1
|
Fatemi SH, Eschenlauer A, Aman J, Folsom TD, Chekouo T. Quantitative proteomics of dorsolateral prefrontal cortex reveals an early pattern of synaptic dysmaturation in children with idiopathic autism. Cereb Cortex 2024; 34:161-171. [PMID: 38696595 DOI: 10.1093/cercor/bhae044] [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: 12/26/2023] [Accepted: 01/23/2024] [Indexed: 05/04/2024] Open
Abstract
Autism spectrum disorder (ASD) is a developmental disorder with a rising prevalence and unknown etiology presenting with deficits in cognition and abnormal behavior. We hypothesized that the investigation of the synaptic component of prefrontal cortex may provide proteomic signatures that may identify the biological underpinnings of cognitive deficits in childhood ASD. Subcellular fractions of synaptosomes from prefrontal cortices of age-, brain area-, and postmortem-interval-matched samples from children and adults with idiopathic ASD vs. controls were subjected to HPLC-tandem mass spectrometry. Analysis of data revealed the enrichment of ASD risk genes that participate in slow maturation of the postsynaptic density (PSD) structure and function during early brain development. Proteomic analysis revealed down regulation of PSD-related proteins including AMPA and NMDA receptors, GRM3, DLG4, olfactomedins, Shank1-3, Homer1, CaMK2α, NRXN1, NLGN2, Drebrin1, ARHGAP32, and Dock9 in children with autism (FDR-adjusted P < 0.05). In contrast, PSD-related alterations were less severe or unchanged in adult individuals with ASD. Network analyses revealed glutamate receptor abnormalities. Overall, the proteomic data support the concept that idiopathic autism is a synaptopathy involving PSD-related ASD risk genes. Interruption in evolutionarily conserved slow maturation of the PSD complex in prefrontal cortex may lead to the development of ASD in a susceptible individual.
Collapse
Affiliation(s)
- S Hossein Fatemi
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Arthur Eschenlauer
- Minnesota Supercomputing Institute, 599 Walter Library, 117 Pleasant Street, Minneapolis, MN 55455, USA
| | - Justin Aman
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Timothy D Folsom
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Thierry Chekouo
- University of Minnesota School of Public Health, Minneapolis, MN 55455, USA
| |
Collapse
|
2
|
Bischof L, Schweitzer F, Schmitz HP, Heinisch JJ. The small yeast GTPase Rho5 requires specific mitochondrial outer membrane proteins for translocation under oxidative stress and interacts with the VDAC Por1. Eur J Cell Biol 2024; 103:151405. [PMID: 38503132 DOI: 10.1016/j.ejcb.2024.151405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 03/21/2024] Open
Abstract
Yeast Rho5 is a small GTPase which mediates the response to nutrient and oxidative stress, and triggers mitophagy and apoptosis. We here studied the rapid translocation of a GFP-tagged Rho5 to mitochondria under such stress conditions by live-cell fluorescence microscopy in the background of strains lacking different mitochondrial outer membrane proteins (MOMP). Fun14, Msp1 and Alo1 were found to be required for efficient recruitment of the GTPase, whereas translocation of Dck1 and Lmo1, the subunits of its dimeric GDP/GTP exchange factor (GEF), remained unaffected. An influence of the voltage-dependent anion channel (VDAC) Por1 on the association of GFP-Rho5 with mitochondria under oxidative stress conditions appeared to be strain-dependent. However, epistasis analyses and bimolecular fluorescence complementation (BiFC) studies indicate a genetic and physical interaction. All four strains lacking a single MOMP were investigated for their effect on mitophagy.
Collapse
Affiliation(s)
- Linnet Bischof
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Genetik, Barbarastr. 11, Osnabrück D-49076, Germany
| | - Franziska Schweitzer
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Genetik, Barbarastr. 11, Osnabrück D-49076, Germany
| | - Hans-Peter Schmitz
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Genetik, Barbarastr. 11, Osnabrück D-49076, Germany
| | - Jürgen J Heinisch
- Universität Osnabrück, Fachbereich Biologie/Chemie, AG Genetik, Barbarastr. 11, Osnabrück D-49076, Germany.
| |
Collapse
|
3
|
Bischof L, Schweitzer F, Heinisch JJ. Functional Conservation of the Small GTPase Rho5/Rac1-A Tale of Yeast and Men. Cells 2024; 13:472. [PMID: 38534316 DOI: 10.3390/cells13060472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024] Open
Abstract
Small GTPases are molecular switches that participate in many essential cellular processes. Amongst them, human Rac1 was first described for its role in regulating actin cytoskeleton dynamics and cell migration, with a close relation to carcinogenesis. More recently, the role of Rac1 in regulating the production of reactive oxygen species (ROS), both as a subunit of NADPH oxidase complexes and through its association with mitochondrial functions, has drawn attention. Malfunctions in this context affect cellular plasticity and apoptosis, related to neurodegenerative diseases and diabetes. Some of these features of Rac1 are conserved in its yeast homologue Rho5. Here, we review the structural and functional similarities and differences between these two evolutionary distant proteins and propose yeast as a useful model and a device for high-throughput screens for specific drugs.
Collapse
Affiliation(s)
- Linnet Bischof
- AG Genetik, Fachbereich Biologie/Chemie, University of Osnabrück, Barbarastrasse 11, D-49076 Osnabrück, Germany
| | - Franziska Schweitzer
- AG Genetik, Fachbereich Biologie/Chemie, University of Osnabrück, Barbarastrasse 11, D-49076 Osnabrück, Germany
| | - Jürgen J Heinisch
- AG Genetik, Fachbereich Biologie/Chemie, University of Osnabrück, Barbarastrasse 11, D-49076 Osnabrück, Germany
| |
Collapse
|
4
|
Herbst C, Bothe V, Wegler M, Axer-Schaefer S, Audebert-Bellanger S, Gecz J, Cogne B, Feldman HB, Horn AHC, Hurst ACE, Kelly MA, Kruer MC, Kurolap A, Laquerriere A, Li M, Mark PR, Morawski M, Nizon M, Pastinen T, Polster T, Saugier-Veber P, SeSong J, Sticht H, Stieler JT, Thifffault I, van Eyk CL, Marcorelles P, Vezain-Mouchard M, Abou Jamra R, Oppermann H. Heterozygous loss-of-function variants in DOCK4 cause neurodevelopmental delay and microcephaly. Hum Genet 2024; 143:455-469. [PMID: 38526744 PMCID: PMC11043173 DOI: 10.1007/s00439-024-02655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024]
Abstract
Neurons form the basic anatomical and functional structure of the nervous system, and defects in neuronal differentiation or formation of neurites are associated with various psychiatric and neurodevelopmental disorders. Dynamic changes in the cytoskeleton are essential for this process, which is, inter alia, controlled by the dedicator of cytokinesis 4 (DOCK4) through the activation of RAC1. Here, we clinically describe 7 individuals (6 males and one female) with variants in DOCK4 and overlapping phenotype of mild to severe global developmental delay. Additional symptoms include coordination or gait abnormalities, microcephaly, nonspecific brain malformations, hypotonia and seizures. Four individuals carry missense variants (three of them detected de novo) and three individuals carry null variants (two of them maternally inherited). Molecular modeling of the heterozygous missense variants suggests that the majority of them affect the globular structure of DOCK4. In vitro functional expression studies in transfected Neuro-2A cells showed that all missense variants impaired neurite outgrowth. Furthermore, Dock4 knockout Neuro-2A cells also exhibited defects in promoting neurite outgrowth. Our results, including clinical, molecular and functional data, suggest that loss-of-function variants in DOCK4 probable cause a variable spectrum of a novel neurodevelopmental disorder with microcephaly.
