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Kyriakopoulou V, Davidson A, Chew A, Gupta N, Arichi T, Nosarti C, Rutherford MA. Characterisation of ASD traits among a cohort of children with isolated fetal ventriculomegaly. Nat Commun 2023; 14:1550. [PMID: 36941265 PMCID: PMC10027681 DOI: 10.1038/s41467-023-37242-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023] Open
Abstract
Fetal ventriculomegaly is the most common antenatally-diagnosed brain abnormality. Imaging studies in antenatal isolated ventriculomegaly demonstrate enlarged ventricles and cortical overgrowth which are also present in children with autism-spectrum disorder/condition (ASD). We investigate the presence of ASD traits in a cohort of children (n = 24 [20 males/4 females]) with isolated fetal ventriculomegaly, compared with 10 controls (n = 10 [6 males/4 females]). Neurodevelopmental outcome at school age included IQ, ASD traits (ADOS-2), sustained attention, neurological functioning, behaviour, executive function, sensory processing, co-ordination, and adaptive behaviours. Pre-school language development was assessed at 2 years. 37.5% of children, all male, in the ventriculomegaly cohort scored above threshold for autism/ASD classification. Pre-school language delay predicted an ADOS-2 autism/ASD classification with 73.3% specificity/66.7% sensitivity. Greater pre-school language delay was associated with more ASD symptoms. In this study, the neurodevelopment of children with isolated fetal ventriculomegaly, associated with altered cortical development, includes ASD traits, difficulties in sustained attention, working memory and sensation-seeking behaviours.
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Affiliation(s)
- Vanessa Kyriakopoulou
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK.
| | - Alice Davidson
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Andrew Chew
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
| | - Nidhi Gupta
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- Department of Paediatric Neurosciences, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Tomoki Arichi
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- Department of Paediatric Neurosciences, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Department of Bioengineering, Imperial College London, London, UK
| | - Chiara Nosarti
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Mary A Rutherford
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
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Wells MF, Nemesh J, Ghosh S, Mitchell JM, Salick MR, Mello CJ, Meyer D, Pietilainen O, Piccioni F, Guss EJ, Raghunathan K, Tegtmeyer M, Hawes D, Neumann A, Worringer KA, Ho D, Kommineni S, Chan K, Peterson BK, Raymond JJ, Gold JT, Siekmann MT, Zuccaro E, Nehme R, Kaykas A, Eggan K, McCarroll SA. Natural variation in gene expression and viral susceptibility revealed by neural progenitor cell villages. Cell Stem Cell 2023; 30:312-332.e13. [PMID: 36796362 PMCID: PMC10581885 DOI: 10.1016/j.stem.2023.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023]
Abstract
Human genome variation contributes to diversity in neurodevelopmental outcomes and vulnerabilities; recognizing the underlying molecular and cellular mechanisms will require scalable approaches. Here, we describe a "cell village" experimental platform we used to analyze genetic, molecular, and phenotypic heterogeneity across neural progenitor cells from 44 human donors cultured in a shared in vitro environment using algorithms (Dropulation and Census-seq) to assign cells and phenotypes to individual donors. Through rapid induction of human stem cell-derived neural progenitor cells, measurements of natural genetic variation, and CRISPR-Cas9 genetic perturbations, we identified a common variant that regulates antiviral IFITM3 expression and explains most inter-individual variation in susceptibility to the Zika virus. We also detected expression QTLs corresponding to GWAS loci for brain traits and discovered novel disease-relevant regulators of progenitor proliferation and differentiation such as CACHD1. This approach provides scalable ways to elucidate the effects of genes and genetic variation on cellular phenotypes.
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Affiliation(s)
- Michael F Wells
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Human Genetics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jana M Mitchell
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Insitro, South San Francisco, CA 94080, USA
| | | | - Curtis J Mello
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Olli Pietilainen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Federica Piccioni
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Ellen J Guss
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Kavya Raghunathan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Derek Hawes
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Anna Neumann
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Kathleen A Worringer
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Daniel Ho
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Sravya Kommineni
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Karrie Chan
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Brant K Peterson
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - Joseph J Raymond
- Department of Neuroscience, Novartis Institute for BioMedical Research, Cambridge, MA 02139, USA
| | - John T Gold
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Department of Biology, Davidson College, Davidson, NC 28035, USA
| | - Marco T Siekmann
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Emanuela Zuccaro
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | | | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA.
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Yde Ohki CM, Walter NM, Bender A, Rickli M, Ruhstaller S, Walitza S, Grünblatt E. Growth rates of human induced pluripotent stem cells and neural stem cells from attention-deficit hyperactivity disorder patients: a preliminary study. J Neural Transm (Vienna) 2023; 130:243-252. [PMID: 36800023 PMCID: PMC10033475 DOI: 10.1007/s00702-023-02600-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023]
Abstract
Attention-deficit hyperactivity disorder (ADHD) is a neurodevelopmental polygenic disorder that affects more than 5% of children and adolescents around the world. Genetic and environmental factors play important roles in ADHD etiology, which leads to a wide range of clinical outcomes and biological phenotypes across the population. Brain maturation delays of a 4-year lag are commonly found in patients, when compared to controls of the same age. Possible differences in cellular growth rates might reflect the clinical observations in ADHD patients. However, the cellular mechanisms are still not elucidated. To test this hypothesis, we analysed the proliferation of induced pluripotent stem cells (iPSCs) and neural stem cells (NSCs) derived from male children and adolescents diagnosed with ADHD and with genetic predisposition to it (assessed using polygenic risk scores), as well as their respective matched controls. In the current pilot study, it was noticeable that NSCs from the ADHD group proliferate less than controls, while no differences were seen at the iPSC developmental stage. Our results from two distinct proliferation methods indicate that the functional and structural delays found in patients might be associated with these in vitro phenotypic differences, but start at a distinct neurodevelopmental stage. These findings are the first ones in the field of disease modelling of ADHD and might be crucial to better understand the pathophysiology of this disorder.
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Affiliation(s)
- Cristine Marie Yde Ohki
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Biomedicine PhD Program, University of Zurich, Zurich, Switzerland
| | - Natalie Monet Walter
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Audrey Bender
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michelle Rickli
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sina Ruhstaller
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, Psychiatric University Hospital Zurich, University of Zurich, Zurich, Switzerland.
- Neuroscience Center Zurich, University of Zurich and the ETH Zurich, Zurich, Switzerland.
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
- Department of Child and Adolescent Psychiatry and Psychotherapy, Translational Molecular Psychiatry, Psychiatric University Hospital Zurich, University Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland.
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Mintz Hemed N, Melosh NA. An integrated perspective for the diagnosis and therapy of neurodevelopmental disorders - From an engineering point of view. Adv Drug Deliv Rev 2023; 194:114723. [PMID: 36746077 DOI: 10.1016/j.addr.2023.114723] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/14/2022] [Accepted: 01/29/2023] [Indexed: 02/05/2023]
Abstract
Neurodevelopmental disorders (NDDs) are complex conditions with largely unknown pathophysiology. While many NDD symptoms are familiar, the cause of these disorders remains unclear and may involve a combination of genetic, biological, psychosocial, and environmental risk factors. Current diagnosis relies heavily on behaviorally defined criteria, which may be biased by the clinical team's professional and cultural expectations, thus a push for new biological-based biomarkers for NDDs diagnosis is underway. Emerging new research technologies offer an unprecedented view into the electrical, chemical, and physiological activity in the brain and with further development in humans may provide clinically relevant diagnoses. These could also be extended to new treatment options, which can start to address the underlying physiological issues. When combined with current speech, language, occupational therapy, and pharmacological treatment these could greatly improve patient outcomes. The current review will discuss the latest technologies that are being used or may be used for NDDs diagnosis and treatment. The aim is to provide an inspiring and forward-looking view for future research in the field.
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Affiliation(s)
- Nofar Mintz Hemed
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Nicholas A Melosh
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
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Thongkorn S, Kanlayaprasit S, Kasitipradit K, Lertpeerapan P, Panjabud P, Hu VW, Jindatip D, Sarachana T. Investigation of autism-related transcription factors underlying sex differences in the effects of bisphenol A on transcriptome profiles and synaptogenesis in the offspring hippocampus. Biol Sex Differ 2023; 14:8. [PMID: 36803626 PMCID: PMC9940328 DOI: 10.1186/s13293-023-00496-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 02/07/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Bisphenol A (BPA) has been linked to susceptibility to autism spectrum disorder (ASD). Our recent studies have shown that prenatal BPA exposure disrupted ASD-related gene expression in the hippocampus, neurological functions, and behaviors associated with ASD in a sex-specific pattern. However, the molecular mechanisms underlying the effects of BPA are still unclear. METHODS Transcriptome data mining and molecular docking analyses were performed to identify ASD-related transcription factors (TFs) and their target genes underlying the sex-specific effects of prenatal BPA exposure. Gene ontology analysis was conducted to predict biological functions associated with these genes. The expression levels of ASD-related TFs and targets in the hippocampus of rat pups prenatally exposed to BPA were measured using qRT-PCR analysis. The role of the androgen receptor (AR) in BPA-mediated regulation of ASD candidate genes was investigated using a human neuronal cell line stably transfected with AR-expression or control plasmid. Synaptogenesis, which is a function associated with genes transcriptionally regulated by ASD-related TFs, was assessed using primary hippocampal neurons isolated from male and female rat pups prenatally exposed to BPA. RESULTS We found that there was a sex difference in ASD-related TFs underlying the effects of prenatal BPA exposure on the transcriptome profiles of the offspring hippocampus. In addition to the known BPA targets AR and ESR1, BPA could directly interact with novel targets (i.e., KDM5B, SMAD4, and TCF7L2). The targets of these TFs were also associated with ASD. Prenatal BPA exposure disrupted the expression of ASD-related TFs and targets in the offspring hippocampus in a sex-dependent manner. Moreover, AR was involved in the BPA-mediated dysregulation of AUTS2, KMT2C, and SMARCC2. Prenatal BPA exposure altered synaptogenesis by increasing synaptic protein levels in males but not in females, but the number of excitatory synapses was increased in female primary neurons only. CONCLUSIONS Our findings suggest that AR and other ASD-related TFs are involved in sex differences in the effects of prenatal BPA exposure on transcriptome profiles and synaptogenesis in the offspring hippocampus. These TFs may play an essential role in an increased ASD susceptibility associated with endocrine-disrupting chemicals, particularly BPA, and the male bias of ASD.
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Affiliation(s)
- Surangrat Thongkorn
- grid.7922.e0000 0001 0244 7875Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Songphon Kanlayaprasit
- grid.7922.e0000 0001 0244 7875SYstems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Wangmai, Pathumwan, Bangkok, 10330 Thailand
| | - Kasidit Kasitipradit
- grid.7922.e0000 0001 0244 7875Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Pattanachat Lertpeerapan
- grid.7922.e0000 0001 0244 7875Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Pawinee Panjabud
- grid.7922.e0000 0001 0244 7875Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Valerie W. Hu
- grid.253615.60000 0004 1936 9510Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, The George Washington University, Washington, DC USA
| | - Depicha Jindatip
- grid.7922.e0000 0001 0244 7875SYstems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Wangmai, Pathumwan, Bangkok, 10330 Thailand ,grid.7922.e0000 0001 0244 7875Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tewarit Sarachana
- SYstems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Wangmai, Pathumwan, Bangkok, 10330, Thailand.
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Mushtaq A, Mir US, Altaf M. Multifaceted functions of RNA-binding protein vigilin in gene silencing, genome stability, and autism-related disorders. J Biol Chem 2023; 299:102988. [PMID: 36758804 PMCID: PMC10011833 DOI: 10.1016/j.jbc.2023.102988] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
RNA-binding proteins (RBPs) are emerging as important players in regulating eukaryotic gene expression and genome stability. Specific RBPs have been shown to mediate various chromatin-associated processes ranging from transcription to gene silencing and DNA repair. One of the prominent classes of RBPs is the KH domain-containing proteins. Vigilin, an evolutionarily conserved KH domain-containing RBP has been shown to be associated with diverse biological processes like RNA transport and metabolism, sterol metabolism, chromosome segregation, and carcinogenesis. We have previously reported that vigilin is essential for heterochromatin-mediated gene silencing in fission yeast. More recently, we have identified that vigilin in humans plays a critical role in efficient repair of DNA double-stranded breaks and functions in homology-directed DNA repair. In this review, we highlight the multifaceted functions of vigilin and discuss the findings in the context of gene expression, genome organization, cancer, and autism-related disorders.
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Affiliation(s)
- Arjamand Mushtaq
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Ulfat Syed Mir
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Mohammad Altaf
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir, India.
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Transition from Animal-Based to Human Induced Pluripotent Stem Cells (iPSCs)-Based Models of Neurodevelopmental Disorders: Opportunities and Challenges. Cells 2023; 12:cells12040538. [PMID: 36831205 PMCID: PMC9954744 DOI: 10.3390/cells12040538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) arise from the disruption of highly coordinated mechanisms underlying brain development, which results in impaired sensory, motor and/or cognitive functions. Although rodent models have offered very relevant insights to the field, the translation of findings to clinics, particularly regarding therapeutic approaches for these diseases, remains challenging. Part of the explanation for this failure may be the genetic differences-some targets not being conserved between species-and, most importantly, the differences in regulation of gene expression. This prompts the use of human-derived models to study NDDS. The generation of human induced pluripotent stem cells (hIPSCs) added a new suitable alternative to overcome species limitations, allowing for the study of human neuronal development while maintaining the genetic background of the donor patient. Several hIPSC models of NDDs already proved their worth by mimicking several pathological phenotypes found in humans. In this review, we highlight the utility of hIPSCs to pave new paths for NDD research and development of new therapeutic tools, summarize the challenges and advances of hIPSC-culture and neuronal differentiation protocols and discuss the best way to take advantage of these models, illustrating this with examples of success for some NDDs.
