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Yang Y, Wang Q, Wang C, Buxbaum J, Ionita-Laza I. KnockoffHybrid: A knockoff framework for hybrid analysis of trio and population designs in genome-wide association studies. Am J Hum Genet 2024:S0002-9297(24)00166-6. [PMID: 38821058 DOI: 10.1016/j.ajhg.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024] Open
Abstract
Both trio and population designs are popular study designs for identifying risk genetic variants in genome-wide association studies (GWASs). The trio design, as a family-based design, is robust to confounding due to population structure, whereas the population design is often more powerful due to larger sample sizes. Here, we propose KnockoffHybrid, a knockoff-based statistical method for hybrid analysis of both the trio and population designs. KnockoffHybrid provides a unified framework that brings together the advantages of both designs and produces powerful hybrid analysis while controlling the false discovery rate (FDR) in the presence of linkage disequilibrium and population structure. Furthermore, KnockoffHybrid has the flexibility to leverage different types of summary statistics for hybrid analyses, including expression quantitative trait loci (eQTL) and GWAS summary statistics. We demonstrate in simulations that KnockoffHybrid offers power gains over non-hybrid methods for the trio and population designs with the same number of cases while controlling the FDR with complex correlation among variants and population structure among subjects. In hybrid analyses of three trio cohorts for autism spectrum disorders (ASDs) from the Autism Speaks MSSNG, Autism Sequencing Consortium, and Autism Genome Project with GWAS summary statistics from the iPSYCH project and eQTL summary statistics from the MetaBrain project, KnockoffHybrid outperforms conventional methods by replicating several known risk genes for ASDs and identifying additional associations with variants in other genes, including the PRAME family genes involved in axon guidance and which may act as common targets for human speech/language evolution and related disorders.
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Affiliation(s)
- Yi Yang
- Department of Biostatistics, City University of Hong Kong, Hong Kong SAR, China; School of Data Science, City University of Hong Kong, Hong Kong SAR, China.
| | - Qi Wang
- School of Data Science, City University of Hong Kong, Hong Kong SAR, China
| | - Chen Wang
- Department of Biostatistics, Columbia University, New York, NY 10032, USA
| | - Joseph Buxbaum
- Departments of Psychiatry, Neuroscience, and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Columbia University, New York, NY 10032, USA; Department of Statistics, Lund University, Lund, Sweden
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2
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Ferranti AS, Luessen DJ, Niswender CM. Novel pharmacological targets for GABAergic dysfunction in ADHD. Neuropharmacology 2024; 249:109897. [PMID: 38462041 DOI: 10.1016/j.neuropharm.2024.109897] [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: 01/01/2024] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
Attention deficit/hyperactivity disorder (ADHD) is a neurodevelopment disorder that affects approximately 5% of the population. The disorder is characterized by impulsivity, hyperactivity, and deficits in attention and cognition, although symptoms vary across patients due to the heterogenous and polygenic nature of the disorder. Stimulant medications are the standard of care treatment for ADHD patients, and their effectiveness has led to the dopaminergic hypothesis of ADHD in which deficits in dopaminergic signaling, especially in cortical brain regions, mechanistically underly ADHD pathophysiology. Despite their effectiveness in many individuals, almost one-third of patients do not respond to stimulant treatments and the long-term negative side effects of these medications remain unclear. Emerging clinical evidence is beginning to highlight an important role of dysregulated excitatory/inhibitory (E/I) balance in ADHD. These deficits in E/I balance are related to functional abnormalities in glutamate and Gamma-Aminobutyric Acid (GABA) signaling in the brain, with increasing emphasis placed on GABAergic interneurons driving specific aspects of ADHD pathophysiology. Recent genome-wide association studies (GWAS) have also highlighted how genes associated with GABA function are mutated in human populations with ADHD, resulting in the generation of several new genetic mouse models of ADHD. This review will discuss how GABAergic dysfunction underlies ADHD pathophysiology, and how specific receptors/proteins related to GABAergic interneuron dysfunction may be pharmacologically targeted to treat ADHD in subpopulations with specific comorbidities and symptom domains. This article is part of the Special Issue on "PFC circuit function in psychiatric disease and relevant models".
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Affiliation(s)
- Anthony S Ferranti
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA; Warren Center for Neuroscience Drug Discovery, Nashville, TN, 37232, USA
| | - Deborah J Luessen
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA; Warren Center for Neuroscience Drug Discovery, Nashville, TN, 37232, USA
| | - Colleen M Niswender
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA; Warren Center for Neuroscience Drug Discovery, Nashville, TN, 37232, USA; Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, 37232, USA; Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37232, USA.
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3
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Cornejo F, Franchini N, Cortés BI, Elgueta D, Cancino GI. Neural conditional ablation of the protein tyrosine phosphatase receptor Delta PTPRD impairs gliogenesis in the developing mouse brain cortex. Front Cell Dev Biol 2024; 12:1357862. [PMID: 38487272 PMCID: PMC10937347 DOI: 10.3389/fcell.2024.1357862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
Neurodevelopmental disorders are characterized by alterations in the development of the cerebral cortex, including aberrant changes in the number and function of neural cells. Although neurogenesis is one of the most studied cellular processes in these pathologies, little evidence is known about glial development. Genetic association studies have identified several genes associated with neurodevelopmental disorders. Indeed, variations in the PTPRD gene have been associated with numerous brain disorders, including autism spectrum disorder, restless leg syndrome, and schizophrenia. We previously demonstrated that constitutive loss of PTPRD expression induces significant alterations in cortical neurogenesis, promoting an increase in intermediate progenitors and neurons in mice. However, its role in gliogenesis has not been evaluated. To assess this, we developed a conditional knockout mouse model lacking PTPRD expression in telencephalon cells. Here, we found that the lack of PTPRD in the mouse cortex reduces glial precursors, astrocytes, and oligodendrocytes. According to our results, this decrease in gliogenesis resulted from a reduced number of radial glia cells at gliogenesis onset and a lower gliogenic potential in cortical neural precursors due to less activation of the JAK/STAT pathway and reduced expression of gliogenic genes. Our study shows PTPRD as a regulator of the glial/neuronal balance during cortical neurodevelopment and highlights the importance of studying glial development to understand the etiology of neurodevelopmental diseases.
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Affiliation(s)
- Francisca Cornejo
- Center for Integrative Biology, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Nayhara Franchini
- Center for Integrative Biology, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Bastián I. Cortés
- Center for Integrative Biology, Faculty of Sciences, Universidad Mayor, Santiago, Chile
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniela Elgueta
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Gonzalo I. Cancino
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
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4
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Antón-Galindo E, Adel MR, García-González J, Leggieri A, López-Blanch L, Irimia M, Norton WHJ, Brennan CH, Fernàndez-Castillo N, Cormand B. Pleiotropic contribution of rbfox1 to psychiatric and neurodevelopmental phenotypes in two zebrafish models. Transl Psychiatry 2024; 14:99. [PMID: 38374212 PMCID: PMC10876957 DOI: 10.1038/s41398-024-02801-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/21/2024] Open
Abstract
RBFOX1 is a highly pleiotropic gene that contributes to several psychiatric and neurodevelopmental disorders. Both rare and common variants in RBFOX1 have been associated with several psychiatric conditions, but the mechanisms underlying the pleiotropic effects of RBFOX1 are not yet understood. Here we found that, in zebrafish, rbfox1 is expressed in spinal cord, mid- and hindbrain during developmental stages. In adults, expression is restricted to specific areas of the brain, including telencephalic and diencephalic regions with an important role in receiving and processing sensory information and in directing behaviour. To investigate the contribution of rbfox1 to behaviour, we used rbfox1sa15940, a zebrafish mutant line with TL background. We found that rbfox1sa15940 mutants present hyperactivity, thigmotaxis, decreased freezing behaviour and altered social behaviour. We repeated these behavioural tests in a second rbfox1 mutant line with a different genetic background (TU), rbfox1del19, and found that rbfox1 deficiency affects behaviour similarly in this line, although there were some differences. rbfox1del19 mutants present similar thigmotaxis, but stronger alterations in social behaviour and lower levels of hyperactivity than rbfox1sa15940 fish. Taken together, these results suggest that mutations in rbfox1 lead to multiple behavioural changes in zebrafish that might be modulated by environmental, epigenetic and genetic background effects, and that resemble phenotypic alterations present in Rbfox1-deficient mice and in patients with different psychiatric conditions. Our study, thus, highlights the evolutionary conservation of rbfox1 function in behaviour and paves the way to further investigate the mechanisms underlying rbfox1 pleiotropy on the onset of neurodevelopmental and psychiatric disorders.
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Affiliation(s)
- Ester Antón-Galindo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalunya, Spain
- Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Catalunya, Spain
| | - Maja R Adel
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, Spain
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Judit García-González
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, NYC 10029, USA
| | - Adele Leggieri
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Laura López-Blanch
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalunya, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalunya, Spain
- Universitat Pompeu Fabra, Barcelona, Catalunya, Spain
- ICREA, Barcelona, Catalunya, Spain
| | - William H J Norton
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, UK
| | - Caroline H Brennan
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalunya, Spain.
- Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Catalunya, Spain.
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalunya, Spain.
- Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Catalunya, Spain.
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Malyshev AV, Pavshintcev VV, Mitkin NA, Sukhanova IA, Gedzun VR, Zlobin AS, Doronin II, Babkin GA, Sawyer TK. The novel peptide LCGM-10 attenuates metabotropic glutamate receptor 5 activity and demonstrates behavioral effects in animal models. Front Behav Neurosci 2024; 18:1333258. [PMID: 38385004 PMCID: PMC10879279 DOI: 10.3389/fnbeh.2024.1333258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024] Open
Abstract
We employed a structural bioinformatics approach to develop novel peptides with predicted affinity to the binding site for negative allosteric modulators (NAMs) of metabotropic glutamate receptor 5 (mGluR5). Primary screening in zebrafish (Danio rerio) revealed a stimulatory effect of two peptides, LCGM-10 and LCGM-15. Target validation studies using calcium ion flux imaging and a luciferase reporter assay confirmed mGluR5 as the target. LCGM-10 showed greater potency than LCGM-15; it was comparable to that of the mGluR5 NAM 2-methyl-6-(phenylethynyl) pyridine (MPEP). Rodent behavioral screening in the open field and elevated plus maze revealed increased locomotor activity in both tests after acute LCGM-10 treatment, supported by further analysis of home cage spontaneous locomotor activity (SLA). The stimulating effect of a single LCGM-10 administration on SLA was evident up to 60 min after administration and was not accompanied by hypokinetic rebound observed for caffeine. According to our results, LCGM-10 has therapeutic potential to treat hypo- and dyskinesias of various etiologies. Further investigation of LCGM-10 effects in the delay discounting model of impulsive choice in rats revealed reduced trait impulsivity after single and chronic administrations, suggesting potential implication for attention deficit hyperactivity disorder, obsessive compulsive disorder, and addictions.
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Antón-Galindo E, Adel M, García-Gonzalez J, Leggieri A, López-Blanch L, Irimia M, Norton WHJ, Brennan CH, Fernàndez-Castillo N, Cormand B. Pleiotropic contribution of rbfox1 to psychiatric and neurodevelopmental phenotypes in a zebrafish model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529711. [PMID: 36865197 PMCID: PMC9980121 DOI: 10.1101/2023.02.23.529711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
RBFOX1 is a highly pleiotropic gene that contributes to several psychiatric and neurodevelopmental disorders. Both rare and common variants in RBFOX1 have been associated with several psychiatric conditions, but the mechanisms underlying the pleiotropic effects of RBFOX1 are not yet understood. Here we found that, in zebrafish, rbfox1 is expressed in spinal cord, mid- and hindbrain during developmental stages. In adults, expression is restricted to specific areas of the brain, including telencephalic and diencephalic regions with an important role in receiving and processing sensory information and in directing behaviour. To investigate the effect of rbfox1 deficiency on behaviour, we used rbfox1sa15940, a rbfox1 loss-of-function line. We found that rbfox1sa15940 mutants present hyperactivity, thigmotaxis, decreased freezing behaviour and altered social behaviour. We repeated these behavioural tests in a second rbfox1 loss-of-function line with a different genetic background, rbfox1del19, and found that rbfox1 deficiency affects behaviour similarly in this line, although there were some differences. rbfox1del19 mutants present similar thigmotaxis, but stronger alterations in social behaviour and lower levels of hyperactivity than rbfox1sa15940 fish. Taken together, these results suggest that rbfox1 deficiency leads to multiple behavioural changes in zebrafish that might be modulated by environmental, epigenetic and genetic background effects, and that resemble phenotypic alterations present in Rbfox1-deficient mice and in patients with different psychiatric conditions. Our study thus highlights the evolutionary conservation of rbfox1 function in behaviour and paves the way to further investigate the mechanisms underlying rbfox1 pleiotropy on the onset of neurodevelopmental and psychiatric disorders.
