Epigenetics and cerebral organoids: promising directions in autism spectrum disorders

NASP gene contributes to autism by epigenetic dysregulation of neural and immune pathways

BACKGROUND

Epigenetics makes substantial contribution to the aetiology of autism spectrum disorder (ASD) and may harbour a unique opportunity to prevent the development of ASD. We aimed to identify novel epigenetic genes involved in ASD aetiology.

METHODS

Trio-based whole exome sequencing was conducted on ASD families. Genome editing technique was used to knock out the candidate causal gene in a relevant cell line. ATAC-seq, ChIP-seq and RNA-seq were performed to investigate the functional impact of knockout (KO) or mutation in the candidate gene.

RESULTS

We identified a novel candidate gene NASP (nuclear autoantigenic sperm protein) for epigenetic dysregulation in ASD in a Chinese nuclear family including one proband with autism and comorbid atopic disease. The de novo likely gene disruptive variant tNASP(Q289X) subjects the expression of tNASP to nonsense-mediated decay. tNASP KO increases chromatin accessibility, promotes the active promoter state of genes enriched in synaptic signalling and leads to upregulated expression of genes in the neural signalling and immune signalling pathways. Compared with wild-type tNASP, tNASP(Q289X) enhances chromatin accessibility of the genes with enriched expression in the brain. RNA-seq revealed that genes involved in neural and immune signalling are affected by the tNASP mutation, consistent with the phenotypic impact and molecular effects of nasp-1 mutations in Caenorhabditis elegans. Two additional patients with ASD were found carrying deletion or deleterious mutation in the NASP gene.

CONCLUSION

We identified novel epigenetic mechanisms mediated by tNASP which may contribute to the pathogenesis of ASD and its immune comorbidity.

Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells

The implications of the early phases of human telencephalic development, involving neural stem cells (NSCs), in the etiology of cortical disorders remain elusive. Here, we explored the expression dynamics of cortical and neuropsychiatric disorder-associated genes in datasets generated from human NSCs across telencephalic fate transitions in vitro and in vivo. We identified risk genes expressed in brain organizers and sequential gene regulatory networks across corticogenesis revealing disease-specific critical phases, when NSCs are more vulnerable to gene dysfunctions, and converging signaling across multiple diseases. Moreover, we simulated the impact of risk transcription factor (TF) depletions on different neural cell types spanning the developing human neocortex and observed a spatiotemporal-dependent effect for each perturbation. Finally, single-cell transcriptomics of newly generated autism-affected patient-derived NSCs in vitro revealed recurrent alterations of TFs orchestrating brain patterning and NSC lineage commitment. This work opens new perspectives to explore human brain dysfunctions at the early phases of development.

One-sentence summary

The temporal analysis of gene regulatory networks in human neural stem cells reveals multiple early critical phases associated with cortical disorders and neuropsychiatric traits.

Induced Pluripotent Stem Cells and Organoids in Advancing Neuropathology Research and Therapies

This review delves into the groundbreaking impact of induced pluripotent stem cells (iPSCs) and three-dimensional organoid models in propelling forward neuropathology research. With a focus on neurodegenerative diseases, neuromotor disorders, and related conditions, iPSCs provide a platform for personalized disease modeling, holding significant potential for regenerative therapy and drug discovery. The adaptability of iPSCs, along with associated methodologies, enables the generation of various types of neural cell differentiations and their integration into three-dimensional organoid models, effectively replicating complex tissue structures in vitro. Key advancements in organoid and iPSC generation protocols, alongside the careful selection of donor cell types, are emphasized as critical steps in harnessing these technologies to mitigate tumorigenic risks and other hurdles. Encouragingly, iPSCs show promising outcomes in regenerative therapies, as evidenced by their successful application in animal models.

Bibliometric analysis of cerebral organoids and diseases in the last 10 years

Cerebral organoids have emerged as a powerful tool for mirroring the brain developmental processes and replicating its unique physiology. This bibliometric analysis aims to delineate the burgeoning trends in the application of cerebral organoids in disease research and offer insights for future investigations. We screened all relevant literature from the Web of Science on cerebral organoids in disease research during the period 2013-2022 and analyzed the research trends in the field using VOSviewer, CiteSpace, and Scimago Graphica software. According to the search strategy, 592 articles were screened out. The United States of America (USA) was the most productive, followed by China and Germany. The top nine institutions in terms of the number of publications include Canada and the United States, with the University of California, San Diego (USA), having the highest number of publications. The International Journal of Molecular Sciences was the most productive journal. Knoblich, Juergen A., and Lancaster, Madeline A. published the highest number of articles. Keyword cluster analysis showed that current research trends focused more on induced pluripotent stem cells to construct organoid models of cerebral diseases and the exploration of their mechanisms and therapeutic modalities. This study provides a comprehensive summary and analysis of global research trends in the field of cerebral organoids in diseases. In the past decade, the number of high-quality papers in this field has increased significantly, and cerebral organoids provide hope for simulating nervous system diseases (such as Alzheimer's disease).

