1
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Zheng JY, Kang T, Jiang C, Lin LK, Gao L, Jin LH, Shu Y, Zhang JJ, Li C, Chen B, Shen YH. Gut microbiome and brain transcriptome analyses reveal the effect of walnut oil in preventing scopolamine-induced cognitive impairment. Food Funct 2023; 14:9707-9724. [PMID: 37814808 DOI: 10.1039/d3fo01893h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Walnut Oil (WO) is recognized for its potential to improve cognition, but the mechanisms of its action related to improving cognitive impairment are not yet clear. In this study, the components of walnut oil were measured, and it was found that WO supplementation for 8 weeks could significantly prevent cognitive behavioral deficits and synaptic dysfunction induced by intraperitoneal injection of scopolamine (SCOP) in mice. By comparing and analyzing the changes in the hippocampal synaptic structure, oxidative stress, neurotransmitter fluctuations, brain transcriptome, inflammatory factors and gut microbiota in mice from different treatment groups, we observed a significant correlation between synaptic transmission genes, gut microbiota and neurotransmission in the WO supplemented group. It was found that WO supplementation could influence the secretion of neurotransmitters Ach and 5-HT by modulating the gut microbiota in vivo, thereby improving cognitive impairment through the central nervous system and hypothalamic-pituitary-adrenal (HPA) axis regulation.
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Affiliation(s)
- Jing Yi Zheng
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an, Shaanxi 710127, China.
| | - Ting Kang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an, Shaanxi 710127, China.
| | - Chao Jiang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an, Shaanxi 710127, China.
| | - Li Ke Lin
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an, Shaanxi 710127, China.
| | - Lu Gao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an, Shaanxi 710127, China.
| | - Li Hua Jin
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an, Shaanxi 710127, China.
| | - Yu Shu
- College of Food Science and Technology, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jing Jing Zhang
- School of Chemical Engineering, Northwest University, Xi'an, Shaanxi 710069, China
| | - Cong Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an, Shaanxi 710127, China.
| | - Bang Chen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an, Shaanxi 710127, China.
| | - Ye Hua Shen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an, Shaanxi 710127, China.
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2
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Ribasés M, Mitjans M, Hartman CA, Soler Artigas M, Demontis D, Larsson H, Ramos-Quiroga JA, Kuntsi J, Faraone SV, Børglum AD, Reif A, Franke B, Cormand B. Genetic architecture of ADHD and overlap with other psychiatric disorders and cognition-related phenotypes. Neurosci Biobehav Rev 2023; 153:105313. [PMID: 37451654 PMCID: PMC10789879 DOI: 10.1016/j.neubiorev.2023.105313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/30/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) co-occurs with many other psychiatric disorders and traits. In this review, we summarize and interpret the existing literature on the genetic architecture of these comorbidities based on hypothesis-generating approaches. Quantitative genetic studies indicate that genetic factors play a substantial role in the observed co-occurrence of ADHD with many different disorders and traits. Molecular genetic correlations derived from genome-wide association studies and results of studies based on polygenic risk scores confirm the general pattern but provide effect estimates that are smaller than those from twin studies. The identification of the specific genetic variants and biological pathways underlying co-occurrence using genome-wide approaches is still in its infancy. The first analyses of causal inference using genetic data support causal relationships between ADHD and comorbid disorders, although bidirectional effects identified in some instances point to complex relationships. While several issues in the methodology and inferences from the results are still to be overcome, this review shows that the co-occurrence of ADHD with many psychiatric disorders and traits is genetically interpretable.
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Affiliation(s)
- M Ribasés
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain; Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - M Mitjans
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain; Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Catalonia, Spain
| | - C A Hartman
- Department of Psychiatry, Interdisciplinary Center Psychopathology and Emotion regulation (ICPE), University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - M Soler Artigas
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain; Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - D Demontis
- Department of Biomedicine/Human Genetics, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark; The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - H Larsson
- School of Medical Sciences, Örebro University, Örebro, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - J A Ramos-Quiroga
- Department of Mental Health, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), Barcelona, Spain; Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J Kuntsi
- Social, Genetic and Developmental Psychiatry Centre; Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - S V Faraone
- Departments of Psychiatry and of Neuroscience and Physiology, Norton College of Medicine, SUNY Upstate Medical University, Syracuse, NY, USA
| | - A D Børglum
- Department of Biomedicine/Human Genetics, Aarhus University, Aarhus, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark; Center for Genomics and Personalized Medicine, Aarhus, Denmark
| | - A Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - B Franke
- Departments of Cognitive Neuroscience and Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - B Cormand
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IRSJD), Esplugues de Llobregat, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Instituto de Salud Carlos III, Madrid, Spain.
