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Bucknor EMV, Johnson E, Efthymiou S, Alvi JR, Sultan T, Houlden H, Maroofian R, Karimiani EG, Finelli MJ, Oliver PL. Neuroinflammation and Lysosomal Abnormalities Characterise the Essential Role for Oxidation Resistance 1 in the Developing and Adult Cerebellum. Antioxidants (Basel) 2024; 13:685. [PMID: 38929124 PMCID: PMC11201099 DOI: 10.3390/antiox13060685] [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: 04/23/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Loss-of-function mutations in the TLDc family of proteins cause a range of severe childhood-onset neurological disorders with common clinical features that include cerebellar neurodegeneration, ataxia and epilepsy. Of these proteins, oxidation resistance 1 (OXR1) has been implicated in multiple cellular pathways related to antioxidant function, transcriptional regulation and cellular survival; yet how this relates to the specific neuropathological features in disease remains unclear. Here, we investigate a range of loss-of-function mouse model systems and reveal that constitutive deletion of Oxr1 leads to a rapid and striking neuroinflammatory response prior to neurodegeneration that is associated with lysosomal pathology. We go on to show that neuroinflammation and cell death in Oxr1 knockouts can be completely rescued by the neuronal expression of Oxr1, suggesting that the phenotype is driven by the cell-intrinsic defects of neuronal cells lacking the gene. Next, we generate a ubiquitous, adult inducible knockout of Oxr1 that surprisingly displays rapid-onset ataxia and cerebellar neurodegeneration, establishing for the first time that the distinctive pathology associated with the loss of Oxr1 occurs irrespective of developmental stage. Finally, we describe two new homozygous human pathogenic variants in OXR1 that cause neurodevelopmental delay, including a novel stop-gain mutation. We also compare functionally two missense human pathogenic mutations in OXR1, including one newly described here, that cause different clinical phenotypes but demonstrate partially retained neuroprotective activity against oxidative stress. Together, these data highlight the essential role of Oxr1 in modulating neuroinflammatory and lysosomal pathways in the mammalian brain and support the hypothesis that OXR1 protein dosage may be critical for pathological outcomes in disease.
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Affiliation(s)
- Eboni M. V. Bucknor
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Errin Johnson
- The Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1B 5EE, UK
| | - Javeria R. Alvi
- Department of Pediatric Neurology, Children Hospital, University of Child Health Sciences, Lahore 54660, Pakistan
| | - Tipu Sultan
- Department of Pediatric Neurology, Children Hospital, University of Child Health Sciences, Lahore 54660, Pakistan
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1B 5EE, UK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1B 5EE, UK
| | - Ehsan G. Karimiani
- Molecular and Clinical Sciences Institute, St. George’s University of London, Cranmer Terrace, London SW18 0RE, UK
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad 009851, Iran
| | - Mattéa J. Finelli
- School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK
| | - Peter L. Oliver
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
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Yahia A, Li D, Lejerkrans S, Rajagopalan S, Kalnak N, Tammimies K. Whole exome sequencing and polygenic assessment of a Swedish cohort with severe developmental language disorder. Hum Genet 2024; 143:169-183. [PMID: 38300321 PMCID: PMC10881898 DOI: 10.1007/s00439-023-02636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
Developmental language disorder (DLD) overlaps clinically, genetically, and pathologically with other neurodevelopmental disorders (NDD), corroborating the concept of the NDD continuum. There is a lack of studies to understand the whole genetic spectrum in individuals with DLD. Previously, we recruited 61 probands with severe DLD from 59 families and examined 59 of them and their families using microarray genotyping with a 6.8% diagnostic yield. Herein, we investigated 53 of those probands using whole exome sequencing (WES). Additionally, we used polygenic risk scores (PRS) to understand the within family enrichment of neurodevelopmental difficulties and examine the associations between the results of language-related tests in the probands and language-related PRS. We identified clinically significant variants in four probands, resulting in a 7.5% (4/53) molecular diagnostic yield. Those variants were in PAK2, MED13, PLCB4, and TNRC6B. We also prioritized additional variants for future studies for their role in DLD, including high-impact variants in PARD3 and DIP2C. PRS did not explain the aggregation of neurodevelopmental difficulties in these families. We did not detect significant associations between the language-related tests and language-related PRS. Our results support using WES as the first-tier genetic test for DLD as it can identify monogenic DLD forms. Large-scale sequencing studies for DLD are needed to identify new genes and investigate the polygenic contribution to the condition.
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Affiliation(s)
- Ashraf Yahia
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Danyang Li
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Sanna Lejerkrans
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Shyam Rajagopalan
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Nelli Kalnak
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Department of Speech-Language Pathology, Helsingborg Hospital, Helsingborg, Sweden
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden.
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van Wijngaarden V, de Wilde H, Mink van der Molen D, Petter J, Stegeman I, Gerrits E, Smit AL, van den Boogaard MJ. Genetic outcomes in children with developmental language disorder: a systematic review. Front Pediatr 2024; 12:1315229. [PMID: 38298611 PMCID: PMC10828955 DOI: 10.3389/fped.2024.1315229] [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: 10/10/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
Introduction Developmental language disorder (DLD) is a common childhood condition negatively influencing communication and psychosocial development. An increasing number of pathogenic variants or chromosomal anomalies possibly related to DLD have been identified. To provide a base for accurate clinical genetic diagnostic work-up for DLD patients, understanding the specific genetic background is crucial. This study aims to give a systematic literature overview of pathogenic variants or chromosomal anomalies causative for DLD in children. Methods We conducted a systematic search in PubMed and Embase on available literature related to the genetic background of diagnosed DLD in children. Included papers were critically appraised before data extraction. An additional search in OMIM was performed to see if the described DLD genes are associated with a broader clinical spectrum. Results The search resulted in 15,842 papers. After assessing eligibility, 47 studies remained, of which 25 studies related to sex chromosome aneuploidies and 15 papers concerned other chromosomal anomalies (SCAs) and/or Copy Number Variants (CNVs), including del15q13.1-13.3 and del16p11.2. The remaining 7 studies displayed a variety of gene variants. 45 (candidate) genes related to language development, including FOXP2, GRIN2A, ERC1, and ATP2C2. After an additional search in the OMIM database, 22 of these genes were associated with a genetic disorder with a broader clinical spectrum, including intellectual disability, epilepsy, and/or autism. Conclusion Our study illustrates that DLD can be related to SCAs and specific CNV's. The reported (candidate) genes (n = 45) in the latter category reflect the genetic heterogeneity and support DLD without any comorbidities and syndromic language disorder have an overlapping genetic etiology.
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Affiliation(s)
| | - Hester de Wilde
- Department of Pediatric Otorhinolaryngology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Jildo Petter
- Faculty of Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Inge Stegeman
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Utrecht, Utrecht, Netherlands
- Brain Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ellen Gerrits
- Research Group Speech and Language Therapy, HU University of Applied Sciences Utrecht, Utrecht, Netherlands
- Department of Languages, Literature and Communication, Faculty of Humanities, Utrecht University, Utrecht, Netherlands
| | - Adriana L. Smit
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Utrecht, Utrecht, Netherlands
- Research Group Speech and Language Therapy, HU University of Applied Sciences Utrecht, Utrecht, Netherlands
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Espinosa-Mojica AA, Varo Varo C. Determining the Linguistic Profile of Children With Rare Genetic Disorders. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2024; 67:170-186. [PMID: 38085694 DOI: 10.1044/2023_jslhr-23-00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
PURPOSE Language studies on populations with rare genetic disorders are limited. Hence, there is little data on commonly found or expected developmental linguistic traits and cognitive mechanisms that may be impaired. Based on the hypothesis that there is a close connection between language and cognition and the relevance of specific genetic changes in the development of each, our goal was to provide linguistic data on relationships with other executive functioning mechanisms. METHOD This study assessed language skills, communicative behaviors, and executive functions in four children, aged 7-9 years, with rare genetic disorders, using standardized protocols and tests. RESULTS The findings revealed different levels of language impairment and executive functioning problems in each case. The overall executive function index performance for each of the four cases studied was clinically significantly high, indicating executive dysfunction. CONCLUSIONS The cases analyzed illustrate different types of atypical development that affect both language and other cognitive mechanisms and underscore the importance of executive skills and the various ways in which they are involved in diverse levels of language that might be affected to a greater or lesser degree in rare genetic disorders. In conclusion, we found that language dysfunction is a salient feature of the rare genetic disorders included in our study, although this is not necessarily true for all genetic disorders. Along with these conclusive results, we performed a qualitative analysis of the linguistic and cognitive components that enable functional communication in order to allow optimal interpretation of the data we have collected, laying the foundations for a more effective therapeutic approach.
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Boerma T, Ter Haar S, Ganga R, Wijnen F, Blom E, Wierenga CJ. What risk factors for Developmental Language Disorder can tell us about the neurobiological mechanisms of language development. Neurosci Biobehav Rev 2023; 154:105398. [PMID: 37741516 DOI: 10.1016/j.neubiorev.2023.105398] [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: 04/21/2023] [Revised: 07/03/2023] [Accepted: 09/17/2023] [Indexed: 09/25/2023]
Abstract
Language is a complex multidimensional cognitive system that is connected to many neurocognitive capacities. The development of language is therefore strongly intertwined with the development of these capacities and their neurobiological substrates. Consequently, language problems, for example those of children with Developmental Language Disorder (DLD), are explained by a variety of etiological pathways and each of these pathways will be associated with specific risk factors. In this review, we attempt to link previously described factors that may interfere with language development to putative underlying neurobiological mechanisms of language development, hoping to uncover openings for future therapeutical approaches or interventions that can help children to optimally develop their language skills.
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Affiliation(s)
- Tessel Boerma
- Institute for Language Sciences, Department of Languages, Literature and Communication, Utrecht University, Utrecht, the Netherlands
| | - Sita Ter Haar
- Institute for Language Sciences, Department of Languages, Literature and Communication, Utrecht University, Utrecht, the Netherlands; Cognitive Neurobiology and Helmholtz Institute, Department of Psychology, Utrecht University/Translational Neuroscience, University Medical Center Utrecht, the Netherlands
| | - Rachida Ganga
- Institute for Language Sciences, Department of Languages, Literature and Communication, Utrecht University, Utrecht, the Netherlands
| | - Frank Wijnen
- Institute for Language Sciences, Department of Languages, Literature and Communication, Utrecht University, Utrecht, the Netherlands
| | - Elma Blom
- Department of Development and Education of youth in Diverse Societies (DEEDS), Utrecht University, Utrecht, the Netherlands; Department of Language and Culture, The Arctic University of Norway UiT, Tromsø, Norway.
| | - Corette J Wierenga
- Biology Department, Faculty of Science, Utrecht University, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands.