Cerebral organoids as an in vitro model to study autism spectrum disorders

Autism spectrum disorders (ASDs) are a set of disorders characterised by social and communication deficits caused by numerous genetic lesions affecting brain development. Progress in ASD research has been hampered by the lack of appropriate models, as both 2D cell culture as well as animal models cannot fully recapitulate the developing human brain or the pathogenesis of ASD. Recently, cerebral organoids have been developed to provide a more accurate, 3D in vitro model of human brain development. Cerebral organoids have been shown to recapitulate the foetal brain gene expression profile, transcriptome, epigenome, as well as disease dynamics of both idiopathic and syndromic ASDs. They are thus an excellent tool to investigate development of foetal stage ASDs, as well as interventions that can reverse or rescue the altered phenotypes observed. In this review, we discuss the development of cerebral organoids, their recent applications in the study of both syndromic and idiopathic ASDs, their use as an ASD drug development platform, as well as limitations of their use in ASD research.

Rare diseases of epigenetic origin: Challenges and opportunities

Rare diseases (RDs), more than 80% of which have a genetic origin, collectively affect approximately 350 million people worldwide. Progress in next-generation sequencing technology has both greatly accelerated the pace of discovery of novel RDs and provided more accurate means for their diagnosis. RDs that are driven by altered epigenetic regulation with an underlying genetic basis are referred to as rare diseases of epigenetic origin (RDEOs). These diseases pose unique challenges in research, as they often show complex genetic and clinical heterogeneity arising from unknown gene-disease mechanisms. Furthermore, multiple other factors, including cell type and developmental time point, can confound attempts to deconvolute the pathophysiology of these disorders. These challenges are further exacerbated by factors that contribute to epigenetic variability and the difficulty of collecting sufficient participant numbers in human studies. However, new molecular and bioinformatics techniques will provide insight into how these disorders manifest over time. This review highlights recent studies addressing these challenges with innovative solutions. Further research will elucidate the mechanisms of action underlying unique RDEOs and facilitate the discovery of treatments and diagnostic biomarkers for screening, thereby improving health trajectories and clinical outcomes of affected patients.

Modeling Autism Spectrum Disorders with Induced Pluripotent Stem Cell-Derived Brain Organoids

Autism spectrum disorders (ASD) are a group of complex neurodevelopmental disorders that affect communication and social interactions and present with restricted interests and repetitive behavior patterns. The susceptibility to ASD is strongly influenced by genetic/heritable factors; however, there is still a large gap in understanding the cellular and molecular mechanisms underlying the neurobiology of ASD. Significant progress has been made in identifying ASD risk genes and the possible convergent pathways regulated by these gene networks during development. The breakthrough of cellular reprogramming technology has allowed the generation of induced pluripotent stem cells (iPSCs) from individuals with syndromic and idiopathic ASD, providing patient-specific cell models for mechanistic studies. In the past decade, protocols for developing brain organoids from these cells have been established, leading to significant advances in the in vitro reproducibility of the early steps of human brain development. Here, we reviewed the most relevant literature regarding the application of brain organoids to the study of ASD, providing the current state of the art, and discussing the impact of such models on the field, limitations, and opportunities for future development.

Multi-omics data integration methods and their applications in psychiatric disorders

To study mental illness and health, in the past researchers have often broken down their complexity into individual subsystems (e.g., genomics, transcriptomics, proteomics, clinical data) and explored the components independently. Technological advancements and decreasing costs of high throughput sequencing has led to an unprecedented increase in data generation. Furthermore, over the years it has become increasingly clear that these subsystems do not act in isolation but instead interact with each other to drive mental illness and health. Consequently, individual subsystems are now analysed jointly to promote a holistic understanding of the underlying biological complexity of health and disease. Complementing the increasing data availability, current research is geared towards developing novel methods that can efficiently combine the information rich multi-omics data to discover biologically meaningful biomarkers for diagnosis, treatment, and prognosis. However, clinical translation of the research is still challenging. In this review, we summarise conventional and state-of-the-art statistical and machine learning approaches for discovery of biomarker, diagnosis, as well as outcome and treatment response prediction through integrating multi-omics and clinical data. In addition, we describe the role of biological model systems and in silico multi-omics model designs in clinical translation of psychiatric research from bench to bedside. Finally, we discuss the current challenges and explore the application of multi-omics integration in future psychiatric research. The review provides a structured overview and latest updates in the field of multi-omics in psychiatry.

