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Alexander MS, Velinov M. DOCK3-Associated Neurodevelopmental Disorder-Clinical Features and Molecular Basis. Genes (Basel) 2023; 14:1940. [PMID: 37895289 PMCID: PMC10606569 DOI: 10.3390/genes14101940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
The protein product of DOCK3 is highly expressed in neurons and has a role in cell adhesion and neuronal outgrowth through its interaction with the actin cytoskeleton and key cell signaling molecules. The DOCK3 protein is essential for normal cell growth and migration. Biallelic variants in DOCK3 associated with complete or partial loss of function of the gene were recently reported in six patients with intellectual disability and muscle hypotonia. Only one of the reported patients had congenital malformations outside of the CNS. Further studies are necessary to better determine the prevalence of DOCK3-associated neurodevelopmental disorders and the frequency of non-CNS clinical manifestations in these patients. Since deficiency of the DOCK3 protein product is now an established pathway of this neurodevelopmental condition, supplementing the deficient gene product using a gene therapy approach may be an efficient treatment strategy.
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Affiliation(s)
- Matthew S. Alexander
- Department of Pediatrics, Division of Neurology, University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294, USA;
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- UAB Civitan International Research Center (CIRC), University of Alabama at Birmingham, Birmingham, AL 35233, USA
- UAB Center for Neurodegeneration and Experimental Therapeutics (CNET), University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Milen Velinov
- Department of Pediatrics, Division of Genetics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
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2
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Samani A, Karuppasamy M, English KG, Siler CA, Wang Y, Widrick JJ, Alexander MS. DOCK3 regulates normal skeletal muscle regeneration and glucose metabolism. FASEB J 2023; 37:e23198. [PMID: 37742307 PMCID: PMC10539028 DOI: 10.1096/fj.202300386rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/26/2023]
Abstract
DOCK (dedicator of cytokinesis) is an 11-member family of typical guanine nucleotide exchange factors (GEFs) expressed in the brain, spinal cord, and skeletal muscle. Several DOCK proteins have been implicated in maintaining several myogenic processes such as fusion. We previously identified DOCK3 as being strongly upregulated in Duchenne muscular dystrophy (DMD), specifically in the skeletal muscles of DMD patients and dystrophic mice. Dock3 ubiquitous KO mice on the dystrophin-deficient background exacerbated skeletal muscle and cardiac phenotypes. We generated Dock3 conditional skeletal muscle knockout mice (Dock3 mKO) to characterize the role of DOCK3 protein exclusively in the adult muscle lineage. Dock3 mKO mice presented with significant hyperglycemia and increased fat mass, indicating a metabolic role in the maintenance of skeletal muscle health. Dock3 mKO mice had impaired muscle architecture, reduced locomotor activity, impaired myofiber regeneration, and metabolic dysfunction. We identified a novel DOCK3 interaction with SORBS1 through the C-terminal domain of DOCK3 that may account for its metabolic dysregulation. Together, these findings demonstrate an essential role for DOCK3 in skeletal muscle independent of DOCK3 function in neuronal lineages.
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Affiliation(s)
- Adrienne Samani
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Muthukumar Karuppasamy
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Katherine G. English
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Colin A. Siler
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Yimin Wang
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Jeffrey J. Widrick
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew S. Alexander
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
- UAB Center for Exercise Medicine at the University of Alabama at Birmingham, Birmingham, AL, 35294
- Department of Genetics at the University of Alabama at Birmingham, Birmingham, AL 35294
- UAB Civitan International Research Center (CIRC), at the University of Alabama at Birmingham, Birmingham, AL 35233
- UAB Center for Neurodegeneration and Experimental Therapeutics (CNET), Birmingham, AL 35294, USA
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3
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Samani A, Karuppasamy M, English KG, Siler CA, Wang Y, Widrick JJ, Alexander MS. DOCK3 regulates normal skeletal muscle regeneration and glucose metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529576. [PMID: 36865261 PMCID: PMC9980075 DOI: 10.1101/2023.02.22.529576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
DOCK (dedicator of cytokinesis) is an 11-member family of typical guanine nucleotide exchange factors (GEFs) expressed in the brain, spinal cord, and skeletal muscle. Several DOCK proteins have been implicated in maintaining several myogenic processes such as fusion. We previously identified DOCK3 as being strongly upregulated in Duchenne muscular dystrophy (DMD), specifically in the skeletal muscles of DMD patients and dystrophic mice. Dock3 ubiquitous KO mice on the dystrophin-deficient background exacerbated skeletal muscle and cardiac phenotypes. We generated Dock3 conditional skeletal muscle knockout mice (Dock3 mKO) to characterize the role of DOCK3 protein exclusively in the adult muscle lineage. Dock3 mKO mice presented with significant hyperglycemia and increased fat mass, indicating a metabolic role in the maintenance of skeletal muscle health. Dock3 mKO mice had impaired muscle architecture, reduced locomotor activity, impaired myofiber regeneration, and metabolic dysfunction. We identified a novel DOCK3 interaction with SORBS1 through the C-terminal domain of DOCK3 that may account for its metabolic dysregulation. Together, these findings demonstrate an essential role for DOCK3 in skeletal muscle independent of DOCK3 function in neuronal lineages.