Collapse
Affiliation(s)
- Charlotte Herbst
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Viktoria Bothe
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Meret Wegler
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Susanne Axer-Schaefer
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | | | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Hagit Baris Feldman
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anselm H C Horn
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Erlangen National High Performance Computing Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Melissa A Kelly
- HudsonAlpha Clinical Services Lab, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital University of Arizona College of Medicine, Phoenix, USA
| | - Alina Kurolap
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Annie Laquerriere
- Department of Anatomy, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Megan Li
- Invitae Corp, San Francisco, CA, USA
| | - Paul R Mark
- Division of Medical Genetics, Helen DeVos Children's Hospital, Corewell Health, Grand Rapids, MI, USA
| | - Markus Morawski
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Tilman Polster
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | - Pascale Saugier-Veber
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Jang SeSong
- Genomic Medicine Institute, Seoul National University, Seoul, Republic of Korea
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jens T Stieler
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Isabelle Thifffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Clare L van Eyk
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Myriam Vezain-Mouchard
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany.
| |
Collapse
|
5
|
Wang W, Wang M, Peng H, Huang J, Wu T. Association of major depressive disorder and increased risk of irritable bowel syndrome: A population-based cohort study and a two-sample Mendelian randomization study in the UK biobank. J Affect Disord 2024; 345:419-426. [PMID: 37852586 DOI: 10.1016/j.jad.2023.10.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/08/2023] [Accepted: 10/15/2023] [Indexed: 10/20/2023]
Abstract
OBJECTIVE To examine the association between depression and the risk of incident irritable bowel syndrome (IBS). METHODS We included 98,564 participants free of IBS in the UK biobank. Depression was defined by self-report and Hospital Episode Statistics. The main outcome was incident IBS. Cox proportional hazards regression models and two-sample mendelian randomization were performed to estimate the risk of incident IBS. RESULTS Among 98,564 participants, 8770 (8.9 %) participants had a depression diagnosis at baseline. During a median of 12.9-year follow-up, 224 cases of incident IBS were identified in patients with depression (2.0 per 1000 person-years), compared with 1625 cases in reference individuals (1.5 per 1000 person-years). After adjustment, the hazard ratio of incident IBS associated with depression was 1.26 (95 % CI: 1.01-1.41). Sensitivity analysis indicated similar results. The two-sample mendelian randomization based on the inverse variance weighted method provided evidence for the harmful role of depression in an increased risk of IBS with an OR of 1.57 (95 % CI: 1.24-1.99). LIMITATIONS Depression was mainly measured by self-report online CIDI-SF in the current study, rather than the gold diagnostic criteria including clinical structured interview, which might lead to potential measurement error. Lifestyle behaviors might change during the long-term follow-up, and time-varying covariates (i.e., smoking and alcohol status) may bias the estimate. CONCLUSIONS Depression is associated with an increased risk of incident IBS. Further studies are warranted to confirm the role of depression on incident IBS and elucidate the underlying mechanisms.
Collapse
Affiliation(s)
- Weiwei Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China; Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders, National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, 5 Ankang Lane, Xicheng District, Beijing 100088, China
| | - Mengying Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China; Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing 100191, China
| | - Hexiang Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China; Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing 100191, China
| | - Jie Huang
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China; Key Laboratory of Epidemiology of Major Diseases, Peking University, Ministry of Education, Beijing 100191, China.
| |
Collapse
|
6
|
Powis G, Meuillet EJ, Indarte M, Booher G, Kirkpatrick L. Pleckstrin Homology [PH] domain, structure, mechanism, and contribution to human disease. Biomed Pharmacother 2023; 165:115024. [PMID: 37399719 DOI: 10.1016/j.biopha.2023.115024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/14/2023] [Indexed: 07/05/2023] Open
Abstract
The pleckstrin homology [PH] domain is a structural fold found in more than 250 proteins making it the 11th most common domain in the human proteome. 25% of family members have more than one PH domain and some PH domains are split by one, or several other, protein domains although still folding to give functioning PH domains. We review mechanisms of PH domain activity, the role PH domain mutation plays in human disease including cancer, hyperproliferation, neurodegeneration, inflammation, and infection, and discuss pharmacotherapeutic approaches to regulate PH domain activity for the treatment of human disease. Almost half PH domain family members bind phosphatidylinositols [PIs] that attach the host protein to cell membranes where they interact with other membrane proteins to give signaling complexes or cytoskeleton scaffold platforms. A PH domain in its native state may fold over other protein domains thereby preventing substrate access to a catalytic site or binding with other proteins. The resulting autoinhibition can be released by PI binding to the PH domain, or by protein phosphorylation thus providing fine tuning of the cellular control of PH domain protein activity. For many years the PH domain was thought to be undruggable until high-resolution structures of human PH domains allowed structure-based design of novel inhibitors that selectively bind the PH domain. Allosteric inhibitors of the Akt1 PH domain have already been tested in cancer patients and for proteus syndrome, with several other PH domain inhibitors in preclinical development for treatment of other human diseases.
Collapse
Affiliation(s)
- Garth Powis
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA.
| | | | - Martin Indarte
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Garrett Booher
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| | - Lynn Kirkpatrick
- PHusis Therapeutics Inc., 6019 Folsom Drive, La Jolla, CA 92037, USA
| |
Collapse
|
7
|
Wang W, Wang Z, Cao J, Dong Y, Chen Y. Roles of Rac1-Dependent Intrinsic Forgetting in Memory-Related Brain Disorders: Demon or Angel. Int J Mol Sci 2023; 24:10736. [PMID: 37445914 DOI: 10.3390/ijms241310736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Animals are required to handle daily massive amounts of information in an ever-changing environment, and the resulting memories and experiences determine their survival and development, which is critical for adaptive evolution. However, intrinsic forgetting, which actively deletes irrelevant information, is equally important for memory acquisition and consolidation. Recently, it has been shown that Rac1 activity plays a key role in intrinsic forgetting, maintaining the balance of the brain's memory management system in a controlled manner. In addition, dysfunctions of Rac1-dependent intrinsic forgetting may contribute to memory deficits in neurological and neurodegenerative diseases. Here, these new findings will provide insights into the neurobiology of memory and forgetting, pathological mechanisms and potential therapies for brain disorders that alter intrinsic forgetting mechanisms.
Collapse
Affiliation(s)
- Wei Wang
- Neurobiology Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zixu Wang
- Neurobiology Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jing Cao
- Neurobiology Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yulan Dong
- Neurobiology Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yaoxing Chen
- Neurobiology Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, Ministry of Education, Beijing Laboratory of Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| |
Collapse
|
8
|
The neurobiology of irritable bowel syndrome. Mol Psychiatry 2023; 28:1451-1465. [PMID: 36732586 DOI: 10.1038/s41380-023-01972-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/06/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023]
Abstract
Irritable bowel syndrome (IBS) is the most prevalent disorder of brain-gut interactions that affects between 5 and 10% of the general population worldwide. The current symptom criteria restrict the diagnosis to recurrent abdominal pain associated with altered bowel habits, but the majority of patients also report non-painful abdominal discomfort, associated psychiatric conditions (anxiety and depression), as well as other visceral and somatic pain-related symptoms. For decades, IBS was considered an intestinal motility disorder, and more recently a gut disorder. However, based on an extensive body of reported information about central, peripheral mechanisms and genetic factors involved in the pathophysiology of IBS symptoms, a comprehensive disease model of brain-gut-microbiome interactions has emerged, which can explain altered bowel habits, chronic abdominal pain, and psychiatric comorbidities. In this review, we will first describe novel insights into several key components of brain-gut microbiome interactions, starting with reported alterations in the gut connectome and enteric nervous system, and a list of distinct functional and structural brain signatures, and comparing them to the proposed brain alterations in anxiety disorders. We will then point out the emerging correlations between the brain networks with the genomic, gastrointestinal, immune, and gut microbiome-related parameters. We will incorporate this new information into a systems-based disease model of IBS. Finally, we will discuss the implications of such a model for the improved understanding of the disorder and the development of more effective treatment approaches in the future.