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Nudel R, Christensen RV, Kalnak N, Schwinn M, Banasik K, Dinh KM, Erikstrup C, Pedersen OB, Burgdorf KS, Ullum H, Ostrowski SR, Hansen TF, Werge T. Developmental language disorder - a comprehensive study of more than 46,000 individuals. Psychiatry Res 2023; 323:115171. [PMID: 36963307 DOI: 10.1016/j.psychres.2023.115171] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/16/2023] [Accepted: 03/14/2023] [Indexed: 03/26/2023]
Abstract
Developmental language disorder (DLD) is characterized by enduring low language abilities with a significant functional impact, in the absence of biomedical conditions in which language impairment is part of a complex of impairments. There is a lack of awareness of DLD even among healthcare professionals. Here we estimated the prevalence of DLD and its links to reading and learning difficulties and physical and mental health in the Danish Blood Donor Study (N = 46,547), where DLD-related information is based on questionnaires (self-report). We compared the questionnaire-derived DLD status with the relevant language-related diagnoses from hospital registers. We also investigated the genetic architecture of DLD in a subset of the cohort (N = 18,380). DLD was significantly associated with reading and learning difficulties and poorer mental and physical health. DLD prevalence was 3.36%-3.70% based on questionnaires, compared with 0.04% in hospital registers. Our genetic analyses identified one genome-wide significant locus, but not a significant heritability estimate. Our study shows that DLD has health-related implications that may last into adulthood, and that DLD may be undiagnosed in general healthcare. Furthermore, DLD is likely more genetically heterogeneous than narrower developmental language phenotypes. Our results emphasize the need to raise awareness of DLD and consider criteria for molecular studies of DLD to reduce case heterogeneity.
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Affiliation(s)
- Ron Nudel
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark.
| | - Rikke Vang Christensen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Emil Holms Kanal 2, Copenhagen 2300, Denmark.
| | - Nelli Kalnak
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden; Department of Speech-Language Pathology, Helsingborg Hospital, Helsingborg, Sweden.
| | - Michael Schwinn
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Karina Banasik
- Novo Nordisk foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Khoa Manh Dinh
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ole Birger Pedersen
- Department of Immunology, Næstved Hospital, Næstved, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer Sølvsten Burgdorf
- Department of Immunology, Rigshospitalet, Copenhagen, Denmark; Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Folkmann Hansen
- Novo Nordisk foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Danish Headache Center, Rigshospitalet Glostrup, Glostrup, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Institute of Biological Psychiatry, Roskilde, Denmark
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Benítez-Burraco A, Jiménez-Romero MS, Fernández-Urquiza M. Delving into the Genetic Causes of Language Impairment in a Case of Partial Deletion of NRXN1. Mol Syndromol 2023; 13:496-510. [PMID: 36660026 PMCID: PMC9843585 DOI: 10.1159/000524710] [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: 02/19/2022] [Accepted: 04/22/2022] [Indexed: 01/22/2023] Open
Abstract
Introduction Copy-number variations (CNVs) impacting on small DNA stretches and associated with language deficits provide a unique window to the role played by specific genes in language function. Methods We report in detail on the cognitive, language, and genetic features of a girl bearing a small deletion (0.186 Mb) in the 2p16.3 region, arr[hg19] 2p16.3(50761778_50947729)×1, affecting exons 3-7 of NRXN1, a neurexin-coding gene previously related to schizophrenia, autism (ASD), attention deficit hyperactivity disorder (ADHD), mood disorder, and intellectual disability (ID). Results The proband exhibits many of the features commonly found in subjects with deletions of NRXN1, like ASD-like traits (including ritualized behaviors, disordered sensory aspects, social disturbances, and impaired theory of mind), ADHD symptoms, moderate ID, and impaired speech and language. Regarding this latter aspect, we observed altered speech production, underdeveloped phonological awareness, minimal syntax, serious shortage of active vocabulary, impaired receptive language, and inappropriate pragmatic behavior (including lack of metapragmatic awareness and communicative use of gaze). Microarray analyses point to the dysregulation of several genes important for language function in the girl compared to her healthy parents. Discussion Although some basic cognitive deficit - such as the impairment of executive function - might contribute to the language problems exhibited by the proband, molecular evidence suggests that they might result, to a great extent, from the abnormal expression of genes directly related to language.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), University of Seville, Seville, Spain,*Antonio Benítez-Burraco,
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An Alzheimer’s Disease Patient-Derived Olfactory Stem Cell Model Identifies Gene Expression Changes Associated with Cognition. Cells 2022; 11:cells11203258. [PMID: 36291125 PMCID: PMC9601087 DOI: 10.3390/cells11203258] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
An early symptom of Alzheimer’s disease (AD) is an impaired sense of smell, for which the molecular basis remains elusive. Here, we generated human olfactory neurosphere-derived (ONS) cells from people with AD and mild cognitive impairment (MCI), and performed global RNA sequencing to determine gene expression changes. ONS cells expressed markers of neuroglial differentiation, providing a unique cellular model to explore changes of early AD-associated pathways. Our transcriptomics data from ONS cells revealed differentially expressed genes (DEGs) associated with cognitive processes in AD cells compared to MCI, or matched healthy controls (HC). A-Kinase Anchoring Protein 6 (AKAP6) was the most significantly altered gene in AD compared to both MCI and HC, and has been linked to cognitive function. The greatest change in gene expression of all DEGs occurred between AD and MCI. Gene pathway analysis revealed defects in multiple cellular processes with aging, intellectual deficiency and alternative splicing being the most significantly dysregulated in AD ONS cells. Our results demonstrate that ONS cells can provide a cellular model for AD that recapitulates disease-associated differences. We have revealed potential novel genes, including AKAP6 that may have a role in AD, particularly MCI to AD transition, and should be further examined.
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Li Y, Sun Y, Liu Y, Wang B, Li J, Wang H, Zhang H, Wang X, Han X, Lin Q, Zhou Y, Hu L, Song Y, Bao J, Gong L, Sun M, Yuan X, Zhang X, Lian M, Xiao X, Miao Q, Wang Q, Li KK, Du S, Ma A, Li Y, Xu J, Tang S, Shi J, Xu Y, Yang L, Zhang J, Huang Z, Zhou L, Cui Y, Seldin MF, Gershwin ME, Yan H, Zou Z, Zuo X, Tang R, Ma X. Genome-wide meta-analysis identifies susceptibility loci for autoimmune hepatitis type 1. Hepatology 2022; 76:564-575. [PMID: 35184318 DOI: 10.1002/hep.32417] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/10/2022] [Accepted: 02/16/2022] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS Autoimmune hepatitis (AIH) is a rare and chronic autoimmune liver disease. While genetic factors are believed to play a crucial role in the etiopathogenesis of AIH, our understanding of these genetic risk factors is still limited. In this study, we aimed to identify susceptibility loci to further understand the pathogenesis of this disease. APPROACH AND RESULTS We conducted a case-control association study of 1,622 Chinese patients with AIH type 1 and 10,466 population controls from two independent cohorts. A meta-analysis was performed to ascertain variants associated with AIH type 1. A single-nucleotide polymorphism within the human leukocyte antigen (HLA) region showed the strongest association with AIH (rs6932730: OR = 2.32; p = 9.21 × 10-73 ). The meta-analysis also identified two non-HLA loci significantly associated with AIH: CD28/CTLA4/ICOS on 2q33.3 (rs72929257: OR = 1.31; p = 2.92 × 10-9 ) and SYNPR on 3p14.2 (rs6809477: OR = 1.25; p = 5.48 × 10-9 ). In silico annotation, reporter gene assays, and CRISPR activation experiments identified a distal enhancer at 2q33.3 that regulated expression of CTLA4. In addition, variants near STAT1/STAT4 (rs11889341: OR = 1.24; p = 1.34 × 10-7 ), LINC00392 (rs9564997: OR = 0.81; p = 2.53 × 10-7 ), IRF8 (rs11117432: OR = 0.72; p = 6.10 × 10-6 ), and LILRA4/LILRA5 (rs11084330: OR = 0.65; p = 5.19 × 10-6 ) had suggestive association signals with AIH. CONCLUSIONS Our study identifies two novel loci (CD28/CTLA4/ICOS and SYNPR) exceeding genome-wide significance and suggests four loci as potential risk factors. These findings highlight the importance of costimulatory signaling and neuro-immune interaction in the pathogenesis of AIH.
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Affiliation(s)
- You Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Ying Sun
- Department of Liver Disease, Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Yanmin Liu
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Jia Li
- Tianjin Second People's Hospital, Tianjin Institute of Hepatology, Tianjin, China
| | - Hanxiao Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Haiping Zhang
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xiaoyi Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Xu Han
- Tianjin Second People's Hospital, Tianjin Institute of Hepatology, Tianjin, China
| | - Qiuxiang Lin
- Department of Hepatology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Yang Zhou
- Department of Hepatology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Lilin Hu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhu Song
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Bao
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ling Gong
- Department of Hepatology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Mengying Sun
- Department of Gastroenterology, The General Hospital of Western Theater Command, Chengdu, China
| | - Xiaoling Yuan
- Department of Infectious Disease, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinhe Zhang
- Department of Gastroenterology, First Affiliated Hospital of China Medical University, ShenYang, China
| | - Min Lian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Xiao Xiao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qi Miao
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Qixia Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Ke-Ke Li
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China.,Graduate School, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Shiyu Du
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Anlin Ma
- Department of infection disease, China-Japan Friendship Hospital, Beijing, China
| | - Yiling Li
- Department of Gastroenterology, First Affiliated Hospital of China Medical University, ShenYang, China
| | - Jie Xu
- Department of Infectious Disease, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shanhong Tang
- Department of Gastroenterology, The General Hospital of Western Theater Command, Chengdu, China
| | - Junping Shi
- Department of Hepatology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Yun Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ling Yang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiming Zhang
- Department of Infectious Diseases, Huashan Hospital and Key Laboratory of Medical Molecular Virology (MOH & MOE), Shanghai Medical College, Fudan University, Shanghai, China
| | - Zuxiong Huang
- Department of Hepatology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Lu Zhou
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, Tianjin, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China.,Graduate School, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Michael F Seldin
- Division of Rheumatology, Department of Medicine, Allergy and Clinical Immunology, University of California at Davis, Davis, California, USA.,Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, California, USA
| | - M Eric Gershwin
- Division of Rheumatology, Department of Medicine, Allergy and Clinical Immunology, University of California at Davis, Davis, California, USA
| | - Huiping Yan
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Zhengsheng Zou
- Department of Liver Disease, Senior Department of Hepatology, The Fifth Medical Center of PLA General Hospital, Beijing, China
| | - Xianbo Zuo
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China.,Institute of Dermatology and Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Department of Pharmacy, China-Japan Friendship Hospital, Beijing, China
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University; Shanghai Institute of Digestive Disease, Shanghai, China
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10
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Mountford HS, Braden R, Newbury DF, Morgan AT. The Genetic and Molecular Basis of Developmental Language Disorder: A Review. CHILDREN (BASEL, SWITZERLAND) 2022; 9:children9050586. [PMID: 35626763 PMCID: PMC9139417 DOI: 10.3390/children9050586] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 04/12/2022] [Indexed: 01/05/2023]
Abstract
Language disorders are highly heritable and are influenced by complex interactions between genetic and environmental factors. Despite more than twenty years of research, we still lack critical understanding of the biological underpinnings of language. This review provides an overview of the genetic landscape of developmental language disorders (DLD), with an emphasis on the importance of defining the specific features (the phenotype) of DLD to inform gene discovery. We review the specific phenotype of DLD in the genetic literature, and the influence of historic variation in diagnostic inclusion criteria on researchers' ability to compare and replicate genotype-phenotype studies. This review provides an overview of the recently identified gene pathways in populations with DLD and explores current state-of-the-art approaches to genetic analysis based on the hypothesised architecture of DLD. We will show how recent global efforts to unify diagnostic criteria have vastly increased sample size and allow for large multi-cohort metanalyses, leading the identification of a growing number of contributory loci. We emphasise the important role of estimating the genetic architecture of DLD to decipher underlying genetic associations. Finally, we explore the potential for epigenetics and environmental interactions to further unravel the biological basis of language disorders.