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Bao B, Zahiri J, Gazestani VH, Lopez L, Xiao Y, Kim R, Wen TH, Chiang AWT, Nalabolu S, Pierce K, Robasky K, Wang T, Hoekzema K, Eichler EE, Lewis NE, Courchesne E. A predictive ensemble classifier for the gene expression diagnosis of ASD at ages 1 to 4 years. Mol Psychiatry 2023; 28:822-833. [PMID: 36266569 PMCID: PMC9908553 DOI: 10.1038/s41380-022-01826-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 09/13/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Abstract
Autism Spectrum Disorder (ASD) diagnosis remains behavior-based and the median age of diagnosis is ~52 months, nearly 5 years after its first-trimester origin. Accurate and clinically-translatable early-age diagnostics do not exist due to ASD genetic and clinical heterogeneity. Here we collected clinical, diagnostic, and leukocyte RNA data from 240 ASD and typically developing (TD) toddlers (175 toddlers for training and 65 for test). To identify gene expression ASD diagnostic classifiers, we developed 42,840 models composed of 3570 gene expression feature selection sets and 12 classification methods. We found that 742 models had AUC-ROC ≥ 0.8 on both Training and Test sets. Weighted Bayesian model averaging of these 742 models yielded an ensemble classifier model with accurate performance in Training and Test gene expression datasets with ASD diagnostic classification AUC-ROC scores of 85-89% and AUC-PR scores of 84-92%. ASD toddlers with ensemble scores above and below the overall ASD ensemble mean of 0.723 (on a scale of 0 to 1) had similar diagnostic and psychometric scores, but those below this ASD ensemble mean had more prenatal risk events than TD toddlers. Ensemble model feature genes were involved in cell cycle, inflammation/immune response, transcriptional gene regulation, cytokine response, and PI3K-AKT, RAS and Wnt signaling pathways. We additionally collected targeted DNA sequencing smMIPs data on a subset of ASD risk genes from 217 of the 240 ASD and TD toddlers. This DNA sequencing found about the same percentage of SFARI Level 1 and 2 ASD risk gene mutations in TD (12 of 105) as in ASD (13 of 112) toddlers, and classification based only on the presence of mutation in these risk genes performed at a chance level of 49%. By contrast, the leukocyte ensemble gene expression classifier correctly diagnostically classified 88% of TD and ASD toddlers with ASD risk gene mutations. Our ensemble ASD gene expression classifier is diagnostically predictive and replicable across different toddler ages, races, and ethnicities; out-performs a risk gene mutation classifier; and has potential for clinical translation.
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Affiliation(s)
- Bokan Bao
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Javad Zahiri
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Vahid H Gazestani
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Linda Lopez
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Yaqiong Xiao
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Center for Language and Brain, Shenzhen Institute of Neuroscience, Shenzhen, China
| | - Raphael Kim
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Teresa H Wen
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Austin W T Chiang
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Srinivasa Nalabolu
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Karen Pierce
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA
| | - Kimberly Robasky
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, US
- School of Information and Library Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Carolina Health and Informatics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tianyun Wang
- Department of Medical Genetics, Center for Medical Genetics, Peking University Health Science Center, 100191, Beijing, China
- Neuroscience Research Institute, Peking University; Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, 100191, Beijing, China
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| | - Eric Courchesne
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA, USA.
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Sathyanarayanan A, Mueller TT, Ali Moni M, Schueler K, Baune BT, Lio P, Mehta D, Baune BT, Dierssen M, Ebert B, Fabbri C, Fusar-Poli P, Gennarelli M, Harmer C, Howes OD, Janzing JGE, Lio P, Maron E, Mehta D, Minelli A, Nonell L, Pisanu C, Potier MC, Rybakowski F, Serretti A, Squassina A, Stacey D, van Westrhenen R, Xicota L. Multi-omics data integration methods and their applications in psychiatric disorders. Eur Neuropsychopharmacol 2023; 69:26-46. [PMID: 36706689 DOI: 10.1016/j.euroneuro.2023.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/22/2022] [Accepted: 01/02/2023] [Indexed: 01/27/2023]
Abstract
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.
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Affiliation(s)
- Anita Sathyanarayanan
- Queensland University of Technology, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Kelvin Grove, Queensland 4059, Australia
| | - Tamara T Mueller
- Institute for Artificial Intelligence and Informatics in Medicine, TU Munich, 80333 Munich, Germany
| | - Mohammad Ali Moni
- Artificial Intelligence and Digital Health Data Science, School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Katja Schueler
- Clinic for Psychosomatics, Hospital zum Heiligen Geist, Frankfurt am Main, Germany; Frankfurt Psychoanalytic Institute, Frankfurt am Main, Germany
| | - Bernhard T Baune
- Department of Psychiatry and Psychotherapy, University of Münster, Germany; Department of Psychiatry, Melbourne Medical School, University of Melbourne, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Australia
| | - Pietro Lio
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Divya Mehta
- Queensland University of Technology, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Kelvin Grove, Queensland 4059, Australia.
| | | | - Bernhard T Baune
- Department of Psychiatry and Psychotherapy, University of Münster, Germany; Department of Psychiatry, Melbourne Medical School, University of Melbourne, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Australia
| | - Mara Dierssen
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bjarke Ebert
- Medical Strategy & Communication, H. Lundbeck A/S, Valby, Denmark
| | - Chiara Fabbri
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy; Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Paolo Fusar-Poli
- Early Psychosis: Intervention and Clinical-detection (EPIC) Lab, Department of Psychosis Studies, King's College London, United Kingdom; Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia; Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | | | - Oliver D Howes
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; Psychiatric Imaging, Medical Research Council Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | | | - Pietro Lio
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Eduard Maron
- Department of Psychiatry, University of Tartu, Tartu, Estonia; Centre for Neuropsychopharmacology, Division of Brain Sciences, Imperial College London, London, United Kingdom; Documental Ltd, Tallin, Estonia; West Tallinn Central Hospital, Tallinn, Estonia
| | - Divya Mehta
- Queensland University of Technology, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Kelvin Grove, Queensland 4059, Australia
| | - Alessandra Minelli
- Department of Molecular and Translational Medicine, University of Brescia; Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Lara Nonell
- MARGenomics, IMIM (Hospital del Mar Research Institute), Barcelona, Spain
| | - Claudia Pisanu
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | | | - Filip Rybakowski
- Department of Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | - Alessandro Serretti
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | - David Stacey
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Roos van Westrhenen
- Parnassia Psychiatric Institute, Amsterdam, the Netherlands; Department of Psychiatry and Neuropsychology, Faculty of Health and Sciences, Maastricht University, Maastricht, the Netherlands; Institute of Psychiatry, Psychology & Neuroscience (IoPPN) King's College London, United Kingdom
| | - Laura Xicota
- Paris Brain Institute ICM, Salpetriere Hospital, Paris, France
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Differential vulnerability of adult neurogenic niches to dosage of the neurodevelopmental-disorder linked gene Foxg1. Mol Psychiatry 2023; 28:497-514. [PMID: 35318461 PMCID: PMC9812795 DOI: 10.1038/s41380-022-01497-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 01/13/2023]
Abstract
The transcription factor FOXG1 serves pleiotropic functions in brain development ranging from the regulation of precursor proliferation to the control of cortical circuit formation. Loss-of-function mutations and duplications of FOXG1 are associated with neurodevelopmental disorders in humans illustrating the importance of FOXG1 dosage for brain development. Aberrant FOXG1 dosage has been found to disrupt the balanced activity of glutamatergic and GABAergic neurons, but the underlying mechanisms are not fully understood. We report that FOXG1 is expressed in the main adult neurogenic niches in mice, i.e. the hippocampal dentate gyrus and the subependymal zone/olfactory bulb system, where neurogenesis of glutamatergic and GABAergic neurons persists into adulthood. These niches displayed differential vulnerability to increased FOXG1 dosage: high FOXG1 levels severely compromised survival and glutamatergic dentate granule neuron fate acquisition in the hippocampal neurogenic niche, but left neurogenesis of GABAergic neurons in the subependymal zone/olfactory bulb system unaffected. Comparative transcriptomic analyses revealed a significantly higher expression of the apoptosis-linked nuclear receptor Nr4a1 in FOXG1-overexpressing hippocampal neural precursors. Strikingly, pharmacological interference with NR4A1 function rescued FOXG1-dependent death of hippocampal progenitors. Our results reveal differential vulnerability of neuronal subtypes to increased FOXG1 dosage and suggest that activity of a FOXG1/NR4A1 axis contributes to such subtype-specific response.
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Dixon TA, Muotri AR. Advancing preclinical models of psychiatric disorders with human brain organoid cultures. Mol Psychiatry 2023; 28:83-95. [PMID: 35948659 PMCID: PMC9812789 DOI: 10.1038/s41380-022-01708-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 01/11/2023]
Abstract
Psychiatric disorders are often distinguished from neurological disorders in that the former do not have characteristic lesions or findings from cerebrospinal fluid, electroencephalograms (EEGs), or brain imaging, and furthermore do not have commonly recognized convergent mechanisms. Psychiatric disorders commonly involve clinical diagnosis of phenotypic behavioral disturbances of mood and psychosis, often with a poorly understood contribution of environmental factors. As such, psychiatric disease has been challenging to model preclinically for mechanistic understanding and pharmaceutical development. This review compares commonly used animal paradigms of preclinical testing with evolving techniques of induced pluripotent cell culture with a focus on emerging three-dimensional models. Advances in complexity of 3D cultures, recapitulating electrical activity in utero, and disease modeling of psychosis, mood, and environmentally induced disorders are reviewed. Insights from these rapidly expanding technologies are discussed as they pertain to the utility of human organoid and other models in finding novel research directions, validating pharmaceutical action, and recapitulating human disease.
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Affiliation(s)
- Thomas Anthony Dixon
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
| | - Alysson R. Muotri
- grid.266100.30000 0001 2107 4242Department of Pediatrics and Department of Cellular & Molecular Medicine, University of California San Diego, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, Archealization Center (ArchC), La Jolla, CA 92037 USA
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62
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Li J, Xu X, Liu J, Zhang S, Tan X, Li Z, Zhang J, Wang Z. Decoding microRNAs in autism spectrum disorder. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 30:535-546. [PMID: 36457702 PMCID: PMC9685394 DOI: 10.1016/j.omtn.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Autism spectrum disorder (ASD)-a congenital mental disorder accompanied by social dysfunction and stereotyped behaviors-has attracted a great deal of attention worldwide. A combination of genetic and environmental factors may determine the pathogenesis of ASD. Recent research of multiple ASD models indicates that microRNAs (miRNAs) play a central role at the onset and progression of ASD by repressing the translation of key mRNAs in neural development and functions. As such, miRNAs show great potential to serve as biomarkers for ASD diagnosis or prognosis and therapeutic targets for the treatment of ASD. In this review, we discuss the regulatory mechanisms by which miRNAs influence ASD phenotypes through various in vivo and in vitro models, including necropsy specimens, animal models, cellular models, and, in particular, induced pluripotent stem cells derived from patients with ASD. We then discuss the potential of miRNA-based therapeutic strategies for ASD currently being evaluated in preclinical studies.
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Affiliation(s)
- Jinyu Li
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, Shandong 266071, China
| | - Xiaohui Xu
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, Shandong 266071, China
| | - Jiane Liu
- Department of Reproductive Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
| | - Sudan Zhang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, Shandong 266071, China
| | - Xiaohua Tan
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, Shandong 266071, China
| | - Zhiqiang Li
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University, Qingdao Branch of SJTU Bio-X Institutes, Qingdao University, Qingdao, Shandong 266003, China
| | - Jian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Zheng Wang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, Shandong 266071, China
- Department of Reproductive Medicine, the Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, China
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63
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Price KM, Wigg KG, Eising E, Feng Y, Blokland K, Wilkinson M, Kerr EN, Guger SL, Fisher SE, Lovett MW, Strug LJ, Barr CL. Hypothesis-driven genome-wide association studies provide novel insights into genetics of reading disabilities. Transl Psychiatry 2022; 12:495. [PMID: 36446759 PMCID: PMC9709072 DOI: 10.1038/s41398-022-02250-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/24/2022] [Accepted: 11/03/2022] [Indexed: 11/30/2022] Open
Abstract
Reading Disability (RD) is often characterized by difficulties in the phonology of the language. While the molecular mechanisms underlying it are largely undetermined, loci are being revealed by genome-wide association studies (GWAS). In a previous GWAS for word reading (Price, 2020), we observed that top single-nucleotide polymorphisms (SNPs) were located near to or in genes involved in neuronal migration/axon guidance (NM/AG) or loci implicated in autism spectrum disorder (ASD). A prominent theory of RD etiology posits that it involves disturbed neuronal migration, while potential links between RD-ASD have not been extensively investigated. To improve power to identify associated loci, we up-weighted variants involved in NM/AG or ASD, separately, and performed a new Hypothesis-Driven (HD)-GWAS. The approach was applied to a Toronto RD sample and a meta-analysis of the GenLang Consortium. For the Toronto sample (n = 624), no SNPs reached significance; however, by gene-set analysis, the joint contribution of ASD-related genes passed the threshold (p~1.45 × 10-2, threshold = 2.5 × 10-2). For the GenLang Cohort (n = 26,558), SNPs in DOCK7 and CDH4 showed significant association for the NM/AG hypothesis (sFDR q = 1.02 × 10-2). To make the GenLang dataset more similar to Toronto, we repeated the analysis restricting to samples selected for reading/language deficits (n = 4152). In this GenLang selected subset, we found significant association for a locus intergenic between BTG3-C21orf91 for both hypotheses (sFDR q < 9.00 × 10-4). This study contributes candidate loci to the genetics of word reading. Data also suggest that, although different variants may be involved, alleles implicated in ASD risk may be found in the same genes as those implicated in word reading. This finding is limited to the Toronto sample suggesting that ascertainment influences genetic associations.