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Affiliation(s)
- Adrienne Samani
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Muthukumar Karuppasamy
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Katherine G. English
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Colin A. Siler
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Yimin Wang
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Jeffrey J. Widrick
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew S. Alexander
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
- UAB Center for Exercise Medicine at the University of Alabama at Birmingham, Birmingham, AL, 35294
- Department of Genetics at the University of Alabama at Birmingham, Birmingham, AL 35294
- UAB Civitan International Research Center (CIRC), at the University of Alabama at Birmingham, Birmingham, AL 35233
- UAB Center for Neurodegeneration and Experimental Therapeutics (CNET), Birmingham, AL 35294, USA
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4
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Key role of Rho GTPases in motor disorders associated with neurodevelopmental pathologies. Mol Psychiatry 2023; 28:118-126. [PMID: 35918397 DOI: 10.1038/s41380-022-01702-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 06/24/2022] [Accepted: 07/02/2022] [Indexed: 01/07/2023]
Abstract
Growing evidence suggests that Rho GTPases and molecules involved in their signaling pathways play a major role in the development of the central nervous system (CNS). Whole exome sequencing (WES) and de novo examination of mutations, including SNP (Single Nucleotide Polymorphism) in genes coding for the molecules of their signaling cascade, has allowed the recent discovery of dominant autosomic mutations and duplication or deletion of candidates in the field of neurodevelopmental diseases (NDD). Epidemiological studies show that the co-occurrence of several of these neurological pathologies may indeed be the rule. The regulators of Rho GTPases have often been considered for cognitive diseases such as intellectual disability (ID) and autism. But, in a remarkable way, mild to severe motor symptoms are now reported in autism and other cognitive NDD. Although a more abundant litterature reports the involvement of Rho GTPases and signaling partners in cognitive development, molecular investigations on their roles in central nervous system (CNS) development or degenerative CNS pathologies also reveal their role in embryonic and perinatal motor wiring through axon guidance and later in synaptic plasticity. Thus, Rho family small GTPases have been revealed to play a key role in brain functions including learning and memory but their precise role in motor development and associated symptoms in NDD has been poorly scoped so far, despite increasing clinical data highlighting the links between cognition and motor development. Indeed, early impairements in fine or gross motor performance is often an associated feature of NDDs, which then impact social communication, cognition, emotion, and behavior. We review here recent insights derived from clinical developmental neurobiology in the field of Rho GTPases and NDD (autism spectrum related disorder (ASD), ID, schizophrenia, hypotonia, spastic paraplegia, bipolar disorder and dyslexia), with a specific focus on genetic alterations affecting Rho GTPases that are involved in motor circuit development.