Collapse
|
9
|
Lin J, de Rezende VL, de Aguiar da Costa M, de Oliveira J, Gonçalves CL. Cholesterol metabolism pathway in autism spectrum disorder: From animal models to clinical observations. Pharmacol Biochem Behav 2023; 223:173522. [PMID: 36717034 DOI: 10.1016/j.pbb.2023.173522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/18/2022] [Accepted: 01/24/2023] [Indexed: 01/29/2023]
Abstract
Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by a persistent impairment of social skills, including aspects of perception, interpretation, and response, combined with restricted and repetitive behavior. ASD is a complex and multifactorial condition, and its etiology could be attributed to genetic and environmental factors. Despite numerous clinical and experimental studies, no etiological factor, biomarker, and specific model of transmission have been consistently associated with ASD. However, an imbalance in cholesterol levels has been observed in many patients, more specifically, a condition of hypocholesterolemia, which seems to be shared between ASD and ASD-related genetic syndromes such as fragile X syndrome (FXS), Rett syndrome (RS), and Smith- Lemli-Opitz (SLO). Furthermore, it is known that alterations in cholesterol levels lead to neuroinflammation, oxidative stress, impaired myelination and synaptogenesis. Thus, the aim of this review is to discuss the cholesterol metabolic pathways in the ASD context, as well as in genetic syndromes related to ASD, through clinical observations and animal models. In fact, SLO, FXS, and RS patients display early behavioral markers of ASD followed by cholesterol disturbances. Several studies have demonstrated the role of cholesterol in psychiatric conditions and how its levels modulate brain neurodevelopment. This review suggests an important relationship between ASD pathology and cholesterol metabolism impairment; thus, some strategies could be raised - at clinical and pre-clinical levels - to explore whether cholesterol metabolism disturbance has a generally adverse effect in exacerbating the symptoms of ASD patients.
Collapse
Affiliation(s)
- Jaime Lin
- Laboratory of Experimental Neurology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - Victória Linden de Rezende
- Laboratory of Experimental Neurology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - Maiara de Aguiar da Costa
- Laboratory of Experimental Neurology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil
| | - Jade de Oliveira
- Laboratory for Research in Metabolic Disorders and Neurodegenerative Diseases, Graduate Program in Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Cinara Ludvig Gonçalves
- Laboratory of Experimental Neurology, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil.
| |
Collapse
|
10
|
Camilleri M, Zhernakova A, Bozzarelli I, D'Amato M. Genetics of irritable bowel syndrome: shifting gear via biobank-scale studies. Nat Rev Gastroenterol Hepatol 2022; 19:689-702. [PMID: 35948782 DOI: 10.1038/s41575-022-00662-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/29/2022] [Indexed: 12/19/2022]
Abstract
The pathophysiology of irritable bowel syndrome (IBS) is multifactorial and probably involves genetic predisposition and the effect of environmental factors. Unlike other gastrointestinal diseases with a heritable component, genetic research in IBS has been scarce and mostly characterized by small underpowered studies, leading to inconclusive results. The availability of genomic and health-related data from large international cohorts and population-based biobanks offers unprecedented opportunities for long-awaited, well-powered genetic studies in IBS. This Review focuses on the latest advances that provide compelling evidence for the importance of genes involved in the digestion of carbohydrates, ion channel function, neurotransmitters and their receptors, neuronal pathways and the control of gut motility. These discoveries have generated novel information that might be further refined for the identification of predisposed individuals and selection of management strategies for patients. This Review presents a conceptual framework, the advantages and potential limitations of modern genetic research in IBS, and a summary of available evidence.
Collapse
Affiliation(s)
- Michael Camilleri
- Clinical Enteric Neuroscience Translational and Epidemiological Research (CENTER) and Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, Netherlands
| | | | - Mauro D'Amato
- Gastrointestinal Genetics Lab, CIC bioGUNE - BRTA, Derio, Spain. .,Ikerbasque, Basque Foundation for Science, Bilbao, Spain. .,Department of Medicine and Surgery, LUM University, Casamassima, Italy.
| |
Collapse
|
11
|
Dall' Aglio L, Rijlaarsdam J, Mulder RH, Neumann A, Felix JF, Kok R, Bakermans-Kranenburg MJ, van Ijzendoorn MH, Tiemeier H, Cecil CAM. Epigenome-wide associations between observed maternal sensitivity and offspring DNA methylation: a population-based prospective study in children. Psychol Med 2022; 52:2481-2491. [PMID: 33267929 DOI: 10.1017/s0033291720004353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Experimental work in animals has shown that DNA methylation (DNAm), an epigenetic mechanism regulating gene expression, is influenced by typical variation in maternal care. While emerging research in humans supports a similar association, studies to date have been limited to candidate gene and cross-sectional approaches, with a focus on extreme deviations in the caregiving environment. METHODS Here, we explored the prospective association between typical variation in maternal sensitivity and offspring epigenome-wide DNAm, in a population-based cohort of children (N = 235). Maternal sensitivity was observed when children were 3- and 4-years-old. DNAm, quantified with the Infinium 450 K array, was extracted at age 6 (whole blood). The influence of methylation quantitative trait loci (mQTLs), DNAm at birth (cord blood), and confounders (socioeconomic status, maternal psychopathology) was considered in follow-up analyses. RESULTS Genome-wide significant associations between maternal sensitivity and offspring DNAm were observed at 13 regions (p < 1.06 × 10-07), but not at single sites. Follow-up analyses indicated that associations at these regions were in part related to genetic factors, confounders, and baseline DNAm levels at birth, as evidenced by the presence of mQTLs at five regions and estimate attenuations. Robust associations with maternal sensitivity were found at four regions, annotated to ZBTB22, TAPBP, ZBTB12, and DOCK4. CONCLUSIONS These findings provide novel leads into the relationship between typical variation in maternal caregiving and offspring DNAm in humans, highlighting robust regions of associations, previously implicated in psychological and developmental problems, immune functioning, and stress responses.
Collapse
Affiliation(s)
- Lorenza Dall' Aglio
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Center Rotterdam-Sophia Children's Hospital, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jolien Rijlaarsdam
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Center Rotterdam-Sophia Children's Hospital, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rosa H Mulder
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Center Rotterdam-Sophia Children's Hospital, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alexander Neumann
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Center Rotterdam-Sophia Children's Hospital, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rianne Kok
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | | | - Marinus H van Ijzendoorn
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam, Rotterdam, The Netherlands
- Primary Care Unit School of Clinical Medicine, University of Cambridge, UK
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Center Rotterdam-Sophia Children's Hospital, Rotterdam, The Netherlands
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry, Erasmus MC, University Medical Center Rotterdam-Sophia Children's Hospital, Rotterdam, The Netherlands
- Department of Psychology, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| |
Collapse
|
12
|
Huang Y, Yang Y, Zhao Y, Guo D, Chen L, Shi L, Xu G. DOCK4 regulates ghrelin production in gastric X/A-like cells. J Endocrinol Invest 2022; 45:1447-1454. [PMID: 35302184 DOI: 10.1007/s40618-022-01785-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/08/2022] [Indexed: 10/18/2022]
Abstract
PURPOSE Ghrelin, a gastric hormone, provides a hunger signal to the central nervous system to stimulate food intake. Ghrelin also modulates neuroinflammatory and apoptotic processes. Dedicator of cytokinesis 4 (DOCK4), a guanine nucleotide exchange factor (GEF), is involved in the regulation of neuronal polarization and axon regeneration. However, the effect of DOCK4 on ghrelin production has not been explored. METHODS The expression of DOCK4 in human and mouse stomach was examined by immunohistochemical staining. The synthesis and secretion of ghrelin in Dock4 null mice were evaluated by real-time quantitative PCR, Western blot and ELISA. The effects of DOCK4 on ghrelin production in mHypoE-42 cells were measured by real-time quantitative PCR and Western blot. RESULTS We showed that DOCK4 was expressed in both human and mouse gastric ghrelin cells. The mRNA and protein levels of gastric ghrelin, as well as ghrelin secretion, were remarkably diminished in Dock4 null mice. Furthermore, we showed that overexpression of Dock4 significantly stimulated ghrelin expression, while siRNA knockdown of endogenous Dock4 resulted in a marked decrease of ghrelin in mHypoE-N42 cells. CONCLUSIONS Our results identify DOCK4 as a critical regulator for ghrelin production in gastric X/A-like cells.