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3
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Domain and cell type-specific immunolocalisation of voltage-gated potassium channels in the mouse striatum. J Chem Neuroanat 2023; 128:102233. [PMID: 36640913 DOI: 10.1016/j.jchemneu.2023.102233] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Diverse classes of voltage-gated potassium channels (Kv) are integral to the variety of electrical activity patterns that distinguish different classes of neurons in the brain. A feature of their heterogenous expression patterns is the highly precise manner in which specific cell types target their location within functionally specialised sub-cellular domains. Although Kv expression profiles in cortical brain regions are widely reported, their immunolocalisation in sub-cortical areas such as the striatum, and in associated diseases such as Parkinson's disease (PD), remain less well described. Therefore, the broad aims of this study were to provide a high resolution immunolocalisation analysis of various Kv subtypes within the mouse striatum and assess their potential plasticity in a model of PD. Immunohistochemistry and confocal microscopy revealed that immunoreactivity for Kv1.1, 1.2 and 1.4 overlapped to varying degrees with excitatory and inhibitory axonal marker proteins suggesting these Kv subtypes are targeted to axons innervating striatal medium spiny neurons (MSNs). Immunoreactivity for Kv1.3 strongly overlapped with signal for mitochondrial marker proteins in MSN somata and dendrites. Kv1.5 immunoreactivity was expressed in parvalbumin-immunopositive neurons whereas Kv1.6 was located in cells immunopositive for microglia. Signal for Kv2.1 was concentrated on the somatic and proximal dendritic plasma membrane of MSNs, whilst immunoreactivity for Kv4.2 was targeted to their distal dendritic regions. Finally, striatal Kv2.1 expression, at both the mRNA and protein levels, was decreased in alpha-synuclein overexpressing mice, yet increased in alpha-synuclein knockout mice, compared to wild-type counterparts. The data indicate a variety of Kv expression patterns that are distinctive to the striatum and susceptible to pathology that mirrors PD. Furthermore, these findings advance our understanding of the molecular diversity of various striatal cell types, and potentially have implications for the homeostatic changes of MSN excitability during associated medical conditions such as PD.
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4
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Leung HW, Foo G, VanDongen A. Arc Regulates Transcription of Genes for Plasticity, Excitability and Alzheimer’s Disease. Biomedicines 2022; 10:biomedicines10081946. [PMID: 36009494 PMCID: PMC9405677 DOI: 10.3390/biomedicines10081946] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 02/06/2023] Open
Abstract
The immediate early gene Arc is a master regulator of synaptic function and a critical determinant of memory consolidation. Here, we show that Arc interacts with dynamic chromatin and closely associates with histone markers for active enhancers and transcription in cultured rat hippocampal neurons. Both these histone modifications, H3K27Ac and H3K9Ac, have recently been shown to be upregulated in late-onset Alzheimer’s disease (AD). When Arc induction by pharmacological network activation was prevented using a short hairpin RNA, the expression profile was altered for over 1900 genes, which included genes associated with synaptic function, neuronal plasticity, intrinsic excitability, and signalling pathways. Interestingly, about 100 Arc-dependent genes are associated with the pathophysiology of AD. When endogenous Arc expression was induced in HEK293T cells, the transcription of many neuronal genes was increased, suggesting that Arc can control expression in the absence of activated signalling pathways. Taken together, these data establish Arc as a master regulator of neuronal activity-dependent gene expression and suggest that it plays a significant role in the pathophysiology of AD.