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Affiliation(s)
- Ester Antón-Galindo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Centro de Investigación Biomédica en Red de Enfermedades raras (CIBERER), Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Institut de recerca Sant Joan de Déu, Espluges de Llobregat, Catalunya, 08950, Spain
| | - Maja Adel
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Judit García-Gonzalez
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
- Icahn School of Medicine, Mount Sinai, NYC 10029, USA
| | - Adele Leggieri
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Laura López-Blanch
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- ICREA, Barcelona, Spain
| | - William HJ Norton
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Caroline H Brennan
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Centro de Investigación Biomédica en Red de Enfermedades raras (CIBERER), Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Institut de recerca Sant Joan de Déu, Espluges de Llobregat, Catalunya, 08950, Spain
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Centro de Investigación Biomédica en Red de Enfermedades raras (CIBERER), Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Catalunya, 08028, Spain
- Institut de recerca Sant Joan de Déu, Espluges de Llobregat, Catalunya, 08950, Spain
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Mukherjee A, Nongthomba U. To RNA-binding and beyond: Emerging facets of the role of Rbfox proteins in development and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1813. [PMID: 37661850 DOI: 10.1002/wrna.1813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 09/05/2023]
Abstract
The RNA-binding Fox-1 homologue (Rbfox) proteins represent an ancient family of splicing factors, conserved through evolution. All members share an RNA recognition motif (RRM), and a particular affinity for the GCAUG signature in target RNA molecules. The role of Rbfox, as a splice factor, deciding the tissue-specific inclusion/exclusion of an exon, depending on its binding position on the flanking introns, is well known. Rbfox often acts in concert with other splicing factors, and forms splicing regulatory networks. Apart from this canonical role, recent studies show that Rbfox can also function as a transcription co-factor, and affects mRNA stability and translation. The repertoire of Rbfox targets is vast, including genes involved in the development of tissue lineages, such as neurogenesis, myogenesis, and erythropoeiesis, and molecular processes, including cytoskeletal dynamics, and calcium handling. A second layer of complexity is added by the fact that Rbfox expression itself is regulated by multiple mechanisms, and, in vertebrates, exhibits tissue-specific expression. The optimum dosage of Rbfox is critical, and its misexpression is etiological to various disease conditions. In this review, we discuss the contextual roles played by Rbfox as a tissue-specific regulator for the expression of many important genes with diverse functions, through the lens of the emerging data which highlights its involvement in many human diseases. Furthermore, we explore the mechanistic details provided by studies in model organisms, with emphasis on the work with Drosophila. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Turnover and Surveillance > Regulation of RNA Stability RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Amartya Mukherjee
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Upendra Nongthomba
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
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Lawther AJ, Zieba J, Fang Z, Furlong TM, Conn I, Govindaraju H, Choong LLY, Turner N, Siddiqui KS, Bridge W, Merlin S, Hyams TC, Killingsworth M, Eapen V, Clarke RA, Walker AK. Antioxidant Behavioural Phenotype in the Immp2l Gene Knock-Out Mouse. Genes (Basel) 2023; 14:1717. [PMID: 37761857 PMCID: PMC10531238 DOI: 10.3390/genes14091717] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Mitochondrial dysfunction is strongly associated with autism spectrum disorder (ASD) and the Inner mitochondrial membrane protein 2-like (IMMP2L) gene is linked to autism inheritance. However, the biological basis of this linkage is unknown notwithstanding independent reports of oxidative stress in association with both IMMP2L and ASD. To better understand IMMP2L's association with behaviour, we developed the Immp2lKD knockout (KO) mouse model which is devoid of Immp2l peptidase activity. Immp2lKD -/- KO mice do not display any of the core behavioural symptoms of ASD, albeit homozygous Immp2lKD -/- KO mice do display increased auditory stimulus-driven instrumental behaviour and increased amphetamine-induced locomotion. Due to reports of increased ROS and oxidative stress phenotypes in an earlier truncated Immp2l mouse model resulting from an intragenic deletion within Immp2l, we tested whether high doses of the synthetic mitochondrial targeted antioxidant (MitoQ) could reverse or moderate the behavioural changes in Immp2lKD -/- KO mice. To our surprise, we observed that ROS levels were not increased but significantly lowered in our new Immp2lKD -/- KO mice and that these mice had no oxidative stress-associated phenotypes and were fully fertile with no age-related ataxia or neurodegeneration as ascertained using electron microscopy. Furthermore, the antioxidant MitoQ had no effect on the increased amphetamine-induced locomotion of these mice. Together, these findings indicate that the behavioural changes in Immp2lKD -/- KO mice are associated with an antioxidant-like phenotype with lowered and not increased levels of ROS and no oxidative stress-related phenotypes. This suggested that treatments with antioxidants are unlikely to be effective in treating behaviours directly resulting from the loss of Immp2l/IMMP2L activity, while any behavioural deficits that maybe associated with IMMP2L intragenic deletion-associated truncations have yet to be determined.
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Affiliation(s)
- Adam J. Lawther
- Laboratory of ImmunoPsychiatry, Neuroscience Research Australia, Randwick, NSW 2031, Australia
| | - Jerzy Zieba
- Laboratory of ImmunoPsychiatry, Neuroscience Research Australia, Randwick, NSW 2031, Australia
- Department of Psychology, University of Rzeszow, 35-310 Rzeszow, Poland
| | - Zhiming Fang
- Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, NSW 2052, Australia
- Ingham Institute for Applied Medical Research, Sydney, NSW 2170, Australia; (T.C.H.)
| | - Teri M. Furlong
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Illya Conn
- Laboratory of ImmunoPsychiatry, Neuroscience Research Australia, Randwick, NSW 2031, Australia
- Schizophrenia Research Laboratory, Neuroscience Research Australia, Randwick, NSW 2031, Australia
| | - Hemna Govindaraju
- Department of Pharmacology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Laura L. Y. Choong
- Department of Pharmacology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Nigel Turner
- Department of Pharmacology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Khawar Sohail Siddiqui
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Wallace Bridge
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sam Merlin
- Medical Science, School of Science, Western Sydney University, Campbelltown, Sydney, NSW 2751, Australia
| | - Tzipi Cohen Hyams
- Ingham Institute for Applied Medical Research, Sydney, NSW 2170, Australia; (T.C.H.)
| | - Murray Killingsworth
- Ingham Institute for Applied Medical Research, Sydney, NSW 2170, Australia; (T.C.H.)
- NSW Health Pathology, Liverpool Hospital Campus, 1 Campbell Street, Liverpool, NSW 2107, Australia
| | - Valsamma Eapen
- Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, NSW 2052, Australia
- Ingham Institute for Applied Medical Research, Sydney, NSW 2170, Australia; (T.C.H.)
- Academic Unit of Infant Child and Adolescent Services (AUCS), South Western Sydney Local Health District, Liverpool, NSW 2170, Australia
| | - Raymond A. Clarke
- Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, NSW 2052, Australia
- Ingham Institute for Applied Medical Research, Sydney, NSW 2170, Australia; (T.C.H.)
- Academic Unit of Infant Child and Adolescent Services (AUCS), South Western Sydney Local Health District, Liverpool, NSW 2170, Australia
| | - Adam K. Walker
- Laboratory of ImmunoPsychiatry, Neuroscience Research Australia, Randwick, NSW 2031, Australia
- Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, NSW 2052, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
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Leung BK, Merlin S, Walker AK, Lawther AJ, Paxinos G, Eapen V, Clarke R, Balleine BW, Furlong TM. Immp2l knockdown in male mice increases stimulus-driven instrumental behaviour but does not alter goal-directed learning or neuron density in cortico-striatal circuits in a model of Tourette syndrome and autism spectrum disorder. Behav Brain Res 2023; 452:114610. [PMID: 37541448 DOI: 10.1016/j.bbr.2023.114610] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/22/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023]
Abstract
Cortico-striatal neurocircuits mediate goal-directed and habitual actions which are necessary for adaptive behaviour. It has recently been proposed that some of the core symptoms of autism spectrum disorder (ASD) and Gilles de la Tourette syndrome (GTS), such as tics and other repetitive behaviours, may emerge because of imbalances in these neurocircuits. We have recently developed a model of ASD and GTS by knocking down Immp2l, a mitochondrial gene frequently associated with these disorders. The current study sought to determine whether Immp2l knockdown (KD) in male mice alters flexible, goal- or cue- driven behaviour using procedures specifically designed to examine response-outcome and stimulus-response associations, which underlie goal-directed and habitual behaviour, respectively. Whether Immp2l KD alters neuron density in cortico-striatal neurocircuits known to regulate these behaviours was also examined. Immp2l KD mice and wild type-like mice (WT) were trained on Pavlovian and instrumental learning procedures where auditory cues predicted food delivery and lever-press responses earned a food outcome. It was demonstrated that goal-directed learning was not changed for Immp2l KD mice compared to WT mice, as lever-press responses were sensitive to changes in the value of the food outcome, and to contingency reversal and degradation. There was also no difference in the capacity of KD mice to form habitual behaviours compared to WT mice following extending training of the instrumental action. However, Immp2l KD mice were more responsive to auditory stimuli paired with food as indicated by a non-specific increase in lever response rates during Pavlovian-to-instrumental transfer. Finally, there were no alterations to neuron density in striatum or any prefrontal cortex or limbic brain structures examined. Thus, the current study suggests that Immp2l is not necessary for learned maladaptive goal or stimulus driven behaviours in ASD or GTS, but that it may contribute to increased capacity for external stimuli to drive behaviour. Alterations to stimulus-driven behaviour could potentially influence the expression of tics and repetitive behaviours, suggesting that genetic alterations to Immp2l may contribute to these core symptoms in ASD and GTS. Given that this is the first application of this battery of instrumental learning procedures to a mouse model of ASD or GTS, it is an important initial step in determining the contribution of known risk-genes to goal-directed versus habitual behaviours, which should be more broadly applied to other rodent models of ASD and GTS in the future.
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Affiliation(s)
- Beatrice K Leung
- Decision Neuroscience Laboratory, School of Psychology, University of New South Wales, Sydney, NSW, Australia
| | - Sam Merlin
- School of Science, Western Sydney University, Campbelltown, Sydney, NSW, Australia
| | - Adam K Walker
- Laboratory of ImmunoPsychiatry, Neuroscience Research Australia, Randwick, NSW, Australia; Discipline of Psychiatry and Mental Health, University of New South Wales, NSW, Australia
| | - Adam J Lawther
- Laboratory of ImmunoPsychiatry, Neuroscience Research Australia, Randwick, NSW, Australia
| | - George Paxinos
- Neuroscience Research Australia, Randwick, NSW, Australia; School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Valsamma Eapen
- Discipline of Psychiatry and Mental Health, University of New South Wales, NSW, Australia; Mental Health Research Unit, South Western Sydney Local Health District, Liverpool, Australia
| | - Raymond Clarke
- Ingham Institute, Discipline of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Bernard W Balleine
- Decision Neuroscience Laboratory, School of Psychology, University of New South Wales, Sydney, NSW, Australia
| | - Teri M Furlong
- Neuroscience Research Australia, Randwick, NSW, Australia; School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia.
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10
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Veneruso I, Ranieri A, Falcone N, Tripodi L, Scarano C, La Monica I, Pastore L, Lombardo B, D’Argenio V. The Potential Usefulness of the Expanded Carrier Screening to Identify Hereditary Genetic Diseases: A Case Report from Real-World Data. Genes (Basel) 2023; 14:1651. [PMID: 37628702 PMCID: PMC10454493 DOI: 10.3390/genes14081651] [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: 07/08/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Expanded carrier screening (ECS) means a comprehensive genetic analysis to evaluate an individual's carrier status. ECS is becoming more frequently used, thanks to the availability of techniques such as next generation sequencing (NGS) and array comparative genomic hybridization (aCGH), allowing for extensive genome-scale analyses. Here, we report the case of a couple who underwent ECS for a case of autism spectrum disorder in the male partner family. aCGH and whole-exome sequencing (WES) were performed in the couple. aCGH analysis identified in the female partner two deletions involving genes associated to behavioral and neurodevelopment disorders. No clinically relevant alterations were identified in the husband. Interestingly, WES analysis identified in the male partner a pathogenic variant in the LPL gene that is emerging as a novel candidate gene for autism. This case shows that ECS may be useful in clinical contexts, especially when both the partners are analyzed before conception, thus allowing the estimation of their risk to transmit an inherited condition. On the other side, there are several concerns related to possible incidental findings and difficult-to-interpret results. Once these limits are defined by the establishment of specific guidelines, ECS may have a greater diffusion.
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Affiliation(s)
- Iolanda Veneruso
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Annaluisa Ranieri
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
| | - Noemi Falcone
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Lorella Tripodi
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Carmela Scarano
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Ilaria La Monica
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
| | - Lucio Pastore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Barbara Lombardo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, via di Val Cannuta 247, 00166 Rome, Italy
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11
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Naudhani S, Ahmad A, Khan Bazai F, Pervez MT, Zafar A, Shah SA, Raheem N, Baloch AH, Mushtaq M, Daud S. A Missense Pathogenic Variant in a Conserved Region of CNTNAP2 Is Associated with Obesity, Seizures, and Language Impairment in a Pakistani Family. Mol Syndromol 2023; 14:293-302. [PMID: 37766826 PMCID: PMC10521233 DOI: 10.1159/000529427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/24/2023] [Indexed: 09/29/2023] Open
Abstract
Introduction In a consanguineous family, seven siblings born in three sibships showed a syndromic disorder characterized by obesity, seizures, and language impairment phenotypes, which appeared at early age or developed during early childhood. Methods By whole-exome sequencing and subsequent Sanger sequencing, a novel homozygous missense variant (c.3371 T>A [p.Ile1124Asn]) in exon 20 of the CNTNAP2 gene was identified. Results The pathogenic variant in this family is located within one of the laminin G-like 4 domains of CASPR2 and may cause loss of hydrophobic interactions of CASPR2 with its partner proteins. Single nucleotide and copy number variants in this gene have previously been related to Gilles de la Tourette syndrome, cortical dysplasia-focal epilepsy syndrome, schizophrenia, Pitt-Hopkins syndrome, and autism spectrum, attention deficit hyperactivity, and obsessive compulsive disorders. Yet, few studies described patients with CNTNAP2 variants showing diet-induced obesity. Conclusion This report expands the phenotypic spectrum of this rare syndrome and provides deeper insights by documenting the clinical features and genetic findings of the patients.
