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Leow KQ, Tonta MA, Lu J, Coleman HA, Parkington HC. Towards understanding sex differences in autism spectrum disorders. Brain Res 2024; 1833:148877. [PMID: 38513995 DOI: 10.1016/j.brainres.2024.148877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental condition characterized by social deficits, repetitive behaviours and lack of empathy. Its significant genetic heritability and potential comorbidities often lead to diagnostic and therapeutic challenges. This review addresses the biological basis of ASD, focusing on the sex differences in gene expression and hormonal influences. ASD is more commonly diagnosed in males at a ratio of 4:1, indicating a potential oversight in female-specific ASD research and a risk of underdiagnosis in females. We consider how ASD manifests differently across sexes by exploring differential gene expression in female and male brains and consider how variations in steroid hormones influence ASD characteristics. Synaptic function, including excitation/inhibition ratio imbalance, is influenced by gene mutations and this is explored as a key factor in the cognitive and behavioural manifestations of ASD. We also discuss the role of micro RNAs (miRNAs) and highlight a novel mutation in miRNA-873, which affects a suite of key synaptic genes, neurexin, neuroligin, SHANK and post-synaptic density proteins, implicated in the pathology of ASD. Our review suggests that genetic predisposition, sex differences in brain gene expression, and hormonal factors significantly contribute to the presentation, identification and severity of ASD, necessitating sex-specific considerations in diagnosis and treatments. These findings advocate for personalized interventions to improve the outcomes for individuals with ASD.
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Affiliation(s)
- Karen Q Leow
- Department of Physiology, Biomedical Discovery Institute, Monash University, Victoria, Australia
| | - Mary A Tonta
- Department of Physiology, Biomedical Discovery Institute, Monash University, Victoria, Australia
| | - Jing Lu
- Tianjin Institute of Infectious Disease, Second Hospital of Tianjin Medical University, China
| | - Harold A Coleman
- Department of Physiology, Biomedical Discovery Institute, Monash University, Victoria, Australia
| | - Helena C Parkington
- Department of Physiology, Biomedical Discovery Institute, Monash University, Victoria, Australia.
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2
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Almansoori S, Alsters SI, Yiorkas AM, Nor Hashim NA, Walters RG, Chahal HS, Purkayastha S, Lessan N, Blakemore AIF. Oligogenic inheritance in severe adult obesity. Int J Obes (Lond) 2024; 48:815-820. [PMID: 38297031 PMCID: PMC11129943 DOI: 10.1038/s41366-024-01476-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 11/13/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND/OBJECTIVE The genetic architecture of extreme non-syndromic obesity in adults remains to be elucidated. A range of genes are known to cause monogenic obesity, but even when pathogenic mutations are present, there may be variable penetrance. METHODS Whole-exome sequencing (WES) was carried out on a 15-year-old male proband of Pakistani ancestry who had severe obesity. This was followed by family segregation analysis, using Sanger sequencing. We also undertook re-analysis of WES data from 91 unrelated adults with severe obesity (86% white European ancestry) from the Personalised Medicine for Morbid Obesity (PMMO) cohort, recruited from the UK National Health Service. RESULTS We identified an oligogenic mode of inheritance of obesity in the proband's family-this provided the impetus to reanalyze existing sequence data in a separate dataset. Analysis of PMMO participant data revealed two further patients who carried more than one rare, predicted-deleterious mutation in a known monogenic obesity gene. In all three cases, the genes involved had known autosomal dominant inheritance, with incomplete penetrance. CONCLUSION Oligogenic inheritance may explain some of the variable penetrance in Mendelian forms of obesity. We caution clinicians and researchers to avoid confining sequence analysis to individual genes and, in particular, not to stop looking when the first potentially-causative mutation is found.
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Affiliation(s)
- Sumaya Almansoori
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, London, UK.
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates.
- Genome Center, Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates.
| | - Suzanne I Alsters
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Andrianos M Yiorkas
- Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, London, UK
| | - Nikman Adli Nor Hashim
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
- Centre for Drug Research in Systems Biology, Structural Bioinformatics and Human Digital Imaging (CRYSTAL), Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Harvinder S Chahal
- Imperial Weight Centre, Imperial College Healthcare NHS Trust, St Mary's Hospital, Praed Street, London, W2 1NY, UK
- Section of Investigative Medicine, Division of Diabetes, Endocrinology and Metabolism, Imperial College London, Hammersmith Campus, Hammersmith Hospital, 6th Floor Commonwealth Building, Du Cane Road, London, W12 0NN, UK
| | | | - Nader Lessan
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Imperial College London Diabetes Centre Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Alexandra I F Blakemore
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, London, UK
- College of Medicine, Nursing, and Health Science, University of Galway, Galway, Republic of Ireland
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Shi X, Lu C, Corman A, Nikish A, Zhou Y, Platt RJ, Iossifov I, Zhang F, Pan JQ, Sanjana NE. Heterozygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction. Am J Hum Genet 2023; 110:1750-1768. [PMID: 37802044 PMCID: PMC10577079 DOI: 10.1016/j.ajhg.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023] Open
Abstract
Whole-exome sequencing of autism spectrum disorder (ASD) probands and unaffected family members has identified many genes harboring de novo variants suspected to play a causal role in the disorder. Of these, chromodomain helicase DNA-binding protein 8 (CHD8) is the most recurrently mutated. Despite the prevalence of CHD8 mutations, we have little insight into how CHD8 loss affects genome organization or the functional consequences of these molecular alterations in neurons. Here, we engineered two isogenic human embryonic stem cell lines with CHD8 loss-of-function mutations and characterized differences in differentiated human cortical neurons. We identified hundreds of genes with altered expression, including many involved in neural development and excitatory synaptic transmission. Field recordings and single-cell electrophysiology revealed a 3-fold decrease in firing rates and synaptic activity in CHD8+/- neurons, as well as a similar firing-rate deficit in primary cortical neurons from Chd8+/- mice. These alterations in neuron and synapse function can be reversed by CHD8 overexpression. Moreover, CHD8+/- neurons displayed a large increase in open chromatin across the genome, where the greatest change in compaction was near autism susceptibility candidate 2 (AUTS2), which encodes a transcriptional regulator implicated in ASD. Genes with changes in chromatin accessibility and expression in CHD8+/- neurons have significant overlap with genes mutated in probands for ASD, intellectual disability, and schizophrenia but not with genes mutated in healthy controls or other disease cohorts. Overall, this study characterizes key molecular alterations in genome structure and expression in CHD8+/- neurons and links these changes to impaired neuronal and synaptic function.
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Affiliation(s)
- Xi Shi
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute, Cambridge, MA, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Congyi Lu
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Alba Corman
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Alexandra Nikish
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute, Cambridge, MA, USA
| | - Yang Zhou
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Montreal Neurological Institute, Montreal, QC, Canada
| | - Randy J Platt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ivan Iossifov
- New York Genome Center, New York, NY, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Feng Zhang
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute, Cambridge, MA, USA
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA.
| | - Neville E Sanjana
- New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA.
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Bayat A, Liu Z, Luo S, Fenger CD, Højte AF, Isidor B, Cogne B, Larson A, Zanus C, Faletra F, Keren B, Musante L, Gourfinkel-An I, Perrine C, Demily C, Lesca G, Liao W, Ren D. A new neurodevelopmental disorder linked to heterozygous variants in UNC79. Genet Med 2023; 25:100894. [PMID: 37183800 DOI: 10.1016/j.gim.2023.100894] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/16/2023] Open
Abstract
PURPOSE The "NALCN channelosome" is an ion channel complex that consists of multiple proteins, including NALCN, UNC79, UNC80, and FAM155A. Only a small number of individuals with a neurodevelopmental syndrome have been reported with disease causing variants in NALCN and UNC80. However, no pathogenic UNC79 variants have been reported, and in vivo function of UNC79 in humans is largely unknown. METHODS We used international gene-matching efforts to identify patients harboring ultrarare heterozygous loss-of-function UNC79 variants and no other putative responsible genes. We used genetic manipulations in Drosophila and mice to test potential causal relationships between UNC79 variants and the pathology. RESULTS We found 6 unrelated and affected patients with UNC79 variants. Five patients presented with overlapping neurodevelopmental features, including mild to moderate intellectual disability and a mild developmental delay, whereas a single patient reportedly had normal cognitive and motor development but was diagnosed with epilepsy and autistic features. All displayed behavioral issues and 4 patients had epilepsy. Drosophila with UNC79 knocked down displayed induced seizure-like phenotype. Mice with a heterozygous loss-of-function variant have a developmental delay in body weight compared with wild type. In addition, they have impaired ability in learning and memory. CONCLUSION Our results demonstrate that heterozygous loss-of-function UNC79 variants are associated with neurologic pathologies.
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Affiliation(s)
- Allan Bayat
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark; Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark; Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
| | - Zhenjiang Liu
- Department of Biology, University of Pennsylvania, Philadelphia, PA; National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
| | - Sheng Luo
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Christina D Fenger
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark; Amplexa Genetics A/S, Odense, Denmark
| | - Anne F Højte
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Bertrand Isidor
- Department of Genetics, CHU Nantes, Nantes, France; University of Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Benjamin Cogne
- Department of Genetics, CHU Nantes, Nantes, France; University of Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Austin Larson
- University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
| | - Caterina Zanus
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," Trieste, Italy
| | - Boris Keren
- Department of Neurology, Epileptology Unit, Reference Center for Rare Epilepsies, Sorbonne University, La Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Luciana Musante
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," Trieste, Italy
| | - Isabelle Gourfinkel-An
- Department of Neurology, Epileptology Unit, Reference Center for Rare Epilepsies, Sorbonne University, La Pitié-Salpêtrière Hospital, AP-HP, Paris, France
| | - Charles Perrine
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP-HP, University of Sorbonne, Paris, France
| | - Caroline Demily
- GénoPsy, Reference Center for Diagnosis and Management of Genetic Psychiatric Disorders, Vinatier Hospital Center and EDR-Psy Team (National Center for Scientific Research and Lyon 1 Claude Bernard University), Lyon, France; iMIND Excellence Center for Autism and Neurodevelopmental Disorders, Lyon, France
| | - Gaeton Lesca
- Department of Medical Genetics, University Hospital of Lyon, Lyon, France
| | - Weiping Liao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Dejian Ren
- Department of Biology, University of Pennsylvania, Philadelphia, PA
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5
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Park G, Jang WE, Kim S, Gonzales EL, Ji J, Choi S, Kim Y, Park JH, Mohammad HB, Bang G, Kang M, Kim S, Jeon SJ, Kim JY, Kim KP, Shin CY, An JY, Kim MS, Lee YS. Dysregulation of the Wnt/β-catenin signaling pathway via Rnf146 upregulation in a VPA-induced mouse model of autism spectrum disorder. Exp Mol Med 2023; 55:1783-1794. [PMID: 37524878 PMCID: PMC10474298 DOI: 10.1038/s12276-023-01065-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 08/02/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder associated with impaired social behavior and communication, repetitive behaviors, and restricted interests. In addition to genetic factors, environmental factors such as prenatal drug exposure contribute to the development of ASD. However, how those prenatal factors induce behavioral deficits in the adult stage is not clear. To elucidate ASD pathogenesis at the molecular level, we performed a high-resolution mass spectrometry-based quantitative proteomic analysis on the prefrontal cortex (PFC) of mice exposed to valproic acid (VPA) in utero, a widely used animal model of ASD. Differentially expressed proteins (DEPs) in VPA-exposed mice showed significant overlap with ASD risk genes, including differentially expressed genes from the postmortem cortex of ASD patients. Functional annotations of the DEPs revealed significant enrichment in the Wnt/β-catenin signaling pathway, which is dysregulated by the upregulation of Rnf146 in VPA-exposed mice. Consistently, overexpressing Rnf146 in the PFC impaired social behaviors and altered the Wnt signaling pathway in adult mice. Furthermore, Rnf146-overexpressing PFC neurons showed increased excitatory synaptic transmission, which may underlie impaired social behavior. These results demonstrate that Rnf146 is critical for social behavior and that dysregulation of Rnf146 underlies social deficits in VPA-exposed mice.
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Affiliation(s)
- Gaeun Park
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Wooyoung Eric Jang
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Seoyeon Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
| | - Edson Luck Gonzales
- School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jungeun Ji
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
| | - Seunghwan Choi
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Yujin Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea
| | - Ji Hwan Park
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | | | - Geul Bang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119, Republic of Korea
| | - Minkyung Kang
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Soobin Kim
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Se Jin Jeon
- School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, 28119, Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin, 17104, Republic of Korea
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Chan Young Shin
- School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea.
| | - Min-Sik Kim
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
- New Biology Research Center, DGIST, Daegu, 42988, Republic of Korea.
- Center for Cell Fate Reprogramming and Control, DGIST, Daegu, 42988, Republic of Korea.
| | - Yong-Seok Lee
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
- Department of Physiology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
- Wide River Institute of Immunology, Seoul National University, Hongcheon, 25159, Republic of Korea.