Associations between parental psychiatric disorders and autism spectrum disorder in the offspring

Whether parental psychiatric disorders are associated with autism spectrum disorder (ASD) in offspring has remained inconclusive. We examined the associations of parental psychiatric disorders with ASD in offspring. This population-based case-control study used Taiwan's National Health Insurance Research Database to identify a cohort of children born from 2004 to 2017 and their parents. A total of 24,279 children with ASD (diagnostic ICD-9-CM code: 299.x or ICD-10 code F84.x) and 97,715 matched controls were included. Parental psychiatric disorders, including depressive disorders, bipolar spectrum disorders, anxiety disorders, obsessive-compulsive disorder, schizophrenia, substance use disorders, autism spectrum disorder, attention-deficit hyperactivity disorder (ADHD), and adjustment disorders were identified. Conditional logistic regressions with covariate adjustment were performed. The results suggest that parental diagnosis with any of the psychiatric disorders is associated with ASD in offspring (adjusted odds ratio [AOR] = 1.45, 95%CI: 1.40-1.51 for mothers; and AOR = 1.12, 95%CI: 1.08-1.17 for fathers). ASD in offspring was associated with schizophrenia, depressive disorders, obsessive-compulsive disorder, adjustment disorders, ADHD and ASD in both parents. The relationship between parental psychiatric disorders and the timing of the child's birth and ASD diagnosis varied across the different psychiatric disorders. The present study provides supportive evidence that parental psychiatric disorders are associated with autistic children. Furthermore, because the associations between parental psychiatric disorders and the timing of child's birth and ASD diagnosis varied across psychiatric disorders, the observed relationships may be affected by both genetic and environmental factors. Future studies are needed to disentangle the potential influence of genetic and environmental factors on the observed associations.

Proteomic phenotype of cerebral organoids derived from autism spectrum disorder patients reveal disrupted energy metabolism, cellular components, and biological processes

The way in which brain morphology and proteome are remodeled during embryonal development, and how they are linked to the cellular metabolism, could be a key for elucidating the pathological mechanisms of certain neurodevelopmental disorders. Cerebral organoids derived from autism spectrum disorder (ASD) patients were generated to capture critical time-points in the neuronal development, and metabolism and protein expression were investigated. The early stages of development, when neurogenesis commences (day in vitro 39), appeared to be a critical timepoint in pathogenesis. In the first month of development, increased size in ASD-derived organoids were detected in comparison to the controls. The size of the organoids correlates with the number of proliferating cells (Ki-67 positive cells). A significant difference in energy metabolism and proteome phenotype was also observed in ASD organoids at this time point, specifically, prevalence of glycolysis over oxidative phosphorylation, decreased ATP production and mitochondrial respiratory chain activity, differently expressed cell adhesion proteins, cell cycle (spindle formation), cytoskeleton, and several transcription factors. Finally, ASD patients and controls derived organoids were clustered based on a differential expression of ten proteins-heat shock protein 27 (hsp27) phospho Ser 15, Pyk (FAK2), Elk-1, Rac1/cdc42, S6 ribosomal protein phospho Ser 240/Ser 244, Ha-ras, mTOR (FRAP) phospho Ser 2448, PKCα, FoxO3a, Src family phospho Tyr 416-at day 39 which could be defined as potential biomarkers and further investigated for potential drug development.

DNA Methylation Profiles of GAD1 in Human Cerebral Organoids of Autism Indicate Disrupted Epigenetic Regulation during Early Development

DNA methylation profiling has become a promising approach towards identifying biomarkers of neuropsychiatric disorders including autism spectrum disorder (ASD). Epigenetic markers capture genetic risk factors and diverse exogenous and endogenous factors, including environmental risk factors and complex disease pathologies. We analysed the differential methylation profile of a regulatory region of the GAD1 gene using cerebral organoids generated from induced pluripotent stem cells (iPSCs) from adults with a diagnosis of ASD and from age- and gender-matched healthy individuals. Both groups showed high levels of methylation across the majority of CpG sites within the profiled GAD1 region of interest. The ASD group exhibited a higher number of unique DNA methylation patterns compared to controls and an increased CpG-wise variance. We detected six differentially methylated CpG sites in ASD, three of which reside within a methylation-dependent transcription factor binding site. In ASD, GAD1 is subject to differential methylation patterns that may not only influence its expression, but may also indicate variable epigenetic regulation among cells.

Everything You Always Wanted to Know About Organoid-Based Models (and Never Dared to Ask)

Homeostatic functions of a living tissue, such as the gastrointestinal tract, rely on highly sophisticated and finely tuned cell-to-cell interactions. These crosstalks evolve and continuously are refined as the tissue develops and give rise to specialized cells performing general and tissue-specific functions. To study these systems, stem cell-based in vitro models, often called organoids, and non-stem cell-based primary cell aggregates (called spheroids) appeared just over a decade ago. These models still are evolving and gaining complexity, making them the state-of-the-art models for studying cellular crosstalk in the gastrointestinal tract, and to investigate digestive pathologies, such as inflammatory bowel disease, colorectal cancer, and liver diseases. However, the use of organoid- or spheroid-based models to recapitulate in vitro the highly complex structure of in vivo tissue remains challenging, and mainly restricted to expert developmental cell biologists. Here, we condense the founding knowledge and key literature information that scientists adopting the organoid technology for the first time need to consider when using these models for novel biological questions. We also include information that current organoid/spheroid users could use to add to increase the complexity to their existing models. We highlight the current and prospective evolution of these models through bridging stem cell biology with biomaterial and scaffold engineering research areas. Linking these complementary fields will increase the in vitro mimicry of in vivo tissue, and potentially lead to more successful translational biomedical applications. Deepening our understanding of the nature and dynamic fine-tuning of intercellular crosstalks will enable identifying novel signaling targets for new or repurposed therapeutics used in many multifactorial diseases.