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Affiliation(s)
- Kaitlyn M Price
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Karen G Wigg
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Else Eising
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Yu Feng
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Kirsten Blokland
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Margaret Wilkinson
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth N Kerr
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Sharon L Guger
- Department of Psychology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Maureen W Lovett
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Lisa J Strug
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Departments of Statistical Sciences and Computer Science, Faculty of Arts and Science and Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Cathy L Barr
- Division of Experimental and Translational Neuroscience, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.
- Program in Neuroscience and Mental Health, Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada.
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64
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Griffin A, Mahesh A, Tiwari VK. Disruption of the gene regulatory programme in neurodevelopmental disorders. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194860. [PMID: 36007842 DOI: 10.1016/j.bbagrm.2022.194860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Cortical development consists of a series of synchronised events, including fate transition of cortical progenitors, neuronal migration, specification and connectivity. It is becoming clear that gene expression programs governing these events rely on the interplay between signalling molecules, transcription factors and epigenetic mechanisms. When genetic or environmental factors disrupt expression of genes involved in important brain development processes, neurodevelopmental disorders can occur. This review aims to highlight how recent advances in technologies have helped uncover and imitate the gene regulatory mechanisms commonly disrupted in neurodevelopmental disorders.
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Affiliation(s)
- Aoife Griffin
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queens University, Belfast BT9 7BL, United Kingdom
| | - Arun Mahesh
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queens University, Belfast BT9 7BL, United Kingdom
| | - Vijay K Tiwari
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry & Biomedical Science, Queens University, Belfast BT9 7BL, United Kingdom.
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65
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Thudium S, Palozola K, L'Her É, Korb E. Identification of a transcriptional signature found in multiple models of ASD and related disorders. Genome Res 2022; 32:1642-1654. [PMID: 36104286 PMCID: PMC9528985 DOI: 10.1101/gr.276591.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022]
Abstract
Epigenetic regulation plays a critical role in many neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD). In particular, many such disorders are the result of mutations in genes that encode chromatin-modifying proteins. However, although these disorders share many features, it is unclear whether they also share gene expression disruptions resulting from the aberrant regulation of chromatin. We examined five chromatin modifiers that are all linked to ASD despite their different roles in regulating chromatin. Specifically, we depleted ASH1L, CHD8, CREBBP, EHMT1, and NSD1 in parallel in a highly controlled neuronal culture system. We then identified sets of shared genes, or transcriptional signatures, that are differentially expressed following loss of multiple ASD-linked chromatin modifiers. We examined the functions of genes within the transcriptional signatures and found an enrichment in many neurotransmitter transport genes and activity-dependent genes. In addition, these genes are enriched for specific chromatin features such as bivalent domains that allow for highly dynamic regulation of gene expression. The down-regulated transcriptional signature is also observed within multiple mouse models of NDDs that result in ASD, but not those only associated with intellectual disability. Finally, the down-regulated transcriptional signature can distinguish between control and idiopathic ASD patient iPSC-derived neurons as well as postmortem tissue, demonstrating that this gene set is relevant to the human disorder. This work identifies a transcriptional signature that is found within many neurodevelopmental syndromes, helping to elucidate the link between epigenetic regulation and the underlying cellular mechanisms that result in ASD.
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Affiliation(s)
- Samuel Thudium
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Katherine Palozola
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Éloïse L'Her
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Erica Korb
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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66
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Baldassari S, Cervetto C, Amato S, Fruscione F, Balagura G, Pelassa S, Musante I, Iacomino M, Traverso M, Corradi A, Scudieri P, Maura G, Marcoli M, Zara F. Vesicular Glutamate Release from Feeder-FreehiPSC-Derived Neurons. Int J Mol Sci 2022; 23:ijms231810545. [PMID: 36142455 PMCID: PMC9501332 DOI: 10.3390/ijms231810545] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Human-induced pluripotent stem cells (hiPSCs) represent one of the main and powerful tools for the in vitro modeling of neurological diseases. Standard hiPSC-based protocols make use of animal-derived feeder systems to better support the neuronal differentiation process. Despite their efficiency, such protocols may not be appropriate to dissect neuronal specific properties or to avoid interspecies contaminations, hindering their future translation into clinical and drug discovery approaches. In this work, we focused on the optimization of a reproducible protocol in feeder-free conditions able to generate functional glutamatergic neurons. This protocol is based on a generation of neuroprecursor cells differentiated into human neurons with the administration in the culture medium of specific neurotrophins in a Geltrex-coated substrate. We confirmed the efficiency of this protocol through molecular analysis (upregulation of neuronal markers and neurotransmitter receptors assessed by gene expression profiling and expression of the neuronal markers at the protein level), morphological analysis, and immunfluorescence detection of pre-synaptic and post-synaptic markers at synaptic boutons. The hiPSC-derived neurons acquired Ca2+-dependent glutamate release properties as a hallmark of neuronal maturation. In conclusion, our study describes a new methodological approach to achieve feeder-free neuronal differentiation from hiPSC and adds a new tool for functional characterization of hiPSC-derived neurons.
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Affiliation(s)
- Simona Baldassari
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
| | - Chiara Cervetto
- Department of Pharmacy (DIFAR), Section of Pharmacology and Toxicology, University of Genoa, Viale Cembrano 4, 16148 Genova, Italy
- Interuniversity Center for the Promotion of the 3Rs Principles in Teaching and Research (Centro 3R), 56100 Pisa, Italy
- Correspondence: (C.C.); (M.M.)
| | - Sarah Amato
- Department of Pharmacy (DIFAR), Section of Pharmacology and Toxicology, University of Genoa, Viale Cembrano 4, 16148 Genova, Italy
| | - Floriana Fruscione
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
| | - Ganna Balagura
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Largo Paolo Daneo 3, 16132 Genova, Italy
| | - Simone Pelassa
- Department of Pharmacy (DIFAR), Section of Pharmacology and Toxicology, University of Genoa, Viale Cembrano 4, 16148 Genova, Italy
| | - Ilaria Musante
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Largo Paolo Daneo 3, 16132 Genova, Italy
| | - Michele Iacomino
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
| | - Monica Traverso
- Paediatric Neurology and Neuromuscular Disorders Unit, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
| | - Anna Corradi
- Department of Experimental Medicine, University of Genoa, Viale Benedetto XV 3, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Paolo Scudieri
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Largo Paolo Daneo 3, 16132 Genova, Italy
| | - Guido Maura
- Department of Pharmacy (DIFAR), Section of Pharmacology and Toxicology, University of Genoa, Viale Cembrano 4, 16148 Genova, Italy
| | - Manuela Marcoli
- Department of Pharmacy (DIFAR), Section of Pharmacology and Toxicology, University of Genoa, Viale Cembrano 4, 16148 Genova, Italy
- Interuniversity Center for the Promotion of the 3Rs Principles in Teaching and Research (Centro 3R), 56100 Pisa, Italy
- Center of Excellence for Biomedical Research, Viale Benedetto XV, 16132 Genova, Italy
- Correspondence: (C.C.); (M.M.)
| | - Federico Zara
- Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, Via G. Gaslini 5, 16147 Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Largo Paolo Daneo 3, 16132 Genova, Italy
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McAfee JC, Bell JL, Krupa O, Matoba N, Stein JL, Won H. Focus on your locus with a massively parallel reporter assay. J Neurodev Disord 2022; 14:50. [PMID: 36085003 PMCID: PMC9463819 DOI: 10.1186/s11689-022-09461-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 09/01/2022] [Indexed: 01/01/2023] Open
Abstract
A growing number of variants associated with risk for neurodevelopmental disorders have been identified by genome-wide association and whole genome sequencing studies. As common risk variants often fall within large haplotype blocks covering long stretches of the noncoding genome, the causal variants within an associated locus are often unknown. Similarly, the effect of rare noncoding risk variants identified by whole genome sequencing on molecular traits is seldom known without functional assays. A massively parallel reporter assay (MPRA) is an assay that can functionally validate thousands of regulatory elements simultaneously using high-throughput sequencing and barcode technology. MPRA has been adapted to various experimental designs that measure gene regulatory effects of genetic variants within cis- and trans-regulatory elements as well as posttranscriptional processes. This review discusses different MPRA designs that have been or could be used in the future to experimentally validate genetic variants associated with neurodevelopmental disorders. Though MPRA has limitations such as it does not model genomic context, this assay can help narrow down the underlying genetic causes of neurodevelopmental disorders by screening thousands of sequences in one experiment. We conclude by describing future directions of this technique such as applications of MPRA for gene-by-environment interactions and pharmacogenetics.
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Affiliation(s)
- Jessica C McAfee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jessica L Bell
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Oleh Krupa
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Hyejung Won
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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68
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Purushotham SS, Reddy NMN, D'Souza MN, Choudhury NR, Ganguly A, Gopalakrishna N, Muddashetty R, Clement JP. A perspective on molecular signalling dysfunction, its clinical relevance and therapeutics in autism spectrum disorder. Exp Brain Res 2022; 240:2525-2567. [PMID: 36063192 DOI: 10.1007/s00221-022-06448-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022]
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are neurodevelopmental disorders that have become a primary clinical and social concern, with a prevalence of 2-3% in the population. Neuronal function and behaviour undergo significant malleability during the critical period of development that is found to be impaired in ID/ASD. Human genome sequencing studies have revealed many genetic variations associated with ASD/ID that are further verified by many approaches, including many mouse and other models. These models have facilitated the identification of fundamental mechanisms underlying the pathogenesis of ASD/ID, and several studies have proposed converging molecular pathways in ASD/ID. However, linking the mechanisms of the pathogenic genes and their molecular characteristics that lead to ID/ASD has progressed slowly, hampering the development of potential therapeutic strategies. This review discusses the possibility of recognising the common molecular causes for most ASD/ID based on studies from the available models that may enable a better therapeutic strategy to treat ID/ASD. We also reviewed the potential biomarkers to detect ASD/ID at early stages that may aid in diagnosis and initiating medical treatment, the concerns with drug failure in clinical trials, and developing therapeutic strategies that can be applied beyond a particular mutation associated with ASD/ID.
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Affiliation(s)
- Sushmitha S Purushotham
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Neeharika M N Reddy
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Michelle Ninochka D'Souza
- Centre for Brain Research, Indian Institute of Science Campus, CV Raman Avenue, Bangalore, 560 012, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, 560064, India
| | - Nilpawan Roy Choudhury
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Anusa Ganguly
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Niharika Gopalakrishna
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India
| | - Ravi Muddashetty
- Centre for Brain Research, Indian Institute of Science Campus, CV Raman Avenue, Bangalore, 560 012, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, 560064, India
| | - James P Clement
- Neuroscience Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, 560064, India.
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69
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Human-Induced Pluripotent Stem Cell Technology: Toward the Future of Personalized Psychiatry. J Pers Med 2022; 12:jpm12081340. [PMID: 36013289 PMCID: PMC9410334 DOI: 10.3390/jpm12081340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
The polygenic and multifactorial nature of many psychiatric disorders has hampered implementation of the personalized medicine approach in clinical practice. However, induced pluripotent stem cell (iPSC) technology has emerged as an innovative tool for patient-specific disease modeling to expand the pathophysiology knowledge and treatment perspectives in the last decade. Current technologies enable adult human somatic cell reprogramming into iPSCs to generate neural cells and direct neural cell conversion to model organisms that exhibit phenotypes close to human diseases, thereby effectively representing relevant aspects of neuropsychiatric disorders. In this regard, iPSCs reflect patient pathophysiology and pharmacological responsiveness, particularly when cultured under conditions that emulate spatial tissue organization in brain organoids. Recently, the application of iPSCs has been frequently associated with gene editing that targets the disease-causing gene to deepen the illness pathophysiology and to conduct drug screening. Moreover, gene editing has provided a unique opportunity to repair the putative causative genetic lesions in patient-derived cells. Here, we review the use of iPSC technology to model and potentially treat neuropsychiatric disorders by illustrating the key studies on a series of mental disorders, including schizophrenia, major depressive disorder, bipolar disorder, and autism spectrum disorder. Future perspectives will involve the development of organ-on-a-chip platforms that control the microenvironmental conditions so as to reflect individual pathophysiological by adjusting physiochemical parameters according to personal health data. This strategy could open new ways by which to build a disease model that considers individual variability and tailors personalized treatments.