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Affiliation(s)
- Sara Naudhani
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
| | - Adeel Ahmad
- Continental Medical College and Hayat Memorial Hospital, Lahore, Pakistan
| | - Fariya Khan Bazai
- Quetta Institute of Medical Sciences/Combined Military Hospital, Quetta, Pakistan
| | - Muhammad Tariq Pervez
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Azqa Zafar
- Lahore General Hospital, Lahore, Pakistan
| | - Sajjad Ali Shah
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | | | - Abdul Hameed Baloch
- Department of Biotechnology, Lasbela University of Agriculture, Water and Marine Sciences (LUAWMS), Uthal, Pakistan
| | | | - Shakeela Daud
- Department of Biotechnology, BUITEMS, Quetta, Pakistan
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12
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Jiang Y, Wei D, Xie Y. Functional modular networks identify the pivotal genes associated with morphine addiction and potential drug therapies. BMC Anesthesiol 2023; 23:151. [PMID: 37138216 PMCID: PMC10155436 DOI: 10.1186/s12871-023-02111-2] [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: 06/13/2022] [Accepted: 04/25/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Chronic morphine usage induces lasting molecular and microcellular adaptations in distinct brain areas, resulting in addiction-related behavioural abnormalities, drug-seeking, and relapse. Nonetheless, the mechanisms of action of the genes responsible for morphine addiction have not been exhaustively studied. METHODS We obtained morphine addiction-related datasets from the Gene Expression Omnibus (GEO) database and screened for Differentially Expressed Genes (DEGs). Weighted Gene Co-expression Network Analysis (WGCNA) functional modularity constructs were analyzed for genes associated with clinical traits. Venn diagrams were filtered for intersecting common DEGs (CDEGs). Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for functional annotation. Protein-protein interaction network (PPI) and CytoHubba were used to screen for hub genes. Potential treatments for morphine addiction were figured out with the help of an online database. RESULTS Sixty-five common differential genes linked to morphine addiction were identified, and functional enrichment analysis showed that they were primarily involved in ion channel activity, protein transport, the oxytocin signalling pathway, neuroactive ligand-receptor interactions, and other signalling pathways. Based on the PPI network, ten hub genes (CHN2, OLIG2, UGT8A, CACNB2, TIMP3, FKBP5, ZBTB16, TSC22D3, ISL1, and SLC2A1) were checked. In the data set GSE7762, all of the Area Under Curve (AUC) values for the hub gene Receiver Operating Characteristic (ROC) curves were greater than 0.8. We also used the DGIdb database to look for eight small-molecule drugs that might be useful for treating morphine addiction. CONCLUSIONS The hub genes are crucial genes associated with morphine addiction in the mouse striatum. The oxytocin signalling pathway may play a vital role in developing morphine addiction.
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Affiliation(s)
- Yage Jiang
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
| | - Donglei Wei
- Department of Traumatology Orthopedic Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
| | - Yubo Xie
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
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13
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Lyulcheva-Bennett E, Genomics England Research Consortium, Bennett D. A retrospective analysis of phosphatase catalytic subunit gene variants in patients with rare disorders identifies novel candidate neurodevelopmental disease genes. Front Cell Dev Biol 2023; 11:1107930. [PMID: 37056996 PMCID: PMC10086149 DOI: 10.3389/fcell.2023.1107930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/03/2023] [Indexed: 03/30/2023] Open
Abstract
Rare genetic disorders represent some of the most severe and life-limiting conditions that constitute a considerable burden on global healthcare systems and societies. Most individuals affected by rare disorders remain undiagnosed, highlighting the unmet need for improved disease gene discovery and novel variant interpretation. Aberrant (de) phosphorylation can have profound pathological consequences underpinning many disease processes. Numerous phosphatases and associated proteins have been identified as disease genes, with many more likely to have gone undiscovered thus far. To begin to address these issues, we have performed a systematic survey of de novo variants amongst 189 genes encoding phosphatase catalytic subunits found in rare disease patients recruited to the 100,000 Genomes Project (100 kGP), the largest national sequencing project of its kind in the United Kingdom. We found that 49% of phosphatases were found to carry de novo mutation(s) in this cohort. Only 25% of these phosphatases have been previously linked to genetic disorders. A gene-to-patient approach matching variants to phenotypic data identified 9 novel candidate rare-disease genes: PTPRD, PTPRG, PTPRT, PTPRU, PTPRZ1, MTMR3, GAK, TPTE2, PTPN18. As the number of patients undergoing whole genome sequencing increases and information sharing improves, we anticipate that reiterative analysis of genomic and phenotypic data will continue to identify candidate phosphatase disease genes for functional validation. This is the first step towards delineating the aetiology of rare genetic disorders associated with altered phosphatase function, leading to new biological insights and improved clinical outcomes for the affected individuals and their families.
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Affiliation(s)
| | | | - Daimark Bennett
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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14
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Jung B, Ahn K, Justice C, Norman L, Price J, Sudre G, Shaw P. Rare copy number variants in males and females with childhood attention-deficit/hyperactivity disorder. Mol Psychiatry 2023; 28:1240-1247. [PMID: 36517639 PMCID: PMC10010944 DOI: 10.1038/s41380-022-01906-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]
Abstract
While childhood attention-deficit/hyperactivity disorder (ADHD) is more prevalent in males than females, genetic contributors to this effect have not been established. Here, we explore sex differences in the contribution of common and/or rare genetic variants to ADHD. Participants were from the Adolescent Brain and Cognitive Development study (N = 1253 youth meeting DSM-5 criteria for ADHD [mean age = 11.46 years [SD = 0.87]; 31% female] and 5577 unaffected individuals [mean age = 11.42 years [SD = 0.89]; 50% female], overall 66% White, non-Hispanic (WNH), 19% Black/African American, and 15% other races. Logistic regression tested for interactions between sex (defined genotypically) and both rare copy number variants (CNV) and polygenic (common variant) risk in association with ADHD. There was a significant interaction between sex and the presence of a CNV deletion larger than 200 kb, both in the entire cohort (β = -0.74, CI = [-1.27 to -0.20], FDR-corrected p = 0.048) and, at nominal significance levels in the WNH ancestry subcohort (β = -0.86, CI = [-1.51 to -0.20], p = 0.010). Additionally, the number of deleted genes interacted with sex in association with ADHD (whole cohort. β = -0.13, CI = [-0.23 to -0.029], FDR-corrected p = 0.048; WNH. β = -0.17, CI = [-0.29 to -0.050], FDR-corrected p = 0.044) as did the total length of CNV deletions (whole cohort. β = -0.12, CI = [-0.19 to -0.044], FDR-corrected p = 0.028; WNH. β = -0.17, CI = [-0.28 to -0.061], FDR-corrected p = 0.034). This sex effect was driven by increased odds of childhood ADHD for females but not males in the presence of CNV deletions. No similar sex effect was found for CNV duplications or polygenic risk scores. The association between CNV deletions and ADHD was partially mediated by measures of cognitive flexibility. In summary, CNV deletions were associated with increased odds for childhood ADHD in females, but not males.
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Affiliation(s)
- Benjamin Jung
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kwangmi Ahn
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cristina Justice
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Luke Norman
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jolie Price
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gustavo Sudre
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Philip Shaw
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20892, USA.
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15
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Liu M, Chen Y, Sun M, Du Y, Bai Y, Lei G, Zhang C, Zhang M, Zhang Y, Xi C, Ma Y, Wang G. Auts2 regulated autism-like behavior, glucose metabolism and oxidative stress in mice. Exp Neurol 2023; 361:114298. [PMID: 36525998 DOI: 10.1016/j.expneurol.2022.114298] [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: 10/17/2022] [Revised: 11/29/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by abnormal social behavior and communication. The autism susceptibility candidate 2 (AUTS2) gene has been associated with multiple neurological diseases, including ASD. Glucose metabolism plays an important role in social behaviors associated with ASD, but the potential role of AUTS2 in glucose metabolism has not been studied. Here, we generated Auts2flox/flox; Emx1Cre+ conditional knockout mice with Auts2 deletion specifically in Exm1-positive neurons in the brain (Auts2-cKO mice) to evaluate the effects of Auts2 knockdown on social behaviors and metabolic pathways. Auts2-cKO mice exhibited ASD-like behaviors, including impaired social interactions and repetitive grooming behaviors. At the molecular level, we found that Auts2 knockdown reduced brain glucose uptake and inhibited the pentose phosphate pathway. Auts2 knockdown also resulted in signs of oxidative stress, and we documented increased levels of reactive oxygen species and malondialdehyde as well as decreased levels of antioxidant molecules, including glutathione and superoxide dismutases in Auts2-cKO mouse brains compared to controls. Finally, Auts2 knockdown significantly disrupted mitochondrial homeostasis and inhibited activity of the SIRT1-SIRT3 axis. Taken together, our findings indicate that loss of AUTS2 expression in Emx1-expressing cells induces multiple changes in metabolic pathways that have been linked to the pathology of ASD. Further characterization of the role of AUTS2 in Emx1-expressing cells in regulating the metabolism of brain neurons may identify opportunities to treat ASD and AUTS2-deficiency disorders with metabolism-targeted therapies.
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Affiliation(s)
- Min Liu
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yimeng Chen
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Miao Sun
- Department of Anesthesiology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou 121000, China
| | - Yingjie Du
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yafan Bai
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Guiyu Lei
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Congya Zhang
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Mingru Zhang
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yue Zhang
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Chunhua Xi
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Yulong Ma
- Department of Anesthesiology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China.
| | - Guyan Wang
- Department of Anesthesiology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China.
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16
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Carter MT, Srour M, Au PYB, Buhas D, Dyack S, Eaton A, Inbar-Feigenberg M, Howley H, Kawamura A, Lewis SME, McCready E, Nelson TN, Vallance H. Genetic and metabolic investigations for neurodevelopmental disorders: position statement of the Canadian College of Medical Geneticists (CCMG). J Med Genet 2023; 60:523-532. [PMID: 36822643 DOI: 10.1136/jmg-2022-108962] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023]
Abstract
PURPOSE AND SCOPE The aim of this position statement is to provide recommendations for clinicians regarding the use of genetic and metabolic investigations for patients with neurodevelopmental disorders (NDDs), specifically, patients with global developmental delay (GDD), intellectual disability (ID) and/or autism spectrum disorder (ASD). This document also provides guidance for primary care and non-genetics specialists caring for these patients while awaiting consultation with a clinical geneticist or metabolic specialist. METHODS OF STATEMENT DEVELOPMENT A multidisciplinary group reviewed existing literature and guidelines on the use of genetic and metabolic investigations for the diagnosis of NDDs and synthesised the evidence to make recommendations relevant to the Canadian context. The statement was circulated for comment to the Canadian College of Medical Geneticists (CCMG) membership-at-large and to the Canadian Pediatric Society (Mental Health and Developmental Disabilities Committee); following incorporation of feedback, it was approved by the CCMG Board of Directors on 1 September 2022. RESULTS AND CONCLUSIONS Chromosomal microarray is recommended as a first-tier test for patients with GDD, ID or ASD. Fragile X testing should also be done as a first-tier test when there are suggestive clinical features or family history. Metabolic investigations should be done if there are clinical features suggestive of an inherited metabolic disease, while the patient awaits consultation with a metabolic physician. Exome sequencing or a comprehensive gene panel is recommended as a second-tier test for patients with GDD or ID. Genetic testing is not recommended for patients with NDDs in the absence of GDD, ID or ASD, unless accompanied by clinical features suggestive of a syndromic aetiology or inherited metabolic disease.
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Affiliation(s)
| | - Myriam Srour
- Division of Neurology, McGill University Health Centre, Montreal, Québec, Canada
- Department of Pediatrics, McGill University, Montréal, QC, Canada
| | - Ping-Yee Billie Au
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Daniela Buhas
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sarah Dyack
- Division of Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Alison Eaton
- Department of Medical Genetics, Stollery Children's Hospital, Edmonton, Alberta, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Michal Inbar-Feigenberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Heather Howley
- Office of Research Services, CHEO Research Institute, Ottawa, Ontario, Canada
| | - Anne Kawamura
- Division of Developmental Pediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Mental Health and Developmental Disability Committee, Canadian Pediatric Society, Ottawa, ON, Canada
- Canadian Paediatric Society, Toronto, Ontario, Canada
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's and Women's Hospital, Vancouver, British Columbia, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, McMaster University, Hamilton, ON, Canada, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Tanya N Nelson
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hilary Vallance
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
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A Systematic Review of the Human Accelerated Regions in Schizophrenia and Related Disorders: Where the Evolutionary and Neurodevelopmental Hypotheses Converge. Int J Mol Sci 2023; 24:ijms24043597. [PMID: 36835010 PMCID: PMC9962562 DOI: 10.3390/ijms24043597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Schizophrenia is a psychiatric disorder that results from genetic and environmental factors interacting and disrupting neurodevelopmental trajectories. Human Accelerated Regions (HARs) are evolutionarily conserved genomic regions that have accumulated human-specific sequence changes. Thus, studies on the impact of HARs in the context of neurodevelopment, as well as with respect to adult brain phenotypes, have increased considerably in the last few years. Through a systematic approach, we aim to offer a comprehensive review of HARs' role in terms of human brain development, configuration, and cognitive abilities, as well as whether HARs modulate the susceptibility to neurodevelopmental psychiatric disorders such as schizophrenia. First, the evidence in this review highlights HARs' molecular functions in the context of the neurodevelopmental regulatory genetic machinery. Second, brain phenotypic analyses indicate that HAR genes' expression spatially correlates with the regions that suffered human-specific cortical expansion, as well as with the regional interactions for synergistic information processing. Lastly, studies based on candidate HAR genes and the global "HARome" variability describe the involvement of these regions in the genetic background of schizophrenia, but also in other neurodevelopmental psychiatric disorders. Overall, the data considered in this review emphasise the crucial role of HARs in human-specific neurodevelopment processes and encourage future research on this evolutionary marker for a better understanding of the genetic basis of schizophrenia and other neurodevelopmental-related psychiatric disorders. Accordingly, HARs emerge as interesting genomic regions that require further study in order to bridge the neurodevelopmental and evolutionary hypotheses in schizophrenia and other related disorders and phenotypes.