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Affiliation(s)
| | - Gabriel Foo
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Antonius VanDongen
- Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
- Correspondence:
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5
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Neurodevelopmental Disorders Associated with PSD-95 and Its Interaction Partners. Int J Mol Sci 2022; 23:ijms23084390. [PMID: 35457207 PMCID: PMC9025546 DOI: 10.3390/ijms23084390] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 01/17/2023] Open
Abstract
The postsynaptic density (PSD) is a massive protein complex, critical for synaptic strength and plasticity in excitatory neurons. Here, the scaffolding protein PSD-95 plays a crucial role as it organizes key PSD components essential for synaptic signaling, development, and survival. Recently, variants in DLG4 encoding PSD-95 were found to cause a neurodevelopmental disorder with a variety of clinical features including intellectual disability, developmental delay, and epilepsy. Genetic variants in several of the interaction partners of PSD-95 are associated with similar phenotypes, suggesting that deficient PSD-95 may affect the interaction partners, explaining the overlapping symptoms. Here, we review the transmembrane interaction partners of PSD-95 and their association with neurodevelopmental disorders. We assess how the structural changes induced by DLG4 missense variants may disrupt or alter such protein-protein interactions, and we argue that the pathological effect of DLG4 variants is, at least partly, exerted indirectly through interaction partners of PSD-95. This review presents a direction for functional studies to elucidate the pathogenic mechanism of deficient PSD-95, providing clues for therapeutic strategies.
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6
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Al-Muhaizea MA, Aldeeb H, Almass R, Jaber H, Binhumaid F, Alquait L, Abukhalid M, Aldhalaan H, Alsagob M, Al-Bakheet A, Aldosary M, Alkofide H, Alrasheed MM, Colak D, Kaya N. Genetics of ataxia telangiectasia in a highly consanguineous population. Ann Hum Genet 2021; 86:34-44. [PMID: 34582042 DOI: 10.1111/ahg.12445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/17/2022]
Abstract
Ataxia telangiectasia (AT) is a rare autosomal recessive multisystemic disorder. It usually presents in toddler years with progressive ataxia and oculomotor apraxia, or less commonly, in the late-first or early-second decade of life with mixed movement disorders. Biallelic mutations in ataxia telangiectasia mutated gene (ATM) cause AT phenotype, a disease not well documented in Saudi Arabia, a highly consanguineous society. We studied several Saudi AT patients, identified ATM variants, and investigated associated clinical features. We included 17 patients from 12 consanguineous families. All patients had comprehensive clinical and radiological assessment, and most were examined through whole-exome sequencing (WES). Selected individuals were analyzed using various genetic approaches. We identified five different ATM variants in our patients: three previously reported mutations, and two novel variants. Nearly all patients had classical AT presentation except for two patients with a milder phenotype. Among the three known variants, a deletion causing truncation (c.381delA resulting in p.(Val128Ter)) was identified in 13 patients. Two patients harboured the other two truncating variants, (c.9001_9002delAG resulting in p.Ser3001Phefs*6) and (c.9066delA resulting in p.Glu3023Alafs*10) and two patients had novel compound heterozygous variants (NM_000051.3:Paternal Allele:c.8762C > G;p.Thr2921Arg and Maternal Allele:c.1057T > C;p.Cys353Arg). We speculate that c.381delA is a founder mutation in our population. This study provides a genotype-phenotype relationship in a previously unstudied consanguineous population. Our findings contribute to improve local clinical care, therapy, and genetic counseling.