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70
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de Toledo VHC, Feltrin AS, Barbosa AR, Tahira AC, Brentani H. Sex differences in gene regulatory networks during mid-gestational brain development. Front Hum Neurosci 2022; 16:955607. [PMID: 36061507 PMCID: PMC9428411 DOI: 10.3389/fnhum.2022.955607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Neurodevelopmental disorders differ considerably between males and females, and fetal brain development is one of the most critical periods to determine risk for these disorders. Transcriptomic studies comparing male and female fetal brain have demonstrated that the highest difference in gene expression occurs in sex chromosomes, but several autossomal genes also demonstrate a slight difference that has not been yet explored. In order to investigate biological pathways underlying fetal brain sex differences, we applied medicine network principles using integrative methods such as co-expression networks (CEMiTool) and regulatory networks (netZoo). The pattern of gene expression from genes in the same pathway tend to reflect biologically relevant phenomena. In this study, network analysis of fetal brain expression reveals regulatory differences between males and females. Integrating two different bioinformatics tools, our results suggest that biological processes such as cell cycle, cell differentiation, energy metabolism and extracellular matrix organization are consistently sex-biased. MSET analysis demonstrates that these differences are relevant to neurodevelopmental disorders, including autism.
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Affiliation(s)
- Victor Hugo Calegari de Toledo
- Departamento e Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Psicopatologia e Terapêutica Psiquiátrica (LIM23), Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Ana Carolina Tahira
- Laboratório de Expressão Gênica, Departamento de Parasitologia, Instituto Butantan, São Paulo, Brazil
| | - Helena Brentani
- Departamento e Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- Laboratório de Psicopatologia e Terapêutica Psiquiátrica (LIM23), Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
- *Correspondence: Helena Brentani
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71
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Keeratitanont K, Theerakulpisut D, Auvichayapat N, Suphakunpinyo C, Patjanasoontorn N, Tiamkao S, Tepmongkol S, Khiewvan B, Raruenrom Y, Srisuruk P, Paholpak S, Auvichayapat P. Brain laterality evaluated by F-18 fluorodeoxyglucose positron emission computed tomography in autism spectrum disorders. Front Mol Neurosci 2022; 15:901016. [PMID: 36034502 PMCID: PMC9399910 DOI: 10.3389/fnmol.2022.901016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/13/2022] [Indexed: 12/04/2022] Open
Abstract
Background and rationale Autism spectrum disorder (ASD) is a neuropsychiatric disorder that has no curative treatment. Little is known about the brain laterality in patients with ASD. F-18 fluorodeoxyglucose positron emission computed tomography (F-18 FDG PET/CT) is a neuroimaging technique that is suitable for ASD owing to its ability to detect whole brain functional abnormalities in a short time and is feasible in ASD patients. The purpose of this study was to evaluate brain laterality using F-18 FDG PET/CT in patients with high-functioning ASD. Materials and methods This case-control study recruited eight ASD patients who met the DSM-5 criteria, the recorded data of eight controls matched for age, sex, and handedness were also enrolled. The resting state of brain glucose metabolism in the regions of interest (ROIs) was analyzed using the Q.Brain software. Brain glucose metabolism and laterality index in each ROI of ASD patients were compared with those of the controls. The pattern of brain metabolism was analyzed using visual analysis and is reported in the data description. Results The ASD group’s overall brain glucose metabolism was lower than that of the control group in both the left and right hemispheres, with mean differences of 1.54 and 1.21, respectively. We found statistically lower mean glucose metabolism for ASD patients than controls in the left prefrontal lateral (Z = 1.96, p = 0.049). The left laterality index was found in nine ROIs for ASD and 11 ROIs for the control. The left laterality index in the ASD group was significantly lower than that in the control group in the prefrontal lateral (Z = 2.52, p = 0.012), precuneus (Z = 2.10, p = 0.036), and parietal inferior (Z = 1.96, p = 0.049) regions. Conclusion Individuals with ASD have lower brain glucose metabolism than control. In addition, the number of ROIs for left laterality index in the ASD group was lower than control. Left laterality defects may be one of the causes of ASD. This knowledge can be useful in the treatment of ASD by increasing the left-brain metabolism. This trial was registered in the Thai Clinical Trials Registry (TCTR20210705005).
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Affiliation(s)
- Keattichai Keeratitanont
- Division of Nuclear Medicine, Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Noninvasive Brain Stimulation Research Group of Thailand, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Daris Theerakulpisut
- Division of Nuclear Medicine, Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Narong Auvichayapat
- Noninvasive Brain Stimulation Research Group of Thailand, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Department of Pediatrics, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Chanyut Suphakunpinyo
- Noninvasive Brain Stimulation Research Group of Thailand, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Department of Pediatrics, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Niramol Patjanasoontorn
- Noninvasive Brain Stimulation Research Group of Thailand, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Department of Psychiatry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Somsak Tiamkao
- Noninvasive Brain Stimulation Research Group of Thailand, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Supatporn Tepmongkol
- Division of Nuclear Medicine, Department of Radiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Chulalongkorn University Biomedical Imaging Group (CUBIG), Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Benjapa Khiewvan
- Division of Nuclear Medicine, Department of Radiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yutapong Raruenrom
- Division of Nuclear Medicine, Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Piyawan Srisuruk
- Department of Educational Psychology and Counseling, Faculty of Education, Khon Kaen University, Khon Kaen, Thailand
- Research and Service Institute for Autism, Khon Kaen University, Khon Kaen, Thailand
| | - Suchat Paholpak
- Department of Psychiatry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Service Institute for Autism, Khon Kaen University, Khon Kaen, Thailand
| | - Paradee Auvichayapat
- Noninvasive Brain Stimulation Research Group of Thailand, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Service Institute for Autism, Khon Kaen University, Khon Kaen, Thailand
- *Correspondence: Paradee Auvichayapat,
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Girault JB, Donovan K, Hawks Z, Talovic M, Forsen E, Elison JT, Shen MD, Swanson MR, Wolff JJ, Kim SH, Nishino T, Davis S, Snyder AZ, Botteron KN, Estes AM, Dager SR, Hazlett HC, Gerig G, McKinstry R, Pandey J, Schultz RT, St John T, Zwaigenbaum L, Todorov A, Truong Y, Styner M, Pruett JR, Constantino JN, Piven J. Infant Visual Brain Development and Inherited Genetic Liability in Autism. Am J Psychiatry 2022; 179:573-585. [PMID: 35615814 PMCID: PMC9356977 DOI: 10.1176/appi.ajp.21101002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Autism spectrum disorder (ASD) is heritable, and younger siblings of ASD probands are at higher likelihood of developing ASD themselves. Prospective MRI studies of siblings report that atypical brain development precedes ASD diagnosis, although the link between brain maturation and genetic factors is unclear. Given that familial recurrence of ASD is predicted by higher levels of ASD traits in the proband, the authors investigated associations between proband ASD traits and brain development among younger siblings. METHODS In a sample of 384 proband-sibling pairs (89 pairs concordant for ASD), the authors examined associations between proband ASD traits and sibling brain development at 6, 12, and 24 months in key MRI phenotypes: total cerebral volume, cortical surface area, extra-axial cerebrospinal fluid, occipital cortical surface area, and splenium white matter microstructure. Results from primary analyses led the authors to implement a data-driven approach using functional connectivity MRI at 6 months. RESULTS Greater levels of proband ASD traits were associated with larger total cerebral volume and surface area and larger surface area and reduced white matter integrity in components of the visual system in siblings who developed ASD. This aligned with weaker functional connectivity between several networks and the visual system among all siblings during infancy. CONCLUSIONS The findings provide evidence that specific early brain MRI phenotypes of ASD reflect quantitative variation in familial ASD traits. Multimodal anatomical and functional convergence on cortical regions, fiber pathways, and functional networks involved in visual processing suggest that inherited liability has a role in shaping the prodromal development of visual circuitry in ASD.
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Affiliation(s)
- Jessica B Girault
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Educational Psychology (Wolff), University of Minnesota, Minneapolis;Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Kevin Donovan
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Zoë Hawks
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Muhamed Talovic
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Elizabeth Forsen
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Jed T Elison
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Mark D Shen
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Meghan R Swanson
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Jason J Wolff
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Sun Hyung Kim
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Tomoyuki Nishino
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Savannah Davis
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Abraham Z Snyder
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Kelly N Botteron
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Annette M Estes
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Stephen R Dager
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Heather C Hazlett
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Guido Gerig
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Robert McKinstry
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Juhi Pandey
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Robert T Schultz
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Tanya St John
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Lonnie Zwaigenbaum
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Alexandre Todorov
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Young Truong
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Martin Styner
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - John R Pruett
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - John N Constantino
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
| | - Joseph Piven
- Carolina Institute for Developmental Disabilities (Girault, Forsen, Shen, Hazlett, Piven), Department of Psychiatry (Girault, Shen, Kim, Hazlett, Styner, Piven), Department of Biostatistics (Donovan, Truong), and ; Department of Psychological and Brain Sciences (Hawks) and Department of Psychiatry (Talovic, Nishino, Davis, Botteron, Todorov, Pruett, Constantino), Washington University School of Medicine in St. Louis; Institute of Child Development (Elison) and Department of Psychology, School of Behavioral and Brain Sciences, University of Texas at Dallas, Richardson, Tex. (Swanson); Department of Radiology, Washington University in St. Louis (Snyder, McKinstry); Department of Speech and Hearing Science, University of Washington, Seattle (Estes, St. John); Department of Radiology, University of Washington Medical Center, Seattle (Dager); Tandon School of Engineering, New York University, New York (Gerig); Center for Autism Research, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia (Pandey, Schultz); Department of Pediatrics, University of Alberta, Edmonton, Canada (Zwaigenbaum)
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73
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Reis L, Raciti M, Rodriguez PG, Joseph B, Al Rayyes I, Uhlén P, Falk A, da Cunha Lima ST, Ceccatelli S. Glyphosate-based herbicide induces long-lasting impairment in neuronal and glial differentiation. ENVIRONMENTAL TOXICOLOGY 2022; 37:2044-2057. [PMID: 35485992 PMCID: PMC9541419 DOI: 10.1002/tox.23549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 05/09/2023]
Abstract
Glyphosate-based herbicides (GBH) are among the most sold pesticides in the world. There are several formulations based on the active ingredient glyphosate (GLY) used along with other chemicals to improve the absorption and penetration in plants. The final composition of commercial GBH may modify GLY toxicological profile, potentially enhancing its neurotoxic properties. The developing nervous system is particularly susceptible to insults occurring during the early phases of development, and exposure to chemicals in this period may lead to persistent impairments on neurogenesis and differentiation. The aim of this study was to evaluate the long-lasting effects of a sub-cytotoxic concentration, 2.5 parts per million of GBH and GLY, on the differentiation of human neuroepithelial stem cells (NES) derived from induced pluripotent stem cells (iPSC). We treated NES cells with each compound and evaluated the effects on key cellular processes, such as proliferation and differentiation in daughter cells never directly exposed to the toxicants. We found that GBH induced a more immature neuronal profile associated to increased PAX6, NESTIN and DCX expression, and a shift in the differentiation process toward glial cell fate at the expense of mature neurons, as shown by an increase in the glial markers GFAP, GLT1, GLAST and a decrease in MAP2. Such alterations were associated to dysregulation of key genes critically involved in neurogenesis, including PAX6, HES1, HES5, and DDK1. Altogether, the data indicate that subtoxic concentrations of GBH, but not of GLY, induce long-lasting impairments on the differentiation potential of NES cells.
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Affiliation(s)
- Luã Reis
- Department of NeuroscienceKarolinska InstitutetStockholmSweden
| | - Marilena Raciti
- Department of NeuroscienceKarolinska InstitutetStockholmSweden
| | | | - Bertrand Joseph
- Institute of Environmental MedicineKarolinska InstitutetStockholmSweden
| | - Ibrahim Al Rayyes
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Per Uhlén
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Anna Falk
- Department of NeuroscienceKarolinska InstitutetStockholmSweden
| | - Suzana Telles da Cunha Lima
- Laboratório de Bioprospecção e Biotecnologia, Instituto de BiologiaUniversidade Federal da Bahia (UFBA)SalvadorBrazil
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74
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Michel N, Young HMR, Atkin ND, Arshad U, Al-Humadi R, Singh S, Manukyan A, Gore L, Burbulis IE, Wang YH, McConnell MJ. Transcription-associated DNA DSBs activate p53 during hiPSC-based neurogenesis. Sci Rep 2022; 12:12156. [PMID: 35840793 PMCID: PMC9287420 DOI: 10.1038/s41598-022-16516-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Neurons are overproduced during cerebral cortical development. Neural progenitor cells (NPCs) divide rapidly and incur frequent DNA double-strand breaks (DSBs) throughout cortical neurogenesis. Although half of the neurons born during neurodevelopment die, many neurons with inaccurate DNA repair survive leading to brain somatic mosaicism. Recurrent DNA DSBs during neurodevelopment are associated with both gene expression level and gene length. We used imaging flow cytometry and a genome-wide DNA DSB capture approach to quantify and map DNA DSBs during human induced pluripotent stem cell (hiPSC)-based neurogenesis. Reduced p53 signaling was brought about by knockdown (p53KD); p53KD led to elevated DNA DSB burden in neurons that was associated with gene expression level but not gene length in neural progenitor cells (NPCs). Furthermore, DNA DSBs incurred from transcriptional, but not replicative, stress lead to p53 activation in neurotypical NPCs. In p53KD NPCs, DNA DSBs accumulate at transcription start sites of genes that are associated with neurological and psychiatric disorders. These findings add to a growing understanding of how neuronal genome dynamics are engaged by high transcriptional or replicative burden during neurodevelopment.