Decellularised extracellular matrix-based biomaterials for repair and regeneration of central nervous system

The central nervous system (CNS), consisting of the brain and spinal cord, regulates the mind and functions of the organs. CNS diseases, leading to changes in neurological functions in corresponding sites and causing long-term disability, represent one of the major public health issues with significant clinical and economic burdens worldwide. In particular, the abnormal changes in the extracellular matrix under various disease conditions have been demonstrated as one of the main factors that can alter normal cell function and reduce the neuroregeneration potential in damaged tissue. Decellularised extracellular matrix (dECM)-based biomaterials have been recently utilised for CNS applications, closely mimicking the native tissue. dECM retains tissue-specific components, including proteoglycan as well as structural and functional proteins. Due to their unique composition, these biomaterials can stimulate sensitive repair mechanisms associated with CNS damages. Herein, we discuss the decellularisation of the brain and spinal cord as well as recellularisation of acellular matrix and the recent progress in the utilisation of brain and spinal cord dECM.

Prenatal GABAB Receptor Agonist Administration Corrects the Inheritance of Autism-Like Core Behaviors in Offspring of Mice Prenatally Exposed to Valproic Acid

This study was performed to evaluate the effects of prenatal baclofen (a GABAB receptor agonist) treatment on the inheritance of autism-like behaviors in valproic acid (VPA)-exposed mice. VPA model mice (first generation, F1) that were prenatally exposed to VPA exhibited robust core autism-like behaviors, and we found that oral administration of baclofen to F1 mice corrected their autism-like behavioral phenotypes at an early age. Based on a previous epigenetics study, we mated the F1 male offspring with litter females to produce the second generation (F2). The F2 male mice showed obvious inheritance of autism-like phenotypes from F1 mice, implying the heritability of autism symptoms in patients with prenatal VPA exposure. Furthermore, we found prenatal baclofen administration was associated with beneficial effects on the autism-like phenotype in F2 male mice. This may have involved corrections in the density of total/mature dendritic spines in the hippocampus (HC) and medial prefrontal cortex (mPFC), normalizing synaptic plasticity. In this research, GABAB receptor agonist administration corrected the core autism-like behaviors of F1 mice and protected against the inheritance of neurodevelopmental disorders in the offspring of F1 mice, suggesting the potential of early intervention with GABAB receptor agonists in the treatment of neurodevelopmental disorders.

Next-Generation Human Cerebral Organoids as Powerful Tools To Advance NeuroHIV Research

Long-term effective use of antiretroviral therapy (ART) among people with HIV (PWH) has significantly reduced the burden of disease, yet a cure for HIV has not been universally achieved, likely due to the persistence of an HIV reservoir. The central nervous system (CNS) is an understudied HIV sanctuary. Importantly, due to viral persistence in the brain, cognitive disturbances persist to various degrees at high rates in PWH despite suppressive ART. Given the complexity and accessibility of the CNS compartment and that it is a physiologically and anatomically unique immune site, human studies to reveal molecular mechanisms of viral entry, reservoir establishment, and the cellular and structural interactions leading to viral persistence and brain injury to advance a cure and either prevent or limit cognitive impairments in PWH remain challenging. Recent advances in human brain organoids show that they can mimic the intercellular dynamics of the human brain and may recapitulate many of the events involved in HIV infection of the brain (neuroHIV). Human brain organoids can be produced, spontaneously or with addition of growth factors and at immature or mature states, and have become stronger models to study neurovirulent viral infections of the CNS. While organoids provide opportunities to study neuroHIV, obstacles such as the need to incorporate microglia need to be overcome to fully utilize this model. Here, we review the current achievements in brain organoid biology and their relevance to neuroHIV research efforts.

Cultures and cures: neurodiversity and brain organoids

BACKGROUND

Research with cerebral organoids is beginning to make significant progress in understanding the etiology of autism spectrum disorder (ASD). Brain organoid models can be grown from the cells of donors with ASD. Researchers can explore the genetic, developmental, and other factors that may give rise to the varieties of autism. Researchers could study all of these factors together with brain organoids grown from cells originating from ASD individuals. This makes brain organoids unique from other forms of ASD research. They are like a multi-tool, one with significant versatility for the scope of ASD research and clinical applications. There is hope that brain organoids could one day be used for precision medicine, like developing tailored ASD drug treatments.