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Affiliation(s)
- Mohammed A Al-Muhaizea
- Department of Neurosciences, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Hanouf Aldeeb
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia.,Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia.,College of Pharmacy, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Rawan Almass
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia.,Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Hadeel Jaber
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia.,College of Pharmacy, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Felwa Binhumaid
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Laila Alquait
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia.,Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Musaad Abukhalid
- Department of Neurosciences, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Hesham Aldhalaan
- Department of Neurosciences, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Maysoon Alsagob
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia.,King Abdulaziz City for Science and Technology, Riyadh, Kingdom of Saudi Arabia
| | - Albandary Al-Bakheet
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia.,Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Mazhor Aldosary
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia.,Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Hadeel Alkofide
- College of Pharmacy, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Maha M Alrasheed
- College of Pharmacy, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Dilek Colak
- Department of Biostatistics, Epidemiology and Scientific Computing, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
| | - Namik Kaya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia.,Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia
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7
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Aldosary M, Baselm S, Abdulrahim M, Almass R, Alsagob M, AlMasseri Z, Huma R, AlQuait L, Al‐Shidi T, Al‐Obeid E, AlBakheet A, Alahideb B, Alahaidib L, Qari A, Taylor RW, Colak D, AlSayed MD, Kaya N. SLC25A42-associated mitochondrial encephalomyopathy: Report of additional founder cases and functional characterization of a novel deletion. JIMD Rep 2021; 60:75-87. [PMID: 34258143 PMCID: PMC8260478 DOI: 10.1002/jmd2.12218] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/09/2021] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
SLC25A42 is the main transporter of coenzyme A (CoA) into mitochondria. To date, 15 individuals have been reported to have one of two bi-allelic homozygous missense variants in the SLC25A42 as the cause of mitochondrial encephalomyopathy, of which 14 of them were of Saudi origin and share the same founder variant, c.871A > G:p.Asn291Asp. The other subject was of German origin with a variant at canonical splice site, c.380 + 2 T > A. Here, we describe the clinical manifestations and the disease course in additional six Saudi patients from four unrelated consanguineous families. While five patients have the Saudi founder p.Asn291Asp variant, one subject has a novel deletion. Functional analyses on fibroblasts obtained from this patient revealed that the deletion causes significant decrease in mitochondrial oxygen consumption and ATP production compared to healthy individuals. Moreover, extracellular acidification rate revealed significantly reduced glycolysis, glycolytic capacity, and glycolytic reserve as compared to control individuals. There were no changes in the mitochondrial DNA (mtDNA) content of patient fibroblasts. Immunoblotting experiments revealed significantly diminished protein expression due to the deletion. In conclusion, we report additional patients with SLC25A42-associated mitochondrial encephalomyopathy. Our study expands the molecular spectrum of this condition and provides further evidence of mitochondrial dysfunction as a central cause of pathology. We therefore propose that this disorder should be included in the differential diagnosis of any patient with an unexplained motor and speech delay, recurrent encephalopathy with metabolic acidosis, intermittent or persistent dystonia, lactic acidosis, basal ganglia lesions and, especially, of Arab ethnicity. Finally, deep brain stimulation should be considered in the management of patients with life altering dystonia.
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Affiliation(s)
- Mazhor Aldosary
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Shahad Baselm
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Maha Abdulrahim
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Rawan Almass
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Maysoon Alsagob
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- King Abdulaziz City for Science and TechnologyRiyadhSaudi Arabia
| | - Zainab AlMasseri
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Rozeena Huma
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Laila AlQuait
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Tarfa Al‐Shidi
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Eman Al‐Obeid
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Albandary AlBakheet
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Basma Alahideb
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Lujane Alahaidib
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Alya Qari
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Mitochondrial Diagnostic LaboratoryNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Dilek Colak
- Department of Biostatistics, Epidemiology, and Scientific ComputingKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
| | - Moeenaldeen D. AlSayed
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- College of MedicineAlfaisal UniversityRiyadhSaudi Arabia
| | - Namik Kaya
- Department of GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Translational Genomics Department, Center for Genomic Medicine (CGM)King Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
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8
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Luo T, Li K, Ling Z, Zhao G, Li B, Wang Z, Wang X, Han Y, Xia L, Zhang Y, Zhou Q, Fang Z, Wang Y, Chen Q, Zhou X, Pan H, Zhao Y, Wang Y, Dong L, Huang Y, Hu Z, Pan Q, Xia K, Li J. De novo mutations in folate-related genes associated with common developmental disorders. Comput Struct Biotechnol J 2021; 19:1414-1422. [PMID: 33777337 PMCID: PMC7966843 DOI: 10.1016/j.csbj.2021.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 01/23/2023] Open