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Vo Ngoc LDT, Osei R, Dohr K, Olsen C, Seneca S, Gheldof A. EDIR: exome database of interspersed repeats. Bioinformatics 2022; 39:6858440. [PMID: 36453866 PMCID: PMC9805566 DOI: 10.1093/bioinformatics/btac771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 11/12/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
MOTIVATION Intragenic exonic deletions are known to contribute to genetic diseases and are often flanked by regions of homology. RESULTS In order to get a more clear view of these interspersed repeats encompassing a coding sequence, we have developed EDIR (Exome Database of Interspersed Repeats) which contains the positions of these structures within the human exome. EDIR has been calculated by an inductive strategy, rather than by a brute force approach and can be queried through an R/Bioconductor package or a web interface allowing the per-gene rapid extraction of homology-flanked sequences throughout the exome. AVAILABILITY AND IMPLEMENTATION The code used to compile EDIR can be found at https://github.com/lauravongoc/EDIR. The full dataset of EDIR can be queried via an Rshiny application at http://193.70.34.71:3857/edir/. The R package for querying EDIR is called 'EDIRquery' and is available on Bioconductor. The full EDIR dataset can be downloaded from https://osf.io/m3gvx/ or http://193.70.34.71/EDIR.tar.gz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Laura D T Vo Ngoc
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Brussels 1090, Belgium
| | - Randy Osei
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Brussels 1090, Belgium
| | - Katrin Dohr
- Department of Paediatrics and Adolescent Medicine, Research Unit of Analytical Mass Spectrometry, Cell Biology and Biochemistry of Inborn Errors of Metabolism, Graz 8010, Austria
| | - Catharina Olsen
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Brussels 1090, Belgium,Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), VUB-ULB, Brussels 1090, Belgium,Interuniversity Institute of Bioinformatics in Brussels (IB)2, VUB-ULB, Brussels 1050, Belgium
| | - Sara Seneca
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Brussels 1090, Belgium
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6
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Samani A, English KG, Lopez MA, Birch CL, Brown DM, Kaur G, Worthey EA, Alexander MS. DOCKopathies: A systematic review of the clinical pathologies associated with human DOCK pathogenic variants. Hum Mutat 2022; 43:1149-1161. [PMID: 35544951 PMCID: PMC9357139 DOI: 10.1002/humu.24398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/29/2022] [Accepted: 05/06/2022] [Indexed: 11/06/2022]
Abstract
The Dedicator of Cytokinesis (DOCK) family (DOCK1-11) of genes are essential mediators of cellular migration, growth, and fusion in a variety of cell types and tissues. Recent advances in whole-genome sequencing of patients with undiagnosed genetic disorders have identified several rare pathogenic variants in DOCK genes. We conducted a systematic review and performed a patient database and literature search of reported DOCK pathogenic variants that have been identified in association with clinical pathologies such as global developmental delay, immune cell dysfunction, muscle hypotonia, and muscle ataxia among other categories. We then categorized these pathogenic DOCK variants and their associated clinical phenotypes under several unique categories: developmental, cardiovascular, metabolic, cognitive, or neuromuscular. Our systematic review of DOCK variants aims to identify and analyze potential DOCK-regulated networks associated with neuromuscular diseases and other disease pathologies, which may identify novel therapeutic strategies and targets. This systematic analysis and categorization of human-associated pathologies with DOCK pathogenic variants is the first report to the best of our knowledge for a unique class in this understudied gene family that has important implications in furthering personalized genomic medicine, clinical diagnoses, and improve targeted therapeutic outcomes across many clinical pathologies.