MAIN BODY

Brain organoid researchers often incorporate the medical model of disability when researching the origins of ASD, especially when the research has the specific aim of potentially finding tailored clinical treatments for ASD individuals. The neurodiversity movement-a developmental disability movement and paradigm that understands autism as a form of natural human diversity-will potentially disagree with approaches or aims of cerebral organoid research on ASD. Neurodiversity advocates incorporate a social model of disability into their movement, which focuses more on the social, attitudinal, and environmental barriers rather than biophysical or psychological deficits. Therefore, a potential conflict may arise between these perspectives on how to proceed with cerebral organoid research regarding neurodevelopmental conditions, especially ASD.

CONCLUSIONS

Here, we present these perspectives and give at least three initial recommendations to achieve a more holistic and inclusive approach to cerebral organoid research on ASD. These three initial starting points can build bridges between researchers and the neurodiversity movement. First, neurodiverse individuals should be included as co-creators in both the scientific process and research communication. Second, clinicians and neurodiverse communities should have open and respectful communication. Finally, we suggest a continual reconceptualization of illness, impairment, disability, behavior, and person.

Myogenic Differentiation of Stem Cells for Skeletal Muscle Regeneration

Stem cells have become a hot research topic in the field of regenerative medicine due to their self-renewal and differentiation capabilities. Skeletal muscle tissue is one of the most important tissues in the human body, and it is difficult to recover when severely damaged. However, conventional treatment methods can cause great pain to patients. Stem cell-based tissue engineering can repair skeletal muscle to the greatest extent with little damage. Therefore, the application of stem cells to skeletal muscle regeneration is very promising. In this review, we discuss scaffolds and stem cells for skeletal muscle regeneration and put forward our ideas for future development.

A Primer on Human Brain Organoids for the Neurosurgeon

Human brain organoids emerged in 2013 as a technology that, unlike prior in Vitro neural models, recapitulates brain development with a high degree of spatial and temporal fidelity. As the platform matured with more accurate reproduction of cerebral architecture, brain organoids became increasingly valuable for studying both normal cortical neurogenesis and a variety of congenital human brain disorders. While the majority of research utilizing human brain organoids has been in the realm of basic science, clinical applications are forthcoming. These present and future translational efforts have the potential to make a considerable impact on the field of neurosurgery. For example, glioma organoids are already being used to study tumor biology and drug responses, and adaptation for the investigation of other neurosurgery-relevant diseases is underway. Moreover, organoids are being explored as a structured neural substrate for repairing brain circuitry. Thus, we believe it is important for our field to be aware and have an accurate understanding of this emerging technology. In this review, we describe the key characteristics of human brain organoids, review their relevant translational applications, and discuss the ethical implications of their use through a neurosurgical lens.

Human iPSC-Based Modeling of Central Nerve System Disorders for Drug Discovery

A high-throughput drug screen identifies potentially promising therapeutics for clinical trials. However, limitations that persist in current disease modeling with limited physiological relevancy of human patients skew drug responses, hamper translation of clinical efficacy, and contribute to high clinical attritions. The emergence of induced pluripotent stem cell (iPSC) technology revolutionizes the paradigm of drug discovery. In particular, iPSC-based three-dimensional (3D) tissue engineering that appears as a promising vehicle of in vitro disease modeling provides more sophisticated tissue architectures and micro-environmental cues than a traditional two-dimensional (2D) culture. Here we discuss 3D based organoids/spheroids that construct the advanced modeling with evolved structural complexity, which propels drug discovery by exhibiting more human specific and diverse pathologies that are not perceived in 2D or animal models. We will then focus on various central nerve system (CNS) disease modeling using human iPSCs, leading to uncovering disease pathogenesis that guides the development of therapeutic strategies. Finally, we will address new opportunities of iPSC-assisted drug discovery with multi-disciplinary approaches from bioengineering to Omics technology. Despite technological challenges, iPSC-derived cytoarchitectures through interactions of diverse cell types mimic patients' CNS and serve as a platform for therapeutic development and personalized precision medicine.

Nuclear receptor corepressors in intellectual disability and autism

Autism spectrum disorder (ASD) is characterized by neurocognitive dysfunctions, such as impaired social interaction and language learning. Gene-environment interactions have a pivotal role in ASD pathogenesis. Nuclear receptor corepressors (NCORs) are transcription co-regulators physically associated with histone deacetylases (HDACs) and many known players in ASD etiology such as transducin β-like 1 X-linked receptor 1 and methyl-CpG binding protein 2. The epigenome-modifying NCOR complex is sensitive to many ASD risk factors, including HDAC inhibitor valproic acid and a variety of endocrine factors, xenobiotic chemicals, or metabolites that can directly bind to multiple nuclear receptors. Here, we review recent studies of NCORs in neurocognition using animal models and human genetics approaches. We discuss functional interplays between NCORs and other known players in ASD etiology. It is conceivable that the NCOR complex may bridge the in utero environmental risk factors of ASD with epigenetic remodeling and can serve as a converging point for many gene-environment interactions in the pathogenesis of ASD and intellectual disability.