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Congiu L, Granato V, Jakovcevski I, Kleene R, Fernandes L, Freitag S, Kneussel M, Schachner M, Loers G. Mice Mutated in the Third Fibronectin Domain of L1 Show Enhanced Hippocampal Neuronal Cell Death, Astrogliosis and Alterations in Behavior. Biomolecules 2023; 13:776. [PMID: 37238646 PMCID: PMC10216033 DOI: 10.3390/biom13050776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Adhesion molecules play major roles in cell proliferation, migration, survival, neurite outgrowth and synapse formation during nervous system development and in adulthood. The neural cell adhesion molecule L1 contributes to these functions during development and in synapse formation and synaptic plasticity after trauma in adulthood. Mutations of L1 in humans result in L1 syndrome, which is associated with mild-to-severe brain malformations and mental disabilities. Furthermore, mutations in the extracellular domain were shown to cause a severe phenotype more often than mutations in the intracellular domain. To explore the outcome of a mutation in the extracellular domain, we generated mice with disruption of the dibasic sequences RK and KR that localize to position 858RKHSKR863 in the third fibronectin type III domain of murine L1. These mice exhibit alterations in exploratory behavior and enhanced marble burying activity. Mutant mice display higher numbers of caspase 3-positive neurons, a reduced number of principle neurons in the hippocampus, and an enhanced number of glial cells. Experiments suggest that disruption of the dibasic sequence in L1 results in subtle impairments in brain structure and functions leading to obsessive-like behavior in males and reduced anxiety in females.
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Affiliation(s)
- Ludovica Congiu
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany (R.K.); (S.F.); (M.K.)
| | - Viviana Granato
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany (R.K.); (S.F.); (M.K.)
| | - Igor Jakovcevski
- Institut für Anatomie und Klinische Morphologie, Universität Witten/Herdecke, 58455 Witten, Germany;
| | - Ralf Kleene
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany (R.K.); (S.F.); (M.K.)
| | - Luciana Fernandes
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany (R.K.); (S.F.); (M.K.)
| | - Sandra Freitag
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany (R.K.); (S.F.); (M.K.)
| | - Matthias Kneussel
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany (R.K.); (S.F.); (M.K.)
| | - Melitta Schachner
- Keck Center for Collaborative Neuroscience, Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08554, USA
| | - Gabriele Loers
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Falkenried 94, 20251 Hamburg, Germany (R.K.); (S.F.); (M.K.)
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7
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Cntnap2-dependent molecular networks in autism spectrum disorder revealed through an integrative multi-omics analysis. Mol Psychiatry 2023; 28:810-821. [PMID: 36253443 PMCID: PMC9908544 DOI: 10.1038/s41380-022-01822-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 09/15/2022] [Accepted: 09/26/2022] [Indexed: 12/28/2022]
Abstract
Autism spectrum disorder (ASD) is a major neurodevelopmental disorder in which patients present with core symptoms of social communication impairment, restricted interest, and repetitive behaviors. Although various studies have been performed to identify ASD-related mechanisms, ASD pathology is still poorly understood. CNTNAP2 genetic variants have been found that represent ASD genetic risk factors, and disruption of Cntnap2 expression has been associated with ASD phenotypes in mice. In this study, we performed an integrative multi-omics analysis by combining quantitative proteometabolomic data obtained with Cntnap2 knockout (KO) mice with multi-omics data obtained from ASD patients and forebrain organoids to elucidate Cntnap2-dependent molecular networks in ASD. To this end, a mass spectrometry-based proteometabolomic analysis of the medial prefrontal cortex in Cntnap2 KO mice led to the identification of Cntnap2-associated molecular features, and these features were assessed in combination with multi-omics data obtained on the prefrontal cortex in ASD patients to identify bona fide ASD cellular processes. Furthermore, a reanalysis of single-cell RNA sequencing data obtained from forebrain organoids derived from patients with CNTNAP2-associated ASD revealed that the aforementioned identified ASD processes were mainly linked to excitatory neurons. On the basis of these data, we constructed Cntnap2-associated ASD network models showing mitochondrial dysfunction, axonal impairment, and synaptic activity. Our results may shed light on the Cntnap2-dependent molecular networks in ASD.
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8
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Ben-Mahmoud A, Jun KR, Gupta V, Shastri P, de la Fuente A, Park Y, Shin KC, Kim CA, da Cruz AD, Pinto IP, Minasi LB, Silva da Cruz A, Faivre L, Callier P, Racine C, Layman LC, Kong IK, Kim CH, Kim WY, Kim HG. A rigorous in silico genomic interrogation at 1p13.3 reveals 16 autosomal dominant candidate genes in syndromic neurodevelopmental disorders. Front Mol Neurosci 2022; 15:979061. [PMID: 36277487 PMCID: PMC9582330 DOI: 10.3389/fnmol.2022.979061] [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: 06/27/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Genome-wide chromosomal microarray is extensively used to detect copy number variations (CNVs), which can diagnose microdeletion and microduplication syndromes. These small unbalanced chromosomal structural rearrangements ranging from 1 kb to 10 Mb comprise up to 15% of human mutations leading to monogenic or contiguous genomic disorders. Albeit rare, CNVs at 1p13.3 cause a variety of neurodevelopmental disorders (NDDs) including development delay (DD), intellectual disability (ID), autism, epilepsy, and craniofacial anomalies (CFA). Most of the 1p13.3 CNV cases reported in the pre-microarray era encompassed a large number of genes and lacked the demarcating genomic coordinates, hampering the discovery of positional candidate genes within the boundaries. In this study, we present four subjects with 1p13.3 microdeletions displaying DD, ID, autism, epilepsy, and CFA. In silico comparative genomic mapping with three previously reported subjects with CNVs and 22 unreported DECIPHER CNV cases has resulted in the identification of four different sub-genomic loci harboring five positional candidate genes for DD, ID, and CFA at 1p13.3. Most of these genes have pathogenic variants reported, and their interacting genes are involved in NDDs. RT-qPCR in various human tissues revealed a high expression pattern in the brain and fetal brain, supporting their functional roles in NDDs. Interrogation of variant databases and interacting protein partners led to the identification of another set of 11 potential candidate genes, which might have been dysregulated by the position effect of these CNVs at 1p13.3. Our studies define 1p13.3 as a genomic region harboring 16 NDD candidate genes and underscore the critical roles of small CNVs in in silico comparative genomic mapping for disease gene discovery. Our candidate genes will help accelerate the isolation of pathogenic heterozygous variants from exome/genome sequencing (ES/GS) databases.
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Affiliation(s)
- Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Ran Jun
- Department of Laboratory Medicine, Inje University Haeundae Paik Hospital, Busan, South Korea
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Pinang Shastri
- Department of Cardiovascular Medicine, Cape Fear Valley Medical Center, Fayetteville, NC, United States
| | - Alberto de la Fuente
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Yongsoo Park
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Chul Shin
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Chong Ae Kim
- Faculdade de Medicina, Unidade de Genética do Instituto da Criança – Hospital das Clínicas HCFMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Aparecido Divino da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Irene Plaza Pinto
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Lysa Bernardes Minasi
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Alex Silva da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Genetics of Developmental Disorders, Université de Bourgogne-Franche Comté, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d’Enfants, Dijon, France
| | - Patrick Callier
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Caroline Racine
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, United States
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, United States
| | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Woo-Yang Kim
- Department of Biological Sciences, Kent State University, Kent, OH, United States
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- *Correspondence: Hyung-Goo Kim,
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9
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Jauhari A, Singh T, Yadav S. Neurodevelopmental Disorders and Neurotoxicity: MicroRNA in Focus. J Chem Neuroanat 2022; 120:102072. [DOI: 10.1016/j.jchemneu.2022.102072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 10/19/2022]
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10
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Marco-Hernández AV, Tomás-Vila M, Montoya-Filardi A, Barranco-González H, Vilchez Padilla JJ, Azorín I, Smeyers Dura P, Monfort-Membrado S, Pitarch-Castellano I, Martínez-Castellano F. Mitochondrial developmental encephalopathy with bilateral optic neuropathy related to homozygous variants in IMMT gene. Clin Genet 2021; 101:233-241. [PMID: 34842280 DOI: 10.1111/cge.14093] [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: 09/15/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/14/2022]
Abstract
IMMT gene codes for mitofilin, a mitochondrial inner membrane protein that regulates the morphology of mitochondrial cristae. The phenotype associated with mutations in this gene has not been yet established, but functional studies carried out show that its loss causes a mitochondrial alteration, both in the morphology of the mitochondrial crests and in their function. We present two cousins from an extended highly consanguineous family with developmental encephalopathy, hypotonia, nystagmus due to optic neuropathy. The likely pathogenic homozygous c.895A>G (p.Lys299Glu) variant in the IMMT gene co-segregates with the disease and associates altered mitochondrial cristae observed by electron microscopy.
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Affiliation(s)
- Ana Victoria Marco-Hernández
- Genomics Unit, La Fe Health Research Institute, Valencia, Spain.,Genetics Unit, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Miguel Tomás-Vila
- Neuropediatrics Section, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | | | | | - Juan Jesus Vilchez Padilla
- Neuromuscular Pathology Laboratory, Health Research Institute La Fe; CIBERER. European Reference for rare Neuromuscular Diseases, Valencia, Spain
| | - Inmaculada Azorín
- Neuromuscular Pathology Laboratory, Health Research Institute La Fe; CIBERER. European Reference for rare Neuromuscular Diseases, Valencia, Spain
| | | | | | | | - Francisco Martínez-Castellano
- Genomics Unit, La Fe Health Research Institute, Valencia, Spain.,Genetics Unit, Hospital Universitari i Politècnic La Fe, Valencia, Spain
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11
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Carollo A, Bonassi A, Lim M, Gabrieli G, Setoh P, Dimitriou D, Aryadoust V, Esposito G. Developmental disabilities across the world: A scientometric review from 1936 to 2020. RESEARCH IN DEVELOPMENTAL DISABILITIES 2021; 117:104031. [PMID: 34333315 DOI: 10.1016/j.ridd.2021.104031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/07/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Developmental disabilities have been largely studied in the past years. Their etiological mechanisms have been underpinned to the interactions between genetic and environmental factors. These factors show variability across the world. Thus, it is important to understand where the set of knowledge obtained on developmental disabilities originates from and whether it is generalizable to low- and middle-income countries. AIMS This study aims to understand the origins of the available literature on developmental disabilities, keeping a focus on parenting, and identify the main trend of research. METHODS AND PROCEDURE A sample of 11,315 publications from 1936 to 2020 were collected from Scopus and a graphical country analysis was conducted. Furthermore, a qualitative approach enabled the clustering of references by keywords into four main areas: "Expression of the disorder", "Physiological Factors", "How it is studied" and "Environmental factors". For each area, a document co-citation analysis (DCA) on CiteSpace software was performed. OUTCOMES AND RESULTS Results highlight the leading role of North America in the study of developmental disabilities. Trends in the literature and the documents' scientific relevance are discussed in details. CONCLUSIONS AND IMPLICATIONS Results demand for investigation in different socio-economical settings to generalize our knowledge. What this paper adds? The current paper tries to provide insight into the origins of the literature on developmental disabilities with a focus on parenting, together with an analysis of the trends of research in the field. The paper consisted of a multi-disciplinary and multi-method review. In fact, the review tried to integrate the analysis of the relation between developmental disabilities with a closer look at the scientific contributions to the field across the world. Specifically, the paper integrates a total of 11,315 papers published on almost a century of research (from 1936 to 2020). An initial qualitative analysis on keywords was combined to a subsequent quantitative approach in order to maximize the comprehension of the impact of almost a century of scientific contributions. Specifically, documents were studied with temporal and structural metrics on a scientometric approach. This allowed the exploration of patterns within the literature available on Scopus in a quantitative way. This method not only assessed the importance of single documents within the network. As a matter of fact, the document co-citation analysis used on CiteSpace software provided insight into the relations existing between multiple documents in the field of research. As a result, the leading role of North America in the literature of developmental disabilities and parenting emerged. This was accompanied by the review of the main trends of research within the existing literature.
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Affiliation(s)
- Alessandro Carollo
- Department of Psychology and Cognitive Science, University of Trento, Rovereto, Italy
| | - Andrea Bonassi
- Department of Psychology and Cognitive Science, University of Trento, Rovereto, Italy; Mobile and Social Computing Lab, Bruno Kessler Foundation, Trento, Italy
| | - Mengyu Lim
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore, Singapore
| | - Giulio Gabrieli
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore, Singapore
| | - Peipei Setoh
- Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore, Singapore
| | - Dagmara Dimitriou
- Sleep Research and Education Laboratory, UCL Institute of Education, London, United Kingdom
| | - Vahid Aryadoust
- National Institute of Education, Nanyang Technological University, Singapore, Singapore
| | - Gianluca Esposito
- Department of Psychology and Cognitive Science, University of Trento, Rovereto, Italy; Psychology Program, School of Social Sciences, Nanyang Technological University, Singapore, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.