Collapse
Affiliation(s)
- Y Huang
- Department of Physiology, School of Medicine, Jinan University, 601 Huangpu Avenue West, Tianhe District, Guangzhou, 510632, Guangdong, China
| | - Y Yang
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan University, Guangzhou, Guangdong, China
| | - Y Zhao
- Department of Physiology, School of Medicine, Jinan University, 601 Huangpu Avenue West, Tianhe District, Guangzhou, 510632, Guangdong, China
| | - D Guo
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan University, Guangzhou, Guangdong, China
- The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, China
| | - L Chen
- Department of Physiology, School of Medicine, Jinan University, 601 Huangpu Avenue West, Tianhe District, Guangzhou, 510632, Guangdong, China
| | - L Shi
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan University, Guangzhou, Guangdong, China.
| | - G Xu
- Department of Physiology, School of Medicine, Jinan University, 601 Huangpu Avenue West, Tianhe District, Guangzhou, 510632, Guangdong, China.
| |
Collapse
|
13
|
Núñez-Rios DL, Martínez-Magaña JJ, Nagamatsu ST, Andrade-Brito DE, Forero DA, Orozco-Castaño CA, Montalvo-Ortiz JL. Central and Peripheral Immune Dysregulation in Posttraumatic Stress Disorder: Convergent Multi-Omics Evidence. Biomedicines 2022; 10:biomedicines10051107. [PMID: 35625844 PMCID: PMC9138536 DOI: 10.3390/biomedicines10051107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/29/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Posttraumatic stress disorder (PTSD) is a chronic and multifactorial disorder with a prevalence ranging between 6–10% in the general population and ~35% in individuals with high lifetime trauma exposure. Growing evidence indicates that the immune system may contribute to the etiology of PTSD, suggesting the inflammatory dysregulation as a hallmark feature of PTSD. However, the potential interplay between the central and peripheral immune system, as well as the biological mechanisms underlying this dysregulation remain poorly understood. The activation of the HPA axis after trauma exposure and the subsequent activation of the inflammatory system mediated by glucocorticoids is the most common mechanism that orchestrates an exacerbated immunological response in PTSD. Recent high-throughput analyses in peripheral and brain tissue from both humans with and animal models of PTSD have found that changes in gene regulation via epigenetic alterations may participate in the impaired inflammatory signaling in PTSD. The goal of this review is to assess the role of the inflammatory system in PTSD across tissue and species, with a particular focus on the genomics, transcriptomics, epigenomics, and proteomics domains. We conducted an integrative multi-omics approach identifying TNF (Tumor Necrosis Factor) signaling, interleukins, chemokines, Toll-like receptors and glucocorticoids among the common dysregulated pathways in both central and peripheral immune systems in PTSD and propose potential novel drug targets for PTSD treatment.
Collapse
Affiliation(s)
- Diana L. Núñez-Rios
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06510, USA; (D.L.N.-R.); (J.J.M.-M.); (S.T.N.); (D.E.A.-B.)
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - José J. Martínez-Magaña
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06510, USA; (D.L.N.-R.); (J.J.M.-M.); (S.T.N.); (D.E.A.-B.)
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Sheila T. Nagamatsu
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06510, USA; (D.L.N.-R.); (J.J.M.-M.); (S.T.N.); (D.E.A.-B.)
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Diego E. Andrade-Brito
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06510, USA; (D.L.N.-R.); (J.J.M.-M.); (S.T.N.); (D.E.A.-B.)
- VA CT Healthcare Center, West Haven, CT 06516, USA
| | - Diego A. Forero
- Health and Sport Sciences Research Group, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá 110231, Colombia; (D.A.F.); (C.A.O.-C.)
| | - Carlos A. Orozco-Castaño
- Health and Sport Sciences Research Group, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá 110231, Colombia; (D.A.F.); (C.A.O.-C.)
| | - Janitza L. Montalvo-Ortiz
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06510, USA; (D.L.N.-R.); (J.J.M.-M.); (S.T.N.); (D.E.A.-B.)
- VA CT Healthcare Center, West Haven, CT 06516, USA
- Correspondence: ; Tel.: +1-(203)-9325711 (ext. 7491)
| |
Collapse
|
14
|
Ding S, Cao Y, Lu X, Zhang H, Cong L, Yi T, Xu M, Wang L. Dedicator of cytokinesis 2 (DOCK2) silencing protects against cerebral ischemia/reperfusion by modulating microglia polarization via the activation of the STAT6 signaling pathway. Neuroscience 2022; 491:110-121. [PMID: 35395356 DOI: 10.1016/j.neuroscience.2022.03.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 12/27/2022]
Abstract
Cerebral ischemia/reperfusion is the major pathophysiological process in stroke and could lead to severe and permanent disability. The current study aimed to investigate the effects of dedicator of cytokinesis 2 (DOCK2) on cerebral ischemia/reperfusion-induced cerebral injury. We established a mouse middle cerebral artery occlusion (MCAO) model with suture-occluded method in vivo. Then, BV-2 cells were conducted to oxygen-glucose deprivation and re-oxygenation (OGD/R) in vitro. The results showed that DOCK2 was highly expressed in ischemic brain following MCAO and in BV-2 cells induced by OGD/R. DOCK2 depletion protected against MCAO-induced brain infarcts and neuron degeneration. DOCK2 downregulation improved long-term neurological function, which was assessed by the Morris water-maze test. Moreover, silencing of DOCK2 promoted M2 polarization (anti-inflammation) and repressed M1 polarization (pro-inflammation) of microglia both in vivo and in vitro. Subsequently, we found that the loss of DOCK2 upregulated the expression of p-STAT6. DOCK2 knockdown-induced microglial cell polarization towards M2 phenotype was partly abrogated by the STAT6 inhibitor AS1517499. In conclusion, DOCK2 downregulation protected against cerebral ischemia/reperfusion by modulating microglia polarization via the activation of the STAT6 signaling pathway.
Collapse
Affiliation(s)
- Siwen Ding
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
| | - Yuze Cao
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
| | - Lin Cong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
| | - Tingting Yi
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
| | - Mei Xu
- Department of Neurology, The Second Hospital of Harbin, Harbin, Heilongjiang, China.
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Eijsbouts C, Zheng T, Kennedy NA, Bonfiglio F, Anderson CA, Moutsianas L, Holliday J, Shi J, Shringarpure S, Voda AI, Farrugia G, Franke A, Hübenthal M, Abecasis G, Zawistowski M, Skogholt AH, Ness-Jensen E, Hveem K, Esko T, Teder-Laving M, Zhernakova A, Camilleri M, Boeckxstaens G, Whorwell PJ, Spiller R, McVean G, D'Amato M, Jostins L, Parkes M. Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders. Nat Genet 2021; 53:1543-1552. [PMID: 34741163 PMCID: PMC8571093 DOI: 10.1038/s41588-021-00950-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022]
Abstract
Irritable bowel syndrome (IBS) results from disordered brain-gut interactions. Identifying susceptibility genes could highlight the underlying pathophysiological mechanisms. We designed a digestive health questionnaire for UK Biobank and combined identified cases with IBS with independent cohorts. We conducted a genome-wide association study with 53,400 cases and 433,201 controls and replicated significant associations in a 23andMe panel (205,252 cases and 1,384,055 controls). Our study identified and confirmed six genetic susceptibility loci for IBS. Implicated genes included NCAM1, CADM2, PHF2/FAM120A, DOCK9, CKAP2/TPTE2P3 and BAG6. The first four are associated with mood and anxiety disorders, expressed in the nervous system, or both. Mirroring this, we also found strong genome-wide correlation between the risk of IBS and anxiety, neuroticism and depression (rg > 0.5). Additional analyses suggested this arises due to shared pathogenic pathways rather than, for example, anxiety causing abdominal symptoms. Implicated mechanisms require further exploration to help understand the altered brain-gut interactions underlying IBS.
Collapse
Affiliation(s)
- Chris Eijsbouts
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tenghao Zheng
- Center for Molecular Medicine & Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Nicholas A Kennedy
- IBD Pharmacogenetics, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Ferdinando Bonfiglio
- Center for Molecular Medicine & Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Carl A Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Loukas Moutsianas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Joanne Holliday
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | - Alexandru-Ioan Voda
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Saint Edmund Hall, University of Oxford, Oxford, UK
| | - Gianrico Farrugia
- Enteric NeuroScience Program, Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- Department of Dermatology, Quincke Research Center, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gonçalo Abecasis
- Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Anne Heidi Skogholt
- Department of Laboratory Medicine, Children's and Women's Health, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Eivind Ness-Jensen
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Medicine, Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kristian Hveem
- Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Maris Teder-Laving
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Michael Camilleri
- Clinical Enteric Neuroscience Translational and Epidemiological Research and Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Guy Boeckxstaens
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter J Whorwell
- Neurogastroenterology Unit, Wythenshawe Hospital, Centre for Gastrointestinal Sciences, University of Manchester, Manchester, UK
| | - Robin Spiller
- Nottingham Digestive Diseases Centre, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Mauro D'Amato
- Center for Molecular Medicine & Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.