Stem Cells for Improving the Treatment of Neurodevelopmental Disorders

Treatment options for neurodevelopmental disorders such as schizophrenia and autism are currently limited. Antipsychotics used to treat schizophrenia are not effective for all patients, do not target all symptoms of the disease, and have serious adverse side effects. There are currently no FDA-approved drugs to treat the core symptoms of autism. In an effort to develop new and more effective treatment strategies, stem cell technologies have been used to reprogram adult somatic cells into induced pluripotent stem cells, which can be differentiated into neuronal cells and even three-dimensional brain organoids. This new technology has the potential to elucidate the complex mechanisms that underlie neurodevelopmental disorders, offer more relevant platforms for drug discovery and personalized medicine, and may even be used to treat the disease.

Risk and Protective Factors in Autism Spectrum Disorders: A Case Control Study in the Lebanese Population

Autism spectrum disorders (ASD) are among the most common childhood neurodevelopmental disorders. Identification of risk and protective factors are necessary to improve the guidance of prevention and intervention strategies. Our study aims to determine the potential risk and protective factors in ASD in the Lebanese population. Our case-control study included 100 ASD patients and 100 healthy matched controls recruited from all the Lebanese districts. The data collected from the questionnaires was analyzed using SPSS 23.0. Independent Student T-test and Chi-Square test were carried out for the bivariate analysis of the data. In addition, the variables revealing a p-value < 0.05 were used for the multivariate logistic regression analysis. Multivitamins intake, especially omega 3 and vitamin B (Odds Ratio (OR) = 0.257; 95% Confidence Interval (CI) [0.115–0.579]), rich cereal diet (OR = 0.212; 95% CI [0.089–0.510]), and supplementation in iron during pregnancy (OR = 0.229; 95% CI [0.083–0.627]) were identified as protective factors against ASD. On the other hand, stress during pregnancy (OR = 6.339; 95% CI [2.845–14.125]), the presence of ASD patients in the family (OR = 7.878; 95% CI [1.877–33.065]) and the presence of attention deficit hyperactivity disorder (ADHD) patients in the family (OR = 6.981; 95% CI [1.362–35.789]) were associated with ASD. This study shed light on risk and protective factors associated with ASD in the Lebanese population. Further rigorous research, taking into consideration these factors, is needed to assist in early detection, prevention and subsequent intervention targeting ASD and its associated comorbidities, given that our study is not experimental and does not prove causality.

Is It Time to Start Transitioning From 2D to 3D Cell Culture?

Cell culture is an important and necessary process in drug discovery, cancer research, as well as stem cell study. Most cells are currently cultured using two-dimensional (2D) methods but new and improved methods that implement three-dimensional (3D) cell culturing techniques suggest compelling evidence that much more advanced experiments can be performed yielding valuable insights. When performing 3D cell culture experiments, the cell environment can be manipulated to mimic that of a cell in vivo and provide more accurate data about cell-to-cell interactions, tumor characteristics, drug discovery, metabolic profiling, stem cell research, and other types of diseases. Scaffold based techniques such as hydrogel-based support, polymeric hard material-based support, hydrophilic glass fiber, and organoids are employed, and each provide their own advantages and applications. Likewise, there are also scaffold free techniques used such as hanging drop microplates, magnetic levitation, and spheroid microplates with ultra-low attachment coating. 3D cell culture has the potential to provide alternative ways to study organ behavior via the use of organoids and is expected to eventually bridge the gap between 2D cell culture and animal models. The present review compares 2D cell culture to 3D cell culture, provides the details surrounding the different 3D culture techniques, as well as focuses on the present and future applications of 3D cell culture.

Detecting multiple differentially methylated CpG sites and regions related to dimensional psychopathology in youths

Background

Psychiatric symptomatology during late childhood and early adolescence tends to persist later in life. In the present longitudinal study, we aimed to identify changes in genome-wide DNA methylation patterns that were associated with the emergence of psychopathology in youths from the Brazilian High-Risk Cohort (HRC) for psychiatric disorders. Moreover, for the differentially methylated genes, we verified whether differences in DNA methylation corresponded to differences in mRNA transcript levels by analyzing the gene expression levels in the blood and by correlating the variation of DNA methylation values with the variation of mRNA levels of the same individuals. Finally, we examined whether the variations in DNA methylation and mRNA levels were correlated with psychopathology measurements over time.

Methods

We selected 24 youths from the HRC who presented with an increase in dimensional psychopathology at a 3-year follow-up as measured by the Child Behavior Checklist (CBCL). The DNA methylation and gene expression data were compared in peripheral blood samples (n = 48) obtained from the 24 youths before and after developing psychopathology. We implemented a methodological framework to reduce the effect of chronological age on DNA methylation using an independent population of 140 youths and the effect of puberty using data from the literature.

Results

We identified 663 differentially methylated positions (DMPs) and 90 differentially methylated regions (DMRs) associated with the emergence of psychopathology. We observed that 15 DMPs were mapped to genes that were differentially expressed in the blood; among these, we found a correlation between the DNA methylation and mRNA levels of RB1CC1 and a correlation between the CBCL and mRNA levels of KMT2E. Of the DMRs, three genes were differentially expressed: ASCL2, which is involved in neurogenesis; HLA-E, which is mapped to the MHC loci; and RPS6KB1, the gene expression of which was correlated with an increase in the CBCL between the time points.