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18
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Talpo F, Spaiardi P, Castagno AN, Maniezzi C, Raffin F, Terribile G, Sancini G, Pisani A, Biella GR. Neuromodulatory functions exerted by oxytocin on different populations of hippocampal neurons in rodents. Front Cell Neurosci 2023; 17:1082010. [PMID: 36816855 PMCID: PMC9932910 DOI: 10.3389/fncel.2023.1082010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Oxytocin (OT) is a neuropeptide widely known for its peripheral hormonal effects (i.e., parturition and lactation) and central neuromodulatory functions, related especially to social behavior and social, spatial, and episodic memory. The hippocampus is a key structure for these functions, it is innervated by oxytocinergic fibers, and contains OT receptors (OTRs). The hippocampal OTR distribution is not homogeneous among its subregions and types of neuronal cells, reflecting the specificity of oxytocin's modulatory action. In this review, we describe the most recent discoveries in OT/OTR signaling in the hippocampus, focusing primarily on the electrophysiological oxytocinergic modulation of the OTR-expressing hippocampal neurons. We then look at the effect this modulation has on the balance of excitation/inhibition and synaptic plasticity in each hippocampal subregion. Additionally, we review OTR downstream signaling, which underlies the OT effects observed in different types of hippocampal neuron. Overall, this review comprehensively summarizes the advancements in unraveling the neuromodulatory functions exerted by OT on specific hippocampal networks.
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Affiliation(s)
- Francesca Talpo
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia, Italy
| | - Paolo Spaiardi
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia, Italy,Istituto Nazionale di Fisica Nucleare, Sezione di Pavia, Pavia, Italy
| | - Antonio Nicolas Castagno
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia, Italy
| | - Claudia Maniezzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Francesca Raffin
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia, Italy
| | - Giulia Terribile
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Giulio Sancini
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy,Nanomedicine Center, Neuroscience Center, School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Antonio Pisani
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy,Neurological Institute Foundation Casimiro Mondino (IRCCS), Pavia, Italy
| | - Gerardo Rosario Biella
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, Pavia, Italy,Istituto Nazionale di Fisica Nucleare, Sezione di Pavia, Pavia, Italy,*Correspondence: Gerardo Rosario Biella,
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19
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Auvinen P, Vehviläinen J, Marjonen H, Modhukur V, Sokka J, Wallén E, Rämö K, Ahola L, Salumets A, Otonkoski T, Skottman H, Ollikainen M, Trokovic R, Kahila H, Kaminen-Ahola N. Chromatin modifier developmental pluripotency associated factor 4 (DPPA4) is a candidate gene for alcohol-induced developmental disorders. BMC Med 2022; 20:495. [PMID: 36581877 PMCID: PMC9801659 DOI: 10.1186/s12916-022-02699-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Prenatal alcohol exposure (PAE) affects embryonic development, causing a variable fetal alcohol spectrum disorder (FASD) phenotype with neuronal disorders and birth defects. We hypothesize that early alcohol-induced epigenetic changes disrupt the accurate developmental programming of embryo and consequently cause the complex phenotype of developmental disorders. To explore the etiology of FASD, we collected unique biological samples of 80 severely alcohol-exposed and 100 control newborns at birth. METHODS We performed genome-wide DNA methylation (DNAm) and gene expression analyses of placentas by using microarrays (EPIC, Illumina) and mRNA sequencing, respectively. To test the manifestation of observed PAE-associated DNAm changes in embryonic tissues as well as potential biomarkers for PAE, we examined if the changes can be detected also in white blood cells or buccal epithelial cells of the same newborns by EpiTYPER. To explore the early effects of alcohol on extraembryonic placental tissue, we selected 27 newborns whose mothers had consumed alcohol up to gestational week 7 at maximum to the separate analyses. Furthermore, to explore the effects of early alcohol exposure on embryonic cells, human embryonic stem cells (hESCs) as well as hESCs during differentiation into endodermal, mesodermal, and ectodermal cells were exposed to alcohol in vitro. RESULTS DPPA4, FOXP2, and TACR3 with significantly decreased DNAm were discovered-particularly the regulatory region of DPPA4 in the early alcohol-exposed placentas. When hESCs were exposed to alcohol in vitro, significantly altered regulation of DPPA2, a closely linked heterodimer of DPPA4, was observed. While the regulatory region of DPPA4 was unmethylated in both control and alcohol-exposed hESCs, alcohol-induced decreased DNAm similar to placenta was seen in in vitro differentiated mesodermal and ectodermal cells. Furthermore, common genes with alcohol-associated DNAm changes in placenta and hESCs were linked exclusively to the neurodevelopmental pathways in the enrichment analysis, which emphasizes the value of placental tissue when analyzing the effects of prenatal environment on human development. CONCLUSIONS Our study shows the effects of early alcohol exposure on human embryonic and extraembryonic cells, introduces candidate genes for alcohol-induced developmental disorders, and reveals potential biomarkers for prenatal alcohol exposure.
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Affiliation(s)
- P Auvinen
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - J Vehviläinen
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - H Marjonen
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - V Modhukur
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia.,Competence Centre on Health Technologies, 50411, Tartu, Estonia
| | - J Sokka
- Research Programs Unit, Stem cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - E Wallén
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - K Rämö
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - L Ahola
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland
| | - A Salumets
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia.,Competence Centre on Health Technologies, 50411, Tartu, Estonia.,Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, S-171 76, Stockholm, Sweden
| | - T Otonkoski
- Research Programs Unit, Stem cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland.,Children's Hospital, Helsinki University Central Hospital, University of Helsinki, 00290, Helsinki, Finland
| | - H Skottman
- Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland
| | - M Ollikainen
- Institute for Molecular Medicine, Finland, FIMM, HiLIFE, University of Helsinki, 00290, Helsinki, Finland
| | - R Trokovic
- Research Programs Unit, Stem cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - H Kahila
- Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, 00290, Helsinki, Finland
| | - N Kaminen-Ahola
- Environmental Epigenetics Laboratory, Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00290, Helsinki, Finland.
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20
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Cabana-Domínguez J, Soler Artigas M, Arribas L, Alemany S, Vilar-Ribó L, Llonga N, Fadeuilhe C, Corrales M, Richarte V, Ramos-Quiroga JA, Ribasés M. Comprehensive analysis of omics data identifies relevant gene networks for Attention-Deficit/Hyperactivity Disorder (ADHD). Transl Psychiatry 2022; 12:409. [PMID: 36153331 PMCID: PMC9509350 DOI: 10.1038/s41398-022-02182-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/23/2022] Open
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a highly prevalent neurodevelopmental disorder that results from the interaction of both genetic and environmental risk factors. Genome-wide association studies have started to identify multiple genetic risk loci associated with ADHD, however, the exact causal genes and biological mechanisms remain largely unknown. We performed a multi-step analysis to identify and characterize modules of co-expressed genes associated with ADHD using data from peripheral blood mononuclear cells of 270 ADHD cases and 279 controls. We identified seven ADHD-associated modules of co-expressed genes, some of them enriched in both genetic and epigenetic signatures for ADHD and in biological pathways relevant for psychiatric disorders, such as the regulation of gene expression, epigenetics and immune system. In addition, for some of the modules, we found evidence of potential regulatory mechanisms, including microRNAs and common genetic variants. In conclusion, our results point to promising genes and pathways for ADHD, supporting the use of peripheral blood to assess gene expression signatures in psychiatric disorders. Furthermore, they highlight that the combination of multi-omics signals provides deeper and broader insights into the biological mechanisms underlying ADHD.
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Affiliation(s)
- Judit Cabana-Domínguez
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. .,Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain. .,Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain. .,Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.
| | - María Soler Artigas
- grid.7080.f0000 0001 2296 0625Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Mental Health, Hospital Universitari Vall d’Hebron, Barcelona, Spain ,grid.469673.90000 0004 5901 7501Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain ,grid.5841.80000 0004 1937 0247Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Lorena Arribas
- grid.7080.f0000 0001 2296 0625Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Mental Health, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Silvia Alemany
- grid.7080.f0000 0001 2296 0625Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Mental Health, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Laura Vilar-Ribó
- grid.7080.f0000 0001 2296 0625Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Mental Health, Hospital Universitari Vall d’Hebron, Barcelona, Spain ,grid.469673.90000 0004 5901 7501Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
| | - Natalia Llonga
- grid.7080.f0000 0001 2296 0625Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Mental Health, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Christian Fadeuilhe
- grid.7080.f0000 0001 2296 0625Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Mental Health, Hospital Universitari Vall d’Hebron, Barcelona, Spain ,grid.469673.90000 0004 5901 7501Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain ,grid.7080.f0000 0001 2296 0625Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Montse Corrales
- grid.7080.f0000 0001 2296 0625Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Mental Health, Hospital Universitari Vall d’Hebron, Barcelona, Spain ,grid.469673.90000 0004 5901 7501Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain ,grid.7080.f0000 0001 2296 0625Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vanesa Richarte
- grid.7080.f0000 0001 2296 0625Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Mental Health, Hospital Universitari Vall d’Hebron, Barcelona, Spain ,grid.469673.90000 0004 5901 7501Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain ,grid.7080.f0000 0001 2296 0625Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Antoni Ramos-Quiroga
- grid.7080.f0000 0001 2296 0625Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain ,grid.411083.f0000 0001 0675 8654Department of Mental Health, Hospital Universitari Vall d’Hebron, Barcelona, Spain ,grid.469673.90000 0004 5901 7501Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain ,grid.7080.f0000 0001 2296 0625Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marta Ribasés
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain. .,Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain. .,Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain. .,Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.
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21
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Exome sequencing analysis of Japanese autism spectrum disorder case-control sample supports an increased burden of synaptic function-related genes. Transl Psychiatry 2022; 12:265. [PMID: 35811316 PMCID: PMC9271461 DOI: 10.1038/s41398-022-02033-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 01/16/2023] Open
Abstract
Autism spectrum disorder (ASD) is a highly heritable, complex disorder in which rare variants contribute significantly to disease risk. Although many genes have been associated with ASD, there have been few genetic studies of ASD in the Japanese population. In whole exomes from a Japanese ASD sample of 309 cases and 299 controls, rare variants were associated with ASD within specific neurodevelopmental gene sets, including highly constrained genes, fragile X mental retardation protein target genes, and genes involved in synaptic function, with the strongest enrichment in trans-synaptic signaling (p = 4.4 × 10-4, Q-value = 0.06). In particular, we strengthen the evidence regarding the role of ABCA13, a synaptic function-related gene, in Japanese ASD. The overall results of this case-control exome study showed that rare variants related to synaptic function are associated with ASD susceptibility in the Japanese population.
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22
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Yoshikawa A, Kushima I, Miyashita M, Suzuki K, Iino K, Toriumi K, Horiuchi Y, Kawaji H, Ozaki N, Itokawa M, Arai M. Exonic deletions in IMMP2L in schizophrenia with enhanced glycation stress subtype. PLoS One 2022; 17:e0270506. [PMID: 35776734 PMCID: PMC9249242 DOI: 10.1371/journal.pone.0270506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/12/2022] [Indexed: 11/24/2022] Open
Abstract
We previously identified a subtype of schizophrenia (SCZ) characterized by increased plasma pentosidine, a marker of glycation and oxidative stress (PEN-SCZ). However, the genetic factors associated with PEN-SCZ have not been fully clarified. We performed a genome-wide copy number variation (CNV) analysis to identify CNVs associated with PEN-SCZ to provide an insight into the novel therapeutic targets for PEN-SCZ. Plasma pentosidine was measured by high-performance liquid chromatography in 185 patients with SCZ harboring rare CNVs detected by array comparative genomic hybridization. In three patients with PEN-SCZ showing additional autistic features, we detected a novel deletion at 7q31.1 within exons 2 and 3 of IMMP2L, which encodes the inner mitochondrial membrane peptidase subunit 2. The deletion was neither observed in non-PEN-SCZ nor in public database of control subjects. IMMP2L is one of the SCZ risk loci genes identified in a previous SCZ genome-wide association study, and its trans-populational association was recently described. Interestingly, deletions in IMMP2L have been previously linked with autism spectrum disorder. Disrupted IMMP2L function has been shown to cause glycation/oxidative stress in neuronal cells in an age-dependent manner. To our knowledge, this is the first genome-wide CNV study to suggest the involvement of IMMP2L exons 2 and 3 in the etiology of PEN-SCZ. The combination of genomic information with plasma pentosidine levels may contribute to the classification of biological SCZ subtypes that show additional autistic features. Modifying IMMP2L functions may be useful for treating PEN-SCZ if the underlying biological mechanism can be clarified in further studies.