- Biodonostia Health Research Institute, San Sebastian, Spain.
- Gastrointestinal Genetics Lab, CIC bioGUNE - Basque Research and Technology Alliance, Derio, Spain.
- IKERBASQUE, The Basque Science Foundation, Bilbao, Spain.
| | - Luke Jostins
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
- Christ Church, University of Oxford, Oxford, UK.
| | - Miles Parkes
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Gastroenterology, Cambridge University Hospital, Cambridge, UK.
| |
Collapse
|
18
|
Panitch R, Hu J, Chung J, Zhu C, Meng G, Xia W, Bennett DA, Lunetta KL, Ikezu T, Au R, Stein TD, Farrer LA, Jun GR. Integrative brain transcriptome analysis links complement component 4 and HSPA2 to the APOE ε2 protective effect in Alzheimer disease. Mol Psychiatry 2021; 26:6054-6064. [PMID: 34480088 PMCID: PMC8758485 DOI: 10.1038/s41380-021-01266-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 07/07/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
Mechanisms underlying the protective effect of apolipoprotein E (APOE) ε2 against Alzheimer disease (AD) are not well understood. We analyzed gene expression data derived from autopsied brains donated by 982 individuals including 135 APOE ɛ2/ɛ3 carriers. Complement pathway genes C4A and C4B were among the most significantly differentially expressed genes between ɛ2/ɛ3 AD cases and controls. We also identified an APOE ε2/ε3 AD-specific co-expression network enriched for astrocytes, oligodendrocytes and oligodendrocyte progenitor cells containing the genes C4A, C4B, and HSPA2. These genes were significantly associated with the ratio of phosphorylated tau at position 231 to total Tau but not with amyloid-β 42 level, suggesting this APOE ɛ2 related co-expression network may primarily be involved with tau pathology. HSPA2 expression was oligodendrocyte-specific and significantly associated with C4B protein. Our findings provide the first evidence of a crucial role of the complement pathway in the protective effect of APOE ε2 for AD.
Collapse
Affiliation(s)
- Rebecca Panitch
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Junming Hu
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Congcong Zhu
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Gaoyuan Meng
- Department of Veterans Affairs Medical Center, Bedford, MA, USA
| | - Weiming Xia
- Department of Veterans Affairs Medical Center, Bedford, MA, USA
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Tsuneya Ikezu
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Center for Systems Neuroscience, Boston University School of Medicine, Boston, MA, USA
| | - Rhoda Au
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Anatomy & Neurobiology, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Thor D Stein
- Department of Veterans Affairs Medical Center, Bedford, MA, USA
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA.
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA.
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, USA.
| | - Gyungah R Jun
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA.
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, USA.
| |
Collapse
|
19
|
Mosaddeghzadeh N, Ahmadian MR. The RHO Family GTPases: Mechanisms of Regulation and Signaling. Cells 2021; 10:1831. [PMID: 34359999 PMCID: PMC8305018 DOI: 10.3390/cells10071831] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 12/27/2022] Open
Abstract
Much progress has been made toward deciphering RHO GTPase functions, and many studies have convincingly demonstrated that altered signal transduction through RHO GTPases is a recurring theme in the progression of human malignancies. It seems that 20 canonical RHO GTPases are likely regulated by three GDIs, 85 GEFs, and 66 GAPs, and eventually interact with >70 downstream effectors. A recurring theme is the challenge in understanding the molecular determinants of the specificity of these four classes of interacting proteins that, irrespective of their functions, bind to common sites on the surface of RHO GTPases. Identified and structurally verified hotspots as functional determinants specific to RHO GTPase regulation by GDIs, GEFs, and GAPs as well as signaling through effectors are presented, and challenges and future perspectives are discussed.
Collapse
Affiliation(s)
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty of the Heinrich Heine University, Universitätsstrasse 1, Building 22.03.05, 40225 Düsseldorf, Germany;
| |
Collapse
|
20
|
Zhang A, Fang J, Hu W, Calhoun VD, Wang YP. A Latent Gaussian Copula Model for Mixed Data Analysis in Brain Imaging Genetics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1350-1360. [PMID: 31689199 PMCID: PMC7756188 DOI: 10.1109/tcbb.2019.2950904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent advances in imaging genetics make it possible to combine different types of data including medical images like functional magnetic resonance imaging (fMRI) and genetic data like single nucleotide polymorphisms (SNPs) for comprehensive diagnosis of mental disorders. Understanding complex interactions among these heterogeneous data may give rise to a new perspective, while at the same time demand statistical models for their integration. Various graphical models have been proposed for the study of interaction or association networks with continuous, binary, and count data as well as the mixture of them. However, limited efforts have been made for the multinomial case, for instance, SNP data. Our goal is therefore to fill the void by developing a graphical model for the integration of fMRI image and SNP data, which can provide deeper understanding of the unknown neurogenetic mechanism. In this article, we propose a latent Gaussian copula model for mixed data containing multinomial components. We assume that the discrete variable is obtained by discretizing a latent (unobserved) continuous variable and then create a semi-rank based estimator of the graph structure. The simulation results demonstrate that the proposed latent correlation has more steady and accurate performance than several existing methods in detecting graph structure. When applying to a real schizophrenia data consisting of SNP array and fMRI image collected by the Mind Clinical Imaging Consortium (MCIC), the proposed method reveals a set of distinct SNP-brain associations, which are verified to be biologically significant. The proposed model is statistically promising in handling mixed types of data including multinomial components, which can find widespread applications. To promote reproducible research, the R code is available at https://github.com/Aiying0512/LGCM.
Collapse
|
21
|
Yousefnezhad S, Gharesouran J, Ghafouri-Fard S, Hosseinzadeh H, Ahmadian-Heris J, Jafari-Rouhi AH, Taheri M, Rezazadeh M. DOCK8-related Immunodeficiency Syndrome (DIDS): Report of Novel Mutations in Iranian Patients. J Mol Neurosci 2021; 71:2456-2461. [PMID: 33948880 DOI: 10.1007/s12031-021-01843-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
DOCK8 immunodeficiency syndrome (DIDS) is a rare autosomal recessive (AR) disorder characterized by elevated serum IgE levels, eosinophilia, recurrent cutaneous infections, severe eczema, and sinopulmonary and gastrointestinal infections. This syndrome is a multisystem disease that is associated with both immune deficiency and neurological complications. In this study, we describe the clinical characteristics of two Iranian patients with DOCK8 deficiency and propose possible mechanisms for this condition. By using whole exome sequencing (WES), we identified two novel mutations, namely c.3233_3234del AG (p.Q1078fs) in exon 6 and a large deletion with 94 kb (c.405-3231 deletion, p.K135fs), in these two patients. These variations are confirmed with Sanger sequencing and CGH array. Subsequent co-segregation analysis is performed to identify inheritance patterns. Both patients were homozygote and their parents were heterozygote for the variations. For further investigation, prediction tools were applied to identify the pathogenicity of the variations and also for modeling the truncated proteins. The patients did not show neurological abnormalities associated with a deficiency of the N terminal region of DOCK8. The absence of neurological complications in the first patient is justifiable due to the maintenance of the proline-rich region in DOCK8, but for the second patient with expanded deletion which is almost like null DOCK8 protein, it is not presumable, pointing to the fact that the C terminal region of the protein might have functions in the proliferation and migration neurons in the peripheral nervous system. Alternatively, it is possible that neurological abnormalities follow an age-dependent pattern, leading to the appearance of related symptoms later in life. Further multiple functional studies are needed to model different identified variants in animal models to confirm our results and suggest possible mechanisms associated with DOCK8 deficiency in this study.