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Affiliation(s)
- Hayley S. Mountford
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (H.S.M.); (D.F.N.)
| | - Ruth Braden
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne 3052, Australia;
| | - Dianne F. Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (H.S.M.); (D.F.N.)
| | - Angela T. Morgan
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne 3052, Australia;
- Correspondence:
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11
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Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex. Brain Sci 2021; 12:brainsci12010047. [PMID: 35053791 PMCID: PMC8773923 DOI: 10.3390/brainsci12010047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/18/2021] [Accepted: 12/27/2021] [Indexed: 12/12/2022] Open
Abstract
Specific language impairment (SLI) is a common neurodevelopmental disorder (NDD) that displays high heritability estimates. Genetic studies have identified several loci, but the molecular basis of SLI remains unclear. With the aim to better understand the genetic architecture of SLI, we performed whole-exome sequencing (WES) in a single family (ID: 489; n = 11). We identified co-segregating rare variants in three new genes: BUD13, APLP2, and NDRG2. To determine the significance of these genes in SLI, we Sanger sequenced all coding regions of each gene in unrelated individuals with SLI (n = 175). We observed 13 additional rare variants in 18 unrelated individuals. Variants in BUD13 reached genome-wide significance (p-value < 0.01) upon comparison with similar variants in the 1000 Genomes Project, providing gene level evidence that BUD13 is involved in SLI. Additionally, five BUD13 variants showed cohesive variant level evidence of likely pathogenicity. Bud13 is a component of the retention and splicing (RES) complex. Additional supportive evidence from studies of an animal model (loss-of-function mutations in BUD13 caused a profound neural phenotype) and individuals with an NDD phenotype (carrying a CNV spanning BUD13), indicates BUD13 could be a target for investigation of the neural basis of language.
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12
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Nudel R, Appadurai V, Buil A, Nordentoft M, Werge T. Pleiotropy between language impairment and broader behavioral disorders-an investigation of both common and rare genetic variants. J Neurodev Disord 2021; 13:54. [PMID: 34773992 PMCID: PMC8590378 DOI: 10.1186/s11689-021-09403-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Language plays a major role in human behavior. For this reason, neurodevelopmental and psychiatric disorders in which linguistic ability is impaired could have a big impact on the individual's social interaction and general wellbeing. Such disorders tend to have a strong genetic component, but most past studies examined mostly the linguistic overlaps across these disorders; investigations into their genetic overlaps are limited. The aim of this study was to assess the potential genetic overlap between language impairment and broader behavioral disorders employing methods capturing both common and rare genetic variants. METHODS We employ polygenic risk scores (PRS) trained on specific language impairment (SLI) to evaluate genetic overlap across several disorders in a large case-cohort sample comprising ~13,000 autism spectrum disorder (ASD) cases, including cases of childhood autism and Asperger's syndrome, ~15,000 attention deficit/hyperactivity disorder (ADHD) cases, ~3000 schizophrenia cases, and ~21,000 population controls. We also examine rare variants in SLI/language-related genes in a subset of the sample that was exome-sequenced using the SKAT-O method. RESULTS We find that there is little evidence for genetic overlap between SLI and ADHD, schizophrenia, and ASD, the latter being in line with results of linguistic analyses in past studies. However, we observe a small, significant genetic overlap between SLI and childhood autism specifically, which we do not observe for SLI and Asperger's syndrome. Moreover, we observe that childhood autism cases have significantly higher SLI-trained PRS compared to Asperger's syndrome cases; these results correspond well to the linguistic profiles of both disorders. Our rare variant analyses provide suggestive evidence of association for specific genes with ASD, childhood autism, and schizophrenia. CONCLUSIONS Our study provides, for the first time, to our knowledge, genetic evidence for ASD subtypes based on risk variants for language impairment.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
| | - Vivek Appadurai
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Alfonso Buil
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
| | - Merete Nordentoft
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- CORE - Copenhagen Research Centre for Mental Health, Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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13
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Soteros BM, Sia GM. Complement and microglia dependent synapse elimination in brain development. WIREs Mech Dis 2021; 14:e1545. [PMID: 34738335 PMCID: PMC9066608 DOI: 10.1002/wsbm.1545] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 01/31/2023]
Abstract
Synapse elimination, also known as synaptic pruning, is a critical step in the maturation of neural circuits during brain development. Mounting evidence indicates that the complement cascade of the innate immune system plays an important role in synapse elimination. Studies indicate that excess synapses during development are opsonized by complement proteins and subsequently phagocytosed by microglia which expresses complement receptors. The process is regulated by diverse molecular signals, including complement inhibitors that affect the activation of complement, as well as signals that affect microglial recruitment and activation. These signals may promote or inhibit the removal of specific sets of synapses during development. The complement-microglia system has also been implicated in the pathogenesis of several developmental brain disorders, suggesting that the dysregulation of mechanisms of synapse pruning may underlie the specific circuitry defects in these diseases. Here, we review the latest evidence on the molecular and cellular mechanisms of complement-dependent and microglia-dependent synapse elimination during brain development, and highlight the potential of this system as a therapeutic target for developmental brain disorders. This article is categorized under: Neurological Diseases > Molecular and Cellular Physiology Neurological Diseases > Stem Cells and Development Immune System Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Breeanne M Soteros
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Gek Ming Sia
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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14
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Andres EM, Neely HL, Hafeez H, Yasmin T, Kausar F, Basra MAR, Raza MH. Study of rare genetic variants in TM4SF20, NFXL1, CNTNAP2, and ATP2C2 in Pakistani probands and families with language impairment. Meta Gene 2021; 30. [PMID: 34540591 DOI: 10.1016/j.mgene.2021.100966] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Language impairment (LI) is highly heritable and aggregates in families. Genetic investigation of LI has revealed many chromosomal regions and genes of interest, though very few studies have focused on rare variant analysis in non-English speaking or non-European samples. We selected four candidate genes (TM4SF20, NFXL1, CNTNAP2 and ATP2C2) strongly suggested for specific language impairment (SLI), a subtype of LI, and investigated rare protein coding variants through Sanger sequencing of probands with LI ascertained from Pakistan. The probands and their family members completed a speech and language family history questionnaire and a vocabulary measure, the Peabody Picture Vocabulary Test-fourth edition (PPVT-4), translated to Urdu, the national language of Pakistan. Our study aimed to determine the significance of rare variants in these SLI candidate genes through segregation analysis in a novel population with a high rate of consanguinity. In total, we identified 16 rare variants (according to the rare MAF in the global population in gnomAD v2.1.1 database exomes), including eight variants with a MAF <0.5 % in the South Asian population. Most of the identified rare variants aggregated in proband's families, one rare variant (c.*9T>C in CNTNAP2) co-segregated in a small family (PKSLI-64) and another (c.2465C>T in ATP2C2) co-segregated in the proband branch (PKSLI-27). The lack of complete co-segregation of most of the identified rare variants indicates that while these genes could be involved in overall risk for LI, other genes are likely involved in LI in this population. Future investigation of these consanguineous families has the potential to expand our understanding of gene function related to language acquisition and impairment.
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Affiliation(s)
- Erin M Andres
- University of Kansas, Child Language Doctoral Program
| | | | - Huma Hafeez
- School of Chemistry, University of the Punjab
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15
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den Hoed J, Devaraju K, Fisher SE. Molecular networks of the FOXP2 transcription factor in the brain. EMBO Rep 2021; 22:e52803. [PMID: 34260143 PMCID: PMC8339667 DOI: 10.15252/embr.202152803] [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: 03/05/2021] [Revised: 05/19/2021] [Accepted: 06/23/2021] [Indexed: 01/06/2023] Open
Abstract
The discovery of the FOXP2 transcription factor, and its implication in a rare severe human speech and language disorder, has led to two decades of empirical studies focused on uncovering its roles in the brain using a range of in vitro and in vivo methods. Here, we discuss what we have learned about the regulation of FOXP2, its downstream effectors, and its modes of action as a transcription factor in brain development and function, providing an integrated overview of what is currently known about the critical molecular networks.
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Affiliation(s)
- Joery den Hoed
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
- International Max Planck Research School for Language SciencesMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - Karthikeyan Devaraju
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - Simon E Fisher
- Language and Genetics DepartmentMax Planck Institute for PsycholinguisticsNijmegenThe Netherlands
- Donders Institute for Brain, Cognition and BehaviourRadboud UniversityNijmegenThe Netherlands
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16
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Benítez-Burraco A, Chekalin E, Bruskin S, Tatarinova T, Morozova I. Recent selection of candidate genes for mammal domestication in Europeans and language change in Europe: a hypothesis. Ann Hum Biol 2021; 48:313-320. [PMID: 34241552 DOI: 10.1080/03014460.2021.1936634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND AND AIM Human evolution resulted from changes in our biology, behaviour, and culture. One source of these changes has been hypothesised to be our self-domestication (that is, the development in humans of features commonly found in domesticated strains of mammals, seemingly as a result of selection for reduced aggression). Signals of domestication, notably brain size reduction, have increased in recent times. METHODS In this paper, we compare whole-genome data between the Late Neolithic/Bronze Age individuals and modern Europeans. RESULTS We show that genes associated with mammal domestication and with neural crest development and function are significantly differently enriched in nonsynonymous single nucleotide polymorphisms between these two groups. CONCLUSION We hypothesise that these changes might account for the increased features of self-domestication in modern humans and, ultimately, for subtle recent changes in human cognition and behaviour, including language.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, Faculty of Philology, University of Seville, Seville, Spain
| | - Evgeny Chekalin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Bruskin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Tatarinova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Department of Biology, University of La Verne, La Verne, CA, USA.,A. A. Kharkevich Institute for Information Transmission Problems, Moscow, Russia.,Department of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
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17
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Benítez-Burraco A, Fernández-Urquiza M, Jiménez-Romero S. Language impairment with a microduplication in 1q42.3q43. CLINICAL LINGUISTICS & PHONETICS 2021; 35:610-635. [PMID: 32856472 DOI: 10.1080/02699206.2020.1812119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/11/2020] [Accepted: 08/16/2020] [Indexed: 06/11/2023]
Abstract
Deletions and duplications of the distal region of the long arm of chromosome 1 are associated with brain abnormalities and developmental delay. Because duplications are less frequent than deletions, no detailed account of the cognitive profile of the affected people is available, particularly, regarding their language (dis)abilities. In this paper we report on the cognitive and language capacities of a girl with one of the smallest interstitial duplications ever described in this region, affecting to 1q42.3q43 (arr[hg19] 1q42.3q43(235,963,632-236,972,276)x3), and advance potential candidate genes for the observed deficits. The proband's speech is severely impaired, exhibiting dysarthric-like features, with speech problems also resulting from a phonological deficit boiling down to a verbal auditory memory deficit. Lexical and grammatical knowledge are also impaired, impacting negatively on both expressive and receptive abilities, seemingly as a consequence of the phonological deficit. Still, her pragmatic abilities seem to be significantly spared, granting her a good command on the principles governing conversational exchanges. Genetic analyses point to several genes of interest. These include one gene within the duplicated region (LYST), one predicted functional partner (CMIP), and three genes outside the 1q42.3q43 region, which are all highly expressed in the cerebellum: DDIT4 and SLC29A1, found strongly downregulated in the proband compared to her healthy parents, and CNTNAP3, found strongly upregulated. The genes highlighted in the paper emerge as potential candidates for the phonological and speech deficits exhibited by the proband and ultimately, for her problems with language.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), University of Seville, Seville, Spain
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18
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Martinelli A, Rice ML, Talcott JB, Diaz R, Smith S, Raza MH, Snowling MJ, Hulme C, Stein J, Hayiou-Thomas ME, Hawi Z, Kent L, Pitt SJ, Newbury DF, Paracchini S. A rare missense variant in the ATP2C2 gene is associated with language impairment and related measures. Hum Mol Genet 2021; 30:1160-1171. [PMID: 33864365 PMCID: PMC8188402 DOI: 10.1093/hmg/ddab111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/02/2023] Open
Abstract
At least 5% of children present unexpected difficulties in expressing and understanding spoken language. This condition is highly heritable and often co-occurs with other neurodevelopmental disorders such as dyslexia and ADHD. Through an exome sequencing analysis, we identified a rare missense variant (chr16:84405221, GRCh38.p12) in the ATP2C2 gene. ATP2C2 was implicated in language disorders by linkage and association studies, and exactly the same variant was reported previously in a different exome sequencing study for language impairment (LI). We followed up this finding by genotyping the mutation in cohorts selected for LI and comorbid disorders. We found that the variant had a higher frequency in LI cases (1.8%, N = 360) compared with cohorts selected for dyslexia (0.8%, N = 520) and ADHD (0.7%, N = 150), which presented frequencies comparable to reference databases (0.9%, N = 24 046 gnomAD controls). Additionally, we observed that carriers of the rare variant identified from a general population cohort (N = 42, ALSPAC cohort) presented, as a group, lower scores on a range of reading and language-related measures compared to controls (N = 1825; minimum P = 0.002 for non-word reading). ATP2C2 encodes for an ATPase (SPCA2) that transports calcium and manganese ions into the Golgi lumen. Our functional characterization suggested that the rare variant influences the ATPase activity of SPCA2. Thus, our results further support the role of ATP2C2 locus in language-related phenotypes and pinpoint the possible effects of a specific rare variant at molecular level.