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Affiliation(s)
- Akane Yoshikawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Mitsuhiro Miyashita
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
- Department of Psychiatry, Takatsuki Clinic, Akishima, Tokyo, Japan
| | - Kazuhiro Suzuki
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
- Department of Psychiatry, Takatsuki Clinic, Akishima, Tokyo, Japan
| | - Kyoka Iino
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Kazuya Toriumi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Yasue Horiuchi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masanari Itokawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
| | - Makoto Arai
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
- Department of Psychiatry, Tokyo Metropolitan Matsuzawa Hospital, Setagaya, Tokyo, Japan
- * E-mail:
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23
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Hohmann S, Häge A, Millenet S, Banaschewski T. [The Genetic Basis of ADHD - An Update]. ZEITSCHRIFT FUR KINDER-UND JUGENDPSYCHIATRIE UND PSYCHOTHERAPIE 2022; 50:203-217. [PMID: 35514173 DOI: 10.1024/1422-4917/a000868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Genetic Basis of ADHD - An Update Abstract. Genetic risks play an important role in the etiology of attention-deficit/hyperactivity disorder (ADHD). This review presents the current state of knowledge concerning the genetic basis of the disorder. It discusses the results of twin- and family-based studies, linkage and association studies as well as recent findings resulting from Genome Wide Association Studies (GWAS). Furthermore, it elaborates on the relevance of polygenic risk scores, rare variants, and epigenetic alterations, especially in light of findings on genetic pleiotropy in the context of frequent psychiatric comorbidities in patients with ADHD.
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Affiliation(s)
- Sarah Hohmann
- Klinik für Psychiatrie und Psychotherapie des Kindes- und Jugendalters, Zentralinstitut für Seelische Gesundheit, Medizinische Fakultät Mannheim der Universität Heidelberg, Mannheim, Deutschland
| | - Alexander Häge
- Klinik für Psychiatrie und Psychotherapie des Kindes- und Jugendalters, Zentralinstitut für Seelische Gesundheit, Medizinische Fakultät Mannheim der Universität Heidelberg, Mannheim, Deutschland
| | - Sabina Millenet
- Klinik für Psychiatrie und Psychotherapie des Kindes- und Jugendalters, Zentralinstitut für Seelische Gesundheit, Medizinische Fakultät Mannheim der Universität Heidelberg, Mannheim, Deutschland
| | - Tobias Banaschewski
- Klinik für Psychiatrie und Psychotherapie des Kindes- und Jugendalters, Zentralinstitut für Seelische Gesundheit, Medizinische Fakultät Mannheim der Universität Heidelberg, Mannheim, Deutschland
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24
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Forastieri C, Italia M, Toffolo E, Romito E, Bonasoni MP, Ranzani V, Bodega B, Rusconi F, Battaglioli E. Evolution Increases Primates Brain Complexity Extending RbFOX1 Splicing Activity to LSD1 Modulation. J Neurosci 2022; 42:3689-3703. [PMID: 35351830 PMCID: PMC9087731 DOI: 10.1523/jneurosci.1782-21.2022] [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: 09/02/2021] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 11/21/2022] Open
Abstract
Recent branching (100 MYA) of the mammalian evolutionary tree has enhanced brain complexity and functions at the putative cost of increased emotional circuitry vulnerability. Thus, to better understand psychopathology, a burden for the modern society, novel approaches should exploit evolutionary aspects of psychiatric-relevant molecular pathways. A handful of genes is nowadays tightly associated to psychiatric disorders. Among them, neuronal-enriched RbFOX1 modifies the activity of synaptic regulators in response to neuronal activity, keeping excitability within healthy domains. We here dissect a higher primates-restricted interaction between RbFOX1 and the transcriptional corepressor Lysine Specific Demethylase 1 (LSD1/KDM1A). A single nucleotide variation (AA to AG) in LSD1 gene appeared in higher primates and humans, endowing RbFOX1 with the ability to promote the alternative usage of a novel 3' AG splice site, which extends LSD1 exon E9 in the upstream intron (E9-long). Exon E9-long regulates LSD1 levels by Nonsense-Mediated mRNA Decay. As reintroduction of the archaic LSD1 variant (AA) abolishes E9-long splicing, the novel 3' AG splice site is necessary for RbFOX1 to control LSD1 levels. LSD1 is a homeostatic immediate early genes (IEGs) regulator playing a relevant part in environmental stress-response. In primates and humans, inclusion of LSD1 as RbFOX1 target provides RbFOX1 with the additional ability to regulate the IEGs. These data, together with extensive RbFOX1 involvement in psychiatric disorders and its stress-dependent regulation in male mice, suggest the RbFOX1-LSD1-IEGs axis as an evolutionary recent psychiatric-relevant pathway. Notably, outside the nervous system, RbFOX2-dependent LSD1 modulation could be a candidate deregulated mechanism in cancer.SIGNIFICANCE STATEMENT To be better understood, anxiety and depression need large human genetics studies aimed at further resolving the often ambiguous, aberrant neuronal pathomechanisms that impact corticolimbic circuitry physiology. Several genetic associations of the alternative splicing regulator RbFOX1 with psychiatric conditions suggest homeostatic unbalance as a neuronal signature of psychopathology. Here we move a step forward, characterizing a disease-relevant higher primates-specific pathway by which RbFOX1 acquires the ability to regulate neuronal levels of Lysine Specific Demethylase 1, an epigenetic modulator of environmental stress response. Thus, two brain-enriched enzymes, independently shown to homeostatically protect neurons with a clear readout in terms of emotional behavior in lower mammals, establish in higher primates and humans a new functional cooperation enhancing the complexity of environmental adaptation and stress vulnerability.
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Affiliation(s)
- Chiara Forastieri
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
| | - Maria Italia
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
| | - Emanuela Toffolo
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
| | - Elena Romito
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
| | | | - Valeria Ranzani
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milano, 20122, Italy
| | - Beatrice Bodega
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milano, 20122, Italy
- Department of Biosciences, Università degli Studi di Milano, Milano, 20133, Italy
| | - Francesco Rusconi
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
| | - Elena Battaglioli
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
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25
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A Pilot Study of Whole-Blood Transcriptomic Analysis to Identify Genes Associated with Repetitive Low-Level Blast Exposure in Career Breachers. Biomedicines 2022; 10:biomedicines10030690. [PMID: 35327492 PMCID: PMC8945695 DOI: 10.3390/biomedicines10030690] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/12/2022] [Accepted: 03/15/2022] [Indexed: 02/06/2023] Open
Abstract
Repetitive low-level blast exposure is one of the major occupational health concerns among US military service members and law enforcement. This study seeks to identify gene expression using microRNA and RNA sequencing in whole-blood samples from experienced breachers and unexposed controls. We performed experimental RNA sequencing using Illumina’s HiSeq 2500 Sequencing System, and microRNA analysis using NanoString Technology nCounter miRNA expression panel in whole-blood total RNA samples from 15 experienced breachers and 14 age-, sex-, and race-matched unexposed controls. We identified 10 significantly dysregulated genes between experienced breachers and unexposed controls, with FDR corrected <0.05: One upregulated gene, LINC00996 (long intergenic non-protein coding RNA 996); and nine downregulated genes, IGLV3-16 (immunoglobulin lambda variable 3-16), CD200 (CD200 molecule), LILRB5 (leukocyte immunoglobulin-like receptor B5), ZNF667-AS1 (ZNF667 antisense RNA 1), LMOD1 (leiomodin 1), CNTNAP2 (contactin-associated protein 2), EVPL (envoplakin), DPF3 (double PHD fingers 3), and IGHV4-34 (immunoglobulin heavy variable 4-34). The dysregulated gene expressions reported here have been associated with chronic inflammation and immune response, suggesting that these pathways may relate to the risk of lasting neurological symptoms following high exposures to blast over a career.
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Kunová N, Havalová H, Ondrovičová G, Stojkovičová B, Bauer JA, Bauerová-Hlinková V, Pevala V, Kutejová E. Mitochondrial Processing Peptidases-Structure, Function and the Role in Human Diseases. Int J Mol Sci 2022; 23:1297. [PMID: 35163221 PMCID: PMC8835746 DOI: 10.3390/ijms23031297] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial proteins are encoded by both nuclear and mitochondrial DNA. While some of the essential subunits of the oxidative phosphorylation (OXPHOS) complexes responsible for cellular ATP production are synthesized directly in the mitochondria, most mitochondrial proteins are first translated in the cytosol and then imported into the organelle using a sophisticated transport system. These proteins are directed mainly by targeting presequences at their N-termini. These presequences need to be cleaved to allow the proper folding and assembly of the pre-proteins into functional protein complexes. In the mitochondria, the presequences are removed by several processing peptidases, including the mitochondrial processing peptidase (MPP), the inner membrane processing peptidase (IMP), the inter-membrane processing peptidase (MIP), and the mitochondrial rhomboid protease (Pcp1/PARL). Their proper functioning is essential for mitochondrial homeostasis as the disruption of any of them is lethal in yeast and severely impacts the lifespan and survival in humans. In this review, we focus on characterizing the structure, function, and substrate specificities of mitochondrial processing peptidases, as well as the connection of their malfunctions to severe human diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Eva Kutejová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (H.H.); (G.O.); (B.S.); (J.A.B.); (V.B.-H.); (V.P.)
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St George-Hyslop F, Kivisild T, Livesey FJ. The role of contactin-associated protein-like 2 in neurodevelopmental disease and human cerebral cortex evolution. Front Mol Neurosci 2022; 15:1017144. [PMID: 36340692 PMCID: PMC9630569 DOI: 10.3389/fnmol.2022.1017144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 12/04/2022] Open
Abstract
The contactin-associated protein-like 2 (CNTNAP2) gene is associated with multiple neurodevelopmental disorders, including autism spectrum disorder (ASD), intellectual disability (ID), and specific language impairment (SLI). Experimental work has shown that CNTNAP2 is important for neuronal development and synapse formation. There is also accumulating evidence for the differential use of CNTNAP2 in the human cerebral cortex compared with other primates. Here, we review the current literature on CNTNAP2, including what is known about its expression, disease associations, and molecular/cellular functions. We also review the evidence for its role in human brain evolution, such as the presence of eight human accelerated regions (HARs) within the introns of the gene. While progress has been made in understanding the function(s) of CNTNAP2, more work is needed to clarify the precise mechanisms through which CNTNAP2 acts. Such information will be crucial for developing effective treatments for CNTNAP2 patients. It may also shed light on the longstanding question of what makes us human.
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Affiliation(s)
- Frances St George-Hyslop
- Zayed Centre for Research Into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Frederick J Livesey
- Zayed Centre for Research Into Rare Disease in Children, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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28
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Wu Q, Li D. CRIA: An Interactive Gene Selection Algorithm for Cancers Prediction Based on Copy Number Variations. FRONTIERS IN PLANT SCIENCE 2022; 13:839044. [PMID: 35386679 PMCID: PMC8978562 DOI: 10.3389/fpls.2022.839044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/19/2022] [Indexed: 05/05/2023]
Abstract
Genomic copy number variations (CNVs) are among the most important structural variations of genes found to be related to the risk of individual cancer and therefore they can be utilized to provide a clue to the research on the formation and progression of cancer. In this paper, an improved computational gene selection algorithm called CRIA (correlation-redundancy and interaction analysis based on gene selection algorithm) is introduced to screen genes that are closely related to cancer from the whole genome based on the value of gene CNVs. The CRIA algorithm mainly consists of two parts. Firstly, the main effect feature is selected out from the original feature set that has the largest correlation with the class label. Secondly, after the analysis involving correlation, redundancy and interaction for each feature in the candidate feature set, we choose the feature that maximizes the value of the custom selection criterion and add it into the selected feature set and then remove it from the candidate feature set in each selection round. Based on the real datasets, CRIA selects the top 200 genes to predict the type of cancer. The experiments' results of our research show that, compared with the state-of-the-art related methods, the CRIA algorithm can extract the key features of CNVs and a better classification performance can be achieved based on them. In addition, the interpretable genes highly related to cancer can be known, which may provide new clues at the genetic level for the treatment of the cancer.
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29
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Cornejo F, Cortés BI, Findlay GM, Cancino GI. LAR Receptor Tyrosine Phosphatase Family in Healthy and Diseased Brain. Front Cell Dev Biol 2021; 9:659951. [PMID: 34966732 PMCID: PMC8711739 DOI: 10.3389/fcell.2021.659951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 11/17/2021] [Indexed: 11/23/2022] Open
Abstract
Protein phosphatases are major regulators of signal transduction and they are involved in key cellular mechanisms such as proliferation, differentiation, and cell survival. Here we focus on one class of protein phosphatases, the type IIA Receptor-type Protein Tyrosine Phosphatases (RPTPs), or LAR-RPTP subfamily. In the last decade, LAR-RPTPs have been demonstrated to have great importance in neurobiology, from neurodevelopment to brain disorders. In vertebrates, the LAR-RPTP subfamily is composed of three members: PTPRF (LAR), PTPRD (PTPδ) and PTPRS (PTPσ), and all participate in several brain functions. In this review we describe the structure and proteolytic processing of the LAR-RPTP subfamily, their alternative splicing and enzymatic regulation. Also, we review the role of the LAR-RPTP subfamily in neural function such as dendrite and axon growth and guidance, synapse formation and differentiation, their participation in synaptic activity, and in brain development, discussing controversial findings and commenting on the most recent studies in the field. Finally, we discuss the clinical outcomes of LAR-RPTP mutations, which are associated with several brain disorders.