Abstract
Folate deficiency is an environmental risk factor for several developmental disorders. De novo mutations (DNMs) also play important etiological roles in various developmental disorders. However, it remains unclear whether DNMs in folate-related genes (FRGs) contribute to developmental disorders. We obtained a list of 1,821 FRGs from folate metabolism pathways and the Comparative Toxicogenomics Database, along with data concerning DNMs in 15,404 cases and 3,391 controls from the Gene4Denovo database. We used a TADA-Denovo model to prioritize candidate disease-associated FRGs, and characterized these genes in terms of genic intolerance, functional networks, and expression patterns. Compared with the controls, FRGs were significantly enriched in likely damaging DNMs (ldDNMs) in patients with developmental disorders (1.54 ≤ odds ratio ≤ 3.39, Padj ≤ 0.0075). Furthermore, FRGs with ldDNMs rather than with likely non-damaging DNMs (lndDNMs) overlapped significantly among the five developmental disorders included in the datasets. The TADA-Denovo model prioritized 96 candidate disease-associated FRGs, which were intolerant to genetic variants. Their functional networks mainly involved pathways associated with chromatin modification, organ development, and signal transduction pathways. DNMT3A, KMT2B, KMT2C, and YY1 emerged as hub FRGs from the protein–protein interaction network. These candidate disease-associated FRGs are preferentially expressed in the excitatory neurones during embryonic development, and in the cortex, cerebellum, striatum, and amygdala during foetal development. Overall, these findings show that DNMs in FRGs are associated with the risk of developmental disorders. Further research on these DNMs may facilitate the discovery of developmental disorder biomarkers and therapeutic targets, enabling detailed, personalized, and precise folate treatment plan.
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Key Words
- ADD, all five developmental disorders
- ASD, autism spectrum disorder
- CHD, congenital heart disease
- Candidate disease-associated genes
- DNMs, De novo mutations
- De novo mutation
- Developmental disorders
- Dmis, deleterious missense variants
- EE, epileptic encephalopathy
- Expression patterns
- FRGs, folate-related genes
- Folate-related gene
- ID, intellectual disability
- PPI, Protein–protein interaction
- PTV, protein-truncating variants
- RVIS, residual variation intolerance scores
- SNPs, single nucleotide polymorphisms
- TADA, Transmitted And De novo Association
- Tmis, tolerant missense variants
- UDD, undiagnosed developmental disorder
- ldDNMs, likely damaging DNMs
- lndDNMs, likely non-damaging DNMs
- pLI, probability of loss-of-function intolerance
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Affiliation(s)
- Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kuokuo Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
| | - Zhengbao Ling
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaomeng Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Ying Han
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhenghuan Fang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yijing Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qian Chen
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xun Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongxu Pan
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuwen Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yige Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lijie Dong
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yuanfeng Huang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhengmao Hu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qian Pan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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9
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Al-Muhaizea MA, AlQuait L, AlRasheed A, AlHarbi S, Albader AA, AlMass R, Albakheet A, Alhumaidan A, AlRasheed MM, Colak D, Kaya N. Pyrostigmine therapy in a patient with VAMP1-related congenital myasthenic syndrome. Neuromuscul Disord 2020; 30:611-615. [DOI: 10.1016/j.nmd.2020.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/25/2020] [Accepted: 04/27/2020] [Indexed: 12/19/2022]
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10
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Kessi M, Chen B, Peng J, Tang Y, Olatoutou E, He F, Yang L, Yin F. Intellectual Disability and Potassium Channelopathies: A Systematic Review. Front Genet 2020; 11:614. [PMID: 32655623 PMCID: PMC7324798 DOI: 10.3389/fgene.2020.00614] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/20/2020] [Indexed: 01/15/2023] Open
Abstract
Intellectual disability (ID) manifests prior to adulthood as severe limitations to intellectual function and adaptive behavior. The role of potassium channelopathies in ID is poorly understood. Therefore, we aimed to evaluate the relationship between ID and potassium channelopathies. We hypothesized that potassium channelopathies are strongly associated with ID initiation, and that both gain- and loss-of-function mutations lead to ID. This systematic review explores the burden of potassium channelopathies, possible mechanisms, advancements using animal models, therapies, and existing gaps. The literature search encompassed both PubMed and Embase up to October 2019. A total of 75 articles describing 338 cases were included in this review. Nineteen channelopathies were identified, affecting the following genes: KCNMA1, KCNN3, KCNT1, KCNT2, KCNJ10, KCNJ6, KCNJ11, KCNA2, KCNA4, KCND3, KCNH1, KCNQ2, KCNAB1, KCNQ3, KCNQ5, KCNC1, KCNB1, KCNC3, and KCTD3. Twelve of these genes presented both gain- and loss-of-function properties, three displayed gain-of-function only, three exhibited loss-of-function only, and one had unknown function. How gain- and loss-of-function mutations can both lead to ID remains largely unknown. We identified only a few animal studies that focused on the mechanisms of ID in relation to potassium channelopathies and some of the few available therapeutic options (channel openers or blockers) appear to offer limited efficacy. In conclusion, potassium channelopathies contribute to the initiation of ID in several instances and this review provides a comprehensive overview of which molecular players are involved in some of the most prominent disease phenotypes.