Collapse
Affiliation(s)
| | - Jalal Gharesouran
- Molecular Genetics Division, GMG center, Tabriz, Iran.,Division of Medical Genetics, Tabriz Children's Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hassan Hosseinzadeh
- Molecular Genetics Division, GMG center, Tabriz, Iran.,Department of Allergy and Clinical Immunology, Tabriz Children's Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javad Ahmadian-Heris
- Division of Medical Genetics, Tabriz Children's Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Maryam Rezazadeh
- Division of Medical Genetics, Tabriz Children's Hospital, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
22
|
Ithal D, Sukumaran SK, Bhattacharjee D, Vemula A, Nadella R, Mahadevan J, Sud R, Viswanath B, Purushottam M, Jain S. Exome hits demystified: The next frontier. Asian J Psychiatr 2021; 59:102640. [PMID: 33892377 DOI: 10.1016/j.ajp.2021.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022]
Abstract
Severe mental illnesses such as schizophrenia and bipolar disorder have complex inheritance patterns, involving both common and rare variants. Whole exome sequencing is a promising approach to find out the rare genetic variants. We had previously reported several rare variants in multiplex families with severe mental illnesses. The current article tries to summarise the biological processes and pattern of expression of genes harbouring the aforementioned variants, linking them to known clinical manifestations through a methodical narrative review. Of the 28 genes considered for this review from 7 families with multiple affected individuals, 6 genes are implicated in various neuropsychiatric manifestations including some variations in the brain morphology assessed by magnetic resonance imaging. Another 15 genes, though associated with neuropsychiatric manifestations, did not have established brain morphological changes whereas the remaining 7 genes did not have any previously recorded neuropsychiatric manifestations at all. Wnt/b-catenin signaling pathway was associated with 6 of these genes and PI3K/AKT, calcium signaling, ERK, RhoA and notch signaling pathways had at least 2 gene associations. We present a comprehensive review of biological and clinical knowledge about the genes previously reported in multiplex families with severe mental illness. A 'disease in dish approach' can be helpful to further explore the fundamental mechanisms.
Collapse
Affiliation(s)
- Dhruva Ithal
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Salil K Sukumaran
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Debanjan Bhattacharjee
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Alekhya Vemula
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Ravi Nadella
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Jayant Mahadevan
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Reeteka Sud
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India.
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| |
Collapse
|
23
|
Thompson AP, Bitsina C, Gray JL, von Delft F, Brennan PE. RHO to the DOCK for GDP disembarking: Structural insights into the DOCK GTPase nucleotide exchange factors. J Biol Chem 2021; 296:100521. [PMID: 33684443 PMCID: PMC8063744 DOI: 10.1016/j.jbc.2021.100521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 01/16/2023] Open
Abstract
The human dedicator of cytokinesis (DOCK) family consists of 11 structurally conserved proteins that serve as atypical RHO guanine nucleotide exchange factors (RHO GEFs). These regulatory proteins act as mediators in numerous cellular cascades that promote cytoskeletal remodeling, playing roles in various crucial processes such as differentiation, migration, polarization, and axon growth in neurons. At the molecular level, DOCK DHR2 domains facilitate nucleotide dissociation from small GTPases, a process that is otherwise too slow for rapid spatiotemporal control of cellular signaling. Here, we provide an overview of the biological and structural characteristics for the various DOCK proteins and describe how they differ from other RHO GEFs and between DOCK subfamilies. The expression of the family varies depending on cell or tissue type, and they are consequently implicated in a broad range of disease phenotypes, particularly in the brain. A growing body of available structural information reveals the mechanism by which the catalytic DHR2 domain elicits nucleotide dissociation and also indicates strategies for the discovery and design of high-affinity small-molecule inhibitors. Such compounds could serve as chemical probes to interrogate the cellular function and provide starting points for drug discovery of this important class of enzymes.
Collapse
Affiliation(s)
- Andrew P Thompson
- Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Christina Bitsina
- Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Janine L Gray
- Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Frank von Delft
- Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom; Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Paul E Brennan
- Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom.
| |
Collapse
|
24
|
Wu CC, Shields JN, Akemann C, Meyer DN, Connell M, Baker BB, Pitts DK, Baker TR. The phenotypic and transcriptomic effects of developmental exposure to nanomolar levels of estrone and bisphenol A in zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143736. [PMID: 33243503 PMCID: PMC7790172 DOI: 10.1016/j.scitotenv.2020.143736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/12/2020] [Accepted: 11/09/2020] [Indexed: 04/14/2023]
Abstract
Estrone and BPA are two endocrine disrupting chemicals (EDCs) that are predicted to be less potent than estrogens such as 17β-estradiol and 17α-ethinylestradiol. Human exposure concentrations to estrone and BPA can be as low as nanomolar levels. However, very few toxicological studies have focused on the nanomolar-dose effects. Low level of EDCs can potentially cause non-monotonic responses. In addition, exposures at different developmental stages can lead to different health outcomes. To identify the nanomolar-dose effects of estrone and BPA, we used zebrafish modeling to study the phenotypic and transcriptomic responses after extended duration exposure from 0 to 5 days post-fertilization (dpf) and short-term exposure at days 4-5 post fertilization. We found that non-monotonic transcriptomic responses occurred after extended duration exposures at 1 nM of estrone or BPA. At this level, estrone also caused hypoactivity locomotive behavior in zebrafish. After both extended duration and short-term exposures, BPA led to more apparent phenotypic responses, i.e. skeletal abnormalities and locomotion changes, and more significant transcriptomic responses than estrone exposure. After short-term exposure, BPA at concentrations equal or above 100 nM affected locomotive behavior and changed the expression of both estrogenic and non-estrogenic genes that are linked to neurological diseases. These data provide gaps of mechanisms between neurological genes expression and associated phenotypic response due to estrone or BPA exposures. This study also provides insights for assessing the acceptable concentration of BPA and estrone in aquatic environments.
Collapse
Affiliation(s)
- Chia-Chen Wu
- Institute of Environmental Health Sciences, Wayne State University, 6135 Woodward Ave, Detroit, MI 48202, USA
| | - Jeremiah N Shields
- Institute of Environmental Health Sciences, Wayne State University, 6135 Woodward Ave, Detroit, MI 48202, USA
| | - Camille Akemann
- Institute of Environmental Health Sciences, Wayne State University, 6135 Woodward Ave, Detroit, MI 48202, USA; Department of Pharmacology, Wayne State University, 540 E Canfield, Detroit, MI 28201, USA
| | - Danielle N Meyer
- Institute of Environmental Health Sciences, Wayne State University, 6135 Woodward Ave, Detroit, MI 48202, USA; Department of Pharmacology, Wayne State University, 540 E Canfield, Detroit, MI 28201, USA
| | - Mackenzie Connell
- Institute of Environmental Health Sciences, Wayne State University, 6135 Woodward Ave, Detroit, MI 48202, USA
| | - Bridget B Baker
- Institute of Environmental Health Sciences, Wayne State University, 6135 Woodward Ave, Detroit, MI 48202, USA
| | - David K Pitts
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Tracie R Baker
- Institute of Environmental Health Sciences, Wayne State University, 6135 Woodward Ave, Detroit, MI 48202, USA; Department of Pharmacology, Wayne State University, 540 E Canfield, Detroit, MI 28201, USA.
| |
Collapse
|
25
|
Benson CE, Southgate L. The DOCK protein family in vascular development and disease. Angiogenesis 2021; 24:417-433. [PMID: 33548004 PMCID: PMC8292242 DOI: 10.1007/s10456-021-09768-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/06/2021] [Accepted: 01/16/2021] [Indexed: 02/07/2023]
Abstract
The vascular network is established and maintained through the processes of vasculogenesis and angiogenesis, which are tightly regulated during embryonic and postnatal life. The formation of a functional vasculature requires critical cellular mechanisms, such as cell migration, proliferation and adhesion, which are dependent on the activity of small Rho GTPases, controlled in part by the dedicator of cytokinesis (DOCK) protein family. Whilst the majority of DOCK proteins are associated with neuronal development, a growing body of evidence has indicated that members of the DOCK family may have key functions in the control of vasculogenic and angiogenic processes. This is supported by the involvement of several angiogenic signalling pathways, including chemokine receptor type 4 (CXCR4), vascular endothelial growth factor (VEGF) and phosphatidylinositol 3-kinase (PI3K), in the regulation of specific DOCK proteins. This review summarises recent progress in understanding the respective roles of DOCK family proteins during vascular development. We focus on existing in vivo and in vitro models and known human disease phenotypes and highlight potential mechanisms of DOCK protein dysfunction in the pathogenesis of vascular disease.