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12
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Marco Hernández AV, Caro A, Montoya Filardi A, Tomás Vila M, Monfort S, Beseler Soto B, Nieto-Barceló JJ, Martínez F. Extending the clinical phenotype of SPTAN1: From DEE5 to migraine, epilepsy, and subependymal heterotopias without intellectual disability. Am J Med Genet A 2021; 188:147-159. [PMID: 34590414 DOI: 10.1002/ajmg.a.62507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/08/2022]
Abstract
Mutations in SPTAN1 gene, encoding the nonerythrocyte αII-spectrin, are responsible for a severe developmental and epileptic encephalopathy (DEE5) and a wide spectrum of neurodevelopmental disorders, as epilepsy with or without intellectual disability (ID) or ID with cerebellar syndrome. A certain genotype-phenotype correlation has been proposed according to the type and location of the mutation. Herein, we report three novel cases with de novo SPTAN1 mutations, one of them associated to a mild phenotype not previously described. They range from (1) severe developmental encephalopathy with ataxia and a mild cerebellar atrophy, without epilepsy; (2) moderate intellectual disability, severe language delay, ataxia and tremor; (3) normal intelligence, chronic migraine, and generalized tonic-clonic seizures. Remarkably, all these patients showed brain MRI abnormalities, being of special interest the subependymal heterotopias detected in the latter patient. Thus we extend the SPTAN1-related phenotypic spectrum, both in its radiological and clinical involvement. Furthermore, after systematic analysis of all the patients so far reported, we noted an excess of male versus female patients (20:9, p = 0.04), more pronounced among the milder phenotypes. Consequently, some protection factor might be suspected among female carriers, which if confirmed should be considered when establishing the pathogenicity of milder genetic variants in this gene.
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Affiliation(s)
- Ana Victoria Marco Hernández
- Genetics Unit, Hospital Universitari i Politècnic La Fe, Valencia, Spain.,Neuropediatrics Section, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Alfonso Caro
- Genetics Unit, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | | | - Miguel Tomás Vila
- Neuropediatrics Section, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Sandra Monfort
- Genetics Unit, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Beatriz Beseler Soto
- Neuropediatrics Section, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | | | - Francisco Martínez
- Genetics Unit, Hospital Universitari i Politècnic La Fe, Valencia, Spain
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13
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Choi L, An JY. Genetic architecture of autism spectrum disorder: Lessons from large-scale genomic studies. Neurosci Biobehav Rev 2021; 128:244-257. [PMID: 34166716 DOI: 10.1016/j.neubiorev.2021.06.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic component. Recently developed genomic technologies, including microarray and next-generation sequencing (NGS), have enabled researchers to genetic analyses aimed at identifying genetic variations associated with ASD and to elucidate the genetic architecture of the disorder. Large-scale microarray, exome sequencing analyses, and robust statistical methods have resulted in successful gene discovery and identification of high-confidence ASD genes from among de novo and inherited variants. Efforts have been made to understand the genetic architecture of ASD using whole-genome sequencing and genome-wide association studies aimed at identifying noncoding mutations and common variants associated with ASD. In addition, the development of systems biology approaches has resulted in the integration of genetic findings with functional genomic datasets, thereby providing a unique insight into the functional convergence of ASD risk genes and their neurobiology. In this review, we summarize the latest findings of ASD genetic studies involving large cohorts and discuss their implications in ASD neurobiology and in clinical practice.
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Affiliation(s)
- Leejee Choi
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea; Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea; Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea; Transdisciplinary Major in Learning Health Systems, Department of Healthcare Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea; BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.
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14
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Roles of HIF and 2-Oxoglutarate-Dependent Dioxygenases in Controlling Gene Expression in Hypoxia. Cancers (Basel) 2021; 13:cancers13020350. [PMID: 33477877 PMCID: PMC7832865 DOI: 10.3390/cancers13020350] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that such dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. Abstract Hypoxia—reduction in oxygen availability—plays key roles in both physiological and pathological processes. Given the importance of oxygen for cell and organism viability, mechanisms to sense and respond to hypoxia are in place. A variety of enzymes utilise molecular oxygen, but of particular importance to oxygen sensing are the 2-oxoglutarate (2-OG) dependent dioxygenases (2-OGDs). Of these, Prolyl-hydroxylases have long been recognised to control the levels and function of Hypoxia Inducible Factor (HIF), a master transcriptional regulator in hypoxia, via their hydroxylase activity. However, recent studies are revealing that dioxygenases are involved in almost all aspects of gene regulation, including chromatin organisation, transcription and translation. We highlight the relevance of HIF and 2-OGDs in the control of gene expression in response to hypoxia and their relevance to human biology and health.
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15
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Dysfunction of NMDA receptors in neuronal models of an autism spectrum disorder patient with a DSCAM mutation and in Dscam-knockout mice. Mol Psychiatry 2021; 26:7538-7549. [PMID: 34253863 PMCID: PMC8873012 DOI: 10.1038/s41380-021-01216-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 06/15/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
Heterogeneity in the etiopathology of autism spectrum disorders (ASD) limits the development of generic remedies, requires individualistic and patient-specific research. Recent progress in human-induced pluripotent stem cell (iPSC) technology provides a novel platform for modeling ASDs for studying complex neuronal phenotypes. In this study, we generated telencephalic induced neuronal (iN) cells from iPSCs derived from an ASD patient with a heterozygous point mutation in the DSCAM gene. The mRNA of DSCAM and the density of DSCAM in dendrites were significantly decreased in ASD compared to control iN cells. RNA sequencing analysis revealed that several synaptic function-related genes including NMDA receptor subunits were downregulated in ASD iN cells. Moreover, NMDA receptor (R)-mediated currents were significantly reduced in ASD compared to control iN cells. Normal NMDA-R-mediated current levels were rescued by expressing wild-type DSCAM in ASD iN cells, and reduced currents were observed by truncated DSCAM expression in control iN cells. shRNA-mediated DSCAM knockdown in control iN cells resulted in the downregulation of an NMDA-R subunit, which was rescued by the overexpression of shRNA-resistant DSCAM. Furthermore, DSCAM was co-localized with NMDA-R components in the dendritic spines of iN cells whereas their co-localizations were significantly reduced in ASD iN cells. Levels of phospho-ERK1/2 were significantly lower in ASD iN cells, suggesting a potential mechanism. A neural stem cell-specific Dscam heterozygous knockout mouse model, showing deficits in social interaction and social memory with reduced NMDA-R currents. These data suggest that DSCAM mutation causes pathological symptoms of ASD by dysregulating NMDA-R function.
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16
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Autism-associated miR-873 regulates ARID1B, SHANK3 and NRXN2 involved in neurodevelopment. Transl Psychiatry 2020; 10:418. [PMID: 33262327 PMCID: PMC7708977 DOI: 10.1038/s41398-020-01106-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/21/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorders (ASD) are highly heritable neurodevelopmental disorders with significant genetic heterogeneity. Noncoding microRNAs (miRNAs) are recognised as playing key roles in development of ASD albeit the function of these regulatory genes remains unclear. We previously conducted whole-exome sequencing of Australian families with ASD and identified four novel single nucleotide variations in mature miRNA sequences. A pull-down transcriptome analysis using transfected SH-SY5Y cells proposed a mechanistic model to examine changes in binding affinity associated with a unique mutation found in the conserved 'seed' region of miR-873-5p (rs777143952: T > A). Results suggested several ASD-risk genes were differentially targeted by wild-type and mutant miR-873 variants. In the current study, a dual-luciferase reporter assay confirmed miR-873 variants have a 20-30% inhibition/dysregulation effect on candidate autism risk genes ARID1B, SHANK3 and NRXN2 and also confirmed the affected expression with qPCR. In vitro mouse hippocampal neurons transfected with mutant miR-873 showed less morphological complexity and enhanced sodium currents and excitatory neurotransmission compared to cells transfected with wild-type miR-873. A second in vitro study showed CRISPR/Cas9 miR-873 disrupted SH-SY5Y neuroblastoma cells acquired a neuronal-like morphology and increased expression of ASD important genes ARID1B, SHANK3, ADNP2, ANK2 and CHD8. These results represent the first functional evidence that miR-873 regulates key neural genes involved in development and cell differentiation.
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17
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Agarwala S, Veerappa AM, Ramachandra NB. Identification of primary copy number variations reveal enrichment of Calcium, and MAPK pathways sensitizing secondary sites for autism. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00091-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Autism is a neurodevelopmental condition with genetic heterogeneity. It is characterized by difficulties in reciprocal social interactions with strong repetitive behaviors and stereotyped interests. Copy number variations (CNVs) are genomic structural variations altering the genomic structure either by duplication or deletion. De novo or inherited CNVs are found in 5–10% of autistic subjects with a size range of few kilobases to several megabases. CNVs predispose humans to various diseases by altering gene regulation, generation of chimeric genes, and disruption of the coding region or through position effect. Although, CNVs are not the initiating event in pathogenesis; additional preceding mutations might be essential for disease manifestation. The present study is aimed to identify the primary CNVs responsible for autism susceptibility in healthy cohorts to sensitize secondary-hits. In the current investigation, primary-hit autism gene CNVs are characterized in 1715 healthy cohorts of varying ethnicities across 12 populations using Affymetrix high-resolution array study. Thirty-eight individuals from twelve families residing in Karnataka, India, with the age group of 13–73 years are included for the comparative CNV analysis. The findings are validated against global 179 autism whole-exome sequence datasets derived from Simons Simplex Collection. These datasets are deposited at the Simons Foundation Autism Research Initiative (SFARI) database.
Results
The study revealed that 34.8% of the subjects carried 2% primary-hit CNV burden with 73 singleton-autism genes in different clusters. Of these, three conserved CNV breakpoints were identified with ARHGAP11B, DUSP22, and CHRNA7 as the target genes across 12 populations. Enrichment analysis of the population-specific autism genes revealed two signaling pathways—calcium and mitogen-activated protein kinases (MAPK) in the CNV identified regions. These impaired pathways affected the downstream cascades of neuronal function and physiology, leading to autism behavior. The pathway analysis of enriched genes unravelled complex protein interaction networks, which sensitized secondary sites for autism. Further, the identification of miRNA targets associated with autism gene CNVs added severity to the condition.
Conclusion
These findings contribute to an atlas of primary-hit genes to detect autism susceptibility in healthy cohorts, indicating their impact on secondary sites for manifestation.
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Ní Ghrálaigh F, Gallagher L, Lopez LM. Autism spectrum disorder genomics: The progress and potential of genomic technologies. Genomics 2020; 112:5136-5142. [DOI: 10.1016/j.ygeno.2020.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/01/2020] [Accepted: 09/08/2020] [Indexed: 12/27/2022]
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19
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Renaux A, Papadimitriou S, Versbraegen N, Nachtegael C, Boutry S, Nowé A, Smits G, Lenaerts T. ORVAL: a novel platform for the prediction and exploration of disease-causing oligogenic variant combinations. Nucleic Acids Res 2020; 47:W93-W98. [PMID: 31147699 PMCID: PMC6602484 DOI: 10.1093/nar/gkz437] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/01/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022] Open
Abstract
A tremendous amount of DNA sequencing data is being produced around the world with the ambition to capture in more detail the mechanisms underlying human diseases. While numerous bioinformatics tools exist that allow the discovery of causal variants in Mendelian diseases, little to no support is provided to do the same for variant combinations, an essential task for the discovery of the causes of oligogenic diseases. ORVAL (the Oligogenic Resource for Variant AnaLysis), which is presented here, provides an answer to this problem by focusing on generating networks of candidate pathogenic variant combinations in gene pairs, as opposed to isolated variants in unique genes. This online platform integrates innovative machine learning methods for combinatorial variant pathogenicity prediction with visualization techniques, offering several interactive and exploratory tools, such as pathogenic gene and protein interaction networks, a ranking of pathogenic gene pairs, as well as visual mappings of the cellular location and pathway information. ORVAL is the first web-based exploration platform dedicated to identifying networks of candidate pathogenic variant combinations with the sole ambition to help in uncovering oligogenic causes for patients that cannot rely on the classical disease analysis tools. ORVAL is available at https://orval.ibsquare.be.
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Affiliation(s)
- Alexandre Renaux
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sofia Papadimitriou
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Nassim Versbraegen
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Charlotte Nachtegael
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Simon Boutry
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Laboratory of Human Molecular Genetics, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Ann Nowé
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Hôpital Universitaire des Enfants Reine Fabiola, 1020 Brussels, Belgium.,Center of Human Genetics, Hôpital Erasme, 1070 Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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20
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Kim Y, An JY. Spatio-Temporal Roles of ASD-Associated Variants in Human Brain Development. Genes (Basel) 2020; 11:genes11050535. [PMID: 32403330 PMCID: PMC7291218 DOI: 10.3390/genes11050535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023] Open
Abstract
Transcriptional regulation of the genome arguably provides the basis for the anatomical elaboration and dynamic operation of the human brain. It logically follows that genetic variations affecting gene transcription contribute to mental health disorders, including autism spectrum disorder (ASD). A number of recent studies have shown the role of de novo variants (DNVs) in disrupting early neurodevelopment. However, there is limited knowledge concerning the role of inherited variants during the early brain development of ASD. In this study, we investigate the role of rare inherited variations in neurodevelopment. We conducted co-expression network analyses using an anatomically comprehensive atlas of the developing human brain and examined whether rare coding and regulatory variants, identified from our genetic screening of Australian families with ASD, work in different spatio-temporal functions.