Conclusions

We observed that changes in DNA methylation and, consequently, in gene expression in the peripheral blood occurred concurrently with the emergence of dimensional psychopathology in youths. Therefore, epigenomic modulations might be involved in the regulation of an individual’s development of psychopathology.

Distinct Vulnerability and Resilience of Human Neuroprogenitor Subtypes in Cerebral Organoid Model of Prenatal Hypoxic Injury

Prenatal hypoxic injury (HI) is a leading cause of neurological disability. The immediate and long-term effects of hypoxia on progenitor homeostasis and developmental progression during early human brain development remain unclear. This gap is due to difficulty to access human fetal brain tissues and inadequate animal models to study human corticogenesis. Recent optimizations of cerebral organoid models derived from human embryonic stem (ES) cells present new opportunities to investigate pathophysiology of prenatal HI. Here, we implemented a transient HI model using human cerebral organoids with dorsal forebrain specification. We demonstrated that transient hypoxia resulted in immediate and prolonged apoptosis in cerebral organoids, with outer radial glia (oRG), a progenitor population more prominent in primates, and differentiating neuroblasts/immature neurons suffering larger losses. In contrast, neural stem cells in ventricular zone displayed relative resilience to HI and exhibited a shift of cleavage plane angle favoring symmetric division, thereby providing a mechanism to replenish the stem cell pool. Furthermore, we defined the vulnerable window and neurodifferentiation stages that are particularly sensitive to HI. Understanding cell type-specific and stage-dependent effects of prenatal HI on survival and mitotic behavior of human neuroprogenitor subtypes during early human corticogenesis helps elucidate the etiology of neurodevelopmental disorders, and provides a therapeutic starting point to protect the vulnerable populations at critical timeframes.

Modelling Protein Synthesis as A Biomarker in Fragile X Syndrome Patient-Derived Cells

The most conserved molecular phenotype of Fragile X Syndrome (FXS) is aberrant protein synthesis. This has been validated in a variety of experimental model systems from zebrafish to rats, patient-derived lymphoblasts and fibroblasts. With the advent of personalized medicine paradigms, patient-derived cells and their derivatives are gaining more translational importance, not only to model disease in a dish, but also for biomarker discovery. Here we review past and current practices of measuring protein synthesis in FXS, studies in patient derived cells and the inherent challenges in measuring protein synthesis in them to offer usable avenues of modeling this important metabolic metric for further biomarker development.

Autism, spectrum or clusters? An EEG coherence study

BACKGROUND

Autism prevalence continues to grow, yet a universally agreed upon etiology is lacking despite manifold evidence of abnormalities especially in terms of genetics and epigenetics. The authors postulate that the broad definition of an omnibus 'spectrum disorder' may inhibit delineation of meaningful clinical correlations. This paper presents evidence that an objectively defined, EEG based brain measure may be helpful in illuminating the autism spectrum versus subgroups (clusters) question.

METHODS

Forty objectively defined EEG coherence factors created in prior studies demonstrated reliable separation of neuro-typical controls from subjects with autism, and reliable separation of subjects with Asperger's syndrome from all other subjects within the autism spectrum and from neurotypical controls. In the current study, these forty previously defined EEG coherence factors were used prospectively within a large (N = 430) population of subjects with autism in order to determine quantitatively the potential existence of separate clusters within this population.

RESULTS

By use of a recently published software package, NbClust, the current investigation determined that the 40 EEG coherence factors reliably identified two distinct clusters within the larger population of subjects with autism. These two clusters demonstrated highly significant differences. Of interest, many more subjects with Asperger's syndrome fell into one rather than the other cluster.

CONCLUSIONS

EEG coherence factors provide evidence of two highly significant separate clusters within the subject population with autism. The establishment of a unitary "Autism Spectrum Disorder" does a disservice to patients and clinicians, hinders much needed scientific exploration, and likely leads to less than optimal educational and/or interventional efforts.

Compartmentalized Devices as Tools for Investigation of Human Brain Network Dynamics

Neuropsychiatric disorders have traditionally been difficult to study due to the complexity of the human brain and limited availability of human tissue. Induced pluripotent stem (iPS) cells provide a promising avenue to further our understanding of human disease mechanisms, but traditional 2D cell cultures can only provide a limited view of the neural circuits. To better model complex brain neurocircuitry, compartmentalized culturing systems and 3D organoids have been developed. Early compartmentalized devices demonstrated how neuronal cell bodies can be isolated both physically and chemically from neurites. Soft lithographic approaches have advanced this approach and offer the tools to construct novel model platforms, enabling circuit-level studies of disease, which can accelerate mechanistic studies and drug candidate screening. In this review, we describe some of the common technologies used to develop such systems and discuss how these lithographic techniques have been used to advance our understanding of neuropsychiatric disease. Finally, we address other in vitro model platforms such as 3D culture systems and organoids and compare these models with compartmentalized models. We ask important questions regarding how we can further harness iPS cells in these engineered culture systems for the development of improved in vitro models. Developmental Dynamics 248:65-77, 2019. © 2018 Wiley Periodicals, Inc.