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Affiliation(s)
| | - Mabel L Rice
- Child Language Doctoral Program, University of Kansas, Lawrence, KS, USA
| | - Joel B Talcott
- Aston Brain Centre, School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Rebeca Diaz
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Shelley Smith
- Department of Neurological Sciences, University of Nebraska Medical Center, Lincoln, NE, USA
| | | | - Margaret J Snowling
- Department of Experimental Psychology and St John's College, University of Oxford, Oxford, UK
| | - Charles Hulme
- Department of Education, University of Oxford, Oxford, UK
| | - John Stein
- Department of Physiology, University of Oxford, Oxford, UK
| | | | - Ziarih Hawi
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University, Clayton, VIC, Australia
| | - Lindsey Kent
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Samantha J Pitt
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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19
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Thomas T, Perdue MV, Khalaf S, Landi N, Hoeft F, Pugh K, Grigorenko EL. Neuroimaging genetic associations between SEMA6D, brain structure, and reading skills. J Clin Exp Neuropsychol 2021; 43:276-289. [PMID: 33960276 PMCID: PMC8225580 DOI: 10.1080/13803395.2021.1912300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/30/2021] [Indexed: 01/15/2023]
Abstract
Specific reading disability (SRD) is defined by genetic and neural risk factors that are not fully understood. The current study used imaging genetics methodology to investigate relationships between SEMA6D, brain structure, and reading. SEMA6D, located on SRD risk locus DYX1, is involved in axon guidance, synapse formation, and dendrite development. SEMA6D's associations with brain structure in reading-related regions of interest (ROIs) were investigated in a sample of children with a range of reading performance, from sites in Connecticut, CT (n = 67, 6-13 years, mean age = 9.07) and San Francisco, SF (n = 28, 5-8 years, mean age = 6.5). Multiple regression analyses revealed significant associations between SEMA6D's rs16959669 and cortical thickness in the fusiform gyrus and rs4270119 and gyrification in the supramarginal gyrus in the CT sample, but this was not replicated in the SF sample. Significant clusters were not associated with reading. For white matter volume, combined analyses across both samples revealed associations between reading and the left transverse temporal gyrus, left pars triangularis, left cerebellum, and right cerebellum. White matter volume in the left transverse temporal gyrus was nominally related to rs1817178, rs12050859, and rs1898110 in SEMA6D, and rs1817178 was significantly related to reading. Haplotype analyses revealed significant associations between the whole gene and brain phenotypes. Results suggest SEMA6D likely has an impact on multiple reading-related neural structures, but only white matter volume in the transverse temporal gyrus was significantly related to reading in the current sample. As the sample was young, the transverse temporal gyrus, involved in auditory perception, may be more strongly involved in reading because phonological processing is still being learned. The relationship between SEMA6D and reading may change as different brain regions are involved during reading development. Future research should examine mediating effects, use additional brain measures, and use an older sample to better understand effects.
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Affiliation(s)
- Tina Thomas
- Department of Psychology, University of Houston, Houston, TX, USA
| | - Meaghan V. Perdue
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Haskins Laboratories, University of Connecticut, New Haven, CT, USA
| | - Shiva Khalaf
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA
| | - Nicole Landi
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Haskins Laboratories, University of Connecticut, New Haven, CT, USA
| | - Fumiko Hoeft
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Department of Psychiatry, University of California, San Francisco, CA, USA
| | - Kenneth Pugh
- University of Connecticut Dept. of Psychological Sciences, Storrs, CT, USA
- Haskins Laboratories, University of Connecticut, New Haven, CT, USA
| | - Elena L. Grigorenko
- Department of Psychology, University of Houston, Houston, TX, USA
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, TX, USA
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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20
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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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21
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Benítez-Burraco A, Fernández-Urquiza M, Jiménez-Romero MS. Language Impairment with a Partial Duplication of DOCK8. Mol Syndromol 2021; 11:243-263. [PMID: 33510598 DOI: 10.1159/000511972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Duplications of the distal region of the short arm of chromosome 9 are rare, but are associated with learning disabilities and behavioral disturbances. We report in detail the cognitive and language features of a child with a duplication in the 9p24.3 region, arr[hg19] 9p24.3(266,045-459,076)×3. The proband exhibits marked expressive and receptive problems, which affect both structural and functional aspects of language. These problems might result from a severe underlying deficit in working memory. Regarding the molecular causes of the observed symptoms, they might result from the altered expression of selected genes involved in procedural learning, particularly some of components of the SLIT/ROBO/FOXP2 network, strongly related to the development and evolution of language. Dysregulation of specific components of this network can result in turn from an altered interaction between DOCK8, affected by the microduplication, and CDC42, acting as the hub component of the network encompassing language-related genes.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), University of Seville, Seville, Spain
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22
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Volkert MR, Crowley DJ. Preventing Neurodegeneration by Controlling Oxidative Stress: The Role of OXR1. Front Neurosci 2020; 14:611904. [PMID: 33384581 PMCID: PMC7770112 DOI: 10.3389/fnins.2020.611904] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/23/2020] [Indexed: 12/31/2022] Open
Abstract
Parkinson’s disease, diabetic retinopathy, hyperoxia induced retinopathy, and neuronal damage resulting from ischemia are among the notable neurodegenerative diseases in which oxidative stress occurs shortly before the onset of neurodegeneration. A shared feature of these diseases is the depletion of OXR1 (oxidation resistance 1) gene products shortly before the onset of neurodegeneration. In animal models of these diseases, restoration of OXR1 has been shown to reduce or eliminate the deleterious effects of oxidative stress induced cell death, delay the onset of symptoms, and reduce overall severity. Moreover, increasing OXR1 expression in cells further increases oxidative stress resistance and delays onset of disease while showing no detectable side effects. Thus, restoring or increasing OXR1 function shows promise as a therapeutic for multiple neurodegenerative diseases. This review examines the role of OXR1 in oxidative stress resistance and its impact on neurodegenerative diseases. We describe the potential of OXR1 as a therapeutic in light of our current understanding of its function at the cellular and molecular level and propose a possible cascade of molecular events linked to OXR1’s regulatory functions.
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Affiliation(s)
- Michael R Volkert
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, United States
| | - David J Crowley
- Department of Biological and Physical Sciences, Assumption University, Worcester, MA, United States
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23
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Andres EM, Earnest KK, Smith SD, Rice ML, Raza MH. Pedigree-Based Gene Mapping Supports Previous Loci and Reveals Novel Suggestive Loci in Specific Language Impairment. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2020; 63:4046-4061. [PMID: 33186502 PMCID: PMC8608229 DOI: 10.1044/2020_jslhr-20-00102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Purpose Specific language impairment (SLI) is characterized by a delay in language acquisition despite a lack of other developmental delays or hearing loss. Genetics of SLI is poorly understood. The purpose of this study is to identify SLI genetic loci through family-based linkage mapping. Method We performed genome-wide parametric linkage analysis in six families segregating with SLI. An age-appropriate standardized omnibus language measure was used to categorically define the SLI phenotype. Results A suggestive linkage region replicated a previous region of interest with the highest logarithm of odds (LOD) score of 2.40 at 14q11.2-q13.3 in Family 489. A paternal parent-of-origin effect associated with SLI and language phenotypes on a nonsynonymous single nucleotide polymorphism (SNP) in NOP9 (14q12) was reported previously. Linkage analysis identified a new SLI locus at 15q24.3-25.3 with the highest parametric LOD score of 3.06 in Family 315 under a recessive mode of inheritance. Suggestive evidence of linkage was also revealed at 4q31.23-q35.2 in Family 300, with the highest LOD score of 2.41. Genetic linkage was not identified in the other three families included in parametric linkage analysis. Conclusions These results are the first to report genome-wide suggestive linkage with a total language standard score on an age-appropriate omnibus language measure across a wide age range. Our findings confirm previous reports of a language-associated locus on chromosome 14q, report new SLI loci, and validate the pedigree-based parametric linkage analysis approach to mapping genes for SLI. Supplemental Material https://doi.org/10.23641/asha.13203218.
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Affiliation(s)
- Erin M. Andres
- Child Language Doctoral Program, University of Kansas, Lawrence
| | | | - Shelley D. Smith
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha
| | - Mabel L. Rice
- Child Language Doctoral Program, University of Kansas, Lawrence
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24
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A genetic window to auditory-verbal problems in bipolar disorder. Psychiatr Genet 2020; 30:169-173. [PMID: 33165203 DOI: 10.1097/ypg.0000000000000265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bipolar disorder is a high prevalent psychiatric condition entailing recurrent episodes of elevated mood and depression, but also diverse cognitive problems. One deficit observed in patients concerns to auditory-verbal processing. Being a hereditary condition with a complex genetic architecture, it is not clear which genes contribute to this deficit. We show that candidates for bipolar disorder significantly overlap with candidates for clinical conditions resulting from a deficit in the phonological loop of working memory, particularly, developmental dyslexia and specific language impairment. The overlapping genes are involved in aspects of brain development and function (particularly, brain oscillations) potentially underlying phonological processing and accordingly, emerge as promising candidates for auditory-verbal deficits in bipolar disorder.