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Affiliation(s)
- Yujin Kim
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul 02841, Korea;
- Department of Integrated Biomedical and Life Science, Korea University, Seoul 02841, Korea
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul 02841, Korea;
- Department of Integrated Biomedical and Life Science, Korea University, Seoul 02841, Korea
- Correspondence: ; Tel.: +82-2-3290-5646
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21
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A Caenorhabditis elegans Model for Integrating the Functions of Neuropsychiatric Risk Genes Identifies Components Required for Normal Dendritic Morphology. G3-GENES GENOMES GENETICS 2020; 10:1617-1628. [PMID: 32132169 PMCID: PMC7202017 DOI: 10.1534/g3.119.400925] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Analysis of patient-derived DNA samples has identified hundreds of variants that are likely involved in neuropsychiatric diseases such as autism spectrum disorder (ASD) and schizophrenia (SCZ). While these studies couple behavioral phenotypes to individual genotypes, the number and diversity of candidate genes implicated in these disorders highlights the fact that the mechanistic underpinnings of these disorders are largely unknown. Here, we describe a RNAi-based screening platform that uses C. elegans to screen candidate neuropsychiatric risk genes (NRGs) for roles in controlling dendritic arborization. To benchmark this approach, we queried published lists of NRGs whose variants in ASD and SCZ are predicted to result in complete or partial loss of gene function. We found that a significant fraction (>16%) of these candidate NRGs are essential for dendritic development. Furthermore, these gene sets are enriched for dendritic arbor phenotypes (>14 fold) when compared to control RNAi datasets of over 500 human orthologs. The diversity of PVD structural abnormalities observed in these assays suggests that the functions of diverse NRGs (encoding transcription factors, chromatin remodelers, molecular chaperones and cytoskeleton-related proteins) converge to regulate neuronal morphology and that individual NRGs may play distinct roles in dendritic branching. We also demonstrate that the experimental value of this platform by providing additional insights into the molecular frameworks of candidate NRGs. Specifically, we show that ANK2/UNC-44 function is directly integrated with known regulators of dendritic arborization and suggest that altering the dosage of ARID1B/LET-526 expression during development affects neuronal morphology without diminishing aspects of cell fate specification.
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22
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Murcia Pienkowski V, Kucharczyk M, Rydzanicz M, Poszewiecka B, Pachota K, Młynek M, Stawiński P, Pollak A, Kosińska J, Wojciechowska K, Lejman M, Cieślikowska A, Wicher D, Stembalska A, Matuszewska K, Materna-Kiryluk A, Gambin A, Chrzanowska K, Krajewska-Walasek M, Płoski R. Breakpoint Mapping of Symptomatic Balanced Translocations Links the EPHA6, KLF13 and UBR3 Genes to Novel Disease Phenotype. J Clin Med 2020; 9:jcm9051245. [PMID: 32344861 PMCID: PMC7287862 DOI: 10.3390/jcm9051245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/19/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
De novo balanced chromosomal aberrations (BCAs), such as reciprocal translocations and inversions, are genomic aberrations that, in approximately 25% of cases, affect the human phenotype. Delineation of the exact structure of BCAs may provide a precise diagnosis and/or point to new disease loci. We report on six patients with de novo balanced chromosomal translocations (BCTs) and one patient with a de novo inversion, in whom we mapped breakpoints to a resolution of 1 bp, using shallow whole-genome mate pair sequencing. In all seven cases, a disruption of at least one gene was found. In two patients, the phenotypic impact of the disrupted genes is well known (NFIA, ATP7A). In five patients, the aberration damaged genes: PARD3, EPHA6, KLF13, STK24, UBR3, MLLT10 and TLE3, whose influence on the human phenotype is poorly understood. In particular, our results suggest novel candidate genes for retinal degeneration with anophthalmia (EPHA6), developmental delay with speech impairment (KLF13), and developmental delay with brain dysembryoplastic neuroepithelial tumor (UBR3). In conclusion, identification of the exact structure of symptomatic BCTs using next generation sequencing is a viable method for both diagnosis and finding novel disease candidate genes in humans.
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Affiliation(s)
- Victor Murcia Pienkowski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Marzena Kucharczyk
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Barbara Poszewiecka
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland; (B.P.); (A.G.)
| | - Katarzyna Pachota
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Marlena Młynek
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Agnieszka Pollak
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
| | - Katarzyna Wojciechowska
- Department of Pediatric Hematology Oncology and Transplantology, University Children’s Hospital, 20-093 Lublin, Poland;
| | - Monika Lejman
- Department of Pediatric Hematology Oncology and Transplantology, Medical University of Lublin, 20-093 Lublin, Poland;
| | - Agata Cieślikowska
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Dorota Wicher
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | | | - Karolina Matuszewska
- Department of Medical Genetics, University of Medical Sciences, 60-806 Poznan, Poland; (K.M.); (A.M.-K.)
- Centers for Medical Genetics GENESIS, Grudzieniec, 60-406 Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, University of Medical Sciences, 60-806 Poznan, Poland; (K.M.); (A.M.-K.)
- Centers for Medical Genetics GENESIS, Grudzieniec, 60-406 Poznan, Poland
| | - Anna Gambin
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland; (B.P.); (A.G.)
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Małgorzata Krajewska-Walasek
- Department of Medical Genetics, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland; (M.K.); (K.P.); (M.M.); (A.C.); (D.W.); (K.C.); (M.K.-W.)
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (V.M.P.); (M.R.); (P.S.); (A.P.); (J.K.)
- Correspondence: ; Tel.: +48-22-572-06-95; Fax: +48-22-572-06-96
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23
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Kang L, Liu Y, Jin Y, Li M, Song J, Zhang Y, Zhang Y, Yang Y. Mutations of MACF1, Encoding Microtubule-Actin Crosslinking-Factor 1, Cause Spectraplakinopathy. Front Neurol 2020; 10:1335. [PMID: 32010038 PMCID: PMC6974614 DOI: 10.3389/fneur.2019.01335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 12/02/2019] [Indexed: 02/01/2023] Open
Abstract
As a member of spectraplakin family of cytoskeletal crosslinking proteins, microtubule-actin crosslinking factor 1 (MACF1) controls cytoskeleton network dynamics. Knockout of Macf1 in mice resulted in the developmental retardation and embryonic lethality. Spectraplakinopathy type I, a novel neuromuscular condition characterized by periodic hypotonia, lax muscles, joint contracture, and diminished motor skill, was reported to be associated with heterozygous genomic duplication involving the MACF1 loci, with incomplete penetrance and highly variable clinical presentation in a single pedigree. In this study, parental-derived compound heterozygous novel missense mutations of MACF1, c.1517C>T (p.Thr506Ile) and c.11654T>C (p.Ile3885Thr), were found to co-segregate with disease status in two affected brothers presenting with progressive spastic tetraplegia, dystonia, joint contracture, feeding difficulty and developmental delay. We speculated that MACF1 mutations cause spectraplakinopathy inherited in an autosomal recessive manner. Our clinical findings expanded the phenotype of this neuromuscular disorder and provided new insights into the function of MACF1.
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Affiliation(s)
- Lulu Kang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yi Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Ying Jin
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Mengqiu Li
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jinqing Song
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | | | - Yao Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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24
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Williams SM, An JY, Edson J, Watts M, Murigneux V, Whitehouse AJO, Jackson CJ, Bellgrove MA, Cristino AS, Claudianos C. An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder. Mol Psychiatry 2019; 24:1707-1719. [PMID: 29703944 DOI: 10.1038/s41380-018-0049-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/16/2018] [Accepted: 02/19/2018] [Indexed: 01/09/2023]
Abstract
A number of genetic studies have identified rare protein-coding DNA variations associated with autism spectrum disorder (ASD), a neurodevelopmental disorder with significant genetic etiology and heterogeneity. In contrast, the contributions of functional, regulatory genetic variations that occur in the extensive non-protein-coding regions of the genome remain poorly understood. Here we developed a genome-wide analysis to identify the rare single nucleotide variants (SNVs) that occur in non-coding regions and determined the regulatory function and evolutionary conservation of these variants. Using publicly available datasets and computational predictions, we identified SNVs within putative regulatory regions in promoters, transcription factor binding sites, and microRNA genes and their target sites. Overall, we found that the regulatory variants in ASD cases were enriched in ASD-risk genes and genes involved in fetal neurodevelopment. As with previously reported coding mutations, we found an enrichment of the regulatory variants associated with dysregulation of neurodevelopmental and synaptic signaling pathways. Among these were several rare inherited SNVs found in the mature sequence of microRNAs predicted to affect the regulation of ASD-risk genes. We show a paternally inherited miR-873-5p variant with altered binding affinity for several risk-genes including NRXN2 and CNTNAP2 putatively overlay maternally inherited loss-of-function coding variations in NRXN1 and CNTNAP2 to likely increase the genetic liability in an idiopathic ASD case. Our analysis pipeline provides a new resource for identifying loss-of-function regulatory DNA variations that may contribute to the genetic etiology of complex disorders.
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Affiliation(s)
- Sarah M Williams
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia.,Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Joon Yong An
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Department of Psychiatry, University of California San Francisco, San Francisco, USA.,Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, USA
| | - Janette Edson
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Michelle Watts
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Valentine Murigneux
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Andrew J O Whitehouse
- Telethon Kids Institute, University of Western Australia, Perth, Australia.,Cooperative Research Centre for Living with Autism, Brisbane, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Mark A Bellgrove
- Monash Institute of Cognitive and Clinical Neuroscience, Monash University, Melbourne, Australia
| | - Alexandre S Cristino
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia.
| | - Charles Claudianos
- Queensland Brain Institute, University of Queensland, Brisbane, Australia. .,Centre for Mental Health Research CMHR, Australian National University, Canberra, Australia.
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25
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Carraro M, Monzon AM, Chiricosta L, Reggiani F, Aspromonte MC, Bellini M, Pagel K, Jiang Y, Radivojac P, Kundu K, Pal LR, Yin Y, Limongelli I, Andreoletti G, Moult J, Wilson SJ, Katsonis P, Lichtarge O, Chen J, Wang Y, Hu Z, Brenner SE, Ferrari C, Murgia A, Tosatto SC, Leonardi E. Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge. Hum Mutat 2019; 40:1330-1345. [PMID: 31144778 PMCID: PMC7341177 DOI: 10.1002/humu.23823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/07/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]
Abstract
The Critical Assessment of Genome Interpretation-5 intellectual disability challenge asked to use computational methods to predict patient clinical phenotypes and the causal variant(s) based on an analysis of their gene panel sequence data. Sequence data for 74 genes associated with intellectual disability (ID) and/or autism spectrum disorders (ASD) from a cohort of 150 patients with a range of neurodevelopmental manifestations (i.e. ID, autism, epilepsy, microcephaly, macrocephaly, hypotonia, ataxia) have been made available for this challenge. For each patient, predictors had to report the causative variants and which of the seven phenotypes were present. Since neurodevelopmental disorders are characterized by strong comorbidity, tested individuals often present more than one pathological condition. Considering the overall clinical manifestation of each patient, the correct phenotype has been predicted by at least one group for 93 individuals (62%). ID and ASD were the best predicted among the seven phenotypic traits. Also, causative or potentially pathogenic variants were predicted correctly by at least one group. However, the prediction of the correct causative variant seems to be insufficient to predict the correct phenotype. In some cases, the correct prediction has been supported by rare or common variants in genes different from the causative one.
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Affiliation(s)
- Marco Carraro
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | | | - Luigi Chiricosta
- Department of Biomedical Sciences, University of Padua, Padua, Italy
| | - Francesco Reggiani
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- Department of Information Engineering, University of Padua, Padua, Italy
| | | | - Mariagrazia Bellini
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
| | - Kymberleigh Pagel
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Yuxiang Jiang
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Predrag Radivojac
- Khoury College of Computer and Information Sciences, Northeastern University, 440, Huntington Avenue, Boston, MA 02115, USA
| | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | | | - Gaia Andreoletti
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Stephen J. Wilson
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Panagiotis Katsonis
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX 77030, USA
| | - Jingqi Chen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Yaqiong Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Carlo Ferrari
- Department of Information Engineering, University of Padua, Padua, Italy
| | - Alessandra Murgia
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
| | - Silvio C.E. Tosatto
- Department of Biomedical Sciences, University of Padua, Padua, Italy
- CNR Institute of Neuroscience, Padua, Italy
| | - Emanuela Leonardi
- Department of Woman and Child Health, University of Padua, Padua, Italy
- Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
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26
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Patowary A, Won SY, Oh SJ, Nesbitt RR, Archer M, Nickerson D, Raskind WH, Bernier R, Lee JE, Brkanac Z. Family-based exome sequencing and case-control analysis implicate CEP41 as an ASD gene. Transl Psychiatry 2019; 9:4. [PMID: 30664616 PMCID: PMC6341097 DOI: 10.1038/s41398-018-0343-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/13/2018] [Indexed: 12/03/2022] Open
Abstract
Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder with a strong genetic component. Although next-generation sequencing (NGS) technologies have been successfully applied to gene identification in de novo ASD, the genetic architecture of familial ASD remains largely unexplored. Our approach, which leverages the high specificity and sensitivity of NGS technology, has focused on rare variants in familial autism. We used NGS exome sequencing in 26 families with distantly related affected individuals to identify genes with private gene disrupting and missense variants of interest (VOI). We found that the genes carrying VOIs were enriched for biological processes related to cell projection organization and neuron development, which is consistent with the neurodevelopmental hypothesis of ASD. For a subset of genes carrying VOIs, we then used targeted NGS sequencing and gene-based variant burden case-control analysis to test for association with ASD. Missense variants in one gene, CEP41, associated significantly with ASD (p = 6.185e-05). Homozygous gene-disrupting variants in CEP41 were initially found to be responsible for recessive Joubert syndrome. Using a zebrafish model, we evaluated the mechanism by which the CEP41 variants might contribute to ASD. We found that CEP41 missense variants affect development of the axonal tract, cranial neural crest migration and social behavior phenotype. Our work demonstrates the involvement of CEP41 heterozygous missense variants in ASD and that biological processes involved in cell projection organization and neuron development are enriched in ASD families we have studied.