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Affiliation(s)
- Nadine Michel
- Neuroscience Graduate Program, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Heather M Raimer Young
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Umar Arshad
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Reem Al-Humadi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Sandeep Singh
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Arkadi Manukyan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Lana Gore
- Lieber Institute for Brain Development, 855 N. Wolfe St., Ste. 300, Baltimore, MD, 21205, USA
| | - Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
- Sede de la Patagonia, Facultad de Medicina y Ciencias, Universidad San Sebastián, Puerto Montt, Chile
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Michael J McConnell
- Lieber Institute for Brain Development, 855 N. Wolfe St., Ste. 300, Baltimore, MD, 21205, USA.
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75
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Jiang CC, Lin LS, Long S, Ke XY, Fukunaga K, Lu YM, Han F. Signalling pathways in autism spectrum disorder: mechanisms and therapeutic implications. Signal Transduct Target Ther 2022; 7:229. [PMID: 35817793 PMCID: PMC9273593 DOI: 10.1038/s41392-022-01081-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/19/2022] [Accepted: 06/23/2022] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a prevalent and complex neurodevelopmental disorder which has strong genetic basis. Despite the rapidly rising incidence of autism, little is known about its aetiology, risk factors, and disease progression. There are currently neither validated biomarkers for diagnostic screening nor specific medication for autism. Over the last two decades, there have been remarkable advances in genetics, with hundreds of genes identified and validated as being associated with a high risk for autism. The convergence of neuroscience methods is becoming more widely recognized for its significance in elucidating the pathological mechanisms of autism. Efforts have been devoted to exploring the behavioural functions, key pathological mechanisms and potential treatments of autism. Here, as we highlight in this review, emerging evidence shows that signal transduction molecular events are involved in pathological processes such as transcription, translation, synaptic transmission, epigenetics and immunoinflammatory responses. This involvement has important implications for the discovery of precise molecular targets for autism. Moreover, we review recent insights into the mechanisms and clinical implications of signal transduction in autism from molecular, cellular, neural circuit, and neurobehavioural aspects. Finally, the challenges and future perspectives are discussed with regard to novel strategies predicated on the biological features of autism.
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Affiliation(s)
- Chen-Chen Jiang
- International Joint Laboratory for Drug Target of Critical Illnesses; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Li-Shan Lin
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Sen Long
- Department of Pharmacy, Hangzhou Seventh People's Hospital, Mental Health Center Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Xiao-Yan Ke
- Child Mental Health Research Center, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Kohji Fukunaga
- Department of CNS Drug Innovation, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Ying-Mei Lu
- Department of Physiology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China.
| | - Feng Han
- International Joint Laboratory for Drug Target of Critical Illnesses; Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
- Institute of Brain Science, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, China.
- Gusu School, Nanjing Medical University, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215002, China.
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76
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Wolter JM, Jimenez JA, Stein JL, Zylka MJ. ToxCast chemical library Wnt screen identifies diethanolamine as an activator of neural progenitor proliferation. FASEB Bioadv 2022; 4:441-453. [PMID: 35812078 PMCID: PMC9254222 DOI: 10.1096/fba.2021-00163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/04/2022] Open
Abstract
Numerous autism spectrum disorder (ASD) risk genes are associated with Wnt signaling, suggesting that brain development may be especially sensitive to genetic perturbation of this pathway. Additionally, valproic acid, which modulates Wnt signaling, increases risk for ASD when taken during pregnancy. We previously found that an autism-linked gain-of-function UBE3A T485A mutant construct hyperactivated canonical Wnt signaling, providing a genetic means to elevate Wnt signaling above baseline levels. To identify environmental use chemicals that enhance or suppress Wnt signaling, we screened the ToxCast Phase I and II libraries in cells expressing this autism-linked UBE3A T485A gain-of-function mutant construct. Using structural comparisons, we identify classes of chemicals that stimulated Wnt signaling, including ethanolamines, as well as chemicals that inhibited Wnt signaling, such as agricultural pesticides, and synthetic hormone analogs. To prioritize chemicals for follow-up, we leveraged predicted human exposure data, and identified diethanolamine (DEA) as a chemical that stimulates Wnt signaling in UBE3A T485A -transfected cells, and has a high potential for prenatal exposure in humans. DEA enhanced proliferation in primary human neural progenitor cell lines (phNPC), but did not affect expression of canonical Wnt target genes in NPCs or primary mouse neuron cultures. Instead, we found DEA increased expression of the H3K9 methylation sensitive gene CALB1, consistent with competitive inhibition of the methyl donor enzymatic pathways.
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Affiliation(s)
- Justin M. Wolter
- UNC Neuroscience CenterThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Department of Cell Biology and PhysiologyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Carolina Institute for Developmental DisabilitiesThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Jessica A. Jimenez
- Curriculum in Toxicology & Environmental MedicineThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Jason L. Stein
- UNC Neuroscience CenterThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Department of GeneticsThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Mark J. Zylka
- UNC Neuroscience CenterThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Department of Cell Biology and PhysiologyThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
- Carolina Institute for Developmental DisabilitiesThe University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
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77
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Doi M, Li M, Usui N, Shimada S. Genomic Strategies for Understanding the Pathophysiology of Autism Spectrum Disorder. Front Mol Neurosci 2022; 15:930941. [PMID: 35813066 PMCID: PMC9263364 DOI: 10.3389/fnmol.2022.930941] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Recent breakthroughs in sequencing technology and technological developments have made it easier to analyze the entire human genome than ever before. In addition to disease-specific genetic mutations and chromosomal aberrations, epigenetic alterations in individuals can also be analyzed using genomics. Autism spectrum disorder (ASD) is a neurodevelopmental disorder (NDD) caused by genetic and/or environmental factors. More than a thousand genes associated with ASD have been identified which are known to be involved in brain development. However, it is difficult to decode the roles of ASD-associated genes without in vitro and in vivo validations, particularly in the process of brain development. In this review, we discuss genomic strategies for understanding the pathological mechanisms underlying ASD. For this purpose, we discuss ASD-associated genes and their functions, as well as analytical strategies and their strengths and weaknesses in cellular and animal models from a basic research perspective.
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Affiliation(s)
- Miyuki Doi
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka, Japan
| | - Mengwei Li
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Noriyoshi Usui
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka, Japan
- United Graduate School of Child Development, Osaka University, Suita, Japan
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Japan
- *Correspondence: Noriyoshi Usui
| | - Shoichi Shimada
- Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Suita, Japan
- Addiction Research Unit, Osaka Psychiatric Research Center, Osaka Psychiatric Medical Center, Osaka, Japan
- United Graduate School of Child Development, Osaka University, Suita, Japan
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Japan
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78
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Rare CACNA1H and RELN variants interact through mTORC1 pathway in oligogenic autism spectrum disorder. Transl Psychiatry 2022; 12:234. [PMID: 35668055 PMCID: PMC9170683 DOI: 10.1038/s41398-022-01997-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/09/2022] Open
Abstract
Oligogenic inheritance of autism spectrum disorder (ASD) has been supported by several studies. However, little is known about how the risk variants interact and converge on causative neurobiological pathways. We identified in an ASD proband deleterious compound heterozygous missense variants in the Reelin (RELN) gene, and a de novo splicing variant in the Cav3.2 calcium channel (CACNA1H) gene. Here, by using iPSC-derived neural progenitor cells (NPCs) and a heterologous expression system, we show that the variant in Cav3.2 leads to increased calcium influx into cells, which overactivates mTORC1 pathway and, consequently, further exacerbates the impairment of Reelin signaling. Also, we show that Cav3.2/mTORC1 overactivation induces proliferation of NPCs and that both mutant Cav3.2 and Reelin cause abnormal migration of these cells. Finally, analysis of the sequencing data from two ASD cohorts-a Brazilian cohort of 861 samples, 291 with ASD; the MSSNG cohort of 11,181 samples, 5,102 with ASD-revealed that the co-occurrence of risk variants in both alleles of Reelin pathway genes and in one allele of calcium channel genes confer significant liability for ASD. Our results support the notion that genes with co-occurring deleterious variants tend to have interconnected pathways underlying oligogenic forms of ASD.
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79
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Aglinskas A, Hartshorne JK, Anzellotti S. Contrastive machine learning reveals the structure of neuroanatomical variation within autism. Science 2022; 376:1070-1074. [PMID: 35653486 DOI: 10.1126/science.abm2461] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Autism spectrum disorder (ASD) is highly heterogeneous. Identifying systematic individual differences in neuroanatomy could inform diagnosis and personalized interventions. The challenge is that these differences are entangled with variation because of other causes: individual differences unrelated to ASD and measurement artifacts. We used contrastive deep learning to disentangle ASD-specific neuroanatomical variation from variation shared with typical control participants. ASD-specific variation correlated with individual differences in symptoms. The structure of this ASD-specific variation also addresses a long-standing debate about the nature of ASD: At least in terms of neuroanatomy, individuals do not cluster into distinct subtypes; instead, they are organized along continuous dimensions that affect distinct sets of regions.
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Affiliation(s)
- Aidas Aglinskas
- Department of Psychology and Neuroscience, Boston College, Boston, MA 02467, USA
| | - Joshua K Hartshorne
- Department of Psychology and Neuroscience, Boston College, Boston, MA 02467, USA
| | - Stefano Anzellotti
- Department of Psychology and Neuroscience, Boston College, Boston, MA 02467, USA
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80
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Willsey HR, Willsey AJ, Wang B, State MW. Genomics, convergent neuroscience and progress in understanding autism spectrum disorder. Nat Rev Neurosci 2022; 23:323-341. [PMID: 35440779 PMCID: PMC10693992 DOI: 10.1038/s41583-022-00576-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/31/2022]
Abstract
More than a hundred genes have been identified that, when disrupted, impart large risk for autism spectrum disorder (ASD). Current knowledge about the encoded proteins - although incomplete - points to a very wide range of developmentally dynamic and diverse biological processes. Moreover, the core symptoms of ASD involve distinctly human characteristics, presenting challenges to interpreting evolutionarily distant model systems. Indeed, despite a decade of striking progress in gene discovery, an actionable understanding of pathobiology remains elusive. Increasingly, convergent neuroscience approaches have been recognized as an important complement to traditional uses of genetics to illuminate the biology of human disorders. These methods seek to identify intersection among molecular-level, cellular-level and circuit-level functions across multiple risk genes and have highlighted developing excitatory neurons in the human mid-gestational prefrontal cortex as an important pathobiological nexus in ASD. In addition, neurogenesis, chromatin modification and synaptic function have emerged as key potential mediators of genetic vulnerability. The continued expansion of foundational 'omics' data sets, the application of higher-throughput model systems and incorporating developmental trajectories and sex differences into future analyses will refine and extend these results. Ultimately, a systems-level understanding of ASD genetic risk holds promise for clarifying pathobiology and advancing therapeutics.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA.
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81
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Zhuang W, Liu H, He Z, Ju J, Gao Q, Shan Z, Lei L. miR-92a-2-5p Regulates the Proliferation and Differentiation of ASD-Derived Neural Progenitor Cells. Curr Issues Mol Biol 2022; 44:2431-2442. [PMID: 35735607 PMCID: PMC9222067 DOI: 10.3390/cimb44060166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorder (ASD) is a group of complex neurodevelopmental disorders with abnormal behavior. However, the pathogenesis of ASD remains to be clarified. It has been demonstrated that miRNAs are essential regulators of ASD. However, it is still unclear how miR-92a-2-5p acts on the developing brain and the cell types directly. In this study, we used neural progenitor cells (NPCs) derived from ASD-hiPSCs as well as from neurotypical controls to examine the effects of miR-92a-2-5p on ASD-NPCs proliferation and neuronal differentiation, and whether miR-92a-2-5p could interact with genetic risk factor, DLG3 for ASD. We observed that miR-92a-2-5p upregulated in ASD-NPCs results in decreased proliferation and neuronal differentiation. Inhibition of miR-92a-2-5p could promote proliferation and neuronal differentiation of ASD-NPCs. DLG3 was negatively regulated by miR-92a-2-5p in NPCs. Our results suggest that miR-92a-2-5p is a strong risk factor for ASD and potentially contributes to neuropsychiatric disorders.
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Affiliation(s)
| | | | | | | | | | | | - Lei Lei
- Correspondence: (Z.S.); (L.L.)