Collapse
Affiliation(s)
- Clare E Benson
- Genetics Research Centre, Molecular and Clinical Sciences Research Institute, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Laura Southgate
- Genetics Research Centre, Molecular and Clinical Sciences Research Institute, St. George's University of London, Cranmer Terrace, London, SW17 0RE, UK. .,Department of Medical & Molecular Genetics, Faculty of Life Sciences & Medicine, King's College London, London, SE1 9RT, UK.
| |
Collapse
|
26
|
Bone WP, Siewert KM, Jha A, Klarin D, Damrauer SM, Chang KM, Tsao PS, Assimes TL, Ritchie MD, Voight BF. Multi-trait association studies discover pleiotropic loci between Alzheimer's disease and cardiometabolic traits. Alzheimers Res Ther 2021; 13:34. [PMID: 33541420 PMCID: PMC7860582 DOI: 10.1186/s13195-021-00773-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Identification of genetic risk factors that are shared between Alzheimer's disease (AD) and other traits, i.e., pleiotropy, can help improve our understanding of the etiology of AD and potentially detect new therapeutic targets. Previous epidemiological correlations observed between cardiometabolic traits and AD led us to assess the pleiotropy between these traits. METHODS We performed a set of bivariate genome-wide association studies coupled with colocalization analysis to identify loci that are shared between AD and eleven cardiometabolic traits. For each of these loci, we performed colocalization with Genotype-Tissue Expression (GTEx) project expression quantitative trait loci (eQTL) to identify candidate causal genes. RESULTS We identified three previously unreported pleiotropic trait associations at known AD loci as well as four novel pleiotropic loci. One associated locus was tagged by a low-frequency coding variant in the gene DOCK4 and is potentially implicated in its alternative splicing. Colocalization with GTEx eQTL data identified additional candidate genes for the loci we detected, including ACE, the target of the hypertensive drug class of ACE inhibitors. We found that the allele associated with decreased ACE expression in brain tissue was also associated with increased risk of AD, providing human genetic evidence of a potential increase in AD risk from use of an established anti-hypertensive therapeutic. CONCLUSION Our results support a complex genetic relationship between AD and these cardiometabolic traits, and the candidate causal genes identified suggest that blood pressure and immune response play a role in the pleiotropy between these traits.
Collapse
Affiliation(s)
- William P Bone
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Katherine M Siewert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Anupama Jha
- Department of Computer and Information Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Derek Klarin
- Boston VA Healthcare System, Boston, MA, 02130, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Scott M Damrauer
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, PA, 19104, Philadelphia, USA
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kyong-Mi Chang
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Philip S Tsao
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Themistocles L Assimes
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Precision Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Benjamin F Voight
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, 19104, USA.
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
27
|
Autism-like social deficit generated by Dock4 deficiency is rescued by restoration of Rac1 activity and NMDA receptor function. Mol Psychiatry 2021; 26:1505-1519. [PMID: 31388105 PMCID: PMC8159750 DOI: 10.1038/s41380-019-0472-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 06/01/2019] [Accepted: 06/24/2019] [Indexed: 12/20/2022]
Abstract
Genetic studies of autism spectrum disorder (ASD) have revealed multigene variations that converge on synaptic dysfunction. DOCK4, a gene at 7q31.1 that encodes the Rac1 guanine nucleotide exchange factor Dock4, has been identified as a risk gene for ASD and other neuropsychiatric disorders. However, whether and how Dock4 disruption leads to ASD features through a synaptic mechanism remain unexplored. We generated and characterized a line of Dock4 knockout (KO) mice, which intriguingly displayed a series of ASD-like behaviors, including impaired social novelty preference, abnormal isolation-induced pup vocalizations, elevated anxiety, and perturbed object and spatial learning. Mice with conditional deletion of Dock4 in hippocampal CA1 recapitulated social preference deficit in KO mice. Examination in CA1 pyramidal neurons revealed that excitatory synaptic transmission was drastically attenuated in KO mice, accompanied by decreased spine density and synaptic content of AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid)- and NMDA (N-methyl-D-aspartate)-type glutamate receptors. Moreover, Dock4 deficiency markedly reduced Rac1 activity in the hippocampus, which resulted in downregulation of global protein synthesis and diminished expression of AMPA and NMDA receptor subunits. Notably, Rac1 replenishment in the hippocampal CA1 of Dock4 KO mice restored excitatory synaptic transmission and corrected impaired social deficits in these mice, and pharmacological activation of NMDA receptors also restored social novelty preference in Dock4 KO mice. Together, our findings uncover a previously unrecognized Dock4-Rac1-dependent mechanism involved in regulating hippocampal excitatory synaptic transmission and social behavior.
Collapse
|
28
|
Umehara H, Nakamura M, Nagai M, Kato Y, Ueno SI, Sano A. Positional cloning and comprehensive mutation analysis of a Japanese family with lithium-responsive bipolar disorder identifies a novel DOCK5 mutation. J Hum Genet 2020; 66:243-249. [PMID: 32920599 DOI: 10.1038/s10038-020-00840-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/09/2022]
Abstract
Bipolar disorder (BD) is a severe psychiatric disorder characterized by the recurrence of depressive and manic episodes. Its heritability is high, and many linkage and association studies have been performed. Although various linkage regions and candidate genes have been reported, few have shown sufficient reproducibility, and none have identified the pathogenic genes based on the results of the linkage analysis. To find functional variants that are expected to be rare and have strong genetic effects, we recruited ten healthy individuals, two individuals with unknown status, and six patients with BD or recurrent major depressive disorder (MDD) from a Japanese family consisting of 21 members. We performed a genome-wide linkage analysis using a 100K single-nucleotide polymorphism (SNP) array and microsatellite markers to narrow linkage regions within this family. Subsequently, we performed whole-exome sequencing for two patients with BD to identify genetic mutations in the narrowed linkage regions. Then, we performed co-segregation analysis for DNA variants obtained from the results of the exome sequencing. Finally, we identified a rare heterozygous mutation in exon 31 of DOCK5 (c.3170A>G, p.E1057G). Convergent functional genomics analysis revealed that DOCK5 was listed as one of the biomarkers for mood state and suicidality. Although DOCK5 is still a functionally unknown gene, our findings highlight the possibility of a pathological relationship between BD and DOCK5.
Collapse
Affiliation(s)
- Hiromi Umehara
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Masayuki Nakamura
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan.
| | - Mio Nagai
- Division of Psychiatry, Matsuyama Red Cross Hospital, Matsuyama, Japan
| | - Yuko Kato
- Division of Psychiatry, Jiundo Hospital, Tokyo, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Akira Sano
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| |
Collapse
|
29
|
Rho GTPases in the Amygdala-A Switch for Fears? Cells 2020; 9:cells9091972. [PMID: 32858950 PMCID: PMC7563696 DOI: 10.3390/cells9091972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 12/28/2022] Open
Abstract
Fear is a fundamental evolutionary process for survival. However, excess or irrational fear hampers normal activity and leads to phobia. The amygdala is the primary brain region associated with fear learning and conditioning. There, Rho GTPases are molecular switches that act as signaling molecules for further downstream processes that modulate, among others, dendritic spine morphogenesis and thereby play a role in fear conditioning. The three main Rho GTPases—RhoA, Rac1, and Cdc42, together with their modulators, are known to be involved in many psychiatric disorders that affect the amygdala′s fear conditioning mechanism. Rich2, a RhoGAP mainly for Rac1 and Cdc42, has been studied extensively in such regard. Here, we will discuss these effectors, along with Rich2, as a molecular switch for fears, especially in the amygdala. Understanding the role of Rho GTPases in fear controlling could be beneficial for the development of therapeutic strategies targeting conditions with abnormal fear/anxiety-like behaviors.