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25
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Cong Q, Soteros BM, Wollet M, Kim JH, Sia GM. The endogenous neuronal complement inhibitor SRPX2 protects against complement-mediated synapse elimination during development. Nat Neurosci 2020; 23:1067-1078. [PMID: 32661396 PMCID: PMC7483802 DOI: 10.1038/s41593-020-0672-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 06/16/2020] [Indexed: 02/06/2023]
Abstract
Complement-mediated synapse elimination has emerged as an important process in both brain development and neurological diseases, but whether neurons express complement inhibitors that protect synapses against complement-mediated synapse elimination remains unknown. Here, we show that the sushi domain protein SRPX2 is a neuronally expressed complement inhibitor that regulates complement-dependent synapse elimination. SRPX2 directly binds to C1q and blocks its activity, and SRPX2-/Y mice show increased C3 deposition and microglial synapse engulfment. They also show a transient decrease in synapse numbers and increase in retinogeniculate axon segregation in the lateral geniculate nucleus. In the somatosensory cortex, SRPX2-/Y mice show decreased thalamocortical synapse numbers and increased spine pruning. C3-/-;SRPX2-/Y double-knockout mice exhibit phenotypes associated with C3-/- mice rather than SRPX2-/Y mice, which indicates that C3 is necessary for the effect of SRPX2 on synapse elimination. Together, these results show that SRPX2 protects synapses against complement-mediated elimination in both the thalamus and the cortex.
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Affiliation(s)
- Qifei Cong
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Breeanne M Soteros
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Mackenna Wollet
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jun Hee Kim
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Gek-Ming Sia
- Department of Pharmacology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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26
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Ho AMC, Cabello-Arreola A, Markota M, Heppelmann CJ, Charlesworth MC, Ozerdem A, Mahajan G, Rajkowska G, Stockmeier CA, Frye MA, Choi DS, Veldic M. Label-free proteomics differences in the dorsolateral prefrontal cortex between bipolar disorder patients with and without psychosis. J Affect Disord 2020; 270:165-173. [PMID: 32339108 PMCID: PMC7234814 DOI: 10.1016/j.jad.2020.03.105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 02/01/2020] [Accepted: 03/28/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Psychosis is common in bipolar disorder (BD) and is related to more severe cognitive impairments. Since the molecular mechanism of BD psychosis is elusive, we conducted this study to explore the proteomic differences associated with BD psychosis in the dorsolateral prefrontal cortex (DLPFC; BA9). METHODS Postmortem DLPFC gray matter tissues from five pairs of age-matched male BD subjects with and without psychosis history were used. Tissue proteomes were identified and quantified by label-free liquid chromatography tandem mass spectrometry and then compared between groups. Statistical significance was set at q < 0.40 and Log2 fold change (Log2FC) ≥ |1|. Protein groups with differential expression between groups at p < 0.05 were subjected to pathway analysis. RESULTS Eleven protein groups differed significantly between groups, including the reduction of tenascin C (q = 0.005, Log2FC = -1.78), the elevations of synaptoporin (q = 0.235, Log2FC = 1.17) and brain-specific angiogenesis inhibitor 1-associated protein 3 (q = 0.241, Log2FC = 2.10) in BD with psychosis. The between-group differences of these proteins were confirmed by Western blots. The top enriched pathways (p < 0.05 with ≥ 3 hits) were the outgrowth of neurons, neuronal cell proliferation, growth of neurites, and outgrowth of neurites, which were all predicted to be upregulated in BD with psychosis. LIMITATIONS Small sample size and uncertain relationships of the observed proteomic differences with illness stage and acute psychosis. CONCLUSIONS These results suggested BD with psychosis history may be associated with abnormalities in neurodevelopment, neuroplasticity, neurotransmission, and neuromodulation in the DLPFC.
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Affiliation(s)
- Ada M.-C. Ho
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | | | - Matej Markota
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Aysegul Ozerdem
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Gouri Mahajan
- Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Grazyna Rajkowska
- Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA
| | - Craig A. Stockmeier
- Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS, USA,Psychiatry, Case Western Reserve University, Cleveland, OH, USA
| | - Mark A. Frye
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Doo-Sup Choi
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Marin Veldic
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA.
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27
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Perrino PA, Talbot L, Kirkland R, Hill A, Rendall AR, Mountford HS, Taylor J, Buscarello AN, Lahiri N, Saggar A, Fitch RH, Newbury DF. Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes. Commun Biol 2020; 3:180. [PMID: 32313182 PMCID: PMC7170883 DOI: 10.1038/s42003-020-0885-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/11/2020] [Indexed: 11/30/2022] Open
Abstract
Language development builds upon a complex network of interacting subservient systems. It therefore follows that variations in, and subclinical disruptions of, these systems may have secondary effects on emergent language. In this paper, we consider the relationship between genetic variants, hearing, auditory processing and language development. We employ whole genome sequencing in a discovery family to target association and gene x environment interaction analyses in two large population cohorts; the Avon Longitudinal Study of Parents and Children (ALSPAC) and UK10K. These investigations indicate that USH2A variants are associated with altered low-frequency sound perception which, in turn, increases the risk of developmental language disorder. We further show that Ush2a heterozygote mice have low-level hearing impairments, persistent higher-order acoustic processing deficits and altered vocalizations. These findings provide new insights into the complexity of genetic mechanisms serving language development and disorders and the relationships between developmental auditory and neural systems. Peter Perrino et al. identify variants in USH2A linked to a dominant language disorder in a human family and find that these variants are also associated with low-frequency hearing at the population level. They investigate the function of USH2A variants in mice, showing that mutations in this gene are responsible for hearing loss.
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Affiliation(s)
- Peter A Perrino
- Department of Psychological Science/Behavioral Neuroscience, University of Connecticut, Storrs, CT, USA.,UConn Institute of Brain and Cognitive Sciences; UConn Murine Behavioral Neurogenetics Facility, Storrs, CT, USA
| | - Lidiya Talbot
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Rose Kirkland
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK.,School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK
| | - Amanda Hill
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Amanda R Rendall
- Department of Psychological Science/Behavioral Neuroscience, University of Connecticut, Storrs, CT, USA.,UConn Institute of Brain and Cognitive Sciences; UConn Murine Behavioral Neurogenetics Facility, Storrs, CT, USA
| | - Hayley S Mountford
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Jenny Taylor
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK.,NIHR Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | | | - Alexzandrea N Buscarello
- Department of Psychological Science/Behavioral Neuroscience, University of Connecticut, Storrs, CT, USA.,UConn Institute of Brain and Cognitive Sciences; UConn Murine Behavioral Neurogenetics Facility, Storrs, CT, USA
| | - Nayana Lahiri
- Institute of Molecular and Clinical Sciences, St George's, University of London & St George's University Hospitals NHS Foundation Trust, London, UK
| | - Anand Saggar
- Institute of Molecular and Clinical Sciences, St George's, University of London & St George's University Hospitals NHS Foundation Trust, London, UK
| | - R Holly Fitch
- Department of Psychological Science/Behavioral Neuroscience, University of Connecticut, Storrs, CT, USA. .,UConn Institute of Brain and Cognitive Sciences; UConn Murine Behavioral Neurogenetics Facility, Storrs, CT, USA.
| | - Dianne F Newbury
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
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28
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Boua PR, Brandenburg JT, Choudhury A, Hazelhurst S, Sengupta D, Agongo G, Nonterah EA, Oduro AR, Tinto H, Mathew CG, Sorgho H, Ramsay M. Novel and Known Gene-Smoking Interactions With cIMT Identified as Potential Drivers for Atherosclerosis Risk in West-African Populations of the AWI-Gen Study. Front Genet 2020; 10:1354. [PMID: 32117412 PMCID: PMC7025492 DOI: 10.3389/fgene.2019.01354] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 12/10/2019] [Indexed: 12/22/2022] Open
Abstract
Introduction Atherosclerosis is a key contributor to the burden of cardiovascular diseases (CVDs) and many epidemiological studies have reported on the effect of smoking on carotid intima-media thickness (cIMT) and its subsequent effect on CVD risk. Gene-environment interaction studies have contributed towards understanding some of the missing heritability of genome-wide association studies. Gene-smoking interactions on cIMT have been studied in non-African populations (European, Latino-American, and African American) but no comparable African research has been reported. Our aim was to investigate smoking-SNP interactions on cIMT in two West African populations by genome-wide analysis. Materials and methods Only male participants from Burkina Faso (Nanoro = 993) and Ghana (Navrongo = 783) were included, as smoking was extremely rare among women. Phenotype and genotype data underwent stringent QC and genotype imputation was performed using the Sanger African Imputation Panel. Smoking prevalence among men was 13.3% in Nanoro and 42.5% in Navrongo. We analyzed gene-smoking interactions with PLINK after adjusting for covariates: age and 6 PCs (Model 1); age, BMI, blood pressure, fasting glucose, cholesterol levels, MVPA, and 6 PCs (Model 2). All analyses were performed at site level and for the combined data set. Results In Nanoro, we identified new gene-smoking interaction variants for cIMT within the previously described RCBTB1 region (rs112017404, rs144170770, and rs4941649) (Model 1: p = 1.35E-07; Model 2: p = 3.08E-08). In the combined sample, two novel intergenic interacting variants were identified, rs1192824 in the regulatory region of TBC1D8 (p = 5.90E-09) and rs77461169 (p = 4.48E-06) located in an upstream region of open chromatin. In silico functional analysis suggests the involvement of genes implicated in biological processes related to cell or biological adhesion and regulatory processes in gene-smoking interactions with cIMT (as evidenced by chromatin interactions and eQTLs). Discussion This is the first gene-smoking interaction study for cIMT, as a risk factor for atherosclerosis, in sub-Saharan African populations. In addition to replicating previously known signals for RCBTB1, we identified two novel genomic regions (TBC1D8, near BCHE) involved in this gene-environment interaction.
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Affiliation(s)
- Palwende Romuald Boua
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso.,Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jean-Tristan Brandenburg
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Engelbert A Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Abraham R Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Halidou Tinto
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | - Christopher G Mathew
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | - Michèle Ramsay
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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29
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Abstract
PURPOSE OF REVIEW To better understand the shared basis of language and mental health, this review examines the behavioral and neurobiological features of aberrant language in five major neuropsychiatric conditions. Special attention is paid to genes implicated in both language and neuropsychiatric disorders, as they reveal biological domains likely to underpin the processes controlling both. RECENT FINDINGS Abnormal language and communication are common manifestations of neuropsychiatric conditions, and children with impaired language are more likely to develop psychiatric disorders than their peers. Major themes in the genetics of both language and psychiatry include master transcriptional regulators, like FOXP2; key developmental regulators, like AUTS2; and mediators of neurotransmission, like GRIN2A and CACNA1C.