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82
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Connacher R, Williams M, Prem S, Yeung PL, Matteson P, Mehta M, Markov A, Peng C, Zhou X, McDermott CR, Pang ZP, Flax J, Brzustowicz L, Lu CW, Millonig JH, DiCicco-Bloom E. Autism NPCs from both idiopathic and CNV 16p11.2 deletion patients exhibit dysregulation of proliferation and mitogenic responses. Stem Cell Reports 2022; 17:1380-1394. [PMID: 35623351 PMCID: PMC9214070 DOI: 10.1016/j.stemcr.2022.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 11/24/2022] Open
Abstract
Neural precursor cell (NPC) dysfunction has been consistently implicated in autism. Induced pluripotent stem cell (iPSC)-derived NPCs from two autism groups (three idiopathic [I-ASD] and two 16p11.2 deletion [16pDel]) were used to investigate if proliferation is commonly disrupted. All five individuals display defects, with all three macrocephalic individuals (two 16pDel, one I-ASD) exhibiting hyperproliferation and the other two I-ASD subjects displaying hypoproliferation. NPCs were challenged with bFGF, and all hyperproliferative NPCs displayed blunted responses, while responses were increased in hypoproliferative cells. mRNA expression studies suggest that different pathways can result in similar proliferation phenotypes. Since 16pDel deletes MAPK3, P-ERK was measured. P-ERK is decreased in hyperproliferative but increased in hypoproliferative NPCs. While these P-ERK changes are not responsible for the phenotypes, P-ERK and bFGF response are inversely correlated with the defects. Finally, we analyzed iPSCs and discovered that 16pDel displays hyperproliferation, while idiopathic iPSCs were normal. These data suggest that NPC proliferation defects are common in ASD. NPC proliferation defects are common in idiopathic and 16p11.2 CNV-deletion ASD All macrocephalic I-ASD and 16pDel individuals have hyperproliferative NPCs NPC proliferative responses to bFGF correlate inversely with P-ERK levels Both NPCs and IPSCs derived from 16pDel individuals exhibit hyperproliferation
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Affiliation(s)
- Robert Connacher
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA; Graduate Program in Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Madeline Williams
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA; Graduate Program in Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Smrithi Prem
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA; Graduate Program in Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Percy L Yeung
- Child Health Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Paul Matteson
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Monal Mehta
- Graduate Program in Neuroscience, Rutgers University, Piscataway, NJ, USA; Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Anna Markov
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ, USA
| | - Cynthia Peng
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Xiaofeng Zhou
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Courtney R McDermott
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA; Graduate Program in Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Zhiping P Pang
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA; Child Health Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Judy Flax
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | | | - Che-Wei Lu
- Child Health Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - James H Millonig
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA; Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA.
| | - Emanuel DiCicco-Bloom
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA; Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
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83
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Papes F, Camargo AP, de Souza JS, Carvalho VMA, Szeto RA, LaMontagne E, Teixeira JR, Avansini SH, Sánchez-Sánchez SM, Nakahara TS, Santo CN, Wu W, Yao H, Araújo BMP, Velho PENF, Haddad GG, Muotri AR. Transcription Factor 4 loss-of-function is associated with deficits in progenitor proliferation and cortical neuron content. Nat Commun 2022; 13:2387. [PMID: 35501322 PMCID: PMC9061776 DOI: 10.1038/s41467-022-29942-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/31/2022] [Indexed: 01/04/2023] Open
Abstract
Transcription Factor 4 (TCF4) has been associated with autism, schizophrenia, and other neuropsychiatric disorders. However, how pathological TCF4 mutations affect the human neural tissue is poorly understood. Here, we derive neural progenitor cells, neurons, and brain organoids from skin fibroblasts obtained from children with Pitt-Hopkins Syndrome carrying clinically relevant mutations in TCF4. We show that neural progenitors bearing these mutations have reduced proliferation and impaired capacity to differentiate into neurons. We identify a mechanism through which TCF4 loss-of-function leads to decreased Wnt signaling and then to diminished expression of SOX genes, culminating in reduced progenitor proliferation in vitro. Moreover, we show reduced cortical neuron content and impaired electrical activity in the patient-derived organoids, phenotypes that were rescued after correction of TCF4 expression or by pharmacological modulation of Wnt signaling. This work delineates pathological mechanisms in neural cells harboring TCF4 mutations and provides a potential target for therapeutic strategies for genetic disorders associated with this gene.
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Affiliation(s)
- Fabio Papes
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil.
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
- Center for Medicinal Chemistry, University of Campinas, Campinas, Sao Paulo, 13083-886, Brazil.
| | - Antonio P Camargo
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil
- Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Janaina S de Souza
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Vinicius M A Carvalho
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil
| | - Ryan A Szeto
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Erin LaMontagne
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - José R Teixeira
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil
| | - Simoni H Avansini
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- School of Medical Sciences, University of Campinas, Campinas, Sao Paulo, 13083-887, Brazil
| | - Sandra M Sánchez-Sánchez
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Thiago S Nakahara
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil
| | - Carolina N Santo
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil
- Center for Medicinal Chemistry, University of Campinas, Campinas, Sao Paulo, 13083-886, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil
| | - Wei Wu
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Hang Yao
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Barbara M P Araújo
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, 13083-862, Brazil
| | - Paulo E N F Velho
- School of Medical Sciences, University of Campinas, Campinas, Sao Paulo, 13083-887, Brazil
| | - Gabriel G Haddad
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- Rady Children's Hospital, San Diego, CA, 92123, USA
| | - Alysson R Muotri
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
- Rady Children's Hospital, San Diego, CA, 92123, USA.
- Department of Cellular & Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
- Kavli Institute for Brain and Mind, University of California San Diego, La Jolla, CA, 92093, USA.
- Center for Academic Research and Training in Anthropogeny (CARTA) and Archealization (ArchC), University of California San Diego, La Jolla, CA, 92093, USA.
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84
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Muhtaseb AW, Duan J. Modeling common and rare genetic risk factors of neuropsychiatric disorders in human induced pluripotent stem cells. Schizophr Res 2022:S0920-9964(22)00156-6. [PMID: 35459617 PMCID: PMC9735430 DOI: 10.1016/j.schres.2022.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022]
Abstract
Recent genome-wide association studies (GWAS) and whole-exome sequencing of neuropsychiatric disorders, especially schizophrenia, have identified a plethora of common and rare disease risk variants/genes. Translating the mounting human genetic discoveries into novel disease biology and more tailored clinical treatments is tied to our ability to causally connect genetic risk variants to molecular and cellular phenotypes. When combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) nuclease-mediated genome editing system, human induced pluripotent stem cell (hiPSC)-derived neural cultures (both 2D and 3D organoids) provide a promising tractable cellular model for bridging the gap between genetic findings and disease biology. In this review, we first conceptualize the advances in understanding the disease polygenicity and convergence from the past decade of iPSC modeling of different types of genetic risk factors of neuropsychiatric disorders. We then discuss the major cell types and cellular phenotypes that are most relevant to neuropsychiatric disorders in iPSC modeling. Finally, we critically review the limitations of iPSC modeling of neuropsychiatric disorders and outline the need for implementing and developing novel methods to scale up the number of iPSC lines and disease risk variants in a systematic manner. Sufficiently scaled-up iPSC modeling and a better functional interpretation of genetic risk variants, in combination with cutting-edge CRISPR/Cas9 gene editing and single-cell multi-omics methods, will enable the field to identify the specific and convergent molecular and cellular phenotypes in precision for neuropsychiatric disorders.
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Affiliation(s)
- Abdurrahman W Muhtaseb
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, United States of America; Department of Human Genetics, The University of Chicago, Chicago, IL 60637, United States of America
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL 60201, United States of America; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, United States of America.
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85
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Casingal CR, Descant KD, Anton ES. Coordinating cerebral cortical construction and connectivity: Unifying influence of radial progenitors. Neuron 2022; 110:1100-1115. [PMID: 35216663 PMCID: PMC8989671 DOI: 10.1016/j.neuron.2022.01.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/15/2021] [Accepted: 01/26/2022] [Indexed: 01/02/2023]
Abstract
Radial progenitor development and function lay the foundation for the construction of the cerebral cortex. Radial glial scaffold, through its functions as a source of neurogenic progenitors and neuronal migration guide, is thought to provide a template for the formation of the cerebral cortex. Emerging evidence is challenging this limited view. Intriguingly, radial glial scaffold may also play a role in axonal growth, guidance, and neuronal connectivity. Radial glial cells not only facilitate the generation, placement, and allocation of neurons in the cortex but also regulate how they wire up. The organization and function of radial glial cells may thus be a unifying feature of the developing cortex that helps to precisely coordinate the right patterns of neurogenesis, neuronal placement, and connectivity necessary for the emergence of a functional cerebral cortex. This perspective critically explores this emerging view and its impact in the context of human brain development and disorders.
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Affiliation(s)
- Cristine R Casingal
- UNC Neuroscience Center, the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Katherine D Descant
- UNC Neuroscience Center, the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - E S Anton
- UNC Neuroscience Center, the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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86
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Gomes AKS, Dantas RM, Yokota BY, Silva ALTE, Griesi-Oliveira K, Passos-Bueno MR, Sertié AL. Interleukin-17a Induces Neuronal Differentiation of Induced-Pluripotent Stem Cell-Derived Neural Progenitors From Autistic and Control Subjects. Front Neurosci 2022; 16:828646. [PMID: 35360153 PMCID: PMC8964130 DOI: 10.3389/fnins.2022.828646] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/07/2022] [Indexed: 12/04/2022] Open
Abstract
Prenatal exposure to maternal immune activation (MIA) has been suggested to increase the probability of autism spectrum disorder (ASD). Recent evidence from animal studies indicates a key role for interleukin-17a (IL-17a) in promoting MIA-induced behavioral and brain abnormalities reminiscent of ASD. However, it is still unclear how IL-17a acts on the human developing brain and the cell types directly affected by IL-17a signaling. In this study, we used iPSC-derived neural progenitor cells (NPCs) from individuals with ASD of known and unknown genetic cause as well as from neurotypical controls to examine the effects of exogenous IL-17a on NPC proliferation, migration and neuronal differentiation, and whether IL-17a and genetic risk factors for ASD interact exacerbating alterations in NPC function. We observed that ASD and control NPCs endogenously express IL-17a receptor (IL17RA), and that IL-17a/IL17RA activation modulates downstream ERK1/2 and mTORC1 signaling pathways. Exogenous IL-17a did not induce abnormal proliferation and migration of ASD and control NPCs but, on the other hand, it significantly increased the expression of synaptic (Synaptophysin-1, Synapsin-1) and neuronal polarity (MAP2) proteins in these cells. Also, as we observed that ASD and control NPCs exhibited similar responses to exogenous IL-17a, it is possible that a more inflammatory environment containing other immune molecules besides IL-17a may be needed to trigger gene-environment interactions during neurodevelopment. In conclusion, our results suggest that exogenous IL-17a positively regulates the neuronal differentiation of human NPCs, which may disturb normal neuronal and synaptic development and contribute to MIA-related changes in brain function and behavior.
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Affiliation(s)
| | | | - Bruno Yukio Yokota
- Hospital Israelita Albert Einstein, Centro de Pesquisa Experimental, São Paulo, Brazil
| | | | | | - Maria Rita Passos-Bueno
- Centro de Estudos do Genoma Humano e Células Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Andréa Laurato Sertié
- Hospital Israelita Albert Einstein, Centro de Pesquisa Experimental, São Paulo, Brazil
- *Correspondence: Andréa Laurato Sertié,
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87
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McCready FP, Gordillo-Sampedro S, Pradeepan K, Martinez-Trujillo J, Ellis J. Multielectrode Arrays for Functional Phenotyping of Neurons from Induced Pluripotent Stem Cell Models of Neurodevelopmental Disorders. BIOLOGY 2022; 11:316. [PMID: 35205182 PMCID: PMC8868577 DOI: 10.3390/biology11020316] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/11/2022]
Abstract
In vitro multielectrode array (MEA) systems are increasingly used as higher-throughput platforms for functional phenotyping studies of neurons in induced pluripotent stem cell (iPSC) disease models. While MEA systems generate large amounts of spatiotemporal activity data from networks of iPSC-derived neurons, the downstream analysis and interpretation of such high-dimensional data often pose a significant challenge to researchers. In this review, we examine how MEA technology is currently deployed in iPSC modeling studies of neurodevelopmental disorders. We first highlight the strengths of in vitro MEA technology by reviewing the history of its development and the original scientific questions MEAs were intended to answer. Methods of generating patient iPSC-derived neurons and astrocytes for MEA co-cultures are summarized. We then discuss challenges associated with MEA data analysis in a disease modeling context, and present novel computational methods used to better interpret network phenotyping data. We end by suggesting best practices for presenting MEA data in research publications, and propose that the creation of a public MEA data repository to enable collaborative data sharing would be of great benefit to the iPSC disease modeling community.
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Affiliation(s)
- Fraser P. McCready
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; (F.P.M.); (S.G.-S.)
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sara Gordillo-Sampedro
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; (F.P.M.); (S.G.-S.)
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Kartik Pradeepan
- Department of Physiology and Pharmacology, Department of Psychiatry, Robarts Research and Brain and Mind Institutes, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada; (K.P.); (J.M.-T.)
| | - Julio Martinez-Trujillo
- Department of Physiology and Pharmacology, Department of Psychiatry, Robarts Research and Brain and Mind Institutes, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5B7, Canada; (K.P.); (J.M.-T.)
| | - James Ellis
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; (F.P.M.); (S.G.-S.)
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
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88
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Whiteley JT, Fernandes S, Sharma A, Mendes APD, Racha V, Benassi SK, Marchetto MC. Reaching into the toolbox: Stem cell models to study neuropsychiatric disorders. Stem Cell Reports 2022; 17:187-210. [PMID: 35063127 PMCID: PMC8828548 DOI: 10.1016/j.stemcr.2021.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in genetics, molecular biology, and stem cell biology have accelerated our understanding of neuropsychiatric disorders, like autism spectrum disorder (ASD), major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SZ). This progress highlights the incredible complexity of both the human brain and mental illnesses from the biochemical to the cellular level. Contributing to the complexity of neuropsychiatric disorders are their polygenic nature, cellular and brain region interconnectivity, and dysregulation of human-specific neurodevelopmental processes. Here, we discuss available tools, including CRISPR-Cas9, and the applications of these tools to develop cell-based two-dimensional (2D) models and 3D brain organoid models that better represent and unravel the intricacies of neuropsychiatric disorder pathophysiology.
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Affiliation(s)
- Jack T Whiteley
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Doctoral Program in Neurobiology and Behavior, Department of Neuroscience, Columbia University, Jerome L. Greene Science Center, 3227 Broadway, L7-028, MC 9872, New York, NY 10027, USA
| | - Sarah Fernandes
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Biological Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Amandeep Sharma
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ana Paula D Mendes
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Vipula Racha
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Simone K Benassi
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Maria C Marchetto
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Anthropology, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.