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Affiliation(s)
- Francisca Cornejo
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Bastián I Cortés
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Greg M Findlay
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Gonzalo I Cancino
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.,Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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30
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AUTS2 Gene: Keys to Understanding the Pathogenesis of Neurodevelopmental Disorders. Cells 2021; 11:cells11010011. [PMID: 35011572 PMCID: PMC8750789 DOI: 10.3390/cells11010011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/08/2021] [Accepted: 12/18/2021] [Indexed: 01/01/2023] Open
Abstract
Neurodevelopmental disorders (NDDs), including autism spectrum disorders (ASD) and intellectual disability (ID), are a large group of neuropsychiatric illnesses that occur during early brain development, resulting in a broad spectrum of syndromes affecting cognition, sociability, and sensory and motor functions. Despite progress in the discovery of various genetic risk factors thanks to the development of novel genomics technologies, the precise pathological mechanisms underlying the onset of NDDs remain elusive owing to the profound genetic and phenotypic heterogeneity of these conditions. Autism susceptibility candidate 2 (AUTS2) has emerged as a crucial gene associated with a wide range of neuropsychological disorders, such as ASD, ID, schizophrenia, and epilepsy. AUTS2 has been shown to be involved in multiple neurodevelopmental processes; in cell nuclei, it acts as a key transcriptional regulator in neurodevelopment, whereas in the cytoplasm, it participates in cerebral corticogenesis, including neuronal migration and neuritogenesis, through the control of cytoskeletal rearrangements. Postnatally, AUTS2 regulates the number of excitatory synapses to maintain the balance between excitation and inhibition in neural circuits. In this review, we summarize the knowledge regarding AUTS2, including its molecular and cellular functions in neurodevelopment, its genetics, and its role in behaviors.
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31
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Liu S, Aldinger KA, Cheng CV, Kiyama T, Dave M, McNamara HK, Zhao W, Stafford JM, Descostes N, Lee P, Caraffi SG, Ivanovski I, Errichiello E, Zweier C, Zuffardi O, Schneider M, Papavasiliou AS, Perry MS, Humberson J, Cho MT, Weber A, Swale A, Badea TC, Mao CA, Garavelli L, Dobyns WB, Reinberg D. NRF1 association with AUTS2-Polycomb mediates specific gene activation in the brain. Mol Cell 2021; 81:4663-4676.e8. [PMID: 34637754 PMCID: PMC8604784 DOI: 10.1016/j.molcel.2021.09.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/21/2021] [Accepted: 09/15/2021] [Indexed: 12/17/2022]
Abstract
The heterogeneous family of complexes comprising Polycomb repressive complex 1 (PRC1) is instrumental for establishing facultative heterochromatin that is repressive to transcription. However, two PRC1 species, ncPRC1.3 and ncPRC1.5, are known to comprise novel components, AUTS2, P300, and CK2, that convert this repressive function to that of transcription activation. Here, we report that individuals harboring mutations in the HX repeat domain of AUTS2 exhibit defects in AUTS2 and P300 interaction as well as a developmental disorder reflective of Rubinstein-Taybi syndrome, which is mainly associated with a heterozygous pathogenic variant in CREBBP/EP300. Moreover, the absence of AUTS2 or mutation in its HX repeat domain gives rise to misregulation of a subset of developmental genes and curtails motor neuron differentiation of mouse embryonic stem cells. The transcription factor nuclear respiratory factor 1 (NRF1) has a novel and integral role in this neurodevelopmental process, being required for ncPRC1.3 recruitment to chromatin.
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Affiliation(s)
- Sanxiong Liu
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Chi Vicky Cheng
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Takae Kiyama
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Mitali Dave
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Hanna K McNamara
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Wukui Zhao
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Nicolas Descostes
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Pedro Lee
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Stefano G Caraffi
- Struttura Semplice Dipartimentale di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Ivan Ivanovski
- Struttura Semplice Dipartimentale di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy; Institute of Medical Genetics, University of Zürich, Zürich, Switzerland
| | - Edoardo Errichiello
- Dipartimento di Medicina Molecolare, Università di Pavia, Pavia, Italy; IRCCS Mondino Foundation, Pavia, Italy
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schwabachanlage 10, 91054 Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Orsetta Zuffardi
- Dipartimento di Medicina Molecolare, Università di Pavia, Pavia, Italy
| | - Michael Schneider
- Carle Physicians Group, Section of Neurology, St. Christopher's Hospital for Children, Urbana, IL, USA
| | | | - M Scott Perry
- Comprehensive Epilepsy Program, Jane and John Justin Neuroscience Center, Cook Children's Medical Center, Fort Worth, TX 76104, USA
| | - Jennifer Humberson
- Division of Genetics, Department of Pediatrics, University of Virginia Children's Hospital, Charlottesville, VA, USA
| | | | | | - Andrew Swale
- Liverpool Women's Hospital, Liverpool, UK; Manchester Centre for Genomic Medicine, Manchester, UK
| | - Tudor C Badea
- National Eye Institute, NIH, Bethesda, MD 20892, USA; Research and Development Institute, Transilvania University of Brasov, School of Medicine, Brasov, Romania
| | - Chai-An Mao
- Ruiz Department of Ophthalmology and Visual Science, McGovern Medical School at The University of Texas Health Science Center at Houston (UTHealth), Houston, TX 77030, USA; National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Livia Garavelli
- Struttura Semplice Dipartimentale di Genetica Medica, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics (Genetic Medicine), University of Washington, Seattle, WA, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University Langone School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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Feng X, Chen L, Qing Y, Li R, Li C, Li SC. SCYN: single cell CNV profiling method using dynamic programming. BMC Genomics 2021; 22:651. [PMID: 34789142 PMCID: PMC8596905 DOI: 10.1186/s12864-021-07941-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Copy number variation is crucial in deciphering the mechanism and cure of complex disorders and cancers. The recent advancement of scDNA sequencing technology sheds light upon addressing intratumor heterogeneity, detecting rare subclones, and reconstructing tumor evolution lineages at single-cell resolution. Nevertheless, the current circular binary segmentation based approach proves to fail to efficiently and effectively identify copy number shifts on some exceptional trails. RESULTS Here, we propose SCYN, a CNV segmentation method powered with dynamic programming. SCYN resolves the precise segmentation on in silico dataset. Then we verified SCYN manifested accurate copy number inferring on triple negative breast cancer scDNA data, with array comparative genomic hybridization results of purified bulk samples as ground truth validation. We tested SCYN on two datasets of the newly emerged 10x Genomics CNV solution. SCYN successfully recognizes gastric cancer cells from 1% and 10% spike-ins 10x datasets. Moreover, SCYN is about 150 times faster than state of the art tool when dealing with the datasets of approximately 2000 cells. CONCLUSIONS SCYN robustly and efficiently detects segmentations and infers copy number profiles on single cell DNA sequencing data. It serves to reveal the tumor intra-heterogeneity. The source code of SCYN can be accessed in https://github.com/xikanfeng2/SCYN .
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Affiliation(s)
- Xikang Feng
- School of Software, Northwestern Polytechnical University, Xi’an Shaanxi, 710072 China
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Lingxi Chen
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Yuhao Qing
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Ruikang Li
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Chaohui Li
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
- Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China
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EWAS of Monozygotic Twins Implicate a Role of mTOR Pathway in Pathogenesis of Tic Spectrum Disorder. Genes (Basel) 2021; 12:genes12101510. [PMID: 34680906 PMCID: PMC8535383 DOI: 10.3390/genes12101510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
Tic spectrum disorder (TSD) is an umbrella term which includes Gilles de la Tourette syndrome (GTS) and chronic tic disorder (CTD). They are considered highly heritable, yet the genetic components remain largely unknown. In this study we aimed to investigate disease-associated DNA methylation differences to identify genes and pathways which may be implicated in TSD aetiology. For this purpose, we performed an exploratory analysis of the genome-wide DNA methylation patterns in whole blood samples of 16 monozygotic twin pairs, of which eight were discordant and six concordant for TSD, while two pairs were asymptomatic. Although no sites reached genome-wide significance, we identified several sites and regions with a suggestive significance, which were located within or in the vicinity of genes with biological functions associated with neuropsychiatric disorders. The two top genes identified (TSC1 and CRYZ/TYW3) and the enriched pathways and components (phosphoinosides and PTEN pathways, and insulin receptor substrate binding) are related to, or have been associated with, the PI3K/AKT/mTOR pathway. Genes in this pathway have previously been associated with GTS, and mTOR signalling has been implicated in a range of neuropsychiatric disorders. It is thus possible that altered mTOR signalling plays a role in the complex pathogenesis of TSD.
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Lopatkina ME, Ivanova SA, Lebedev IN. Estimation of the Prevalence and Parental Origin of Chromosomal Microdeletions and Microduplications Affecting the CNTN6 Gene in Patients with Neurodevelopmental Disorders and Healthy Individuals. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421070103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Erotomania and phenotypic continuum in a family frameshift variant of AUTS2: a case report and review. BMC Psychiatry 2021; 21:360. [PMID: 34273950 PMCID: PMC8285776 DOI: 10.1186/s12888-021-03342-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/25/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Pathogenic variants of the AUTS2 (Autism Susceptibility candidate 2) gene predispose to intellectual disability, autism spectrum disorder, attention deficit hyperactivity disorder, facial dysmorphism and short stature. This phenotype is therefore associated with neurocognitive disturbances and social cognition, indicating potential functional maladjustment in the affected subjects, and a potentially significant impact on quality of life. Although many isolated cases have been reported in the literature, to date no families have been described. This case reports on a family (three generations) with a frameshift variant in the AUTS2 gene. CASE PRESENTATION The proband is 13 years old with short stature, dysmorphic features, moderate intellectual disability and autism spectrum disorder. His mother is 49 years old and also has short stature and similar dysmorphic features. She does not have autism disorder but presents an erotomaniac delusion. Her cognitive performance is heterogeneous. The two aunts are also of short stature. The 50-year-old aunt has isolated social cognition disorders. The 45-year-old aunt has severe cognitive impairment and autism spectrum disorder. The molecular analysis of the three sisters and the proband shows the same AUTS2 heterozygous duplication leading to a frame shift expected to produce a premature stop codon, p.(Met593Tyrfs*85). Previously reported isolated cases revealed phenotypic and cognitive impairment variability. In this case report, these variabilities are present within the same family, presenting the same variant. CONCLUSIONS The possibility of a phenotypic spectrum within the same family highlights the need for joint psychiatry and genetics research.
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Liu Y, Qu HQ, Chang X, Nguyen K, Qu J, Tian L, Glessner J, Sleiman PM, Hakonarson H. Deep learning prediction of attention-deficit hyperactivity disorder in African Americans by copy number variation. Exp Biol Med (Maywood) 2021; 246:2317-2323. [PMID: 34233526 DOI: 10.1177/15353702211018970] [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] [Indexed: 11/15/2022] Open
Abstract
Current understanding of the underlying molecular network and mechanism for attention-deficit hyperactivity disorder (ADHD) is lacking and incomplete. Previous studies suggest that genomic structural variations play an important role in the pathogenesis of ADHD. For effective modeling, deep learning approaches have become a method of choice, with ability to predict the impact of genetic variations involving complicated mechanisms. In this study, we examined copy number variation in whole genome sequencing from 116 African Americans ADHD children and 408 African American controls. We divided the human genome into 150 regions, and the variation intensity in each region was applied as feature vectors for deep learning modeling to classify ADHD patients. The accuracy of deep learning for predicting ADHD diagnosis is consistently around 78% in a two-fold shuffle test, compared with ∼50% by traditional k-mean clustering methods. Additional whole genome sequencing data from 351 European Americans children, including 89 ADHD cases and 262 controls, were applied as independent validation using feature vectors obtained from the African American ethnicity analysis. The accuracy of ADHD labeling was lower in this setting (∼70-75%) but still above the results from traditional methods. The regions with highest weight overlapped with the previously reported ADHD-associated copy number variation regions, including genes such as GRM1 and GRM8, key drivers of metabotropic glutamate receptor signaling. A notable discovery is that structural variations in non-coding genomic (intronic/intergenic) regions show prediction weights that can be as high as prediction weight from variations in coding regions, results that were unexpected.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hui-Qi Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Xiao Chang
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kenny Nguyen
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jingchun Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lifeng Tian
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Joseph Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Patrick Ma Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Individualization of attention-deficit/hyperactivity disorder treatment: pharmacotherapy considerations by age and co-occurring conditions. CNS Spectr 2021; 26:202-221. [PMID: 32054558 DOI: 10.1017/s1092852919001822] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder that manifests in childhood and can persist into adolescence and adulthood. Impairments associated with ADHD can impact quality of life, social interactions, and increase the risk of morbidity and mortality; however, for many patients, effective treatment can lessen these effects. Pharmacotherapy with stimulants or nonstimulants is recommended in conjunction with psychosocial therapy for most patients. Determining the optimal pharmacotherapy can be complex, and the clinician needs to consider many factors such as the patient's age, comorbidities, and lifestyle. Furthermore, the needs of the patient with ADHD will change over time, with specific challenges to consider at each stage of life. A variety of Food and Drug Administration (FDA)-approved stimulant and nonstimulant formulations are available with different modes of delivery and durations of effect. This armamentarium of ADHD medications can be used to individualize ADHD treatment for each patient's needs. This article combines current information from the literature and the first-hand experience of the authors to provide guidance on ADHD treatment options for patients of different ages and for some of the more common comorbidities.