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Affiliation(s)
- Miriam Kessi
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China.,Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Mawenzi Regional Referral Hospital, Moshi, Tanzania
| | - Baiyu Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Yulin Tang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Eleonore Olatoutou
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
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11
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Seidahmed MZ, Hamad MH, AlBakheet A, Elmalik SA, AlDrees A, Al-Sufayan J, Alorainy I, Ghozzi IM, Colak D, Salih MA, Kaya N. Ancient founder mutation in RUBCN: a second unrelated family confirms Salih ataxia (SCAR15). BMC Neurol 2020; 20:207. [PMID: 32450808 PMCID: PMC7249383 DOI: 10.1186/s12883-020-01761-w] [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: 02/05/2020] [Accepted: 05/03/2020] [Indexed: 11/24/2022] Open
Abstract
Background Homozygous frameshift mutation in RUBCN (KIAA0226), known to result in endolysosomal machinery defects, has previously been reported in a single Saudi family with autosomal recessive spinocerebellar ataxia (Salih ataxia, SCAR15, OMIM # 615705). The present report describes the clinical, neurophysiologic, neuroimaging, and genetic findings in a second unrelated Saudi family with two affected children harboring identical homozygous frameshift mutation in the gene. It also explores and documents an ancient founder cerebellar ataxia mutation in the Arabian Peninsula. Case presentation The present family has two affected males (aged 6.5 and 17 years) with unsteady gait apparent since learning to walk at 2.5 and 3 years, respectively. The younger patient showed gait ataxia and normal reflexes. The older patient had saccadic eye movement, dysarthria, mild upper and lower limb and gait ataxia (on tandem walking), and enhanced reflexes in the lower limbs. Cognitive abilities were mildly impaired in the younger sibling (IQ 67) and borderline in the older patient (IQ 72). Nerve conduction studies were normal in both patients. MRI was normal at 2.5 years in the younger sibling. Brain MRI showed normal cerebellar volume and folia in the older sibling at the age of 6 years, and revealed minimal superior vermian atrophy at the age of 16 years. Autozygome and exome analysis showed both affected have previously reported homoallelic mutation in RUBCN (NM_014687:exon18:c.2624delC:p.A875fs), whereas the parents are carriers. Autozygosity mapping focused on smallest haplotype on chromosome 3 and mutation age analysis revealed the mutation occurred approximately 1550 years ago spanning about 62 generations. Conclusions Our findings validate the slowly progressive phenotype of Salih ataxia (SCAR15, OMIM # 615705) by an additional family. Haplotype sharing attests to a common founder, an ancient RUBCN mutation in the Arab population.
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Affiliation(s)
- Mohammed Z Seidahmed
- Neonatology Unit, Department of Pediatrics, Security Forces Hospital, Riyadh, 11481, Saudi Arabia.
| | - Muddathir H Hamad
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Albandary AlBakheet
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, MBC: 03, P.O. Box 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Salah A Elmalik
- Department of Physiology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Abdulmajeed AlDrees
- Department of Physiology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jumanah Al-Sufayan
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, MBC: 03, P.O. Box 3354, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Ibrahim Alorainy
- Department of Radiology and Diagnostic Imaging, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ibrahim M Ghozzi
- Department of Internal Medicine, Division of Neurology, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Dilek Colak
- Department of Biostatistics, Epidemiology, and Scientific Computing, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, MBC: 03, P.O. Box 3354, Riyadh, 11211, Kingdom of Saudi Arabia.