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30
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Rakhlin N, Landi N, Lee M, Magnuson JS, Naumova OY, Ovchinnikova IV, Grigorenko EL. Cohesion of Cortical Language Networks During Word Processing Is Predicted by a Common Polymorphism in the
SETBP1
Gene. New Dir Child Adolesc Dev 2020; 2020:131-155. [DOI: 10.1002/cad.20331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | | | | | | | | | - Elena L. Grigorenko
- Haskins Laboratories
- Yale University
- University of Houston
- Saint-Petersburg State University
- Moscow State University for Psychology and Education
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31
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Wendt FR, Muniz Carvalho C, Pathak GA, Gelernter J, Polimanti R. Deciphering the Biological Mechanisms Underlying the Genome-Wide Associations between Computerized Device Use and Psychiatric Disorders. J Clin Med 2019; 8:E2040. [PMID: 31766499 PMCID: PMC6947231 DOI: 10.3390/jcm8122040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/05/2019] [Accepted: 11/20/2019] [Indexed: 12/14/2022] Open
Abstract
Computerized device use (CDU) is societally ubiquitous but its effects on mental health are unknown. We performed genetic correlation, Mendelian randomization, and latent causal variable analyses to identify shared genetic mechanisms between psychiatric disorders (Psychiatric Genomics Consortium; 14,477 < N < 150,064) and CDU (UK Biobank; N = 361,194 individuals). Using linkage disequilibrium score regression, we detected strong genetic correlations between "weekly usage of mobile phone in last 3 months" (PhoneUse) vs. attention deficit hyperactivity disorder (ADHD; rg = 0.425, p = 4.59 × 10-29) and "plays computer games" (CompGaming) vs. schizophrenia (SCZ; rg = -0.271, p = 7.16 × 10-26). Focusing on these correlations, we used two sample MRs to detect the causal relationships between trait pairs by treating single nucleotide polymorphisms as non-modifiable risk factors underlying both phenotypes. Significant bidirectional associations were detected (PhoneUse→ADHD β = 0.132, p = 1.89 × 10-4 and ADHD→PhoneUse β = 0.084, p = 2.86 × 10-10; CompGaming→SCZ β = -0.02, p = 6.46 × 10-25 and CompGaming→SCZ β = -0.194, p = 0.005) and the latent causal variable analyses did not support a causal relationship independent of the genetic correlations between these traits. This suggests that molecular pathways contribute to the genetic overlap between these traits. Dopamine transport enrichment (Gene Ontology:0015872, pSCZvsCompGaming = 2.74 × 10-10) and DRD2 association (pSCZ = 7.94 × 10-8; pCompGaming = 3.98 × 10-25) were detected in SCZ and CompGaming and support their negative correlative relationship. FOXP2 was significantly associated with ADHD (p = 9.32 × 10-7) and PhoneUse (p = 9.00 × 10-11) with effect directions concordant with their positive genetic correlation. Our study demonstrates that epidemiological associations between psychiatric disorders and CDUs are due, in part, to the molecular mechanisms shared between them rather than a causal relationship. Our findings imply that biological mechanisms underlying CDU contribute to the psychiatric phenotype manifestation.
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Affiliation(s)
- Frank R Wendt
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Carolina Muniz Carvalho
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA
- Universidade Federal de São Paulo (UNIFESP), São Paulo, SP 04021-001, Brazil
| | - Gita A. Pathak
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA
- Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale School of Medicine and VA CT Healthcare Center, West Haven, CT 06516, USA
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32
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Myers SJ, Yuan H, Kang JQ, Tan FCK, Traynelis SF, Low CM. Distinct roles of GRIN2A and GRIN2B variants in neurological conditions. F1000Res 2019; 8:F1000 Faculty Rev-1940. [PMID: 31807283 PMCID: PMC6871362 DOI: 10.12688/f1000research.18949.1] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2019] [Indexed: 12/12/2022] Open
Abstract
Rapid advances in sequencing technology have led to an explosive increase in the number of genetic variants identified in patients with neurological disease and have also enabled the assembly of a robust database of variants in healthy individuals. A surprising number of variants in the GRIN genes that encode N-methyl-D-aspartate (NMDA) glutamatergic receptor subunits have been found in patients with various neuropsychiatric disorders, including autism spectrum disorders, epilepsy, intellectual disability, attention-deficit/hyperactivity disorder, and schizophrenia. This review compares and contrasts the available information describing the clinical and functional consequences of genetic variations in GRIN2A and GRIN2B. Comparison of clinical phenotypes shows that GRIN2A variants are commonly associated with an epileptic phenotype but that GRIN2B variants are commonly found in patients with neurodevelopmental disorders. These observations emphasize the distinct roles that the gene products serve in circuit function and suggest that functional analysis of GRIN2A and GRIN2B variation may provide insight into the molecular mechanisms, which will allow more accurate subclassification of clinical phenotypes. Furthermore, characterization of the pharmacological properties of variant receptors could provide the first opportunity for translational therapeutic strategies for these GRIN-related neurological and psychiatric disorders.
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Affiliation(s)
- Scott J Myers
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA
| | - Hongjie Yuan
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA
| | - Jing-Qiong Kang
- Department of Neurology, Vanderbilt Brain Institute, Vanderbilt Kennedy Center of Human Development, Vanderbilt University, Nashville, TN, USA
| | - Francis Chee Kuan Tan
- Department of Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Stephen F Traynelis
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University, Atlanta, GA, USA
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA, USA
| | - Chian-Ming Low
- Department of Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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33
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Weisner PA, Chen CY, Sun Y, Yoo J, Kao WC, Zhang H, Baltz ET, Troy JM, Stubbs L. A Mouse Mutation That Dysregulates Neighboring Galnt17 and Auts2 Genes Is Associated with Phenotypes Related to the Human AUTS2 Syndrome. G3 (BETHESDA, MD.) 2019; 9:3891-3906. [PMID: 31554716 PMCID: PMC6829118 DOI: 10.1534/g3.119.400723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/19/2019] [Indexed: 01/23/2023]
Abstract
AUTS2 was originally discovered as the gene disrupted by a translocation in human twins with Autism spectrum disorder, intellectual disability, and epilepsy. Since that initial finding, AUTS2-linked mutations and variants have been associated with a very broad array of neuropsychiatric disorders, sugg esting that AUTS2 is required for fundamental steps of neurodevelopment. However, genotype-phenotype correlations in this region are complicated, because most mutations could also involve neighboring genes. Of particular interest is the nearest downstream neighbor of AUTS2, GALNT17, which encodes a brain-expressed N-acetylgalactosaminyltransferase of unknown brain function. Here we describe a mouse (Mus musculus) mutation, T(5G2;8A1)GSO (abbreviated 16Gso), a reciprocal translocation that breaks between Auts2 and Galnt17 and dysregulates both genes. Despite this complex regulatory effect, 16Gso homozygotes model certain human AUTS2-linked phenotypes very well. In addition to abnormalities in growth, craniofacial structure, learning and memory, and behavior, 16Gso homozygotes display distinct pathologies of the cerebellum and hippocampus that are similar to those associated with autism and other types of AUTS2-linked neurological disease. Analyzing mutant cerebellar and hippocampal transcriptomes to explain this pathology, we identified disturbances in pathways related to neuron and synapse maturation, neurotransmitter signaling, and cellular stress, suggesting possible cellular mechanisms. These pathways, coupled with the translocation's selective effects on Auts2 isoforms and coordinated dysregulation of Galnt17, suggest novel hypotheses regarding the etiology of the human "AUTS2 syndrome" and the wide array of neurodevelopmental disorders linked to variance in this genomic region.
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Affiliation(s)
- P Anne Weisner
- Carl R. Woese Institute for Genomic Biology
- Neuroscience Program
| | - Chih-Ying Chen
- Carl R. Woese Institute for Genomic Biology
- Department of Cell and Developmental Biology, and
| | - Younguk Sun
- Carl R. Woese Institute for Genomic Biology
- Department of Cell and Developmental Biology, and
| | | | | | | | | | - Joseph M Troy
- Carl R. Woese Institute for Genomic Biology
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana IL 61802
| | - Lisa Stubbs
- Carl R. Woese Institute for Genomic Biology,
- Neuroscience Program
- Department of Cell and Developmental Biology, and
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana IL 61802
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34
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Gender Related Changes in Gene Expression Induced by Valproic Acid in A Mouse Model of Autism and the Correction by S-adenosyl Methionine. Does It Explain the Gender Differences in Autistic Like Behavior? Int J Mol Sci 2019; 20:ijms20215278. [PMID: 31652960 PMCID: PMC6862653 DOI: 10.3390/ijms20215278] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
In previous studies we produced autism like behavioral changes in mice by Valproic acid (VPA) with significant differences between genders. S-adenosine methionine (SAM) prevented the autism like behavior in both genders. The expression of 770 genes of pathways involved in neurophysiology and neuropathology was studied in the prefrontal cortex of 60 days old male and female mice using the NanoString nCounter. In females, VPA induced statistically significant changes in the expression of 146 genes; 71 genes were upregulated and 75 downregulated. In males, VPA changed the expression of only 19 genes, 16 were upregulated and 3 downregulated. Eight genes were similarly changed in both genders. When considering only the genes that were changed by at least 50%, VPA changed the expression of 15 genes in females and 3 in males. Only Nts was similarly downregulated in both genders. SAM normalized the expression of most changed genes in both genders. We presume that genes that are involved in autism like behavior in our model were similarly changed in both genders and corrected by SAM. The behavioral and other differences between genders may be related to genes that were differently affected by VPA in males and females and/or differently affected by SAM.
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35
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Nudel R, Christiani CAJ, Ohland J, Uddin MJ, Hemager N, Ellersgaard DV, Spang KS, Burton BK, Greve AN, Gantriis DL, Bybjerg-Grauholm J, Jepsen JRM, Thorup AAE, Mors O, Nordentoft M, Werge T. Language deficits in specific language impairment, attention deficit/hyperactivity disorder, and autism spectrum disorder: An analysis of polygenic risk. Autism Res 2019; 13:369-381. [PMID: 31577390 PMCID: PMC7078922 DOI: 10.1002/aur.2211] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/04/2019] [Indexed: 12/27/2022]
Abstract
Language is one of the cognitive domains often impaired across many neurodevelopmental disorders. While for some disorders the linguistic deficit is the primary impairment (e.g., specific language impairment, SLI), for others it may accompany broader behavioral problems (e.g., autism). The precise nature of this phenotypic overlap has been the subject of debate. Moreover, several studies have found genetic overlaps across neurodevelopmental disorders. This raises the question of whether these genetic overlaps may correlate with phenotypic overlaps and, if so, in what manner. Here, we apply a genome‐wide approach to the study of the linguistic deficit in SLI, autism spectrum disorder (ASD), and attention deficit/hyperactivity disorder (ADHD). Using a discovery genome‐wide association study of SLI, we generate polygenic risk scores (PRS) in an independent sample which includes children with language impairment, SLI, ASD or ADHD and age‐matched controls and perform regression analyses across groups. The SLI‐trained PRS significantly predicted risk in the SLI case–control group (adjusted R2 = 6.24%; P = 0.024) but not in the ASD or ADHD case‐control groups (adjusted R2 = 0.0004%, 0.01%; P = 0.984, 0.889, respectively) nor for height, used as a negative control (R2 = 0.2%; P = 0.452). Additionally, there was a significant difference in the normalized PRS between children with SLI and children with ASD (common language effect size = 0.66; P = 0.044). Our study suggests no additive common‐variant genetic overlap between SLI and ASD and ADHD. This is discussed in the context of phenotypic studies of SLI and related disorders. Autism Res 2020, 13: 369–381. © 2019 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals, Inc. Lay Summary Language deficits are characteristic of specific language impairment (SLI), but may also be found in other neurodevelopmental disorders, such as autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD). Many studies examined the overlaps and differences across the language deficits in these disorders, but few studies have examined the genetic aspect thereof. In this study, we use a genome‐wide approach to evaluate whether common genetic variants increasing risk of SLI may also be associated with ASD and ADHD in the same manner. Our results suggest that this is not the case, and we discuss this finding in the context of theories concerning the etiologies of these disorders.