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Affiliation(s)
- Adrienne Samani
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Katherine G. English
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Michael A. Lopez
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
| | - Camille L. Birch
- Department of Pediatrics, Division of Pediatric Hematology and Oncology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
- Center for Computational Genomics and Data Science at Children’s of Alabama, Birmingham, AL 35294
| | - Donna M. Brown
- Department of Pediatrics, Division of Pediatric Hematology and Oncology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
- Center for Computational Genomics and Data Science at Children’s of Alabama, Birmingham, AL 35294
| | - Gurpreet Kaur
- Department of Pediatrics, Division of Pediatric Hematology and Oncology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
- Center for Computational Genomics and Data Science at Children’s of Alabama, Birmingham, AL 35294
| | - Elizabeth A. Worthey
- Department of Pediatrics, Division of Pediatric Hematology and Oncology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
- Center for Computational Genomics and Data Science at Children’s of Alabama, Birmingham, AL 35294
| | - Matthew S. Alexander
- Department of Pediatrics, Division of Neurology at the University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294
- UAB Center for Exercise Medicine at the University of Alabama at Birmingham, Birmingham, AL, 35294
- Department of Genetics at the University of Alabama at Birmingham, Birmingham, AL 35294
- UAB Civitan International Research Center (CIRC), at the University of Alabama at Birmingham, Birmingham, AL 35233
- UAB Center for Neurodegeneration and Experimental Therapeutics (CNET), Birmingham, AL 35294, USA
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7
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Lange LM, Gonzalez-Latapi P, Rajalingam R, Tijssen MAJ, Ebrahimi-Fakhari D, Gabbert C, Ganos C, Ghosh R, Kumar KR, Lang AE, Rossi M, van der Veen S, van de Warrenburg B, Warner T, Lohmann K, Klein C, Marras C. Nomenclature of Genetic Movement Disorders: Recommendations of the International Parkinson and Movement Disorder Society Task Force - An Update. Mov Disord 2022; 37:905-935. [PMID: 35481685 DOI: 10.1002/mds.28982] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/28/2022] [Accepted: 02/14/2022] [Indexed: 12/13/2022] Open
Abstract
In 2016, the Movement Disorder Society Task Force for the Nomenclature of Genetic Movement Disorders presented a new system for naming genetically determined movement disorders and provided a criterion-based list of confirmed monogenic movement disorders. Since then, a substantial number of novel disease-causing genes have been described, which warrant classification using this system. In addition, with this update, we further refined the system and propose dissolving the imaging-based categories of Primary Familial Brain Calcification and Neurodegeneration with Brain Iron Accumulation and reclassifying these genetic conditions according to their predominant phenotype. We also introduce the novel category of Mixed Movement Disorders (MxMD), which includes conditions linked to multiple equally prominent movement disorder phenotypes. In this article, we present updated lists of newly confirmed monogenic causes of movement disorders. We found a total of 89 different newly identified genes that warrant a prefix based on our criteria; 6 genes for parkinsonism, 21 for dystonia, 38 for dominant and recessive ataxia, 5 for chorea, 7 for myoclonus, 13 for spastic paraplegia, 3 for paroxysmal movement disorders, and 6 for mixed movement disorder phenotypes; 10 genes were linked to combined phenotypes and have been assigned two new prefixes. The updated lists represent a resource for clinicians and researchers alike and they have also been published on the website of the Task Force for the Nomenclature of Genetic Movement Disorders on the homepage of the International Parkinson and Movement Disorder Society (https://www.movementdisorders.org/MDS/About/Committees--Other-Groups/MDS-Task-Forces/Task-Force-on-Nomenclature-in-Movement-Disorders.htm). © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson Movement Disorder Society.
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Affiliation(s)
- Lara M Lange
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Paulina Gonzalez-Latapi
- The Edmond J. Safra Program in Parkinson's Disease and The Morton and Gloria Shulman Movement Disorder Clinic, Toronto Western Hospital, University of Toronto, Toronto, Canada.,Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rajasumi Rajalingam
- The Edmond J. Safra Program in Parkinson's Disease and The Morton and Gloria Shulman Movement Disorder Clinic, Toronto Western Hospital, University of Toronto, Toronto, Canada
| | - Marina A J Tijssen
- UMCG Expertise Centre Movement Disorders, Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Darius Ebrahimi-Fakhari
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Carolin Gabbert
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christos Ganos
- Department of Neurology, Charité University Hospital Berlin, Berlin, Germany
| | - Rhia Ghosh
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Kishore R Kumar