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12
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González-Alvarado MN, Rötger C, Berger L, London B, Haase S, Kuhbandner K, Lee DH, Linker RA. Functional role of endogenous Kv1.4 in experimental demyelination. J Neuroimmunol 2020; 343:577227. [PMID: 32247877 DOI: 10.1016/j.jneuroim.2020.577227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 03/13/2020] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
Abstract
During neuroinflammation, the shaker type potassium channel Kv1.4 is re-expressed in oligodendrocytes (Ol), but not immune cells. Here, we analyze the role of endogenous Kv1.4 in two demyelinating animal models of multiple sclerosis. While Kv1.4 deficiency in primary murine Ol led to a decreased proliferation rate in vitro, it did not exert an effect on Ol proliferation or on the extent of de- or remyelination in the cuprizone model in vivo. However, in experimental autoimmune encephalomyelitis, Kv1.4-/- mice exhibited a milder disease course and reduced Th1 responses. These data argue for an indirect effect of Kv1.4 on immune cells, possibly via glial cells.
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Affiliation(s)
- María Nazareth González-Alvarado
- Department of Neurology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany; Department of Neurology, University of Regensburg, Regensburg, Germany
| | - Caroline Rötger
- Department of Neurology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Laura Berger
- Department of Neurology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Barry London
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Stefanie Haase
- Department of Neurology, University of Regensburg, Regensburg, Germany
| | - Kristina Kuhbandner
- Department of Neurology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - De-Hyung Lee
- Department of Neurology, University of Regensburg, Regensburg, Germany
| | - Ralf A Linker
- Department of Neurology, University of Regensburg, Regensburg, Germany.
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13
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Jędrychowska J, Korzh V. Kv2.1 voltage-gated potassium channels in developmental perspective. Dev Dyn 2019; 248:1180-1194. [PMID: 31512327 DOI: 10.1002/dvdy.114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 11/11/2022] Open
Abstract
Kv2.1 voltage-gated potassium channels consist of two types of α-subunits: (a) electrically-active Kcnb1 α-subunits and (b) silent or modulatory α-subunits plus β-subunits that, similar to silent α-subunits, also regulate electrically-active subunits. Voltage-gated potassium channels were traditionally viewed, mainly by electrophysiologists, as regulators of the electrical activity of the plasma membrane in excitable cells, a role that is performed by transmembrane protein domains of α-subunits that form the electric pore. Genetic studies revealed a role for this region of α-subunits of voltage-gated potassium channels in human neurodevelopmental disorders, such as epileptic encephalopathy. The N- and C-terminal domains of α-subunits interact to form the cytoplasmic subunit of heterotetrameric potassium channels that regulate electric pores. Subsequent animal studies revealed the developmental functions of Kcnb1-containing voltage-gated potassium channels and illustrated their role during brain development and reproduction. These functions of potassium channels are discussed in this review in the context of regulatory interactions between electrically-active and regulatory subunits.
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Affiliation(s)
- Justyna Jędrychowska
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Warsaw Medical University, Warsaw, Poland
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
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14
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Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity. Nat Genet 2018; 51:106-116. [PMID: 30559488 PMCID: PMC6309590 DOI: 10.1038/s41588-018-0288-4] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/23/2018] [Indexed: 12/11/2022]
Abstract
We combined de novo mutation (DNM) data from 10,927 individuals with developmental delay and autism to identify 253 candidate neurodevelopmental disease genes with an excess of missense and/or likely gene-disruptive (LGD) mutations. Of these genes, 124 reach exome-wide significance (P < 5 × 10-7) for DNM. Intersecting these results with copy number variation (CNV) morbidity data shows an enrichment for genomic disorder regions (30/253, likelihood ratio (LR) +1.85, P = 0.0017). We identify genes with an excess of missense DNMs overlapping deletion syndromes (for example, KIF1A and the 2q37 deletion) as well as duplication syndromes, such as recurrent MAPK3 missense mutations within the chromosome 16p11.2 duplication, recurrent CHD4 missense DNMs in the 12p13 duplication region, and recurrent WDFY4 missense DNMs in the 10q11.23 duplication region. Network analyses of genes showing an excess of DNMs highlights functional networks, including cell-specific enrichments in the D1+ and D2+ spiny neurons of the striatum.