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Affiliation(s)
- Ron Nudel
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Camilla A J Christiani
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Jessica Ohland
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Md Jamal Uddin
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.,Section for Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Nicoline Hemager
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Ditte V Ellersgaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark
| | - Katrine S Spang
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Birgitte K Burton
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Aja N Greve
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Ditte L Gantriis
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jens Richardt M Jepsen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark.,Center for Neuropsychiatric Schizophrenia Research and Center for Clinical Intervention and Neuropsychiatric Schizophrenia Research, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Anne A E Thorup
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre for Child and Adolescent Psychiatry - Research Unit, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Mental Health Centre Copenhagen, University of Copenhagen Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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36
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Mountford HS, Villanueva P, Fernández MA, Barbieri ZD, Cazier JB, Newbury DF. Candidate gene variant effects on language disorders in Robinson Crusoe Island. Ann Hum Biol 2019; 46:109-119. [DOI: 10.1080/03014460.2019.1622776] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Hayley S. Mountford
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Pía Villanueva
- Department of Speech Language and Hearing Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Institute of Biomedical Sciences, Human Genetics Division, Faculty of Medicine, University of Chile, Santiago, Chile
| | - María Angélica Fernández
- Department of Speech Language and Hearing Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Zulema De Barbieri
- Department of Speech Language and Hearing Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | | | - Dianne F. Newbury
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
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37
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Benítez-Burraco A, Kimura R. Robust Candidates for Language Development and Evolution Are Significantly Dysregulated in the Blood of People With Williams Syndrome. Front Neurosci 2019; 13:258. [PMID: 30971880 PMCID: PMC6444191 DOI: 10.3389/fnins.2019.00258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/05/2019] [Indexed: 01/06/2023] Open
Abstract
Williams syndrome (WS) is a clinical condition, involving cognitive deficits and an uneven language profile, which has been the object of intense inquiry over the last decades. Although WS results from the hemideletion of around two dozen genes in chromosome 7, no gene has yet been probed to account for, or contribute significantly to, the language problems exhibited by the affected people. In this paper we have relied on gene expression profiles in the peripheral blood of WS patients obtained by microarray analysis and show that several robust candidates for language disorders and/or for language evolution in the species, all of them located outside the hemideleted region, are up- or downregulated in the blood of subjects with WS. Most of these genes play a role in the development and function of brain areas involved in language processing, which exhibit structural and functional anomalies in people with this condition. Overall, these genes emerge as robust candidates for language dysfunction in WS.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain
| | - Ryo Kimura
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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38
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Rahul DR, Ponniah RJ. Decoding the biology of language and its implications in language acquisition. J Biosci 2019; 44:25. [PMID: 30837376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Associating human genetic makeup with the faculty of language has long been a goal for biolinguistics. This stimulated the idea that language is attributed to genes and language disabilities are caused by genetic mutations. However, application of genetic knowledge on language intervention is still a gap in the existing literature. In an effort to bridge this gap, this article presents an account of genetic and neural associations of language and synthesizes the genetic, neural, epigenetic and environmental facets involved in language. In addition to describing the association of genes with language, the neural and epigenetic aspects of language are also explored. Further, the environmental aspects of language such as language input, emotion and cognition are also traced back to gene expressions. Therefore, effective language intervention for language learning difficulties must offer genetics-informed solutions, both linguistic and medical.
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Affiliation(s)
- D R Rahul
- National Institute of Technology, Tiruchirappalli, Tamil Nadu, India
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39
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Gene-Specific Intron Retention Serves as Molecular Signature that Distinguishes Melanoma from Non-Melanoma Cancer Cells in Greek Patients. Int J Mol Sci 2019; 20:ijms20040937. [PMID: 30795533 PMCID: PMC6412294 DOI: 10.3390/ijms20040937] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/15/2019] [Accepted: 02/20/2019] [Indexed: 12/19/2022] Open
Abstract
Background: Skin cancer represents the most common human malignancy, and it includes BCC, SCC, and melanoma. Since melanoma is one of the most aggressive types of cancer, we have herein attempted to develop a gene-specific intron retention signature that can distinguish BCC and SCC from melanoma biopsy tumors. Methods: Intron retention events were examined through RT-sqPCR protocols, using total RNA preparations derived from BCC, SCC, and melanoma Greek biopsy specimens. Intron-hosted miRNA species and their target transcripts were predicted via the miRbase and miRDB bioinformatics platforms, respectively. Ιntronic ORFs were recognized through the ORF Finder application. Generation and visualization of protein interactomes were achieved by the IntAct and Cytoscape softwares, while tertiary protein structures were produced by using the I-TASSER online server. Results: c-MYC and Sestrin-1 genes proved to undergo intron retention specifically in melanoma. Interaction maps of proteins encoded by genes being potentially targeted by retained intron-accommodated miRNAs were generated and SRPX2 was additionally delivered to our melanoma-specific signature. Novel ORFs were identified in MCT4 and Sestrin-1 introns, with potentially critical roles in melanoma development. Conclusions: The property of c-MYC, Sestrin-1, and SRPX2 genes to retain specific introns could be clinically used to molecularly differentiate non-melanoma from melanoma tumors.
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40
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A set of regulatory genes co-expressed in embryonic human brain is implicated in disrupted speech development. Mol Psychiatry 2019; 24:1065-1078. [PMID: 29463886 PMCID: PMC6756287 DOI: 10.1038/s41380-018-0020-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/03/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022]
Abstract
Genetic investigations of people with impaired development of spoken language provide windows into key aspects of human biology. Over 15 years after FOXP2 was identified, most speech and language impairments remain unexplained at the molecular level. We sequenced whole genomes of nineteen unrelated individuals diagnosed with childhood apraxia of speech, a rare disorder enriched for causative mutations of large effect. Where DNA was available from unaffected parents, we discovered de novo mutations, implicating genes, including CHD3, SETD1A and WDR5. In other probands, we identified novel loss-of-function variants affecting KAT6A, SETBP1, ZFHX4, TNRC6B and MKL2, regulatory genes with links to neurodevelopment. Several of the new candidates interact with each other or with known speech-related genes. Moreover, they show significant clustering within a single co-expression module of genes highly expressed during early human brain development. This study highlights gene regulatory pathways in the developing brain that may contribute to acquisition of proficient speech.
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41
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Sriganesh R, Joseph Ponniah R. Genetics of language and its implications on language interventions. J Genet 2018; 97:1485-1491. [PMID: 30555099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Genetic variation of language genes affect neurophysiology of brain and can thus influence the way people respond to environmental language input, leading to differences in terms of their response to environmental language learning. Conversely, language learning environment too can affect gene expressions through neuroepigenetic mechanisms, leading to increasedinterindividual differences. Further, language-related cognitive processes such as learning, working memory and perception; and language-related affective factors such as stress and positive emotion involve neuroplasticity, which is also epigenetically regulated. Language intervention methods must understand the extent and the type of difficulties, and must offer personalized learning andmedical solutions. Medical intervention in terms of epigenetics and neurotransmitter regulation is proposed in addition to effectiveteaching methods to aid in effective language acquisition.
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42
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Murphy E, Benítez-Burraco A. Toward the Language Oscillogenome. Front Psychol 2018; 9:1999. [PMID: 30405489 PMCID: PMC6206218 DOI: 10.3389/fpsyg.2018.01999] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/28/2018] [Indexed: 12/20/2022] Open
Abstract
Language has been argued to arise, both ontogenetically and phylogenetically, from specific patterns of brain wiring. We argue that it can further be shown that core features of language processing emerge from particular phasal and cross-frequency coupling properties of neural oscillations; what has been referred to as the language ‘oscillome.’ It is expected that basic aspects of the language oscillome result from genetic guidance, what we will here call the language ‘oscillogenome,’ for which we will put forward a list of candidate genes. We have considered genes for altered brain rhythmicity in conditions involving language deficits: autism spectrum disorders, schizophrenia, specific language impairment and dyslexia. These selected genes map on to aspects of brain function, particularly on to neurotransmitter function. We stress that caution should be adopted in the construction of any oscillogenome, given the range of potential roles particular localized frequency bands have in cognition. Our aim is to propose a set of genome-to-language linking hypotheses that, given testing, would grant explanatory power to brain rhythms with respect to language processing and evolution.
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Affiliation(s)
- Elliot Murphy
- Division of Psychology and Language Sciences, University College London, London, United Kingdom.,Department of Psychology, University of Westminster, London, United Kingdom
| | - Antonio Benítez-Burraco
- Department of Spanish Language, Linguistics and Literary Theory, University of Seville, Seville, Spain
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43
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Haehner A, Hummel T, Heinritz W, Krueger S, Meinhardt M, Whitcroft KL, Sabatowski R, Gossrau G. Mutation in Nav
1.7 causes high olfactory sensitivity. Eur J Pain 2018; 22:1767-1773. [DOI: 10.1002/ejp.1272] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2018] [Indexed: 12/11/2022]
Affiliation(s)
- A. Haehner
- Smell & Taste Clinic; Department of Otorhinolaryngology; TU Dresden; Germany
| | - T. Hummel
- Smell & Taste Clinic; Department of Otorhinolaryngology; TU Dresden; Germany
| | - W. Heinritz
- ÜBAG for Human Genetics Oberelbe/Spree; Cottbus/Dresden Germany
| | - S. Krueger
- ÜBAG for Human Genetics Oberelbe/Spree; Cottbus/Dresden Germany
| | | | - K. L. Whitcroft
- Smell & Taste Clinic; Department of Otorhinolaryngology; TU Dresden; Germany
- UCL Ear Institute; University College London; UK
- Centre for the Study of the Senses; School of Advanced Study; London UK
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44
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Soteros BM, Cong Q, Palmer CR, Sia GM. Sociability and synapse subtype-specific defects in mice lacking SRPX2, a language-associated gene. PLoS One 2018; 13:e0199399. [PMID: 29920554 PMCID: PMC6007900 DOI: 10.1371/journal.pone.0199399] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/06/2018] [Indexed: 01/05/2023] Open
Abstract
The FoxP2 transcription factor and its target genes have been implicated in developmental brain diseases with a prominent language component, such as developmental verbal dyspraxia and specific language impairment. How FoxP2 affects neural circuitry development remains poorly understood. The sushi domain protein SRPX2 is a target of FoxP2, and mutations in SRPX2 are associated with language defects in humans. We have previously shown that SRPX2 is a synaptogenic protein that increases excitatory synapse density. Here we provide the first characterization of mice lacking the SRPX2 gene, and show that these mice exhibit defects in both neural circuitry and communication and social behaviors. Specifically, we show that mice lacking SRPX2 show a specific reduction in excitatory VGlut2 synapses in the cerebral cortex, while VGlut1 and inhibitory synapses were largely unaffected. SRPX2 KO mice also exhibit an abnormal ultrasonic vocalization ontogenetic profile in neonatal pups, and reduced preference for social novelty. These data demonstrate a functional role for SRPX2 during brain development, and further implicate FoxP2 and its targets in regulating the development of vocalization and social circuits.