- Molecular Medicine Laboratory and Department of Neurology, Concord Repatriation General Hospital, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Anthony E Lang
- The Edmond J. Safra Program in Parkinson's Disease and The Morton and Gloria Shulman Movement Disorder Clinic, Toronto Western Hospital, University of Toronto, Toronto, Canada
| | - Malco Rossi
- Movement Disorders Section, Neuroscience Department, Raul Carrea Institute for Neurological Research (FLENI), Buenos Aires, Argentina
| | - Sterre van der Veen
- UMCG Expertise Centre Movement Disorders, Department of Neurology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Center of Expertise for Parkinson and Movement Disorders, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tom Warner
- Department of Clinical & Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Connie Marras
- The Edmond J. Safra Program in Parkinson's Disease and The Morton and Gloria Shulman Movement Disorder Clinic, Toronto Western Hospital, University of Toronto, Toronto, Canada
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8
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Chen X, Bai X, Liu H, Zhao B, Yan Z, Hou Y, Chu Q. Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken. Front Genet 2022; 13:830393. [PMID: 35391799 PMCID: PMC8980806 DOI: 10.3389/fgene.2022.830393] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/14/2022] [Indexed: 12/31/2022] Open
Abstract
Copy number variation (CNV) is an important genetic mechanism that drives evolution and generates new phenotypic variations. To explore the impact of CNV on chicken domestication and breed shaping, the whole-genome CNVs were detected via multiple methods. Using the whole-genome sequencing data from 51 individuals, corresponding to six domestic breeds and wild red jungle fowl (RJF), we determined 19,329 duplications and 98,736 deletions, which covered 11,123 copy number variation regions (CNVRs) and 2,636 protein-coding genes. The principal component analysis (PCA) showed that these individuals could be divided into four populations according to their domestication and selection purpose. Seventy-two highly duplicated CNVRs were detected across all individuals, revealing pivotal roles of nervous system (NRG3, NCAM2), sensory (OR), and follicle development (VTG2) in chicken genome. When contrasting the CNVs of domestic breeds to those of RJFs, 235 CNVRs harboring 255 protein-coding genes, which were predominantly involved in pathways of nervous, immunity, and reproductive system development, were discovered. In breed-specific CNVRs, some valuable genes were identified, including HOXB7 for beard trait in Beijing You chicken; EDN3, SLMO2, TUBB1, and GFPT1 for melanin deposition in Silkie chicken; and SORCS2 for aggressiveness in Luxi Game fowl. Moreover, CSMD1 and NTRK3 with high duplications found exclusively in White Leghorn chicken, and POLR3H, MCM9, DOCK3, and AKR1B1L found in Recessive White Rock chicken may contribute to high egg production and fast-growing traits, respectively. The candidate genes of breed characteristics are valuable resources for further studies on phenotypic variation and the artificial breeding of chickens.
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Affiliation(s)
- Xia Chen
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xue Bai
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Binbin Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China
| | - Zhixun Yan
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yali Hou
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,China National Center for Bioinformation, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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9
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Tran V, Goyette MA, Martínez-García M, Jiménez de Domingo A, Fernández-Mayoralas DM, Fernández-Perrone AL, Tirado P, Calleja-Pérez B, Álvarez S, Côté JF, Fernández-Jaén A. Biallelic ELMO3 mutations and loss of function for DOCK-mediated RAC1 activation result in intellectual disability. Small GTPases 2022; 13:48-55. [PMID: 33660564 PMCID: PMC9707537 DOI: 10.1080/21541248.2021.1888557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The engulfment and cell motility 3 (ELMO3) protein belongs to the ELMO-family of proteins. ELMO proteins form a tight complex with the DOCK1-5 guanine nucleotide exchange factors that regulate RAC1 spatiotemporal activation and signalling. DOCK proteins and RAC1 are known to have fundamental roles in central nervous system development. Here, we searched for homozygous or compound heterozygous mutations in the ELMO3 gene in 390 whole exomes sequenced in trio in individuals with neurodevelopmental disorders compatible with a genetic origin. We found a compound heterozygous mutation in ELMO3 (c.1153A>T, p.Ser385Cys and c.1009 G > A, p.Val337Ile) in a 5 year old male child with autism spectrum disorder (ASD) and developmental delay. These mutations did not interfere with the formation of an ELMO3/DOCK1 complex, but markedly impaired the ability of the complex to promote RAC1-GTP-loading. Consequently, cells expressing DOCK1 and either of the ELMO3 mutants displayed impaired migration and invasion. Collectively, our results suggest that biallelic loss-of-function mutations in ELMO3 may cause a developmental delay and provide new insight into the role of ELMO3 in neurodevelopmental as well as the pathological consequences of ELMO3 mutations.