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15
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Hubert JN, Zerjal T, Hospital F. Cancer- and behavior-related genes are targeted by selection in the Tasmanian devil (Sarcophilus harrisii). PLoS One 2018; 13:e0201838. [PMID: 30102725 PMCID: PMC6089428 DOI: 10.1371/journal.pone.0201838] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/22/2018] [Indexed: 12/27/2022] Open
Abstract
Devil Facial Tumor Disease (DFTD) is an aggressive cancer notorious for its rare etiology and its impact on Tasmanian devil populations. Two regions underlying an evolutionary response to this cancer were recently identified using genomic time-series pre- and post-DTFD arrival. Here, we support that DFTD shaped the genome of the Tasmanian devil in an even more extensive way than previously reported. We detected 97 signatures of selection, including 148 protein coding genes having a human orthologue, linked to DFTD. Most candidate genes are associated with cancer progression, and an important subset of candidate genes has additional influence on social behavior. This confirms the influence of cancer on the ecology and evolution of the Tasmanian devil. Our work also demonstrates the possibility to detect highly polygenic footprints of short-term selection in very small populations.
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Affiliation(s)
- Jean-Noël Hubert
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
| | - Tatiana Zerjal
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Frédéric Hospital
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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16
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Shi Z, Piccus Z, Zhang X, Yang H, Jarrell H, Ding Y, Teng Z, Tchernichovski O, Li X. miR-9 regulates basal ganglia-dependent developmental vocal learning and adult vocal performance in songbirds. eLife 2018; 7:29087. [PMID: 29345619 PMCID: PMC5800847 DOI: 10.7554/elife.29087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 01/17/2018] [Indexed: 12/15/2022] Open
Abstract
miR-9 is an evolutionarily conserved miRNA that is abundantly expressed in Area X, a basal ganglia nucleus required for vocal learning in songbirds. Here, we report that overexpression of miR-9 in Area X of juvenile zebra finches impairs developmental vocal learning, resulting in a song with syllable omission, reduced similarity to the tutor song, and altered acoustic features. miR-9 overexpression in juveniles also leads to more variable song performance in adulthood, and abolishes social context-dependent modulation of song variability. We further show that these behavioral deficits are accompanied by downregulation of FoxP1 and FoxP2, genes that are known to be associated with language impairments, as well as by disruption of dopamine signaling and widespread changes in the expression of genes that are important in circuit development and functions. These findings demonstrate a vital role for miR-9 in basal ganglia function and vocal communication, suggesting that dysregulation of miR-9 in humans may contribute to language impairments and related neurodevelopmental disorders.
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Affiliation(s)
- Zhimin Shi
- Neuroscience Center of Excellence, Louisiana State University School of Medicine, New Orleans, United States
| | - Zoe Piccus
- Neuroscience Center of Excellence, Louisiana State University School of Medicine, New Orleans, United States
| | - Xiaofang Zhang
- Neuroscience Center of Excellence, Louisiana State University School of Medicine, New Orleans, United States
| | - Huidi Yang
- Neuroscience Center of Excellence, Louisiana State University School of Medicine, New Orleans, United States
| | - Hannah Jarrell
- Neuroscience Center of Excellence, Louisiana State University School of Medicine, New Orleans, United States
| | - Yan Ding
- Neuroscience Center of Excellence, Louisiana State University School of Medicine, New Orleans, United States
| | - Zhaoqian Teng
- Neuroscience Center of Excellence, Louisiana State University School of Medicine, New Orleans, United States
| | | | - XiaoChing Li
- Neuroscience Center of Excellence, Louisiana State University School of Medicine, New Orleans, United States
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