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Li D, Zhang L, Bai T, Huang W, Ji GJ, Yang T, Zhang Y, Tian Y, Qiu B, Wang K. Common variants of the autism-associated CNTNAP2 gene contribute to the modulatory effect of social function mediated by temporal cortex. Behav Brain Res 2021; 409:113319. [PMID: 33901431 DOI: 10.1016/j.bbr.2021.113319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/26/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Autistic traits are highly heritable and characterized by social deficits. Common genetic variants of the autism-related CNTNAP2 gene have been linked with social impairments, but the neural substrates are poorly understood. In the present study, we investigated the genetic effect of common variants of CNTNAP2 (rs2710102 and rs7794745) on gray matter volume and its association with social performance among 442 healthy participants. Our results showed that individuals with rs2710102 GG homozygotes had smaller left superior temporal gyrus (STG)/insular volume than A-allele carriers (AA and AG), while individuals with rs7794745 TT and AT showed smaller right parahippocampal, right STG/insular, and left inferior parietal lobule (IPL) cortex volume than those with rs7794745 AA. Smaller volume of the STG/insular and parahippocampal cortex was associated with poorer social performance. An indirect effect of CNTNAP2 rs7794745 and rs2710102 genotype on the social performance was mediated by the STG/insular cortex and parahippocampal cortex volume. These findings provided insight into the genetic effect of CNTNAP2 variants on social behavior, which may be moderated by the temporal cortex.
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Affiliation(s)
- Dandan Li
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, 230022, China; Collaborative Innovation Center of Neuropsychiatric Disorders and Mental Health, Hefei, 230022, China; School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, 230022, China
| | - Long Zhang
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, 230022, China; Collaborative Innovation Center of Neuropsychiatric Disorders and Mental Health, Hefei, 230022, China
| | - Tongjian Bai
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, 230022, China; Collaborative Innovation Center of Neuropsychiatric Disorders and Mental Health, Hefei, 230022, China
| | - Wanling Huang
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Gong-Jun Ji
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, 230022, China; Collaborative Innovation Center of Neuropsychiatric Disorders and Mental Health, Hefei, 230022, China; School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, 230022, China
| | - Tingting Yang
- School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, 230022, China
| | - Yifan Zhang
- School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, 230022, China
| | - Yanghua Tian
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, 230022, China; Collaborative Innovation Center of Neuropsychiatric Disorders and Mental Health, Hefei, 230022, China
| | - Bensheng Qiu
- Center for Biomedical Engineering, University of Science and Technology of China, Hefei, Anhui, 230022, China
| | - Kai Wang
- Department of Neurology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China; Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, 230022, China; Collaborative Innovation Center of Neuropsychiatric Disorders and Mental Health, Hefei, 230022, China; School of Mental Health and Psychological Sciences, Anhui Medical University, Hefei, 230022, China; Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, 230022, China.
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Pang W, Yi X, Li L, Liu L, Xiang W, Xiao L. Untangle the Multi-Facet Functions of Auts2 as an Entry Point to Understand Neurodevelopmental Disorders. Front Psychiatry 2021; 12:580433. [PMID: 33967843 PMCID: PMC8102784 DOI: 10.3389/fpsyt.2021.580433] [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: 07/06/2020] [Accepted: 03/22/2021] [Indexed: 12/27/2022] Open
Abstract
Neurodevelopmental disorders are psychiatric diseases that are usually first diagnosed in infancy, childhood and adolescence. Autism spectrum disorder (ASD) is a neurodevelopmental disorder, characterized by core symptoms including impaired social communication, cognitive rigidity and repetitive behavior, accompanied by a wide range of comorbidities such as intellectual disability (ID) and dysmorphisms. While the cause remains largely unknown, genetic, epigenetic, and environmental factors are believed to contribute toward the onset of the disease. Autism Susceptibility Candidate 2 (Auts2) is a gene highly associated with ID and ASD. Therefore, understanding the function of Auts2 gene can provide a unique entry point to untangle the complex neuronal phenotypes of neurodevelpmental disorders. In this review, we discuss the recent discoveries regarding the molecular and cellular functions of Auts2. Auts2 was shown to be a key-regulator of transcriptional network and a mediator of epigenetic regulation in neurodevelopment, the latter potentially providing a link for the neuronal changes of ASD upon environmental risk-factor exposure. In addition, Auts2 could synchronize the balance between excitation and inhibition through regulating the number of excitatory synapses. Cytoplasmic Auts2 could join the fine-tuning of actin dynamics during neuronal migration and neuritogenesis. Furthermore, Auts2 was expressed in developing mouse and human brain regions such as the frontal cortex, dorsal thalamus, and hippocampus, which have been implicated in the impaired cognitive and social function of ASD. Taken together, a comprehensive understanding of Auts2 functions can give deep insights into the cause of the heterogenous manifestation of neurodevelopmental disorders such as ASD.
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Affiliation(s)
- Wenbin Pang
- Key Laboratory of Brain Science Research & Transformation in Tropical Environment of Hainan Province, Hainan Medical University, Haikou, China
- National Health Commission (NHC) Key Laboratory of Control of Tropical Diseases, Hainan Medical University, Haikou, China
| | - Xinan Yi
- Key Laboratory of Brain Science Research & Transformation in Tropical Environment of Hainan Province, Hainan Medical University, Haikou, China
| | - Ling Li
- Department of Pediatric Rehabilitation, Hainan Women and Children's Medical Center, Haikou, China
| | - Liyan Liu
- Department of Pediatric Rehabilitation, Hainan Women and Children's Medical Center, Haikou, China
| | - Wei Xiang
- National Health Commission (NHC) Key Laboratory of Control of Tropical Diseases, Hainan Medical University, Haikou, China
| | - Le Xiao
- Key Laboratory of Brain Science Research & Transformation in Tropical Environment of Hainan Province, Hainan Medical University, Haikou, China
- Department of Pediatric Rehabilitation, Hainan Women and Children's Medical Center, Haikou, China
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Vasilyev SA, Skryabin NA, Kashevarova AA, Tolmacheva EN, Savchenko RR, Vasilyeva OY, Lopatkina ME, Zarubin AA, Fishman VS, Belyaeva EO, Filippova MO, Shorina AR, Maslennikov AB, Shestovskikh OL, Gayner TA, Čulić V, Vulić R, Nazarenko LP, Lebedev IN. Differential DNA Methylation of the IMMP2L Gene in Families with Maternally Inherited 7q31.1 Microdeletions is Associated with Intellectual Disability and Developmental Delay. Cytogenet Genome Res 2021; 161:105-119. [PMID: 33849037 DOI: 10.1159/000514491] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/18/2021] [Indexed: 11/19/2022] Open
Abstract
Most copy number variations (CNVs) in the human genome display incomplete penetrance with unknown underlying mechanisms. One such mechanism may be epigenetic modification, particularly DNA methylation. The IMMP2L gene is located in a critical region for autism susceptibility on chromosome 7q (AUTS1). The level of DNA methylation was assessed by bisulfite sequencing of 87 CpG sites in the IMMP2L gene in 3 families with maternally inherited 7q31.1 microdeletions affecting the IMMP2L gene alone. Bisulfite sequencing revealed comparable levels of DNA methylation in the probands, healthy siblings without microdeletions, and their fathers. In contrast, a reduced DNA methylation index and increased IMMP2L expression were observed in lymphocytes from the healthy mothers compared with the probands. A number of genes were upregulated in the healthy mothers compared to controls and downregulated in probands compared to mothers. These genes were enriched in components of the ribosome and electron transport chain, as well as oxidative phosphorylation and various degenerative conditions. Differential expression in probands and mothers with IMMP2L deletions relative to controls may be due to compensatory processes in healthy mothers with IMMP2L deletions and disturbances of these processes in probands with intellectual disability. The results suggest a possible partial compensation for IMMP2L gene haploinsufficiency in healthy mothers with the 7q31.1 microdeletion by reducing the DNA methylation level. Differential DNA methylation of intragenic CpG sites may affect the phenotypic manifestation of CNVs and explain the incomplete penetrance of chromosomal microdeletions.
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Affiliation(s)
- Stanislav A Vasilyev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Nikolay A Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Anna A Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Ekaterina N Tolmacheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Renata R Savchenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Oksana Yu Vasilyeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Maria E Lopatkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Alexei A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Veniamin S Fishman
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russian Federation
| | - Elena O Belyaeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Miroslava O Filippova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Asia R Shorina
- Novosibirsk City Clinical Hospital, Novosibirsk, Russian Federation
| | | | | | - Tatyana A Gayner
- Group of Companies "Center of New Medical Technologies,", Novosibirsk, Russian Federation.,Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russian Federation
| | - Vida Čulić
- Gynecology and Obstetrics Private Outpatient Clinic, Split, Croatia
| | - Robert Vulić
- Gynecology and Obstetrics Private Outpatient Clinic, Split, Croatia
| | - Lyudmila P Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
| | - Igor N Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russian Federation
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Young KA, Biggins L, Sharpe HJ. Protein tyrosine phosphatases in cell adhesion. Biochem J 2021; 478:1061-1083. [PMID: 33710332 PMCID: PMC7959691 DOI: 10.1042/bcj20200511] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 02/07/2023]
Abstract
Adhesive structures between cells and with the surrounding matrix are essential for the development of multicellular organisms. In addition to providing mechanical integrity, they are key signalling centres providing feedback on the extracellular environment to the cell interior, and vice versa. During development, mitosis and repair, cell adhesions must undergo extensive remodelling. Post-translational modifications of proteins within these complexes serve as switches for activity. Tyrosine phosphorylation is an important modification in cell adhesion that is dynamically regulated by the protein tyrosine phosphatases (PTPs) and protein tyrosine kinases. Several PTPs are implicated in the assembly and maintenance of cell adhesions, however, their signalling functions remain poorly defined. The PTPs can act by directly dephosphorylating adhesive complex components or function as scaffolds. In this review, we will focus on human PTPs and discuss their individual roles in major adhesion complexes, as well as Hippo signalling. We have collated PTP interactome and cell adhesome datasets, which reveal extensive connections between PTPs and cell adhesions that are relatively unexplored. Finally, we reflect on the dysregulation of PTPs and cell adhesions in disease.
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Affiliation(s)
- Katherine A. Young
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Laura Biggins
- Bioinformatics, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Hayley J. Sharpe
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
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Salesse C, Charest J, Doucet-Beaupré H, Castonguay AM, Labrecque S, De Koninck P, Lévesque M. Opposite Control of Excitatory and Inhibitory Synapse Formation by Slitrk2 and Slitrk5 on Dopamine Neurons Modulates Hyperactivity Behavior. Cell Rep 2021; 30:2374-2386.e5. [PMID: 32075770 DOI: 10.1016/j.celrep.2020.01.084] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 12/03/2019] [Accepted: 01/24/2020] [Indexed: 11/26/2022] Open
Abstract
The neurodevelopmental origin of hyperactivity disorder has been suggested to involve the dopaminergic system, but the underlying mechanisms are still unknown. Here, transcription factors Lmx1a and Lmx1b are shown to be essential for midbrain dopaminergic (mDA) neuron excitatory synaptic inputs and dendritic development. Strikingly, conditional knockout (cKO) of Lmx1a/b in postmitotic mDA neurons results in marked hyperactivity. In seeking Lmx1a/b target genes, we identify positively regulated Slitrk2 and negatively regulated Slitrk5. These two synaptic adhesion proteins promote excitatory and inhibitory synapses on mDA neurons, respectively. Knocking down Slitrk2 reproduces some of the Lmx1a/b cKO cellular and behavioral phenotypes, whereas Slitrk5 knockdown has opposite effects. The hyperactivity caused by this imbalance in excitatory/inhibitory synaptic inputs on dopamine neurons is reproduced by chronically inhibiting the ventral tegmental area during development using pharmacogenetics. Our study shows that alterations in developing dopaminergic circuits strongly impact locomotor activity, shedding light on mechanisms causing hyperactivity behaviors.
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Affiliation(s)
- Charleen Salesse
- CERVO Brain Research Centre, 2601 de la Canardière, Québec, QC G1J 2G3, Canada
| | - Julien Charest
- CERVO Brain Research Centre, 2601 de la Canardière, Québec, QC G1J 2G3, Canada
| | | | | | - Simon Labrecque
- CERVO Brain Research Centre, 2601 de la Canardière, Québec, QC G1J 2G3, Canada
| | - Paul De Koninck
- CERVO Brain Research Centre, 2601 de la Canardière, Québec, QC G1J 2G3, Canada; Department of Biochemistry, Microbiology and Bioinformatics, Faculty of Science and Engineering, Université Laval, Québec, QC G1V 0A6, Canada
| | - Martin Lévesque
- CERVO Brain Research Centre, 2601 de la Canardière, Québec, QC G1J 2G3, Canada; Department of Psychiatry and Neuroscience, Faculty of Medicine, Université Laval, Québec, QC G1V 0A6, Canada.
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Levy G, Barak B. Postnatal therapeutic approaches in genetic neurodevelopmental disorders. Neural Regen Res 2021; 16:414-422. [PMID: 32985459 PMCID: PMC7996025 DOI: 10.4103/1673-5374.293133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 02/28/2020] [Accepted: 03/28/2020] [Indexed: 12/16/2022] Open
Abstract
Genetic neurodevelopmental disorders are characterized by abnormal neurophysiological and behavioral phenotypes, affecting individuals worldwide. While the subject has been heavily researched, current treatment options relate mostly to alleviating symptoms, rather than targeting the altered genome itself. In this review, we address the neurogenetic basis of neurodevelopmental disorders, genetic tools that are enabling precision research of these disorders in animal models, and postnatal gene-therapy approaches for neurodevelopmental disorders derived from preclinical studies in the laboratory.
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Affiliation(s)
- Gilad Levy
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Boaz Barak
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, Israel
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Abstract
Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.