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Affiliation(s)
- Viviane Tran
- Laboratory of Cytoskeletal Organization and Cell Migration, Montreal Clinical Research Institute (IRCM), Montréal, QC, Canada,Department of Biochemistry and Molecular Medicine, Université De Montréal, Montréal, QC, Canada
| | - Marie-Anne Goyette
- Laboratory of Cytoskeletal Organization and Cell Migration, Montreal Clinical Research Institute (IRCM), Montréal, QC, Canada,Molecular Biology Programs, Université De Montréal, Montréal, QC, Canada
| | | | | | | | | | - Pilar Tirado
- Department of Pediatric Neurology. Hospital Universitario La Paz. Madrid. Spain
| | | | - Sara Álvarez
- Department of Genomics and Medicine, NIMGenetics, Madrid, Spain
| | - Jean-François Côté
- Laboratory of Cytoskeletal Organization and Cell Migration, Montreal Clinical Research Institute (IRCM), Montréal, QC, Canada,Department of Biochemistry and Molecular Medicine, Université De Montréal, Montréal, QC, Canada,Molecular Biology Programs, Université De Montréal, Montréal, QC, Canada,Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada
| | - Alberto Fernández-Jaén
- Department of Pediatric Neurology. ónsalud. Madrid. Spain,Department of Pediatric Neurology, Medicine School. Universidad Europea De, Madrid, Spain,CONTACT Alberto Fernández-Jaén Cytoskeletal Organization and Cell Migration Laboratory Montreal Clinical Research Institute (IRCM)110 Avenue Des, Pins, Ouest, Canada
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10
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Scala M, Nishikawa M, Nagata KI, Striano P. Pathophysiological Mechanisms in Neurodevelopmental Disorders Caused by Rac GTPases Dysregulation: What's behind Neuro-RACopathies. Cells 2021; 10:3395. [PMID: 34943902 PMCID: PMC8699292 DOI: 10.3390/cells10123395] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/23/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Rho family guanosine triphosphatases (GTPases) regulate cellular signaling and cytoskeletal dynamics, playing a pivotal role in cell adhesion, migration, and cell cycle progression. The Rac subfamily of Rho GTPases consists of three highly homologous proteins, Rac 1-3. The proper function of Rac1 and Rac3, and their correct interaction with guanine nucleotide-exchange factors (GEFs) and GTPase-activating proteins (GAPs) are crucial for neural development. Pathogenic variants affecting these delicate biological processes are implicated in different medical conditions in humans, primarily neurodevelopmental disorders (NDDs). In addition to a direct deleterious effect produced by genetic variants in the RAC genes, a dysregulated GTPase activity resulting from an abnormal function of GEFs and GAPs has been involved in the pathogenesis of distinctive emerging conditions. In this study, we reviewed the current pertinent literature on Rac-related disorders with a primary neurological involvement, providing an overview of the current knowledge on the pathophysiological mechanisms involved in the neuro-RACopathies.
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Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132 Genoa, Italy;
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Masashi Nishikawa
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai 480-0392, Japan; (M.N.); (K.-i.N.)
| | - Koh-ichi Nagata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, 713-8 Kamiya, Kasugai 480-0392, Japan; (M.N.); (K.-i.N.)
- Department of Neurochemistry, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Nagoya 466-8550, Japan
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16132 Genoa, Italy;
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
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11
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Reid AL, Wang Y, Samani A, Hightower RM, Lopez MA, Gilbert SR, Ianov L, Crossman DK, Dell’Italia LJ, Millay DP, van Groen T, Halade GV, Alexander MS. DOCK3 is a dosage-sensitive regulator of skeletal muscle and Duchenne muscular dystrophy-associated pathologies. Hum Mol Genet 2020; 29:2855-2871. [PMID: 32766788 PMCID: PMC7566544 DOI: 10.1093/hmg/ddaa173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/07/2020] [Accepted: 07/29/2020] [Indexed: 12/26/2022] Open
Abstract
DOCK3 is a member of the DOCK family of guanine nucleotide exchange factors that regulate cell migration, fusion and viability. Previously, we identified a dysregulated miR-486/DOCK3 signaling cascade in dystrophin-deficient muscle, which resulted in the overexpression of DOCK3; however, little is known about the role of DOCK3 in muscle. Here, we characterize the functional role of DOCK3 in normal and dystrophic skeletal muscle. Utilizing Dock3 global knockout (Dock3 KO) mice, we found that the haploinsufficiency of Dock3 in Duchenne muscular dystrophy mice improved dystrophic muscle pathologies; however, complete loss of Dock3 worsened muscle function. Adult Dock3 KO mice have impaired muscle function and Dock3 KO myoblasts are defective for myogenic differentiation. Transcriptomic analyses of Dock3 KO muscles reveal a decrease in myogenic factors and pathways involved in muscle differentiation. These studies identify DOCK3 as a novel modulator of muscle health and may yield therapeutic targets for treating dystrophic muscle symptoms.