Systemic Oxidative Stress: A key Point in Neurodegeneration - A Review

Systemic oxidative stress (SOS) has an important role in the mechanisms activation of neuronal death, involved in the neurodegenerative disease (ND) etiology. Brain is susceptible to oxidative stress injuries due to its high energy and metabolic request, therefore minimal imbalances of the redox state, as occurs in mitochondrial dysfunction, favour tissue injury and neuroinflammatory mechanisms activation. ND affect around the world about a billion people, without distinction of sex, educational level and economic status. Public measures generation that prevent ND from the SOS are possible promising therapeutic targets that could reduce the ND incidence. We discuss here the effects and mechanisms of SOS derived neurodegeneration, as well as the neuroinflammation repercussions for some cerebral structures.

Vascularization and Engraftment of Transplanted Human Cerebral Organoids in Mouse Cortex

Neural stem cells (NSCs) hold great promise for neural repair in cases of CNS injury and neurodegeneration; however, conventional cell-based transplant methods face the challenges of poor survival and inadequate neuronal differentiation. Here, we report an alternative, tissue-based transplantation strategy whereby cerebral organoids derived from human pluripotent stem cells (PSCs) were grafted into lesioned mouse cortex. Cerebral organoid transplants exhibited enhanced survival and robust vascularization from host brain as compared to transplants of dissociated neural progenitor cells (NPCs). Engrafted cerebral organoids harbored a large NSC pool and displayed multilineage neurodifferentiation at two and four weeks after grafting. Cerebral organoids therefore represent a promising alternative source to NSCs or fetal tissues for transplantation, as they contain a large set of neuroprogenitors and differentiated neurons in a structured organization. Engrafted cerebral organoids may also offer a unique experimental paradigm for modeling human neurodevelopment and CNS diseases in the context of vascularized cortical tissue.

Applications of Human Brain Organoids to Clinical Problems

Brain organoids are an exciting new technology with the potential to significantly change how diseases of the brain are understood and treated. These three-dimensional neural tissues are derived from the self-organization of pluripotent stem cells, and they recapitulate the developmental process of the human brain, including progenitor zones and rudimentary cortical layers. Brain organoids have been valuable in investigating different aspects of developmental neurobiology and comparative biology. Several characteristics of organoids also make them attractive as models of brain disorders. Data generated from human organoids are more generalizable to patients because of the match in species background. Personalized organoids also can be generated from patient-derived induced pluripotent stem cells. Furthermore, the three-dimensionality of brain organoids supports cellular, mechanical, and topographical cues that are lacking in planar systems. In this review, we discuss the translational potential of brain organoids, using the examples of Zika virus, autism-spectrum disorder, and glioblastoma multiforme to consider how they could contribute to disease modeling, personalized medicine, and testing of therapeutics. We then discuss areas of improvement in organoid technology that will enhance the translational potential of brain organoids, as well as the possibility of their use as substrates for repairing cerebral circuitry after injury. Developmental Dynamics 248:53-64, 2019. © 2018 Wiley Periodicals, Inc.

Modeling Neurological Diseases With Human Brain Organoids

The complexity and delicacy of human brain make it challenging to recapitulate its development, function and disorders. Brain organoids derived from human pluripotent stem cells (PSCs) provide a new tool to model both normal and pathological human brain, and greatly enhance our ability to study brain biology and diseases. Currently, human brain organoids are increasingly used in modeling neurological disorders and relative therapeutic discovery. This review article focuses on recent advances in human brain organoid system and its application in disease modeling. It also discusses the limitations and future perspective of human brain organoids in modeling neurological diseases.

Organoids Provide an Important Window on Inflammation in Cancer

Inflammation is a primary driver of cancer initiation and progression. However, the complex and dynamic nature of an inflammatory response make this a very difficult process to study. Organoids are a new model system where complex multicellular structures of primary cells can be grown in a 3D matrix to recapitulate the biology of the parent tissue. This experimental model offers several distinct advantages over alternatives including the ability to be genetically engineered, implanted in vivo and reliably derived from a wide variety of normal and cancerous tissue from patients. Furthermore, long-term organoid cultures reproduce many features of their source tissue, including genetic and epigenetic alterations and drug sensitivity. Perhaps most significantly, cancer organoids can be cocultured in a variety of different systems with a patients’ own immune cells, uniquely permitting the study of autologous cancer-immune cell interactions. Experiments with such systems promise to shed light on the mechanisms governing inflammation-associated cancer while also providing prognostic information on an individual patient’s responsiveness to immunotherapeutic anti-cancer drugs. Thanks to their ability to capture important features of the complex relationship between a cancer and its microenvironment, organoids are poised to become an essential tool for unraveling the mechanisms by which inflammation promotes cancer.