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Affiliation(s)
- Ashok Patowary
- 0000000122986657grid.34477.33Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA USA
| | - So Yeon Won
- 0000 0001 2181 989Xgrid.264381.aDepartment of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Shin Ji Oh
- 0000 0001 2181 989Xgrid.264381.aDepartment of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Ryan R Nesbitt
- 0000000122986657grid.34477.33Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA USA
| | - Marilyn Archer
- 0000000122986657grid.34477.33Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA USA
| | - Debbie Nickerson
- 0000000122986657grid.34477.33Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Wendy H. Raskind
- 0000000122986657grid.34477.33Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA USA ,0000000122986657grid.34477.33Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA USA
| | - Raphael Bernier
- 0000000122986657grid.34477.33Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA USA
| | - Ji Eun Lee
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea. .,Division of Medical Science Research, Samsung Medical Center, Seoul, Korea.
| | - Zoran Brkanac
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA.
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27
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Ka M, Moffat JJ, Kim WY. MACF1 Controls Migration and Positioning of Cortical GABAergic Interneurons in Mice. Cereb Cortex 2018; 27:5525-5538. [PMID: 27756764 DOI: 10.1093/cercor/bhw319] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/23/2016] [Indexed: 01/08/2023] Open
Abstract
GABAergic interneurons develop in the ganglionic eminence in the ventral telencephalon and tangentially migrate into the cortical plate during development. However, key molecules controlling interneuron migration remain poorly identified. Here, we show that microtubule-actin cross-linking factor 1 (MACF1) regulates GABAergic interneuron migration and positioning in the developing mouse brain. To investigate the role of MACF1 in developing interneurons, we conditionally deleted the MACF1 gene in mouse interneuron progenitors and their progeny using Dlx5/6-Cre-IRES-EGFP and Nkx2.1-Cre drivers. We found that MACF1 deletion results in a marked reduction and defective positioning of interneurons in the mouse cerebral cortex and hippocampus, suggesting abnormal interneuron migration. Indeed, the speed and mode of interneuron migration were abnormal in the MACF1-mutant brain, compared with controls. Additionally, MACF1-deleted interneurons showed a significant reduction in the length of their leading processes and dendrites in the mouse brain. Finally, loss of MACF1 decreased microtubule stability in cortical interneurons. Our findings suggest that MACF1 plays a critical role in cortical interneuron migration and positioning in the developing mouse brain.
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Affiliation(s)
- Minhan Ka
- Department of Developmental Neuroscience, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jeffrey J Moffat
- Department of Developmental Neuroscience, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Woo-Yang Kim
- Department of Developmental Neuroscience, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA
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28
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Wanke KA, Devanna P, Vernes SC. Understanding Neurodevelopmental Disorders: The Promise of Regulatory Variation in the 3'UTRome. Biol Psychiatry 2018; 83:548-557. [PMID: 29289333 DOI: 10.1016/j.biopsych.2017.11.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 11/02/2017] [Accepted: 11/02/2017] [Indexed: 01/28/2023]
Abstract
Neurodevelopmental disorders have a strong genetic component, but despite widespread efforts, the specific genetic factors underlying these disorders remain undefined for a large proportion of affected individuals. Given the accessibility of exome sequencing, this problem has thus far been addressed from a protein-centric standpoint; however, protein-coding regions only make up ∼1% to 2% of the human genome. With the advent of whole genome sequencing we are in the midst of a paradigm shift as it is now possible to interrogate the entire sequence of the human genome (coding and noncoding) to fill in the missing heritability of complex disorders. These new technologies bring new challenges, as the number of noncoding variants identified per individual can be overwhelming, making it prudent to focus on noncoding regions of known function, for which the effects of variation can be predicted and directly tested to assess pathogenicity. The 3'UTRome is a region of the noncoding genome that perfectly fulfills these criteria and is of high interest when searching for pathogenic variation related to complex neurodevelopmental disorders. Herein, we review the regulatory roles of the 3'UTRome as binding sites for microRNAs or RNA binding proteins, or during alternative polyadenylation. We detail existing evidence that these regions contribute to neurodevelopmental disorders and outline strategies for identification and validation of novel putatively pathogenic variation in these regions. This evidence suggests that studying the 3'UTRome will lead to the identification of new risk factors, new candidate disease genes, and a better understanding of the molecular mechanisms contributing to neurodevelopmental disorders.
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Affiliation(s)
- Kai A Wanke
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Paolo Devanna
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands.
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29
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Rai-Bhogal R, Ahmad E, Li H, Crawford DA. Microarray analysis of gene expression in the cyclooxygenase knockout mice - a connection to autism spectrum disorder. Eur J Neurosci 2017; 47:750-766. [PMID: 29161772 DOI: 10.1111/ejn.13781] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 11/11/2017] [Accepted: 11/14/2017] [Indexed: 02/07/2023]
Abstract
The cellular and molecular events that take place during brain development play an important role in governing function of the mature brain. Lipid-signalling molecules such as prostaglandin E2 (PGE2 ) play an important role in healthy brain development. Abnormalities along the COX-PGE2 signalling pathway due to genetic or environmental causes have been linked to autism spectrum disorder (ASD). This study aims to evaluate the effect of altered COX-PGE2 signalling on development and function of the prenatal brain using male mice lacking cyclooxygenase-1 and cyclooxygenase-2 (COX-1-/- and COX-2-/- ) as potential model systems of ASD. Microarray analysis was used to determine global changes in gene expression during embryonic days 16 (E16) and 19 (E19). Gene Ontology: Biological Process (GO:BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were implemented to identify affected developmental genes and cellular processes. We found that in both knockouts the brain at E16 had nearly twice as many differentially expressed genes, and affected biological pathways containing various ASD-associated genes important in neuronal function. Interestingly, using GeneMANIA and Cytoscape we also show that the ASD-risk genes identified in both COX-1-/- and COX-2-/- models belong to protein-interaction networks important for brain development despite of different cellular localization of these enzymes. Lastly, we identified eight genes that belong to the Wnt signalling pathways exclusively in the COX-2-/- mice at E16. The level of PKA-phosphorylated β-catenin (S552), a major activator of the Wnt pathway, was increased in this model, suggesting crosstalk between the COX-2-PGE2 and Wnt pathways during early brain development. Overall, these results provide further molecular insight into the contribution of the COX-PGE2 pathways to ASD and demonstrate that COX-1-/- and COX-2-/- animals might be suitable new model systems for studying the disorders.
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Affiliation(s)
- Ravneet Rai-Bhogal
- Neuroscience Graduate Diploma Program, York University, Toronto, ON, M3J 1P3, Canada.,Department of Biology, York University, Toronto, ON, Canada
| | - Eizaaz Ahmad
- Neuroscience Graduate Diploma Program, York University, Toronto, ON, M3J 1P3, Canada.,Department of Biology, York University, Toronto, ON, Canada
| | - Hongyan Li
- School of Kinesiology and Health Science, York University, Toronto, ON, Canada
| | - Dorota A Crawford
- Neuroscience Graduate Diploma Program, York University, Toronto, ON, M3J 1P3, Canada.,Department of Biology, York University, Toronto, ON, Canada.,School of Kinesiology and Health Science, York University, Toronto, ON, Canada
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30
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Hansen RD, Christensen AF, Olesen J. Family studies to find rare high risk variants in migraine. J Headache Pain 2017; 18:32. [PMID: 28255817 PMCID: PMC5334193 DOI: 10.1186/s10194-017-0729-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Migraine has long been known as a common complex disease caused by genetic and environmental factors. The pathophysiology and the specific genetic susceptibility are poorly understood. Common variants only explain a small part of the heritability of migraine. It is thought that rare genetic variants with bigger effect size may be involved in the disease. Since migraine has a tendency to cluster in families, a family approach might be the way to find these variants. This is also indicated by identification of migraine-associated loci in classical linkage-analyses in migraine families. A single migraine study using a candidate-gene approach was performed in 2010 identifying a rare mutation in the TRESK potassium channel segregating in a large family with migraine with aura, but this finding has later become questioned. The technologies of next-generation sequencing (NGS) now provides an affordable tool to investigate the genetic variation in the entire exome or genome. The family-based study design using NGS is described in this paper. We also review family studies using NGS that have been successful in finding rare variants in other common complex diseases in order to argue the promising application of a family approach to migraine. METHOD PubMed was searched to find studies that looked for rare genetic variants in common complex diseases through a family-based design using NGS, excluding studies looking for de-novo mutations, or using a candidate-gene approach and studies on cancer. All issues from Nature Genetics and PLOS genetics 2014, 2015 and 2016 (UTAI June) were screened for relevant papers. Reference lists from included and other relevant papers were also searched. For the description of the family-based study design using NGS an in-house protocol was used. RESULTS Thirty-two successful studies, which covered 16 different common complex diseases, were included in this paper. We also found a single migraine study. Twenty-three studies found one or a few family specific variants (less than five), while other studies found several possible variants. Not all of them were genome wide significant. Four studies performed follow-up analyses in unrelated cases and controls and calculated odds ratios that supported an association between detected variants and risk of disease. Studies of 11 diseases identified rare variants that segregated fully or to a large degree with the disease in the pedigrees. CONCLUSION It is possible to find rare high risk variants for common complex diseases through a family-based approach. One study using a family approach and NGS to find rare variants in migraine has already been published but with strong limitations. More studies are under way.
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Affiliation(s)
- Rikke Dyhr Hansen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
| | - Anne Francke Christensen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
| | - Jes Olesen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
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31
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Syrbe S, Harms FL, Parrini E, Montomoli M, Mütze U, Helbig KL, Polster T, Albrecht B, Bernbeck U, van Binsbergen E, Biskup S, Burglen L, Denecke J, Heron B, Heyne HO, Hoffmann GF, Hornemann F, Matsushige T, Matsuura R, Kato M, Korenke GC, Kuechler A, Lämmer C, Merkenschlager A, Mignot C, Ruf S, Nakashima M, Saitsu H, Stamberger H, Pisano T, Tohyama J, Weckhuysen S, Werckx W, Wickert J, Mari F, Verbeek NE, Møller RS, Koeleman B, Matsumoto N, Dobyns WB, Battaglia D, Lemke JR, Kutsche K, Guerrini R. Delineating SPTAN1 associated phenotypes: from isolated epilepsy to encephalopathy with progressive brain atrophy. Brain 2017; 140:2322-2336. [PMID: 29050398 DOI: 10.1093/brain/awx195] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/13/2017] [Indexed: 12/21/2022] Open
Abstract
De novo in-frame deletions and duplications in the SPTAN1 gene, encoding the non-erythrocyte αII spectrin, have been associated with severe West syndrome with hypomyelination and pontocerebellar atrophy. We aimed at comprehensively delineating the phenotypic spectrum associated with SPTAN1 mutations. Using different molecular genetic techniques, we identified 20 patients with a pathogenic or likely pathogenic SPTAN1 variant and reviewed their clinical, genetic and imaging data. SPTAN1 de novo alterations included seven unique missense variants and nine in-frame deletions/duplications of which 12 were novel. The recurrent three-amino acid duplication p.(Asp2303_Leu2305dup) occurred in five patients. Our patient cohort exhibited a broad spectrum of neurodevelopmental phenotypes, comprising six patients with mild to moderate intellectual disability, with or without epilepsy and behavioural disorders, and 14 patients with infantile epileptic encephalopathy, of which 13 had severe neurodevelopmental impairment and four died in early childhood. Imaging studies suggested that the severity of neurological impairment and epilepsy correlates with that of structural abnormalities as well as the mutation type and location. Out of seven patients harbouring mutations outside the α/β spectrin heterodimerization domain, four had normal brain imaging and three exhibited moderately progressive brain and/or cerebellar atrophy. Twelve of 13 patients with mutations located within the spectrin heterodimer contact site exhibited severe and progressive brain, brainstem and cerebellar atrophy, with hypomyelination in most. We used fibroblasts from five patients to study spectrin aggregate formation by Triton-X extraction and immunocytochemistry followed by fluorescence microscopy. αII/βII aggregates and αII spectrin in the insoluble protein fraction were observed in fibroblasts derived from patients with the mutations p.(Glu2207del), p.(Asp2303_Leu2305dup) and p.(Arg2308_Met2309dup), all falling in the nucleation site of the α/β spectrin heterodimer region. Molecular modelling of the seven SPTAN1 amino acid changes provided preliminary evidence for structural alterations of the A-, B- and/or C-helices within each of the mutated spectrin repeats. We conclude that SPTAN1-related disorders comprise a wide spectrum of neurodevelopmental phenotypes ranging from mild to severe and progressive. Spectrin aggregate formation in fibroblasts with mutations in the α/β heterodimerization domain seems to be associated with a severe neurodegenerative course and suggests that the amino acid stretch from Asp2303 to Met2309 in the α20 repeat is important for α/β spectrin heterodimer formation and/or αII spectrin function.