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Affiliation(s)
- Andrea L Reid
- Division of Neurology, Department of Pediatrics, The University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294, USA
| | - Yimin Wang
- Division of Neurology, Department of Pediatrics, The University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294, USA
| | - Adrienne Samani
- Division of Neurology, Department of Pediatrics, The University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294, USA
| | - Rylie M Hightower
- Division of Neurology, Department of Pediatrics, The University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294, USA
- UAB Center for Exercise Medicine, Birmingham, AL 35294, USA
| | - Michael A Lopez
- Division of Neurology, Department of Pediatrics, The University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294, USA
- UAB Center for Exercise Medicine, Birmingham, AL 35294, USA
| | - Shawn R Gilbert
- Department of Orthopedic Surgery, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lara Ianov
- Civitan International Research Center, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David K Crossman
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Louis J Dell’Italia
- Birmingham Veteran Affairs Medical Center, Birmingham, AL 35233, USA
- Division of Cardiovascular Disease, Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Douglas P Millay
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Thomas van Groen
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ganesh V Halade
- Division of Cardiovascular Sciences, Department of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Matthew S Alexander
- Division of Neurology, Department of Pediatrics, The University of Alabama at Birmingham and Children’s of Alabama, Birmingham, AL 35294, USA
- UAB Center for Exercise Medicine, Birmingham, AL 35294, USA
- Civitan International Research Center, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
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12
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Wiltrout K, Ferrer A, van de Laar I, Namekata K, Harada T, Klee EW, Zimmerman MT, Cousin MA, Kempainen JL, Babovic-Vuksanovic D, van Slegtenhorst MA, Aarts-Tesselaar CD, Schnur RE, Andrews M, Shinawi M. Variants in DOCK3 cause developmental delay and hypotonia. Eur J Hum Genet 2019; 27:1225-1234. [PMID: 30976111 DOI: 10.1038/s41431-019-0397-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 03/13/2019] [Accepted: 03/26/2019] [Indexed: 01/05/2023] Open
Abstract
The DOCK3 gene encodes the Dedicator of cytokinesis 3 (DOCK3) protein, which belongs to the family of guanine nucleotide exchange factors and is expressed almost exclusively in the brain and spinal cord. We used whole exome sequencing (WES) to investigate the molecular cause of developmental delay and hypotonia in three unrelated probands. WES identified truncating and splice site variants in Patient 1 and compound heterozygous and homozygous missense variants in Patients 2 and 3, respectively. We studied the effect of the three missense variants in vitro by using site-directed mutagenesis and pull-down assay and show that the induction of Rac1 activation was significantly lower in DOCK3 mutant cells compared with wild type human DOCK3 (P < 0.05). We generated a protein model to further examine the effect of the two missense variants within or adjacent to the DHR-2 domain in DOCK3 and this model supports pathogenicity. Our results support a loss of function mechanism but the data on the patients with missense variants should be cautiously interpreted because of the variability of the phenotypes and limited number of cases. Prior studies have described DOCK3 bi-allelic loss of function variants in two families with ataxia, hypotonia, and developmental delay. Here, we report on three patients with DOCK3-related developmental delay, wide-based or uncoordinated gait, and hypotonia, further supporting DOCK3's role in a neurodevelopmental syndrome and expanding the spectrum of phenotypic and genotypic variability.
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Affiliation(s)
- Kimberly Wiltrout
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alejandro Ferrer
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ingrid van de Laar
- Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Kazuhiko Namekata
- Visual Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Takayuki Harada
- Visual Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michael T Zimmerman
- Genomics Sciences & Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | - Marisa Andrews
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
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