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Affiliation(s)
- Juliann M. Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, United States
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Whole Exome Sequencing Reveals a Novel AUTS2 In-Frame Deletion in a Boy with Global Developmental Delay, Absent Speech, Dysmorphic Features, and Cerebral Anomalies. Genes (Basel) 2021; 12:genes12020229. [PMID: 33562463 PMCID: PMC7915150 DOI: 10.3390/genes12020229] [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] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 12/19/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are a group of highly prevalent, clinically and genetically heterogeneous pediatric disorders comprising, according to the Diagnostic and Statistical Manual of Mental Disorders 5th edition (DSM-V), intellectual disability, developmental delay, autism spectrum disorders, and other neurological and cognitive disorders manifesting in the developmental age. To date, more than 1000 genes have been implicated in the etiopathogenesis of NNDs. Among them, AUTS2 (OMIM # 607270) encodes a protein involved in neural migration and neuritogenesis, and causes NNDs with different molecular mechanisms including copy number variations, single or multiple exonic deletion and single nucleotide variants. We describes a 9-year-old boy with global developmental delay, absent speech, minor craniofacial anomalies, hypoplasia of the cerebellar vermis and thinning of the corpus callosum, resulted carrier of the de novo AUTS2 c.1603_1626del deletion at whole exome sequencing (WES) predicted to cause the loss of eight amino acids [p.(His535_Thr542del)]. Notably, our patient is the first reported so far in medical literature carrying an in-frame deletion and the first in which absent language, hypoplasia of the cerebellar vermis and thinning of the corpus callosum has been observed thus useful to expand the molecular spectrum of AUTS2 pathogenic variants and to broaden our knowledge on the clinical phenotype associated.
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Burton CL, Lemire M, Xiao B, Corfield EC, Erdman L, Bralten J, Poelmans G, Yu D, Shaheen SM, Goodale T, Sinopoli VM, Soreni N, Hanna GL, Fitzgerald KD, Rosenberg D, Nestadt G, Paterson AD, Strug LJ, Schachar RJ, Crosbie J, Arnold PD. Genome-wide association study of pediatric obsessive-compulsive traits: shared genetic risk between traits and disorder. Transl Psychiatry 2021; 11:91. [PMID: 33531474 PMCID: PMC7870035 DOI: 10.1038/s41398-020-01121-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 12/02/2022] Open
Abstract
Using a novel trait-based measure, we examined genetic variants associated with obsessive-compulsive (OC) traits and tested whether OC traits and obsessive-compulsive disorder (OCD) shared genetic risk. We conducted a genome-wide association analysis (GWAS) of OC traits using the Toronto Obsessive-Compulsive Scale (TOCS) in 5018 unrelated Caucasian children and adolescents from the community (Spit for Science sample). We tested the hypothesis that genetic variants associated with OC traits from the community would be associated with clinical OCD using a meta-analysis of all currently available OCD cases. Shared genetic risk was examined between OC traits and OCD in the respective samples using polygenic risk score and genetic correlation analyses. A locus tagged by rs7856850 in an intron of PTPRD (protein tyrosine phosphatase δ) was significantly associated with OC traits at the genome-wide significance level (p = 2.48 × 10-8). rs7856850 was also associated with OCD in a meta-analysis of OCD case/control genome-wide datasets (p = 0.0069). The direction of effect was the same as in the community sample. Polygenic risk scores from OC traits were significantly associated with OCD in case/control datasets and vice versa (p's < 0.01). OC traits were highly, but not significantly, genetically correlated with OCD (rg = 0.71, p = 0.062). We report the first validated genome-wide significant variant for OC traits in PTPRD, downstream of the most significant locus in a previous OCD GWAS. OC traits measured in the community sample shared genetic risk with OCD case/control status. Our results demonstrate the feasibility and power of using trait-based approaches in community samples for genetic discovery.
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Affiliation(s)
| | | | - Bowei Xiao
- Genetics and Genome Biology Hospital for Sick Children, Toronto, Canada
| | | | - Lauren Erdman
- Genetics and Genome Biology Hospital for Sick Children, Toronto, Canada
| | - Janita Bralten
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Dongmei Yu
- The Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- The Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - S-M Shaheen
- The Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Calgary, Canada
- Departments of Psychiatry and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Tara Goodale
- Neurosciences and Mental Health, Toronto, Canada
| | - Vanessa M Sinopoli
- Genetics and Genome Biology Hospital for Sick Children, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Noam Soreni
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Ontario, Canada
| | - Gregory L Hanna
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Kate D Fitzgerald
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - David Rosenberg
- Department of Psychiatry and Behavioural Neurosciences, Wayne State University, Detroit, MI, USA
| | - Gerald Nestadt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew D Paterson
- Genetics and Genome Biology Hospital for Sick Children, Toronto, Canada
- Divisions of Epidemiology and Biostatistics, Dalla Lana School of Public Health, Toronto, Canada
| | - Lisa J Strug
- Genetics and Genome Biology Hospital for Sick Children, Toronto, Canada
- Department of Statistical Sciences, Faculty of Arts and Science, Toronto, Canada
| | - Russell J Schachar
- Neurosciences and Mental Health, Toronto, Canada
- Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Jennifer Crosbie
- Neurosciences and Mental Health, Toronto, Canada
- Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Paul D Arnold
- Genetics and Genome Biology Hospital for Sick Children, Toronto, Canada
- The Mathison Centre for Mental Health Research and Education, Hotchkiss Brain Institute, Calgary, Canada
- Departments of Psychiatry and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, Canada
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AUTS2 isoforms control neuronal differentiation. Mol Psychiatry 2021; 26:666-681. [PMID: 30953002 DOI: 10.1038/s41380-019-0409-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 01/07/2023]
Abstract
Mutations in AUTS2 are associated with autism, intellectual disability, and microcephaly. AUTS2 is expressed in the brain and interacts with polycomb proteins, yet it is still unclear how mutations in AUTS2 lead to neurodevelopmental phenotypes. Here we report that when neuronal differentiation is initiated, there is a shift in expression from a long isoform to a short AUTS2 isoform. Yeast two-hybrid screen identified the splicing factor SF3B1 as an interactor of both isoforms, whereas the polycomb group proteins, PCGF3 and PCGF5, were found to interact exclusively with the long AUTS2 isoform. Reporter assays showed that the first exons of the long AUTS2 isoform function as a transcription repressor, but the part that consist of the short isoform acts as a transcriptional activator, both influenced by the cellular context. The expression levels of PCGF3 influenced the ability of the long AUTS2 isoform to activate or repress transcription. Mouse embryonic stem cells (mESCs) with heterozygote mutations in Auts2 had an increase in cell death during in vitro corticogenesis, which was significantly rescued by overexpressing the human AUTS2 transcripts. mESCs with a truncated AUTS2 protein (missing exons 12-20) showed premature neuronal differentiation, whereas cells overexpressing AUTS2, especially the long transcript, showed increase in expression of pluripotency markers and delayed differentiation. Taken together, our data suggest that the precise expression of AUTS2 isoforms is essential for regulating transcription and the timing of neuronal differentiation.
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Integrative analysis of genome-wide association studies identifies novel loci associated with neuropsychiatric disorders. Transl Psychiatry 2021; 11:69. [PMID: 33479212 PMCID: PMC7820351 DOI: 10.1038/s41398-020-01195-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 01/30/2023] Open
Abstract
Neuropsychiatric disorders, such as autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), schizophrenia (SCZ), bipolar disorder (BIP), and major depressive disorder (MDD) share common clinical presentations, suggesting etiologic overlap. A substantial proportion of SNP-based heritability for neuropsychiatric disorders is attributable to genetic components, and genome-wide association studies (GWASs) focusing on individual diseases have identified multiple genetic loci shared between these diseases. Here, we aimed at identifying novel genetic loci associated with individual neuropsychiatric diseases and genetic loci shared by neuropsychiatric diseases. We performed multi-trait joint analyses and meta-analysis across five neuropsychiatric disorders based on their summary statistics from the Psychiatric Genomics Consortium (PGC), and further carried out a replication study of ADHD among 2726 cases and 16299 controls in an independent pediatric cohort. In the multi-trait joint analyses, we found five novel genome-wide significant loci for ADHD, one novel locus for BIP, and ten novel loci for MDD. We further achieved modest replication in our independent pediatric dataset. We conducted fine-mapping and functional annotation through an integrative multi-omics approach and identified causal variants and potential target genes at each novel locus. Gene expression profile and gene-set enrichment analysis further suggested early developmental stage expression pattern and postsynaptic membrane compartment enrichment of candidate genes at the genome-wide significant loci of these neuropsychiatric disorders. Therefore, through a multi-omics approach, we identified novel genetic loci associated with the five neuropsychiatric disorders which may help to better understand the underlying molecular mechanism of neuropsychiatric diseases.
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Takeda K, Watanabe T, Oyabu K, Tsukamoto S, Oba Y, Nakano T, Kubota K, Katsurabayashi S, Iwasaki K. Valproic acid-exposed astrocytes impair inhibitory synapse formation and function. Sci Rep 2021; 11:23. [PMID: 33420078 PMCID: PMC7794250 DOI: 10.1038/s41598-020-79520-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Valproic acid (VPA) is widely prescribed to treat epilepsy. Maternal VPA use is, however, clinically restricted because of the severe risk that VPA may cause neurodevelopmental disorders in offspring, such as autism spectrum disorder. Understanding the negative action of VPA may help to prevent VPA-induced neurodevelopmental disorders. Astrocytes play a vital role in neurodevelopment and synapse function; however, the impact of VPA on astrocyte involvement in neurodevelopment and synapse function has not been examined. In this study, we examined whether exposure of cultured astrocytes to VPA alters neuronal morphology and synapse function of co-cultured neurons. We show that synaptic transmission by inhibitory neurons was small because VPA-exposed astrocytes reduced the number of inhibitory synapses. However, synaptic transmission by excitatory neurons and the number of excitatory synapses were normal with VPA-exposed astrocytes. VPA-exposed astrocytes did not affect the morphology of inhibitory neurons. These data indicate that VPA-exposed astrocytes impair synaptogenesis specifically of inhibitory neurons. Our results indicate that maternal use of VPA would affect not only neurons but also astrocytes and would result in perturbed astrocyte-mediated neurodevelopment.
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Affiliation(s)
- Kotomi Takeda
- Department of Neuropharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Takuya Watanabe
- Department of Neuropharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, 814-0180, Japan. .,A.I.G. Collaborative Research Institute for Aging and Brain Sciences, Fukuoka University, Fukuoka, 814-0180, Japan.
| | - Kohei Oyabu
- Department of Neuropharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Shuntaro Tsukamoto
- Department of Neuropharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Yuki Oba
- Department of Neuropharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Takafumi Nakano
- Department of Pharmaceutical and Health Care Management, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Kaori Kubota
- Department of Neuropharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, 814-0180, Japan.,A.I.G. Collaborative Research Institute for Aging and Brain Sciences, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Shutaro Katsurabayashi
- Department of Neuropharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, 814-0180, Japan
| | - Katsunori Iwasaki
- Department of Neuropharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, 814-0180, Japan.,A.I.G. Collaborative Research Institute for Aging and Brain Sciences, Fukuoka University, Fukuoka, 814-0180, Japan
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Tomita H, Cornejo F, Aranda-Pino B, Woodard CL, Rioseco CC, Neel BG, Alvarez AR, Kaplan DR, Miller FD, Cancino GI. The Protein Tyrosine Phosphatase Receptor Delta Regulates Developmental Neurogenesis. Cell Rep 2021; 30:215-228.e5. [PMID: 31914388 DOI: 10.1016/j.celrep.2019.11.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 10/10/2019] [Accepted: 11/07/2019] [Indexed: 12/26/2022] Open
Abstract
PTPRD is a receptor protein tyrosine phosphatase that is genetically associated with neurodevelopmental disorders. Here, we asked whether Ptprd mutations cause aberrant neural development by perturbing neurogenesis in the murine cortex. We show that loss of Ptprd causes increases in neurogenic transit-amplifying intermediate progenitor cells and cortical neurons and perturbations in neuronal localization. These effects are intrinsic to neural precursor cells since acute Ptprd knockdown causes similar perturbations. PTPRD mediates these effects by dephosphorylating receptor tyrosine kinases, including TrkB and PDGFRβ, and loss of Ptprd causes the hyperactivation of TrkB and PDGFRβ and their downstream MEK-ERK signaling pathway in neural precursor cells. Moreover, inhibition of aberrant TrkB or MEK activation rescues the increased neurogenesis caused by knockdown or homozygous loss of Ptprd. These results suggest that PTPRD regulates receptor tyrosine kinases to ensure appropriate numbers of intermediate progenitor cells and neurons, suggesting a mechanism for its genetic association with neurodevelopmental disorders.
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Affiliation(s)
- Hideaki Tomita
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto M5G 1X8, ON, Canada
| | - Francisca Cornejo
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Begoña Aranda-Pino
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - Cameron L Woodard
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto M5G 1X8, ON, Canada
| | - Constanza C Rioseco
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto M5G 1X8, ON, Canada
| | - Benjamin G Neel
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016, USA
| | - Alejandra R Alvarez
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
| | - David R Kaplan
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto M5G 1X8, ON, Canada; Institute of Medical Science, University of Toronto, Toronto M5S 1A8, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, ON, Canada
| | - Freda D Miller
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto M5G 1X8, ON, Canada; Institute of Medical Science, University of Toronto, Toronto M5S 1A8, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, ON, Canada; Department of Physiology, University of Toronto, Toronto M5S 1A8, ON, Canada
| | - Gonzalo I Cancino
- Program in Neurosciences and Mental Health, Hospital for Sick Children, Toronto M5G 1X8, ON, Canada; Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile.
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