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89
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Paulsen B, Velasco S, Kedaigle AJ, Pigoni M, Quadrato G, Deo AJ, Adiconis X, Uzquiano A, Sartore R, Yang SM, Simmons SK, Symvoulidis P, Kim K, Tsafou K, Podury A, Abbate C, Tucewicz A, Smith SN, Albanese A, Barrett L, Sanjana NE, Shi X, Chung K, Lage K, Boyden ES, Regev A, Levin JZ, Arlotta P. Autism genes converge on asynchronous development of shared neuron classes. Nature 2022; 602:268-273. [PMID: 35110736 PMCID: PMC8852827 DOI: 10.1038/s41586-021-04358-6] [Citation(s) in RCA: 171] [Impact Index Per Article: 85.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/14/2021] [Indexed: 02/08/2023]
Abstract
Genetic risk for autism spectrum disorder (ASD) is associated with hundreds of genes spanning a wide range of biological functions1-6. The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals7,8. Here we used organoid models of the human cerebral cortex to identify cell-type-specific developmental abnormalities that result from haploinsufficiency in three ASD risk genes-SUV420H1 (also known as KMT5B), ARID1B and CHD8-in multiple cell lines from different donors, using single-cell RNA-sequencing (scRNA-seq) analysis of more than 745,000 cells and proteomic analysis of individual organoids, to identify phenotypic convergence. Each of the three mutations confers asynchronous development of two main cortical neuronal lineages-γ-aminobutyric-acid-releasing (GABAergic) neurons and deep-layer excitatory projection neurons-but acts through largely distinct molecular pathways. Although these phenotypes are consistent across cell lines, their expressivity is influenced by the individual genomic context, in a manner that is dependent on both the risk gene and the developmental defect. Calcium imaging in intact organoids shows that these early-stage developmental changes are followed by abnormal circuit activity. This research uncovers cell-type-specific neurodevelopmental abnormalities that are shared across ASD risk genes and are finely modulated by human genomic context, finding convergence in the neurobiological basis of how different risk genes contribute to ASD pathology.
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Affiliation(s)
- Bruna Paulsen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Silvia Velasco
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Murdoch Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia.
| | - Amanda J Kedaigle
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martina Pigoni
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Giorgia Quadrato
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anthony J Deo
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
- Rutgers University Behavioral Health Care, Piscataway, NJ, USA
| | - Xian Adiconis
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ana Uzquiano
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rafaela Sartore
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sung Min Yang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean K Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Panagiotis Symvoulidis
- MIT Center for Neurobiological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Kwanho Kim
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kalliopi Tsafou
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Archana Podury
- MIT Center for Neurobiological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Harvard-MIT Health Sciences & Technology Program (HST), Harvard Medical School, Boston, MA, USA
| | - Catherine Abbate
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashley Tucewicz
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samantha N Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alexandre Albanese
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Lindy Barrett
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Neville E Sanjana
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- New York Genome Center, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - Xi Shi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Picower Institute for Learning and Memory, Departments of Chemical Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- New York Genome Center, New York, NY, USA
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Edward S Boyden
- MIT Center for Neurobiological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Harvard-MIT Health Sciences & Technology Program (HST), Harvard Medical School, Boston, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA, USA
- Department of Brain of Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Media Arts and Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Genentech, South San Francisco, CA, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Abnormal mTOR Activity in Pediatric Autoimmune Neuropsychiatric and MIA-Associated Autism Spectrum Disorders. Int J Mol Sci 2022; 23:ijms23020967. [PMID: 35055151 PMCID: PMC8781199 DOI: 10.3390/ijms23020967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/14/2022] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by the early onset of communication and behavioral problems. ASD is highly heritable; however, environmental factors also play a considerable role in this disorder. A significant part of both syndromic and idiopathic autism cases could be attributed to disorders caused by mammalian target of rapamycin (mTOR)-dependent translation deregulation. This narrative review analyzes both bioinformatic and experimental evidence that connects mTOR signaling to the maternal autoantibody-related (MAR) autism spectrum and autoimmune neuropsychiatric disorders simultaneously. In addition, we reconstruct a network presenting the interactions between the mTOR signaling and eight MAR ASD genes coding for ASD-specific maternal autoantibody target proteins. The research discussed in this review demonstrates novel perspectives and validates the need for a subtyping of ASD on the grounds of pathogenic mechanisms. The utter necessity of designing ELISA-based test panels to identify all antibodies related to autism-like behavior is also considered.
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91
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Lu X, Yang J, Xiang Y. Modeling human neurodevelopmental diseases with brain organoids. CELL REGENERATION (LONDON, ENGLAND) 2022; 11:1. [PMID: 34982276 PMCID: PMC8727646 DOI: 10.1186/s13619-021-00103-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/24/2021] [Indexed: 04/25/2023]
Abstract
Studying the etiology of human neurodevelopmental diseases has long been a challenging task due to the brain's complexity and its limited accessibility. Human pluripotent stem cells (hPSCs)-derived brain organoids are capable of recapitulating various features and functionalities of the human brain, allowing the investigation of intricate pathogenesis of developmental abnormalities. Over the past years, brain organoids have facilitated identifying disease-associated phenotypes and underlying mechanisms for human neurodevelopmental diseases. Integrating with more cutting-edge technologies, particularly gene editing, brain organoids further empower human disease modeling. Here, we review the latest progress in modeling human neurodevelopmental disorders with brain organoids.
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Affiliation(s)
- Xiaoxiang Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jiajie Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yangfei Xiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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92
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Takahashi E, Allan N, Peres R, Ortug A, van der Kouwe AJW, Valli B, Ethier E, Levman J, Baumer N, Tsujimura K, Vargas-Maya NI, McCracken TA, Lee R, Maunakea AK. Integration of structural MRI and epigenetic analyses hint at linked cellular defects of the subventricular zone and insular cortex in autism: Findings from a case study. Front Neurosci 2022; 16:1023665. [PMID: 36817099 PMCID: PMC9935943 DOI: 10.3389/fnins.2022.1023665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/20/2022] [Indexed: 02/05/2023] Open
Abstract
Introduction Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social interaction, communication and repetitive, restrictive behaviors, features supported by cortical activity. Given the importance of the subventricular zone (SVZ) of the lateral ventrical to cortical development, we compared molecular, cellular, and structural differences in the SVZ and linked cortical regions in specimens of ASD cases and sex and age-matched unaffected brain. Methods We used magnetic resonance imaging (MRI) and diffusion tractography on ex vivo postmortem brain samples, which we further analyzed by Whole Genome Bisulfite Sequencing (WGBS), Flow Cytometry, and RT qPCR. Results Through MRI, we observed decreased tractography pathways from the dorsal SVZ, increased pathways from the posterior ventral SVZ to the insular cortex, and variable cortical thickness within the insular cortex in ASD diagnosed case relative to unaffected controls. Long-range tractography pathways from and to the insula were also reduced in the ASD case. FACS-based cell sorting revealed an increased population of proliferating cells in the SVZ of ASD case relative to the unaffected control. Targeted qPCR assays of SVZ tissue demonstrated significantly reduced expression levels of genes involved in differentiation and migration of neurons in ASD relative to the control counterpart. Finally, using genome-wide DNA methylation analyses, we identified 19 genes relevant to neurological development, function, and disease, 7 of which have not previously been described in ASD, that were significantly differentially methylated in autistic SVZ and insula specimens. Conclusion These findings suggest a hypothesis that epigenetic changes during neurodevelopment alter the trajectory of proliferation, migration, and differentiation in the SVZ, impacting cortical structure and function and resulting in ASD phenotypes.
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Affiliation(s)
- Emi Takahashi
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States.,Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Nina Allan
- Epigenomics Research Program, Department of Anatomy, Institute for Biogenesis Research, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Rafael Peres
- Epigenomics Research Program, Department of Anatomy, Institute for Biogenesis Research, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Alpen Ortug
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States.,Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Andre J W van der Kouwe
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States.,Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Briana Valli
- Department of Behavioral Neuroscience, Northeastern University, Boston, MA, United States
| | - Elizabeth Ethier
- Department of Behavioral Neuroscience, Northeastern University, Boston, MA, United States
| | - Jacob Levman
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States.,Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States.,Department of Mathematics, Statistics and Computer Science, St. Francis Xavier University, Antigonish, NS, Canada
| | - Nicole Baumer
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Keita Tsujimura
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States.,Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Nauru Idalia Vargas-Maya
- Epigenomics Research Program, Department of Anatomy, Institute for Biogenesis Research, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Trevor A McCracken
- Epigenomics Research Program, Department of Anatomy, Institute for Biogenesis Research, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Rosa Lee
- Epigenomics Research Program, Department of Anatomy, Institute for Biogenesis Research, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Alika K Maunakea
- Epigenomics Research Program, Department of Anatomy, Institute for Biogenesis Research, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawai'i at Mānoa, Honolulu, HI, United States
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93
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van Rhijn JR, Shi Y, Bormann M, Mossink B, Frega M, Recaioglu H, Hakobjan M, Klein Gunnewiek T, Schoenmaker C, Palmer E, Faivre L, Kittel-Schneider S, Schubert D, Brunner H, Franke B, Nadif Kasri N. Brunner syndrome associated MAOA mutations result in NMDAR hyperfunction and increased network activity in human dopaminergic neurons. Neurobiol Dis 2021; 163:105587. [PMID: 34923109 DOI: 10.1016/j.nbd.2021.105587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/01/2021] [Accepted: 12/15/2021] [Indexed: 01/15/2023] Open
Abstract
Monoamine neurotransmitter abundance affects motor control, emotion, and cognitive function and is regulated by monoamine oxidases. Among these, Monoamine oxidase A (MAOA) catalyzes the degradation of dopamine, norepinephrine, and serotonin into their inactive metabolites. Loss-of-function mutations in the X-linked MAOA gene have been associated with Brunner syndrome, which is characterized by various forms of impulsivity, maladaptive externalizing behavior, and mild intellectual disability. Impaired MAOA activity in individuals with Brunner syndrome results in bioamine aberration, but it is currently unknown how this affects neuronal function, specifically in dopaminergic (DA) neurons. Here we generated human induced pluripotent stem cell (hiPSC)-derived DA neurons from three individuals with Brunner syndrome carrying different mutations and characterized neuronal properties at the single cell and neuronal network level in vitro. DA neurons of Brunner syndrome patients showed reduced synaptic density but exhibited hyperactive network activity. Intrinsic functional properties and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR)-mediated synaptic transmission were not affected in DA neurons of individuals with Brunner syndrome. Instead, we show that the neuronal network hyperactivity is mediated by upregulation of the GRIN2A and GRIN2B subunits of the N-methyl-d-aspartate receptor (NMDAR), resulting in increased NMDAR-mediated currents. By correcting a MAOA missense mutation with CRISPR/Cas9 genome editing we normalized GRIN2A and GRIN2B expression, NMDAR function and neuronal population activity to control levels. Our data suggest that MAOA mutations in Brunner syndrome increase the activity of dopaminergic neurons through upregulation of NMDAR function, which may contribute to the etiology of Brunner syndrome associated phenotypes.
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Affiliation(s)
- Jon-Ruben van Rhijn
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yan Shi
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Maren Bormann
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Britt Mossink
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Monica Frega
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical neurophysiology, University of Twente, 7522 NB Enschede, Netherlands
| | - Hatice Recaioglu
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marina Hakobjan
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Teun Klein Gunnewiek
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Anatomy, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Chantal Schoenmaker
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elizabeth Palmer
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Randwick, NSW, Australia
| | - Laurence Faivre
- Centre de Référence Anomalies du développement et Syndromes malformatifs and FHU TRANSLAD, Hôpital d'Enfants, Dijon, France; INSERM UMR1231 GAD, Faculté de Médecine, Université de Bourgogne, Dijon, France
| | - Sarah Kittel-Schneider
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe-University, Frankfurt, Germany; Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Würzburg, Würzburg, Germany
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Han Brunner
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Genetics, MUMC+, GROW School of Oncology and Developmental Biology, and MHeNS School of Neuroscience and Maastricht University, Maastricht, the Netherlands
| | - Barbara Franke
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Psychiatry, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nael Nadif Kasri
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.
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Figueiredo CP, Fontes-Dantas FL, da Poian AT, Clarke JR. SARS-CoV-2-associated cytokine storm during pregnancy as a possible risk factor for neuropsychiatric disorder development in post-pandemic infants. Neuropharmacology 2021; 201:108841. [PMID: 34666076 PMCID: PMC8519783 DOI: 10.1016/j.neuropharm.2021.108841] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/07/2021] [Accepted: 10/15/2021] [Indexed: 01/23/2023]
Abstract
A strong association between perinatal viral infections and neurodevelopmental disorders has been established. Both the direct contact of the virus with the developing brain and the strong maternal immune response originated by viral infections can impair proper neurodevelopment. Coronavirus disease 2019 (COVID-19), caused by the highly-infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is currently responsible for a large global outbreak and is a major public health issue. While initial studies focused on the viral impact on the respiratory system, increasing evidence suggest that SARS-CoV-2 infects other organs and tissues including the mature brain. While studies continue to determine the neuropathology associated to COVID-19, the consequences of SARS-CoV-2 infection to the developing brain remain largely unexplored. The present review discusses evidence suggesting that SARS-CoV-2 infection may have persistent effects on the course of pregnancy and on brain development. Studies have shown that several proinflammatory mediators which are increased in the SARS-CoV-2-associated cytokine storm, are also modified in other viral infections known to increase the risk of neurodevelopmental disorders. In this sense, further studies should assess the genuine effects of SARS-CoV-2 infection during pregnancy and delivery along with an extended follow-up of the offspring, including neurocognitive, neuroimaging, and electrophysiological examination. It also remains to be determined whether and by which mechanisms SARS-CoV-2 intrauterine and early life infection could lead to an increased risk of developing neuropsychiatric disorders, such as autism (ASD) and schizophrenia (SZ), in the offspring.