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Affiliation(s)
- Steffen Syrbe
- Department of General Paediatrics, Division of Child Neurology and Inherited Metabolic Diseases, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elena Parrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Martino Montomoli
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Ulrike Mütze
- Department of General Paediatrics, Division of Child Neurology and Inherited Metabolic Diseases, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Katherine L Helbig
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Tilman Polster
- Bethel Epilepsy Center - Krankenhaus Mara GmbH Bielefeld, Germany
| | - Beate Albrecht
- Institut für Humangenetik, Universitaetsklinikum Essen, Universitaet Duisburg-Essen, Germany
| | - Ulrich Bernbeck
- Rems-Murr-Kliniken GmbH, Klinik für Kinder- und Jugendmedizin, Winnenden, Germany
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Saskia Biskup
- CeGaT-Center for Genomics and Transcriptomics GmbH, Tuebingen, Germany
| | - Lydie Burglen
- Centre de référence des Malformations et maladies congénitales du cervelet and Département de Génétique et embryologie médicales, AP-HP, GHUEP, Hôpital Trousseau 75012 Paris, France.,GRC ConCer-LD, Sorbonne Universités, UPMC Univ 06, Paris, France
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bénédicte Heron
- GRC ConCer-LD, Sorbonne Universités, UPMC Univ 06, Paris, France.,AP-HP, Hôpital Trousseau, Service de Neurologie Pédiatrique; Paris, France
| | - Henrike O Heyne
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Georg F Hoffmann
- Department of General Paediatrics, Division of Child Neurology and Inherited Metabolic Diseases, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Frauke Hornemann
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Takeshi Matsushige
- Department of Pediatrics, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Ryuki Matsuura
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Hatanodai, Shinagawa-ku, Tokyo, Japan
| | - G Christoph Korenke
- Klinikum Oldenburg, Zentrum für Kinder- und Jugendmedizin, Klinik für Neuropaediatrie u. angeborene Stoffwechselerkrankungen, Oldenburg, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitaetsklinikum Essen, Universitaet Duisburg-Essen, Germany
| | | | - Andreas Merkenschlager
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Cyril Mignot
- AP-HP, Département de Génétique and Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris, France.,GRC UPMC "Déficiences Intellectuelles et Autisme", Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Susanne Ruf
- Department of Pediatric Neurology and Developmental Medicine, University Children's Hospital, Tübingen, Germany
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hannah Stamberger
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Belgium.,Division of Neurology; Antwerp University Hospital, Antwerp, Belgium
| | - Tiziana Pisano
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Jun Tohyama
- Department of Pediatrics, Nishi-Niigata Chuo National Hospital, Niigata, Japan
| | - Sarah Weckhuysen
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium.,Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Belgium.,Division of Neurology; Antwerp University Hospital, Antwerp, Belgium
| | | | - Julia Wickert
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,IRCCS Stella Maris Foundation, Pisa, Italy
| | - Francesco Mari
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Nienke E Verbeek
- Department of Genetics, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Rikke S Møller
- Danish Epilepsy Centre, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Bobby Koeleman
- Department of Genetics, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - William B Dobyns
- Departments of Pediatrics and Neurology, University of Washington, Seattle, Washington, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Domenica Battaglia
- Child Neurology and Psychiatry Unit, Catholic University, Largo Gemelli 18, Rome, Italy
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A Meyer Children's Hospital, University of Florence, Florence, Italy.,IRCCS Stella Maris Foundation, Pisa, Italy
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32
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Hypermasculinised facial morphology in boys and girls with Autism Spectrum Disorder and its association with symptomatology. Sci Rep 2017; 7:9348. [PMID: 28839245 PMCID: PMC5570931 DOI: 10.1038/s41598-017-09939-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/31/2017] [Indexed: 12/17/2022] Open
Abstract
Elevated prenatal testosterone exposure has been associated with Autism Spectrum Disorder (ASD) and facial masculinity. By employing three-dimensional (3D) photogrammetry, the current study investigated whether prepubescent boys and girls with ASD present increased facial masculinity compared to typically-developing controls. There were two phases to this research. 3D facial images were obtained from a normative sample of 48 boys and 53 girls (3.01-12.44 years old) to determine typical facial masculinity/femininity. The sexually dimorphic features were used to create a continuous 'gender score', indexing degree of facial masculinity. Gender scores based on 3D facial images were then compared for 54 autistic and 54 control boys (3.01-12.52 years old), and also for 20 autistic and 60 control girls (4.24-11.78 years). For each sex, increased facial masculinity was observed in the ASD group relative to control group. Further analyses revealed that increased facial masculinity in the ASD group correlated with more social-communication difficulties based on the Social Affect score derived from the Autism Diagnostic Observation Scale-Generic (ADOS-G). There was no association between facial masculinity and the derived Restricted and Repetitive Behaviours score. This is the first study demonstrating facial hypermasculinisation in ASD and its relationship to social-communication difficulties in prepubescent children.
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33
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C Yuen RK, Merico D, Bookman M, L Howe J, Thiruvahindrapuram B, Patel RV, Whitney J, Deflaux N, Bingham J, Wang Z, Pellecchia G, Buchanan JA, Walker S, Marshall CR, Uddin M, Zarrei M, Deneault E, D'Abate L, Chan AJS, Koyanagi S, Paton T, Pereira SL, Hoang N, Engchuan W, Higginbotham EJ, Ho K, Lamoureux S, Li W, MacDonald JR, Nalpathamkalam T, Sung WWL, Tsoi FJ, Wei J, Xu L, Tasse AM, Kirby E, Van Etten W, Twigger S, Roberts W, Drmic I, Jilderda S, Modi BM, Kellam B, Szego M, Cytrynbaum C, Weksberg R, Zwaigenbaum L, Woodbury-Smith M, Brian J, Senman L, Iaboni A, Doyle-Thomas K, Thompson A, Chrysler C, Leef J, Savion-Lemieux T, Smith IM, Liu X, Nicolson R, Seifer V, Fedele A, Cook EH, Dager S, Estes A, Gallagher L, Malow BA, Parr JR, Spence SJ, Vorstman J, Frey BJ, Robinson JT, Strug LJ, Fernandez BA, Elsabbagh M, Carter MT, Hallmayer J, Knoppers BM, Anagnostou E, Szatmari P, Ring RH, Glazer D, Pletcher MT, Scherer SW. Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. Nat Neurosci 2017; 20:602-611. [PMID: 28263302 DOI: 10.1038/nn.4524] [Citation(s) in RCA: 525] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 02/01/2017] [Indexed: 12/13/2022]
Abstract
We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10-4). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.
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Affiliation(s)
- Ryan K C Yuen
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Deep Genomics Inc., Toronto, Canada
| | - Matt Bookman
- Google, Mountain View, California, USA.,Verily Life Sciences, South San Francisco, California, USA
| | - Jennifer L Howe
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Rohan V Patel
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Joe Whitney
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Nicole Deflaux
- Google, Mountain View, California, USA.,Verily Life Sciences, South San Francisco, California, USA
| | - Jonathan Bingham
- Google, Mountain View, California, USA.,Verily Life Sciences, South San Francisco, California, USA
| | - Zhuozhi Wang
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Janet A Buchanan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Susan Walker
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Mohammed Uddin
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Eric Deneault
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Lia D'Abate
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Ada J S Chan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Stephanie Koyanagi
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Tara Paton
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Ny Hoang
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Autism Research Unit, The Hospital for Sick Children, Toronto, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Karen Ho
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Weili Li
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Wilson W L Sung
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Fiona J Tsoi
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - John Wei
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Lizhen Xu
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Anne-Marie Tasse
- Public Population Project in Genomics and Society, McGill University, Montreal, Canada
| | - Emily Kirby
- Public Population Project in Genomics and Society, McGill University, Montreal, Canada
| | | | | | - Wendy Roberts
- Autism Research Unit, The Hospital for Sick Children, Toronto, Canada
| | - Irene Drmic
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Autism Research Unit, The Hospital for Sick Children, Toronto, Canada
| | - Sanne Jilderda
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Autism Research Unit, The Hospital for Sick Children, Toronto, Canada
| | - Bonnie MacKinnon Modi
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Autism Research Unit, The Hospital for Sick Children, Toronto, Canada
| | - Barbara Kellam
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Michael Szego
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Dalla Lana School of Public Health and the Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl Cytrynbaum
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Dalla Lana School of Public Health and the Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
| | - Rosanna Weksberg
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
| | | | - Marc Woodbury-Smith
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Canada
| | - Jessica Brian
- Bloorview Research Institute, University of Toronto, Toronto, Canada.
| | - Lili Senman
- Bloorview Research Institute, University of Toronto, Toronto, Canada.
| | - Alana Iaboni
- Bloorview Research Institute, University of Toronto, Toronto, Canada.
| | | | - Ann Thompson
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Canada
| | - Christina Chrysler
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Canada
| | - Jonathan Leef
- Bloorview Research Institute, University of Toronto, Toronto, Canada.
| | | | - Isabel M Smith
- Departments of Pediatrics and of Psychology &Neuroscience, Dalhousie University and Autism Research Centre, IWK Health Centre, Halifax, Canada
| | - Xudong Liu
- Department of Psychiatry, Queen's University, Kinston, Canada
| | - Rob Nicolson
- Children's Health Research Institute, London, Ontario, Canada.,Western University, London, Ontario, Canada
| | | | | | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Stephen Dager
- Department of Radiology, University of Washington, Seattle, Washington, USA
| | - Annette Estes
- Department of Speech and Hearing Sciences, University of Washington, Seattle, Washington, USA
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Beth A Malow
- Sleep Disorders Division, Department of Neurology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jeremy R Parr
- Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, UK
| | - Sarah J Spence
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jacob Vorstman
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Brendan J Frey
- Deep Genomics Inc., Toronto, Canada.,Department of Electrical and Computer Engineering and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - James T Robinson
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Lisa J Strug
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Canada
| | - Bridget A Fernandez
- Disciplines of Genetics and Medicine, Memorial University of Newfoundland and Provincial Medical Genetic Program, Eastern Health, St. John's, Canada
| | | | - Melissa T Carter
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada.,Regional Genetics Program, The Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, USA
| | | | | | - Peter Szatmari
- Child Youth and Family Services, Centre for Addiction and Mental Health, Toronto, Canada.,Department of Psychiatry, University of Toronto, Toronto, Canada.,Department of Psychiatry, The Hospital for Sick Children, Toronto, Canada
| | - Robert H Ring
- Department of Pharmacology &Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - David Glazer
- Google, Mountain View, California, USA.,Verily Life Sciences, South San Francisco, California, USA
| | | | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,McLaughlin Centre, University of Toronto, Toronto, Canada
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Anatomy and Cell Biology of Autism Spectrum Disorder: Lessons from Human Genetics. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2017; 224:1-25. [PMID: 28551748 DOI: 10.1007/978-3-319-52498-6_1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Until recently autism spectrum disorder (ASD) was regarded as a neurodevelopmental condition with unknown causes and pathogenesis. In the footsteps of the revolution of genome technologies and genetics, and with its high degree of heritability, ASD became the first neuropsychiatric disorder for which clues towards molecular and cellular pathogenesis were uncovered by genetic identification of susceptibility genes. Currently several hundreds of risk genes have been assigned, with a recurrence below 1% in the ASD population. The multitude and diversity of known ASD genes has extended the clinical notion that ASD comprises very heterogeneous conditions ranging from severe intellectual disabilities to mild high-functioning forms. The results of genetics have allowed to pinpoint a limited number of cellular and molecular processes likely involved in ASD including protein synthesis, signal transduction, transcription/chromatin remodelling and synaptic function all playing an essential role in the regulation of synaptic homeostasis during brain development. In this context, we highlight the role of protein synthesis as a key process in ASD pathogenesis as it might be central in synaptic deregulation and a potential target for intervention. These current insights should lead to a rational design of interventions in molecular and cellular pathways of ASD pathogenesis that may be applied to affected individuals in the future.
