Only one randomised controlled trial (RCT) was identified. The remaining seventeen articles included one open-label trial, three uncontrolled before-and-after trials, two case series and 11 case reports, thus the risk of bias was high. Despite growing community and scientific interest, our systematic review identified limited and generally poor-quality evidence for the efficacy of CBP in neuropsychiatric and neurodevelopmental disorders in children and adolescents. Large rigorous RCTs are required to inform clinical care. In the meantime, clinicians must balance patient expectations with the limited evidence available.

Further studies of GABA and Glutamate imbalances in autism are important challenges for future research.

Neurodevelopmental and neuropsychiatric disorders, such as autism spectrum disorders (ASD), anorexia nervosa (AN), Alzheimer’s disease (AD), and schizophrenia (SZ), are heterogeneous brain disorders with unknown etiology. Genome wide studies have revealed a wide variety of risk genes for these disorders, indicating a biological link between genetic signaling pathways and brain pathology. A unique risk gene is Contactin 4 (Cntn4), an Ig cell adhesion molecule (IgCAM) gene, which has been associated with several neuropsychiatric disorders including ASD, AN, AD, and SZ. Here, we investigated the Cntn4 gene knockout (KO) mouse model to determine whether memory dysfunction and altered brain plasticity, common neuropsychiatric symptoms, are affected by Cntn4 genetic disruption. For that purpose, we tested if Cntn4 genetic disruption affects CA1 synaptic transmission and the ability to induce LTP in hippocampal slices. Stimulation in CA1 striatum radiatum significantly decreased synaptic potentiation in slices of Cntn4 KO mice. Neuroanatomical analyses showed abnormal dendritic arborization and spines of hippocampal CA1 neurons. Short- and long-term recognition memory, spatial memory, and fear conditioning responses were also assessed. These behavioral studies showed increased contextual fear conditioning in heterozygous and homozygous KO mice, quantified by a gene-dose dependent increase in freezing response. In comparison to wild-type mice, Cntn4-deficient animals froze significantly longer and groomed more, indicative of increased stress responsiveness under these test conditions. Our electrophysiological, neuro-anatomical, and behavioral results in Cntn4 KO mice suggest that Cntn4 has important functions related to fear memory possibly in association with the neuronal morphological and synaptic plasticity changes in hippocampus CA1 neurons.

Genome-environment interaction and epigenome plasticity significantly influence the pathogenesis of neurodegenerative and neuropsychiatric disorders. Recent advancements in the field to study genome wide chromatin modifications provide a comprehensive view of the epigenome. Dysregulation of epigenetic machinery has emerged as a major genetic driver of neuro developmental and neuro degenerative disorders, intellectual disabilities and autism spectrum disorders. Emerging evidences point to the involvement of the epigenome in the onset and progression of Alzheimer’s disease, Parkinson’s disease and Huntington’s disease. This review focusses on the changes in epigenetic machinery, specifically on the histone methylation and DNA methylation patterns during the onset and progression of neurodegenerative diseases and neuropsychiatric disorders. The power of epigenetic inhibitors to function as potential diagnostic and therapeutic markers is also discussed.

This article is part of a mini review series: "Synaptic Function and Dysfunction in Brain Diseases".

Caspase-3 Is Enriched in Postsynaptic Densities and Increased in Alzheimer's Disease

Familial and genetic associations between autism spectrum disorder (ASD) and other neurodevelopmental and psychiatric disorders have been reported, sometimes with conflicting results. We estimated familial and genetic associations between ASD and nine disorder groups, and explored differences in these associations for ASD in the context of intellectual disability, epilepsy, chromosomal abnormalities, and congenital malformations. Individuals born between 1985 and 2009 living in Sweden on their seventh birthday were linked to their biological parents in order to identify different types of relatives. We retrieved information on all the disorders considered from the National Patient Register. Logistic regression was used to estimate the familial association between ASD and other neurodevelopmental and psychiatric disorders in the different groups of relatives. Structural equation modeling was used to estimate phenotypic (rp ) and genetic associations (rg ), as well as the contribution of genetic influences to rp . The study included 2,398,608 individuals. Among relatives of individuals diagnosed with ASD, there was an increased risk of the disorders considered, compared to relatives of individuals who were not diagnosed with ASD. Stronger associations were detected for ASD without any additional diagnosis of intellectual disability, epilepsy, chromosomal abnormalities, and congenital malformations. The strongest genetic correlation was estimated between ASD and other neurodevelopmental disorders (rg =0.73; 95% CI=0.66-0.79). Moderate genetic correlations were estimated for anxiety disorders (rg =0.47; 95% CI=0.33-0.61), depression (rg =0.52; 95% CI=0.37-0.66), and intentional self-harm (rg =0.54; 95% CI=0.36-0.71). ASD shows familial and genetic association not only with other neurodevelopmental disorders, but also with other psychiatric disorders, such as anxiety, depression, and intentional self-harm. Family history of ASD comorbid with intellectual disability, epilepsy, congenital malformations, or chromosomal abnormalities is less related to other psychiatric disorders, potentially suggesting a different etiology for this subgroup of patients.