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Affiliation(s)
- Claudia P Figueiredo
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil; Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | | | - Andrea T da Poian
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Julia R Clarke
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil; Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil.
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95
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Räsänen N, Tiihonen J, Koskuvi M, Lehtonen Š, Koistinaho J. The iPSC perspective on schizophrenia. Trends Neurosci 2021; 45:8-26. [PMID: 34876311 DOI: 10.1016/j.tins.2021.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/29/2021] [Accepted: 11/10/2021] [Indexed: 12/17/2022]
Abstract
Over a decade of schizophrenia research using human induced pluripotent stem cell (iPSC)-derived neural models has provided substantial data describing neurobiological characteristics of the disorder in vitro. Simultaneously, translation of the results into general mechanistic concepts underlying schizophrenia pathophysiology has been trailing behind. Given that modeling brain function using cell cultures is challenging, the gap between the in vitro models and schizophrenia as a clinical disorder has remained wide. In this review, we highlight reproducible findings and emerging trends in recent schizophrenia-related iPSC studies. We illuminate the relevance of the results in the context of human brain development, with a focus on processes coinciding with critical developmental periods for schizophrenia.
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Affiliation(s)
- Noora Räsänen
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Jari Tiihonen
- Neuroscience Center, University of Helsinki, Helsinki, Finland; Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden; Center for Psychiatric Research, Stockholm City Council, Stockholm, Sweden; Department of Forensic Psychiatry, University of Eastern Finland, Niuvanniemi Hospital, Kuopio, Finland
| | - Marja Koskuvi
- Neuroscience Center, University of Helsinki, Helsinki, Finland; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Šárka Lehtonen
- Neuroscience Center, University of Helsinki, Helsinki, Finland; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jari Koistinaho
- Neuroscience Center, University of Helsinki, Helsinki, Finland; A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
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96
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Kanlayaprasit S, Thongkorn S, Panjabud P, Jindatip D, Hu VW, Kikkawa T, Osumi N, Sarachana T. Autism-Related Transcription Factors Underlying the Sex-Specific Effects of Prenatal Bisphenol A Exposure on Transcriptome-Interactome Profiles in the Offspring Prefrontal Cortex. Int J Mol Sci 2021; 22:13201. [PMID: 34947998 PMCID: PMC8708761 DOI: 10.3390/ijms222413201] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 11/16/2022] Open
Abstract
Bisphenol A (BPA) is an environmental risk factor for autism spectrum disorder (ASD). BPA exposure dysregulates ASD-related genes in the hippocampus and neurological functions of offspring. However, whether prenatal BPA exposure has an impact on genes in the prefrontal cortex, another brain region highly implicated in ASD, and through what mechanisms have not been investigated. Here, we demonstrated that prenatal BPA exposure disrupts the transcriptome-interactome profiles of the prefrontal cortex of neonatal rats. Interestingly, the list of BPA-responsive genes was significantly enriched with known ASD candidate genes, as well as genes that were dysregulated in the postmortem brain tissues of ASD cases from multiple independent studies. Moreover, several differentially expressed genes in the offspring's prefrontal cortex were the targets of ASD-related transcription factors, including AR, ESR1, and RORA. The hypergeometric distribution analysis revealed that BPA may regulate the expression of such genes through these transcription factors in a sex-dependent manner. The molecular docking analysis of BPA and ASD-related transcription factors revealed novel potential targets of BPA, including RORA, SOX5, TCF4, and YY1. Our findings indicated that prenatal BPA exposure disrupts ASD-related genes in the offspring's prefrontal cortex and may increase the risk of ASD through sex-dependent molecular mechanisms, which should be investigated further.
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Grants
- FRB65_hea(80)_175_37_05 Fundamental Fund, Chulalongkorn University
- AHS-CU 61004 Faculty of Allied Health Sciences Research Fund, Chulalongkorn University
- GRU 6300437001-1 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- GRU_64_033_37_004 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship, Graduate School, Chulalongkorn University
- The Overseas Research Experience Scholarship for Graduate Students from Graduate School, Chulalongkorn University
- PHD/0029/2561 The Royal Golden Jubilee Ph.D. Programme Scholarship, Thailand Research Fund and National Research Council of Thailand
- National Research Council of Thailand (NRCT)
- GCUGR1125623067D-67 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- GCUGR1125632108D-108 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- 2073011 Chulalongkorn University Laboratory Animal Center (CULAC) Grant
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Affiliation(s)
- Songphon Kanlayaprasit
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (S.T.); (P.P.)
| | - Surangrat Thongkorn
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (S.T.); (P.P.)
| | - Pawinee Panjabud
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (S.T.); (P.P.)
| | - Depicha Jindatip
- Systems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand;
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Valerie W. Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20052, USA;
| | - Takako Kikkawa
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai 980-8577, Miyagi, Japan; (T.K.); (N.O.)
| | - Noriko Osumi
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai 980-8577, Miyagi, Japan; (T.K.); (N.O.)
| | - Tewarit Sarachana
- Systems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand;
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97
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Li D, Xu J, Yang MQ. Gene Regulation Analysis Reveals Perturbations of Autism Spectrum Disorder during Neural System Development. Genes (Basel) 2021; 12:genes12121901. [PMID: 34946850 PMCID: PMC8700980 DOI: 10.3390/genes12121901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 01/21/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder that impedes patients' cognition, social, speech and communication skills. ASD is highly heterogeneous with a variety of etiologies and clinical manifestations. The prevalence rate of ASD increased steadily in recent years. Presently, molecular mechanisms underlying ASD occurrence and development remain to be elucidated. Here, we integrated multi-layer genomics data to investigate the transcriptome and pathway dysregulations in ASD development. The RNA sequencing (RNA-seq) expression profiles of induced pluripotent stem cells (iPSCs), neural progenitor cells (NPCs) and neuron cells from ASD and normal samples were compared in our study. We found that substantially more genes were differentially expressed in the NPCs than the iPSCs. Consistently, gene set variation analysis revealed that the activity of the known ASD pathways in NPCs and neural cells were significantly different from the iPSCs, suggesting that ASD occurred at the early stage of neural system development. We further constructed comprehensive brain- and neural-specific regulatory networks by incorporating transcription factor (TF) and gene interactions with long 5 non-coding RNA(lncRNA) and protein interactions. We then overlaid the transcriptomes of different cell types on the regulatory networks to infer the regulatory cascades. The variations of the regulatory cascades between ASD and normal samples uncovered a set of novel disease-associated genes and gene interactions, particularly highlighting the functional roles of ELF3 and the interaction between STAT1 and lncRNA ELF3-AS 1 in the disease development. These new findings extend our understanding of ASD and offer putative new therapeutic targets for further studies.
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Affiliation(s)
- Dan Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA;
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA;
- Correspondence: (J.X.); (M.Q.Y.)
| | - Mary Qu Yang
- MidSouth Bioinformatics Center, Joint Bioinformatics Graduate Program of University of Arkansas at Little Rock, University of Arkansas for Medical Sciences, Little Rock, AR 72204, USA
- Correspondence: (J.X.); (M.Q.Y.)
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98
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Zaghi M, Banfi F, Bellini E, Sessa A. Rare Does Not Mean Worthless: How Rare Diseases Have Shaped Neurodevelopment Research in the NGS Era. Biomolecules 2021; 11:1713. [PMID: 34827709 PMCID: PMC8616022 DOI: 10.3390/biom11111713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/20/2022] Open
Abstract
The advent of next-generation sequencing (NGS) is heavily changing both the diagnosis of human conditions and basic biological research. It is now possible to dig deep inside the genome of hundreds of thousands or even millions of people and find both common and rare genomic variants and to perform detailed phenotypic characterizations of both physiological organs and experimental models. Recent years have seen the introduction of multiple techniques using NGS to profile transcription, DNA and chromatin modifications, protein binding, etc., that are now allowing us to profile cells in bulk or even at a single-cell level. Although rare and ultra-rare diseases only affect a few people, each of these diseases represent scholarly cases from which a great deal can be learned about the pathological and physiological function of genes, pathways, and mechanisms. Therefore, for rare diseases, state-of-the-art investigations using NGS have double valence: their genomic cause (new variants) and the characterize the underlining the mechanisms associated with them (discovery of gene function) can be found. In a non-exhaustive manner, this review will outline the main usage of NGS-based techniques for the diagnosis and characterization of neurodevelopmental disorders (NDDs), under whose umbrella many rare and ultra-rare diseases fall.
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Affiliation(s)
- Mattia Zaghi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
| | - Federica Banfi
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
- CNR Institute of Neuroscience, 20129 Milan, Italy
| | - Edoardo Bellini
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
| | - Alessandro Sessa
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (M.Z.); (F.B.); (E.B.)
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99
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Caracci MO, Avila ME, Espinoza-Cavieres FA, López HR, Ugarte GD, De Ferrari GV. Wnt/β-Catenin-Dependent Transcription in Autism Spectrum Disorders. Front Mol Neurosci 2021; 14:764756. [PMID: 34858139 PMCID: PMC8632544 DOI: 10.3389/fnmol.2021.764756] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorders (ASD) is a heterogeneous group of neurodevelopmental disorders characterized by synaptic dysfunction and defects in dendritic spine morphology. In the past decade, an extensive list of genes associated with ASD has been identified by genome-wide sequencing initiatives. Several of these genes functionally converge in the regulation of the Wnt/β-catenin signaling pathway, a conserved cascade essential for stem cell pluripotency and cell fate decisions during development. Here, we review current information regarding the transcriptional program of Wnt/β-catenin signaling in ASD. First, we discuss that Wnt/β-catenin gain and loss of function studies recapitulate brain developmental abnormalities associated with ASD. Second, transcriptomic approaches using patient-derived induced pluripotent stem cells (iPSC) cells, featuring mutations in high confidence ASD genes, reveal a significant dysregulation in the expression of Wnt signaling components. Finally, we focus on the activity of chromatin-remodeling proteins and transcription factors considered high confidence ASD genes, including CHD8, ARID1B, ADNP, and TBR1, that regulate Wnt/β-catenin-dependent transcriptional activity in multiple cell types, including pyramidal neurons, interneurons and oligodendrocytes, cells which are becoming increasingly relevant in the study of ASD. We conclude that the level of Wnt/β-catenin signaling activation could explain the high phenotypical heterogeneity of ASD and be instrumental in the development of new diagnostics tools and therapies.
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Affiliation(s)
- Mario O. Caracci
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Miguel E. Avila
- Faculty of Veterinary Medicine and Agronomy, Nucleus of Applied Research in Veterinary and Agronomic Sciences (NIAVA), Institute of Natural Sciences, Universidad de Las Américas, Santiago, Chile
| | - Francisca A. Espinoza-Cavieres
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Héctor R. López
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Giorgia D. Ugarte
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
| | - Giancarlo V. De Ferrari
- Faculty of Medicine, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
- Faculty of Life Sciences, Institute of Biomedical Sciences, Universidad Andres Bello, Santiago, Chile
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100
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Nadeem MS, Hosawi S, Alshehri S, Ghoneim MM, Imam SS, Murtaza BN, Kazmi I. Symptomatic, Genetic, and Mechanistic Overlaps between Autism and Alzheimer's Disease. Biomolecules 2021; 11:1635. [PMID: 34827633 PMCID: PMC8615882 DOI: 10.3390/biom11111635] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 02/02/2023] Open
Abstract
Autism spectrum disorder (ASD) and Alzheimer's disease (AD) are neurodevelopmental and neurodegenerative disorders affecting two opposite ends of life span, i.e., childhood and old age. Both disorders pose a cumulative threat to human health, with the rate of incidences increasing considerably worldwide. In the context of recent developments, we aimed to review correlated symptoms and genetics, and overlapping aspects in the mechanisms of the pathogenesis of ASD and AD. Dementia, insomnia, and weak neuromuscular interaction, as well as communicative and cognitive impairments, are shared symptoms. A number of genes and proteins linked with both disorders have been tabulated, including MECP2, ADNP, SCN2A, NLGN, SHANK, PTEN, RELN, and FMR1. Theories about the role of neuron development, processing, connectivity, and levels of neurotransmitters in both disorders have been discussed. Based on the recent literature, the roles of FMRP (Fragile X mental retardation protein), hnRNPC (heterogeneous ribonucleoprotein-C), IRP (Iron regulatory proteins), miRNAs (MicroRNAs), and α-, β0, and γ-secretases in the posttranscriptional regulation of cellular synthesis and processing of APP (amyloid-β precursor protein) have been elaborated to describe the parallel and overlapping routes and mechanisms of ASD and AD pathogenesis. However, the interactive role of genetic and environmental factors, oxidative and metal ion stress, mutations in the associated genes, and alterations in the related cellular pathways in the development of ASD and AD needs further investigation.
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Affiliation(s)
- Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.S.N.); (S.H.)
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.S.N.); (S.H.)
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (S.S.I.)
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Syed Sarim Imam
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (S.S.I.)
| | - Bibi Nazia Murtaza
- Department of Zoology, Abbottabad University of Science and Technology (AUST), Abbottabad 22310, Pakistan;
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.S.N.); (S.H.)
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