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Lin YC, Frei JA, Kilander MBC, Shen W, Blatt GJ. A Subset of Autism-Associated Genes Regulate the Structural Stability of Neurons. Front Cell Neurosci 2016; 10:263. [PMID: 27909399 PMCID: PMC5112273 DOI: 10.3389/fncel.2016.00263] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/28/2016] [Indexed: 12/15/2022] Open
Abstract
Autism spectrum disorder (ASD) comprises a range of neurological conditions that affect individuals’ ability to communicate and interact with others. People with ASD often exhibit marked qualitative difficulties in social interaction, communication, and behavior. Alterations in neurite arborization and dendritic spine morphology, including size, shape, and number, are hallmarks of almost all neurological conditions, including ASD. As experimental evidence emerges in recent years, it becomes clear that although there is broad heterogeneity of identified autism risk genes, many of them converge into similar cellular pathways, including those regulating neurite outgrowth, synapse formation and spine stability, and synaptic plasticity. These mechanisms together regulate the structural stability of neurons and are vulnerable targets in ASD. In this review, we discuss the current understanding of those autism risk genes that affect the structural connectivity of neurons. We sub-categorize them into (1) cytoskeletal regulators, e.g., motors and small RhoGTPase regulators; (2) adhesion molecules, e.g., cadherins, NCAM, and neurexin superfamily; (3) cell surface receptors, e.g., glutamatergic receptors and receptor tyrosine kinases; (4) signaling molecules, e.g., protein kinases and phosphatases; and (5) synaptic proteins, e.g., vesicle and scaffolding proteins. Although the roles of some of these genes in maintaining neuronal structural stability are well studied, how mutations contribute to the autism phenotype is still largely unknown. Investigating whether and how the neuronal structure and function are affected when these genes are mutated will provide insights toward developing effective interventions aimed at improving the lives of people with autism and their families.
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Affiliation(s)
- Yu-Chih Lin
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Jeannine A Frei
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Michaela B C Kilander
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Wenjuan Shen
- Laboratory of Neuronal Connectivity, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
| | - Gene J Blatt
- Laboratory of Autism Neurocircuitry, Program in Neuroscience, Hussman Institute for Autism, Baltimore MD, USA
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36
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An JY, Claudianos C. Genetic heterogeneity in autism: From single gene to a pathway perspective. Neurosci Biobehav Rev 2016; 68:442-453. [DOI: 10.1016/j.neubiorev.2016.06.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 05/15/2016] [Accepted: 06/14/2016] [Indexed: 12/22/2022]
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37
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Sener EF, Canatan H, Ozkul Y. Recent Advances in Autism Spectrum Disorders: Applications of Whole Exome Sequencing Technology. Psychiatry Investig 2016; 13:255-64. [PMID: 27247591 PMCID: PMC4878959 DOI: 10.4306/pi.2016.13.3.255] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 09/22/2015] [Accepted: 10/02/2015] [Indexed: 02/07/2023] Open
Abstract
Autism spectrum disorders (ASD) is characterized by three core symptoms with impaired reciprocal social interaction and communication, a pattern of repetitive behavior and/or restricted interests in early childhood. The prevalence is higher in male children than in female children. As a complex neurodevelopmental disorder, the phenotype and severity of autism are extremely heterogeneous with differences from one patient to another. Genetics has a key role in the etiology of autism. Environmental factors are also interacting with the genetic profile and cause abnormal changes in neuronal development, brain growth, and functional connectivity. The term of exome represents less than 1% of the human genome, but contains 85% of known disease-causing variants. Whole-exome sequencing (WES) is an application of the next generation sequencing technology to determine the variations of all coding regions, or exons of known genes. For this reason, WES has been extensively used for clinical studies in the recent years. WES has achieved great success in the past years for identifying Mendelian disease genes. This review evaluates the potential of current findings in ASD for application in next generation sequencing technology, particularly WES. WES and whole-genome sequencing (WGS) approaches may lead to the discovery of underlying genetic factors for ASD and may thereby identify novel therapeutic targets for this disorder.
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Affiliation(s)
- Elif Funda Sener
- Department of Medical Biology, Erciyes University Medical Faculty, Kayseri, Turkey
- Erciyes University Genome and Stem Cell Center, Kayseri, Turkey
| | - Halit Canatan
- Department of Medical Biology, Erciyes University Medical Faculty, Kayseri, Turkey
| | - Yusuf Ozkul
- Department of Medical Genetics, Erciyes University Medical Faculty, Kayseri, Turkey
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38
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Huguet G, Benabou M, Bourgeron T. The Genetics of Autism Spectrum Disorders. RESEARCH AND PERSPECTIVES IN ENDOCRINE INTERACTIONS 2016. [DOI: 10.1007/978-3-319-27069-2_11] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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39
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Bitsika V, Sharpley CF. Variation in the Profile of Anxiety Disorders in Boys with an ASD According to Method and Source of Assessment. J Autism Dev Disord 2015; 45:1825-35. [PMID: 25503485 DOI: 10.1007/s10803-014-2343-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To determine any variation that might occur due to the type of assessment and source used to assess them, the prevalence of 7 anxiety disorders were investigated in a sample of 140 boys with an Autism spectrum disorder (ASD) and 50 non-ASD (NASD) boys via the Child and Adolescent Symptom Inventory and the KIDSCID Clinical Interview. Boys with an ASD were significantly more anxious than their NASD peers. Data collected from the boys with an ASD themselves showed differences in the severity and diagnostic criterion of anxiety disorders to data collected from the boys' parents. There were age-related variations to the pattern of anxiety disorder differences across reports from the boys with an ASD and reports from their parents.
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Affiliation(s)
- Vicki Bitsika
- Centre for Autism Spectrum Disorders, Bond University, Robina, QLD, 4229, Australia
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40
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Cherukuri PF, Maduro V, Fuentes-Fajardo KV, Lam K, Adams DR, Tifft CJ, Mullikin JC, Gahl WA, Boerkoel CF. Replicate exome-sequencing in a multiple-generation family: improved interpretation of next-generation sequencing data. BMC Genomics 2015; 16:998. [PMID: 26602380 PMCID: PMC4659195 DOI: 10.1186/s12864-015-2107-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 10/16/2015] [Indexed: 12/18/2022] Open
Abstract
Background Whole-exome sequencing (WES) is rapidly evolving into a tool of choice for rapid, and inexpensive identification of molecular genetic lesions within targeted regions of the human genome. While biases in WES coverage of nucleotides in targeted regions are recognized, it is not well understood how repetition of WES improves the interpretation of sequencing results in a clinical diagnostic setting. Method To address this, we compared independently generated exome-capture of six individuals from three-generations sequenced in triplicate. This generated between 48x-86x mean target depth of high-quality mapped bases (>Q20) for each technical replicate library. Cumulatively, we achieved 179 - 208x average target coverage for each individual in the pedigree. Using this experimental design, we evaluated stochastics in WES interpretation, genotyping sensitivity, and accuracy to detect de novo variants. Results In this study, we show that repetition of WES improved the interpretation of the capture target regions after aggregating the data (93.5 - 93.9 %). Compared to 81.2 - 89.6 % (50.2-55.4 Mb of 61.7 M) coverage of targeted bases at ≥20x in the individual technical replicates, the aggregated data covered 93.5 - 93.9 % of targeted bases (57.7 – 58.0 of 61.7 M) at ≥20x threshold, suggesting a 4.3 – 12.7 % improvement in coverage. Each individual’s aggregate dataset recovered 3.4 – 6.4 million bases within variable targeted regions. We uncovered technical variability (2-5 %) inherent to WES technique. We also show improved interpretation in assessing clinically important regions that lack interpretation under current conditions, affecting 12–16 of the 56 genes recommended for secondary analysis by American College of Medical Genetics (ACMG). We demonstrate that comparing technical replicate WES datasets and their derived aggregate data can effectively address overall WES genotyping discrepancies. Conclusion We describe a method to evaluate the reproducibility and stochastics in exome library preparation, and delineate the advantages of aggregating the data derived from technical replicates. The implications of this study are directly applicable to improved experimental design and provide an opportunity to rapidly, efficiently, and accurately arrive at reliable candidate nucleotide variants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2107-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Praveen F Cherukuri
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA.
| | - Valerie Maduro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
| | - Karin V Fuentes-Fajardo
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
| | - Kevin Lam
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
| | | | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - Cynthia J Tifft
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA. .,Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA.
| | - Cornelius F Boerkoel
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, USA.
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Burrows EL, Laskaris L, Koyama L, Churilov L, Bornstein JC, Hill-Yardin EL, Hannan AJ. A neuroligin-3 mutation implicated in autism causes abnormal aggression and increases repetitive behavior in mice. Mol Autism 2015; 6:62. [PMID: 26583067 PMCID: PMC4650404 DOI: 10.1186/s13229-015-0055-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/05/2015] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Aggression is common in patients with autism spectrum disorders (ASD) along with the core symptoms of impairments in social communication and repetitive behavior. Risperidone, an atypical antipsychotic, is widely used to treat aggression in ASD. In order to understand the neurobiological underpinnings of these challenging behaviors, a thorough characterisation of behavioral endophenotypes in animal models is required. METHODS We investigated aggression in mice containing the ASD-associated R451C (arginine to cysteine residue 451 substitution) mutation in neuroligin-3 (NL3). Furthermore, we sought to verify social interaction impairments and assess olfaction, anxiety, and repetitive and restrictive behavior in NL3(R451C) mutant mice. RESULTS We show a pronounced elevation in aggressive behavior in NL3(R451C) mutant mice. Treatment with risperidone reduced this aggression to wild-type (WT) levels. Juvenile and adult social interactions were also investigated, and subtle differences in initiation of interaction were seen in juvenile NL3(R451C) mice. No genotype differences in olfactory discrimination or anxiety were observed indicating that aggression was not dependent on altered olfaction, stress response, or social preference. We also describe repetitive behavior in NL3(R451C) mice as assessed by a clinically relevant object exploration task. CONCLUSIONS The presence of aberrant aggression and other behavioral phenotypes in NL3(R451C) mice consistent with clinical traits strengthen face validity of this model of ASD. Furthermore, we demonstrate predictive validity in this model through the reversal of the aggressive phenotype with risperidone. This is the first demonstration that risperidone can ameliorate aggression in an animal model of ASD and will inform mechanistic and therapeutic research into the neurobiology underlying abnormal behaviors in ASD.
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Affiliation(s)
- Emma L Burrows
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Kenneth Myer Building, Melbourne Brain Centre, Cnr Genetics Lane and Royal Pde, Parkville, Victoria 3010 Australia
| | - Liliana Laskaris
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Kenneth Myer Building, Melbourne Brain Centre, Cnr Genetics Lane and Royal Pde, Parkville, Victoria 3010 Australia
| | - Lynn Koyama
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Kenneth Myer Building, Melbourne Brain Centre, Cnr Genetics Lane and Royal Pde, Parkville, Victoria 3010 Australia
| | - Leonid Churilov
- Florey Institute of Neuroscience and Mental Health, 245 Burgundy St, Heidelberg, Victoria 3084 Australia
| | - Joel C Bornstein
- Department of Physiology, The University of Melbourne, Royal Pde, Parkville, Victoria 3010 Australia
| | - Elisa L Hill-Yardin
- Department of Physiology, The University of Melbourne, Royal Pde, Parkville, Victoria 3010 Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Kenneth Myer Building, Melbourne Brain Centre, Cnr Genetics Lane and Royal Pde, Parkville, Victoria 3010 Australia.,Department of Anatomy and Neuroscience, The University of Melbourne, Royal Pde, Parkville, Victoria 3010 Australia
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42
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Lim CS, Yang JE, Lee YK, Lee K, Lee JA, Kaang BK. Understanding the molecular basis of autism in a dish using hiPSCs-derived neurons from ASD patients. Mol Brain 2015; 8:57. [PMID: 26419846 PMCID: PMC4589208 DOI: 10.1186/s13041-015-0146-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/11/2015] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder characterized by deficits in social cognition, language development, and repetitive/restricted behaviors. Due to the complexity and heterogeneity of ASD and lack of a proper human cellular model system, the pathophysiological mechanism of ASD during the developmental process is largely unknown. However, recent progress in induced pluripotent stem cell (iPSC) technology as well as in vitro neural differentiation techniques have allowed us to functionally characterize neurons and analyze cortical development during neural differentiation. These technical advances will increase our understanding of the pathogenic mechanisms of heterogeneous ASD and help identify molecular biomarkers for patient stratification as well as personalized medicine. In this review, we summarize our current knowledge of iPSC generation, differentiation of specific neuronal subtypes from iPSCs, and phenotypic characterizations of human ASD patient-derived iPSC models. Finally, we discuss the current limitations of iPSC technology and future directions of ASD pathophysiology studies using iPSCs.