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Affiliation(s)
- Breeanne M. Soteros
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Qifei Cong
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
| | - Christian R. Palmer
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, United States of America
| | - Gek-Ming Sia
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States of America
- * E-mail:
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45
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Devanna P, Chen XS, Ho J, Gajewski D, Smith SD, Gialluisi A, Francks C, Fisher SE, Newbury DF, Vernes SC. Next-gen sequencing identifies non-coding variation disrupting miRNA-binding sites in neurological disorders. Mol Psychiatry 2018; 23:1375-1384. [PMID: 28289279 PMCID: PMC5474318 DOI: 10.1038/mp.2017.30] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/17/2016] [Accepted: 01/12/2017] [Indexed: 12/26/2022]
Abstract
Understanding the genetic factors underlying neurodevelopmental and neuropsychiatric disorders is a major challenge given their prevalence and potential severity for quality of life. While large-scale genomic screens have made major advances in this area, for many disorders the genetic underpinnings are complex and poorly understood. To date the field has focused predominantly on protein coding variation, but given the importance of tightly controlled gene expression for normal brain development and disorder, variation that affects non-coding regulatory regions of the genome is likely to play an important role in these phenotypes. Herein we show the importance of 3 prime untranslated region (3'UTR) non-coding regulatory variants across neurodevelopmental and neuropsychiatric disorders. We devised a pipeline for identifying and functionally validating putatively pathogenic variants from next generation sequencing (NGS) data. We applied this pipeline to a cohort of children with severe specific language impairment (SLI) and identified a functional, SLI-associated variant affecting gene regulation in cells and post-mortem human brain. This variant and the affected gene (ARHGEF39) represent new putative risk factors for SLI. Furthermore, we identified 3'UTR regulatory variants across autism, schizophrenia and bipolar disorder NGS cohorts demonstrating their impact on neurodevelopmental and neuropsychiatric disorders. Our findings show the importance of investigating non-coding regulatory variants when determining risk factors contributing to neurodevelopmental and neuropsychiatric disorders. In the future, integration of such regulatory variation with protein coding changes will be essential for uncovering the genetic causes of complex neurological disorders and the fundamental mechanisms underlying health and disease.
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Affiliation(s)
- P Devanna
- Neurogenetics of Vocal Communication
Group, Max Planck Institute for Psycholinguistics, Nijmegen,
The Netherlands
| | - X S Chen
- Language and Genetics Department, Max
Planck Institute for Psycholinguistics, Nijmegen, The
Netherlands
| | - J Ho
- Neurogenetics of Vocal Communication
Group, Max Planck Institute for Psycholinguistics, Nijmegen,
The Netherlands
- Language and Genetics Department, Max
Planck Institute for Psycholinguistics, Nijmegen, The
Netherlands
| | - D Gajewski
- Neurogenetics of Vocal Communication
Group, Max Planck Institute for Psycholinguistics, Nijmegen,
The Netherlands
| | - S D Smith
- Department of Developmental Neuroscience,
Munroe Meyer Institute, University of Nebraska Medical Center,
Omaha, NE, USA
| | - A Gialluisi
- Language and Genetics Department, Max
Planck Institute for Psycholinguistics, Nijmegen, The
Netherlands
- Department of Translational Research in
Psychiatry, Max Planck Institute of Psychiatry, Munich,
Germany
| | - C Francks
- Language and Genetics Department, Max
Planck Institute for Psycholinguistics, Nijmegen, The
Netherlands
- Donders Institute for Brain, Cognition
and Behaviour, Nijmegen, The Netherlands
| | - S E Fisher
- Language and Genetics Department, Max
Planck Institute for Psycholinguistics, Nijmegen, The
Netherlands
- Donders Institute for Brain, Cognition
and Behaviour, Nijmegen, The Netherlands
| | - D F Newbury
- Wellcome Trust Centre for Human Genetics,
University of Oxford, Oxford, UK
- Department of Biological and Medical
Sciences, Faculty of Health and Life Sciences, Oxford Brookes University,
Oxford, UK
| | - S C Vernes
- Neurogenetics of Vocal Communication
Group, Max Planck Institute for Psycholinguistics, Nijmegen,
The Netherlands
- Donders Institute for Brain, Cognition
and Behaviour, Nijmegen, The Netherlands
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46
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Jiménez-Romero S, Carrasco-Salas P, Benítez-Burraco A. Language and Cognitive Impairment Associated with a Novel p.Cys63Arg Change in the MED13L Transcriptional Regulator. Mol Syndromol 2018; 9:83-91. [PMID: 29593475 DOI: 10.1159/000485638] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2017] [Indexed: 12/12/2022] Open
Abstract
Mutations in the MED13L gene, which encodes a subunit of a transcriptional regulatory complex, result in a complex phenotype entailing physical and cognitive anomalies. Deep language impairment has been reported in affected individuals, mostly in patients with copy number variations. We report on a child with a nonsynonymous p.Cys63Arg change in MED13L (chr12:116675396A>G, GRCh37) who exhibits profound language impairment in the expressive domain, cognitive delay, behavioral disturbances, and an autism-like phenotype. Because of the brain areas in which MED13L is expressed and because of the functional links between MED13L and the products of selected candidate genes for cognitive disorders involving language deficits, the proband's linguistic phenotype may result from changes in a functional network important for language development and evolution.
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Affiliation(s)
- Salud Jiménez-Romero
- Maimónides Institute of Biomedical Research, Córdoba, Spain.,Department of Psychology, University of Córdoba, Córdoba, Spain
| | | | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, University of Seville, Seville, Spain
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Benítez-Burraco A, Barcos-Martínez M, Espejo-Portero I, Fernández-Urquiza M, Torres-Ruiz R, Rodríguez-Perales S, Jiménez-Romero MS. Narrowing the Genetic Causes of Language Dysfunction in the 1q21.1 Microduplication Syndrome. Front Pediatr 2018; 6:163. [PMID: 29922639 PMCID: PMC5996825 DOI: 10.3389/fped.2018.00163] [Citation(s) in RCA: 14] [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: 02/12/2018] [Accepted: 05/15/2018] [Indexed: 12/22/2022] Open
Abstract
The chromosome 1q21.1 duplication syndrome (OMIM# 612475) is characterized by head anomalies, mild facial dysmorphisms, and cognitive problems, including autistic features, mental retardation, developmental delay, and learning disabilities. Speech and language development are sometimes impaired, but no detailed characterization of language problems in this condition has been provided to date. We report in detail on the cognitive and language phenotype of a child who presents with a duplication in 1q21.1 (arr[hg19] 1q21.1q21.2(145,764,455-147,824,207) × 3), and who exhibits cognitive delay and behavioral disturbances. Language is significantly perturbed, being the expressive domain the most impaired area (with significant dysphemic features in absence of pure motor speech deficits), although language comprehension and use (pragmatics) are also affected. Among the genes found duplicated in the child, CDH1L is upregulated in the blood of the proband. ROBO1, a candidate for dyslexia, is also highly upregulated, whereas, TLE3, a target of FOXP2, is significantly downregulated. These changes might explain language, and particularly speech dysfunction in the proband.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, University of Seville, Seville, Spain
| | - Montserrat Barcos-Martínez
- Laboratory of Molecular Genetics, University Hospital "Reina Sofía", Córdoba, Spain.,Maimónides Institute of Biomedical Research, Córdoba, Spain
| | - Isabel Espejo-Portero
- Laboratory of Molecular Genetics, University Hospital "Reina Sofía", Córdoba, Spain.,Maimónides Institute of Biomedical Research, Córdoba, Spain
| | | | - Raúl Torres-Ruiz
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncológicas, Madrid, Spain
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XiangWei W, Jiang Y, Yuan H. De Novo Mutations and Rare Variants Occurring in NMDA Receptors. CURRENT OPINION IN PHYSIOLOGY 2017; 2:27-35. [PMID: 29756080 DOI: 10.1016/j.cophys.2017.12.013] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A significant number of variants/mutations in the N-methyl-D-aspartate glutamatergic receptor (NMDAR) gene family (GRIN) have been identified along with stunning advances in the technologies of next generation of whole-exome sequencing. Mutations in human GRIN genes are distributed throughout the entire gene, from amino terminal domain to C-terminal domain, in patients with various neuropsychiatric disorders, including autism spectrum disorders, epilepsy, intellectual disability, attention deficit hyperactivity disorder, and schizophrenia. Analyzing the currently available human genetic variations illustrates the genetic variation intolerance to missense mutations differs significantly among domains within the GRIN genes. Functional analyses of these mutations and their pharmacological profiles provide the first opportunity to understand the molecular mechanism and targeted therapeutic strategies for these neurological and psychiatric disorders, as well as unfold novel clues to channel function.
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Affiliation(s)
- Wenshu XiangWei
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing 100034, China
| | - Yuwu Jiang
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing 100034, China.,Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing 100069, China
| | - Hongjie Yuan
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA 30322, USA
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49
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Deriziotis P, Fisher SE. Speech and Language: Translating the Genome. Trends Genet 2017; 33:642-656. [DOI: 10.1016/j.tig.2017.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/11/2017] [Accepted: 07/12/2017] [Indexed: 01/30/2023]
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50
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Okamoto N, Tsuchiya Y, Miya F, Tsunoda T, Yamashita K, Boroevich KA, Kato M, Saitoh S, Yamasaki M, Kanemura Y, Kosaki K, Kitagawa D. A novel genetic syndrome with STARD9 mutation and abnormal spindle morphology. Am J Med Genet A 2017; 173:2690-2696. [PMID: 28777490 DOI: 10.1002/ajmg.a.38391] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 05/06/2017] [Accepted: 07/14/2017] [Indexed: 11/10/2022]
Abstract
Intellectual disability (ID) is one of neurodevelopmental disorders characterized by serious defects in both intelligence and adaptive behavior. Although it has been suggested that genetic aberrations associated with the process of cell division underlie ID, the cytological evidence for mitotic defects in actual patient's cells is rarely reported. Here, we report a novel mutation in the STARD9 (also known as KIF16A) gene found in a patient with severe ID, characteristic features, epilepsy, acquired microcephaly, and blindness. Using whole-exome sequence analysis, we sequenced potential candidate genes in the patient. We identified a homozygous single-nucleotide deletion creating a premature stop codon in the STARD9 gene. STARD9 encodes a 4,700 amino acid protein belonging to the kinesin superfamily. Depletion of STARD9 or overexpression of C-terminally truncated STARD9 mutants were known to induce spindle assembly defects in human culture cells. To determine cytological features in the patient cells, we isolated lymphoblast cells from the patient, and performed immunofluorescence analysis. Remarkably, mitotic defects, including multipolar spindle formation, fragmentation of pericentriolar materials and centrosome amplification, were observed in the cells. Taken together, our findings raise the possibility that controlled expression of full-length STARD9 is necessary for proper spindle assembly in cell division during human development. We propose that mutations in STARD9 result in abnormal spindle morphology and cause a novel genetic syndrome with ID.
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Affiliation(s)
- Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Osaka, Japan.,Department of Molecular Medicine, Osaka Women's and Children's Hospital, Izumi, Osaka, Japan
| | - Yuki Tsuchiya
- National Institute of Genetics, Department of Molecular Genetics, Division of Centrosome Biology, Mishima, Shizuoka, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Fuyuki Miya
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Tatsuhiko Tsunoda
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Kumiko Yamashita
- Biwako Gakuen Kusatsu Medical and Welfare Center for Children and Persons with Severe Motor and Intellectual Disabilities, Kusatsu, Japan
| | - Keith A Boroevich
- Laboratory for Medical Science Mathematics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Mami Yamasaki
- Department of Pediatric Neurosurgery, Takatsuki General Hospital, Osaka, Japan
| | - Yonehiro Kanemura
- Division of Regenerative Medicine, Institute for Clinical Research, Osaka National Hospital, National Hospital Organization, Osaka, Japan.,Department of Neurosurgery, Osaka National Hospital, National Hospital Organization, Osaka, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Daiju Kitagawa
- National Institute of Genetics, Department of Molecular Genetics, Division of Centrosome Biology, Mishima, Shizuoka, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
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