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Affiliation(s)
- Chae-Seok Lim
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanangno 599, Seoul, Gwanak-gu, 151-747, Korea
| | - Jung-Eun Yang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanangno 599, Seoul, Gwanak-gu, 151-747, Korea
| | - You-Kyung Lee
- Department of Biological Sciences and Biotechnology, College of Life Science and NanoTechnology, Hannam University, Jeonmin-dong 461-6, Daejeon, Yuseong-gu, 305-811, Korea
| | - Kyungmin Lee
- Department of Anatomy, Kyungpook National University Graduate School of Medicine, Dongin-dong 2-101, Daegu, Jung-gu, 700-422, Korea
| | - Jin-A Lee
- Department of Biological Sciences and Biotechnology, College of Life Science and NanoTechnology, Hannam University, Jeonmin-dong 461-6, Daejeon, Yuseong-gu, 305-811, Korea.
| | - Bong-Kiun Kaang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanangno 599, Seoul, Gwanak-gu, 151-747, Korea.
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Larkin A, Chen MY, Kirszenblat L, Reinhard J, van Swinderen B, Claudianos C. Neurexin-1 regulates sleep and synaptic plasticity in Drosophila melanogaster. Eur J Neurosci 2015. [PMID: 26201245 DOI: 10.1111/ejn.13023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Neurexins are cell adhesion molecules that are important for synaptic plasticity and homeostasis, although links to sleep have not yet been investigated. We examined the effects of neurexin-1 perturbation on sleep in Drosophila, showing that neurexin-1 nulls displayed fragmented sleep and altered circadian rhythm. Conversely, the over-expression of neurexin-1 could increase and consolidate night-time sleep. This was not solely due to developmental effects as it could be induced acutely in adulthood, and was coupled with evidence of synaptic growth. The timing of over-expression could differentially impact sleep patterns, with specific night-time effects. These results show that neurexin-1 was dynamically involved in synaptic plasticity and sleep in Drosophila. Neurexin-1 and a number of its binding partners have been repeatedly associated with mental health disorders, including autism spectrum disorders, schizophrenia and Tourette syndrome, all of which are also linked to altered sleep patterns. How and when plasticity-related proteins such as neurexin-1 function during sleep can provide vital information on the interaction between synaptic homeostasis and sleep, paving the way for more informed treatments of human disorders.
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Affiliation(s)
- Aoife Larkin
- Queensland Brain Institute, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Ming-Yu Chen
- Queensland Brain Institute, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Leonie Kirszenblat
- Queensland Brain Institute, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Judith Reinhard
- Queensland Brain Institute, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Bruno van Swinderen
- Queensland Brain Institute, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Charles Claudianos
- Queensland Brain Institute, The University of Queensland, St Lucia, Qld, 4072, Australia.,School of Psychological Sciences, Faculty of Biomedical and Psychological Sciences, Monash University, Melbourne, Vic., Australia
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Espinosa F, Xuan Z, Liu S, Powell CM. Neuroligin 1 modulates striatal glutamatergic neurotransmission in a pathway and NMDAR subunit-specific manner. Front Synaptic Neurosci 2015; 7:11. [PMID: 26283958 PMCID: PMC4518159 DOI: 10.3389/fnsyn.2015.00011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/18/2015] [Indexed: 12/18/2022] Open
Abstract
Together with its presynaptic partner Neurexin 1 (Nxn1), Neuroligin 1 (NL1) participates in synapse specification and synapse maintenance. We and others have shown that NL1 can also modulate glutamatergic synaptic function in the central nervous system of rodent models. These molecular/cellular changes can translate into altered animal behaviors that are thought to be analogous to symptomatology of neuropsychiatric disorders. For example, in dorsal striatum of NL1 deletion mice, we previously reported that the ratio N-methyl-D-aspartate receptor (NMDAR) mediated synaptic currents to α-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate receptor (AMPAR) mediated synaptic currents (NMDA/AMPA) is reduced in medium spiny neuron (MSNs). Importantly, this reduction in NMDA/AMPA ratio correlated with increased repetitive grooming. The striatum is the input nucleus of the basal ganglia (BG). Classical models of this circuitry imply that there are two principal pathways that render distinct and somewhat opposite striatal outputs critical to the function of these nuclei in modulating motor behavior. Thus, we set out to better characterize the effects of NL1 deletion on direct and indirect pathways of the dorsal striatum by genetically labeling MSNs participating in the direct and indirect pathways. We demonstrate that a decrease in NMDAR-mediated currents is limited to MSNs of the direct pathway. Furthermore, the decrease in NMDAR-mediated currents is largely due to a reduction in function of NMDARs containing the GluN2A subunit. In contrast, indirect pathway MSNs in NL1 knockout (KO) mice showed a reduction in the frequency of miniature excitatory neurotransmission not observed in the direct pathway. Thus, NL1 deletion differentially affects direct and indirect pathway MSNs in dorsal striatum. These findings have potential implications for striatal function in NL1 KO mice.
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Affiliation(s)
- Felipe Espinosa
- Department of Neurology and Neurotherapeutics, The University of Texas Southwestern Medical Center Dallas, TX, USA
| | - Zhong Xuan
- Department of Neurology and Neurotherapeutics, The University of Texas Southwestern Medical Center Dallas, TX, USA
| | - Shunan Liu
- Department of Neurology and Neurotherapeutics, The University of Texas Southwestern Medical Center Dallas, TX, USA
| | - Craig M Powell
- Department of Neurology and Neurotherapeutics, The University of Texas Southwestern Medical Center Dallas, TX, USA ; Neuroscience Graduate Program, The University of Texas Southwestern Medical Center Dallas, TX, USA ; Department of Psychiatry, The University of Texas Southwestern Medical Center Dallas, TX, USA
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Loke YJ, Hannan AJ, Craig JM. The Role of Epigenetic Change in Autism Spectrum Disorders. Front Neurol 2015; 6:107. [PMID: 26074864 PMCID: PMC4443738 DOI: 10.3389/fneur.2015.00107] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/28/2015] [Indexed: 12/14/2022] Open
Abstract
Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders characterized by problems with social communication, social interaction, and repetitive or restricted behaviors. ASD are comorbid with other disorders including attention deficit hyperactivity disorder, epilepsy, Rett syndrome, and Fragile X syndrome. Neither the genetic nor the environmental components have been characterized well enough to aid diagnosis or treatment of non-syndromic ASD. However, genome-wide association studies have amassed evidence suggesting involvement of hundreds of genes and a variety of associated genetic pathways. Recently, investigators have turned to epigenetics, a prime mediator of environmental effects on genomes and phenotype, to characterize changes in ASD that constitute a molecular level on top of DNA sequence. Though in their infancy, such studies have the potential to increase our understanding of the etiology of ASD and may assist in the development of biomarkers for its prediction, diagnosis, prognosis, and eventually in its prevention and intervention. This review focuses on the first few epigenome-wide association studies of ASD and discusses future directions.
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Affiliation(s)
- Yuk Jing Loke
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne , Parkville, VIC , Australia
| | - Anthony John Hannan
- Melbourne Brain Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne , Parkville, VIC , Australia
| | - Jeffrey Mark Craig
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne , Parkville, VIC , Australia
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Pinggera A, Lieb A, Benedetti B, Lampert M, Monteleone S, Liedl KR, Tuluc P, Striessnig J. CACNA1D de novo mutations in autism spectrum disorders activate Cav1.3 L-type calcium channels. Biol Psychiatry 2015; 77:816-22. [PMID: 25620733 PMCID: PMC4401440 DOI: 10.1016/j.biopsych.2014.11.020] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/08/2014] [Accepted: 11/20/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Cav1.3 voltage-gated L-type calcium channels (LTCCs) are part of postsynaptic neuronal signaling networks. They play a key role in brain function, including fear memory and emotional and drug-taking behaviors. A whole-exome sequencing study identified a de novo mutation, p.A749G, in Cav1.3 α1-subunits (CACNA1D), the second main LTCC in the brain, as 1 of 62 high risk-conferring mutations in a cohort of patients with autism and intellectual disability. We screened all published genetic information available from whole-exome sequencing studies and identified a second de novo CACNA1D mutation, p.G407R. Both mutations are present only in the probands and not in their unaffected parents or siblings. METHODS We functionally expressed both mutations in tsA-201 cells to study their functional consequences using whole-cell patch-clamp. RESULTS The mutations p.A749G and p.G407R caused dramatic changes in channel gating by shifting (~15 mV) the voltage dependence for steady-state activation and inactivation to more negative voltages (p.A749G) or by pronounced slowing of current inactivation during depolarizing stimuli (p.G407R). In both cases, these changes are compatible with a gain-of-function phenotype. CONCLUSIONS Our data, together with the discovery that Cav1.3 gain-of-function causes primary aldosteronism with seizures, neurologic abnormalities, and intellectual disability, suggest that Cav1.3 gain-of-function mutations confer a major part of the risk for autism in the two probands and may even cause the disease. Our findings have immediate clinical relevance because blockers of LTCCs are available for therapeutic attempts in affected individuals. Patients should also be explored for other symptoms likely resulting from Cav1.3 hyperactivity, in particular, primary aldosteronism.
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Affiliation(s)
- Alexandra Pinggera
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Andreas Lieb
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Bruno Benedetti
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Michaela Lampert
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Stefania Monteleone
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Petronel Tuluc
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Jörg Striessnig
- Department of Pharmacology and Toxicology, Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria..
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Sullivan PF, Posthuma D. Biological pathways and networks implicated in psychiatric disorders. Curr Opin Behav Sci 2015. [DOI: 10.1016/j.cobeha.2014.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Contribution of common and rare variants of the PTCHD1 gene to autism spectrum disorders and intellectual disability. Eur J Hum Genet 2015; 23:1694-701. [PMID: 25782667 DOI: 10.1038/ejhg.2015.37] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/20/2015] [Accepted: 02/03/2015] [Indexed: 11/09/2022] Open
Abstract
Recent findings revealed rare copy number variants and missense changes in the X-linked gene PTCHD1 in autism spectrum disorder (ASD) and intellectual disability (ID). Here, we aim to explore the contribution of common PTCHD1 variants in ASD and gain additional evidence for the role of rare variants of this gene in ASD and ID. A two-stage case-control association study investigated 28 tag single nucleotide polymorphisms (SNPs) in 994 ASD cases and 1035 controls from four European populations. Mutation screening was performed in 673 individuals who included 240 ASD cases, 183 ID patients and 250 controls. The case-control association study showed a significant association with rs7052177 (P=6.13E-4) in the ASD discovery sample that was replicated in an independent sample (P=0.03). A Mantel-Haenszel meta-analysis for rs7052177T considering the four European populations showed an odds ratio of 0.58 (P=7E-05). This SNP is predicted to be located in a transcription factor binding site. No rare missense PTCHD1 variants were found in our ASD cohort and only one was identified in the ID sample. A duplication (27 bp) in the promoter region, absent from 590 controls, was found in three ASD patients (Fisher exact test, P=0.024). A gene reporter assay showed a significant decrease in the transcriptional activity (26%) driven by this variant. Moreover, we found that the longest allele of a trinucleotide repeat located upstream from PTCHD1 was associated with ASD (P=0.003, permP=0.0186). Our results further support the involvement of PTCHD1 in ASD, suggesting that both common and rare variants contribute to the disorder.
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Li J, Shi M, Ma Z, Zhao S, Euskirchen G, Ziskin J, Urban A, Hallmayer J, Snyder M. Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. Mol Syst Biol 2014; 10:774. [PMID: 25549968 PMCID: PMC4300495 DOI: 10.15252/msb.20145487] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Autism is a complex disease whose etiology remains elusive. We integrated previously and newly generated data and developed a systems framework involving the interactome, gene expression and genome sequencing to identify a protein interaction module with members strongly enriched for autism candidate genes. Sequencing of 25 patients confirmed the involvement of this module in autism, which was subsequently validated using an independent cohort of over 500 patients. Expression of this module was dichotomized with a ubiquitously expressed subcomponent and another subcomponent preferentially expressed in the corpus callosum, which was significantly affected by our identified mutations in the network center. RNA-sequencing of the corpus callosum from patients with autism exhibited extensive gene mis-expression in this module, and our immunochemical analysis showed that the human corpus callosum is predominantly populated by oligodendrocyte cells. Analysis of functional genomic data further revealed a significant involvement of this module in the development of oligodendrocyte cells in mouse brain. Our analysis delineates a natural network involved in autism, helps uncover novel candidate genes for this disease and improves our understanding of its molecular pathology.
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Affiliation(s)
- Jingjing Li
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine Stanford University School of Medicine, Stanford, CA, USA
| | - Minyi Shi
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine Stanford University School of Medicine, Stanford, CA, USA
| | - Zhihai Ma
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine Stanford University School of Medicine, Stanford, CA, USA
| | - Shuchun Zhao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ghia Euskirchen
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine Stanford University School of Medicine, Stanford, CA, USA
| | - Jennifer Ziskin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexander Urban
- Department of Psychiatry & Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Joachim Hallmayer
- Department of Psychiatry & Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine Stanford University School of Medicine, Stanford, CA, USA
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Bitsika V, Sharpley CF, Mailli R. The influence of gender, age, Psychological resilience and family interaction factors upon anxiety and depression in non-autism spectrum disorder siblings of children with an autism spectrum disorder. BRITISH JOURNAL OF GUIDANCE & COUNSELLING 2014. [DOI: 10.1080/03069885.2014.950944] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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