Collapse
|
30
|
DOCK6 promotes chemo- and radioresistance of gastric cancer by modulating WNT/β-catenin signaling and cancer stem cell traits. Oncogene 2020; 39:5933-5949. [PMID: 32753649 DOI: 10.1038/s41388-020-01390-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 07/07/2020] [Indexed: 01/01/2023]
Abstract
Gastric cancer (GC) is the third leading cause of cancer-related mortality worldwide and prognosis after potentially curative gastrectomy remains poor. Administration of GC-targeting molecules in combination with adjuvant chemo- or radiotherapy following surgical resection has been proposed as a potentially effective treatment option. Here, we have identified DOCK6, a guanine nucleotide exchange factor (GEF) for Rac1 and CDC42, as an independent biomarker for GC prognosis. Clinical findings indicate the positive correlation of higher DOCK6 expression with tumor size, depth of invasion, lymph node metastasis, vascular invasion, and pathological stage. Furthermore, elevated DOCK6 expression was significantly associated with shorter cumulative survival in both univariate and multivariate analyses. Gene ontology analysis of three independent clinical GC cohorts revealed significant involvement of DOCK6-correlated genes in the WNT/β-catenin signaling pathway. Ectopic expression of DOCK6 promoted GC cancer stem cell (CSC) characteristics and chemo- or radioresistance concomitantly through Rac1 activation. Conversely, depletion of DOCK6 suppressed CSC phenotypes and progression of GC, further demonstrating the pivotal role of DOCK6 in GC progression. Our results demonstrate a novel mechanistic link between DOCK6, Rac1, and β-catenin in GCCSC for the first time, supporting the utility of DOCK6 as an independent marker of GC.
Collapse
|
31
|
Rho GTPase Regulators and Effectors in Autism Spectrum Disorders: Animal Models and Insights for Therapeutics. Cells 2020; 9:cells9040835. [PMID: 32244264 PMCID: PMC7226772 DOI: 10.3390/cells9040835] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/22/2020] [Accepted: 03/26/2020] [Indexed: 12/18/2022] Open
Abstract
The Rho family GTPases are small G proteins that act as molecular switches shuttling between active and inactive forms. Rho GTPases are regulated by two classes of regulatory proteins, guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Rho GTPases transduce the upstream signals to downstream effectors, thus regulating diverse cellular processes, such as growth, migration, adhesion, and differentiation. In particular, Rho GTPases play essential roles in regulating neuronal morphology and function. Recent evidence suggests that dysfunction of Rho GTPase signaling contributes substantially to the pathogenesis of autism spectrum disorder (ASD). It has been found that 20 genes encoding Rho GTPase regulators and effectors are listed as ASD risk genes by Simons foundation autism research initiative (SFARI). This review summarizes the clinical evidence, protein structure, and protein expression pattern of these 20 genes. Moreover, ASD-related behavioral phenotypes in animal models of these genes are reviewed, and the therapeutic approaches that show successful treatment effects in these animal models are discussed.
Collapse
|
32
|
Huang M, Liang C, Li S, Zhang J, Guo D, Zhao B, Liu Y, Peng Y, Xu J, Liu W, Guo G, Shi L. Two Autism/Dyslexia Linked Variations of DOCK4 Disrupt the Gene Function on Rac1/Rap1 Activation, Neurite Outgrowth, and Synapse Development. Front Cell Neurosci 2020; 13:577. [PMID: 32009906 PMCID: PMC6974517 DOI: 10.3389/fncel.2019.00577] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/16/2019] [Indexed: 11/13/2022] Open
Abstract
Autism spectrum disorder (ASD) and dyslexia are both neurodevelopmental disorders with high prevalence in children. Both disorders have strong genetic basis, and share similar social communication deficits co-occurring with impairments of reading or language. However, whether these two disorders share common genetic risks remain elusive. DOCK4 (dedicator for cytokinesis 4), a guanine nucleotide exchange factor (GEF) for the small GTPase Rac1, is one of few genes that are associated with both ASD and dyslexia. Dock4 is important for neuronal development and social behaviors. Two DOCK4 variations, Exon27-52 deletion (protein product: Dock4-945VS) and a missense mutation at rs2074130 (protein product: Dock4-R853H), are associated with dyslexia and/or ASD with reading difficulties. The present study explores the molecular and cellular functions of these two DOCK4 variants on neuronal development, by comparing them with the wild-type Dock4 protein. Notably, it is revealed that both mutants of Dock4 showed decreased ability to activate not only Rac1, but also another small GTPase Rap1. Consistently, both mutants were dysfunctional for regulation of cell morphology and cytoskeleton. Using Neuro-2a cells and hippocampus neurons as models, we found that both mutants had compromised function in promoting neurite outgrowth and dendritic spine formation. Electrophysiological recordings further showed that R853H partially lost the ability to promote excitatory synaptic transmission, whereas 945VS totally lost the ability. Together, we identified R853 as a previously uncharacterized site for the regulation of the integrity of Dock4 function, and provides insights in understanding the common molecular pathophysiology of ASD and dyslexia.
Collapse
Affiliation(s)
- Miaoqi Huang
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Chunmei Liang
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Shengnan Li
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Jifeng Zhang
- Department of Anatomy, Medical College of Jinan University, Guangzhou, China
| | - Daji Guo
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Bo Zhao
- Department of Anatomy, Medical College of Jinan University, Guangzhou, China
| | - Yuyang Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Yinghui Peng
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Junyu Xu
- Department of Neurobiology, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Liu
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Guoqing Guo
- Department of Anatomy, Medical College of Jinan University, Guangzhou, China
| | - Lei Shi
- JNU-HKUST Joint Laboratory for Neuroscience and Innovative Drug Research, College of Pharmacy, Jinan University, Guangzhou, China
| |
Collapse
|
33
|
TrkB hyperactivity contributes to brain dysconnectivity, epileptogenesis, and anxiety in zebrafish model of Tuberous Sclerosis Complex. Proc Natl Acad Sci U S A 2020; 117:2170-2179. [PMID: 31932427 PMCID: PMC6995026 DOI: 10.1073/pnas.1910834117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Tuberous Sclerosis Complex (TSC) is a rare genetic disease that manifests with early symptoms, including cortical malformations, childhood epilepsy, and TSC-associated neuropsychiatric disorders (TANDs). Cortical malformations arise during embryonic development and have been linked to childhood epilepsy before, but the underlying mechanisms of this relationship remain insufficiently understood. Zebrafish have emerged as a convenient model to study elementary neurodevelopment; however, without in-depth functional analysis, the Tsc2-deficient zebrafish line cannot be used for studies of TANDs or new drug screening. In this study, we found that the lack of Tsc2 in zebrafish resulted in heterotopias and hyperactivation of the mTorC1 pathway in pallial regions, which are homologous to the mammalian cortex. We observed commissural thinning that was responsible for brain dysconnectivity, recapitulating TSC pathology in human patients. The lack of Tsc2 also delayed axonal development and caused aberrant tract fasciculation, corresponding to the abnormal expression of genes involved in axon navigation. The mutants underwent epileptogenesis that resulted in nonmotor seizures and exhibited increased anxiety-like behavior. We further mapped discrete parameters of locomotor activity to epilepsy-like and anxiety-like behaviors, which were rescued by reducing tyrosine receptor kinase B (TrkB) signaling. Moreover, in contrast to treatment with vigabatrin and rapamycin, TrkB inhibition rescued brain dysconnectivity and anxiety-like behavior. These data reveal that commissural thinning results in the aberrant regulation of anxiety, providing a mechanistic link between brain anatomy and human TANDs. Our findings also implicate TrkB signaling in the complex pathology of TSC and reveal a therapeutic target.
Collapse
|
34
|
Trifonova EA, Klimenko AI, Mustafin ZS, Lashin SA, Kochetov AV. The mTOR Signaling Pathway Activity and Vitamin D Availability Control the Expression of Most Autism Predisposition Genes. Int J Mol Sci 2019; 20:ijms20246332. [PMID: 31847491 PMCID: PMC6940974 DOI: 10.3390/ijms20246332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) has a strong and complex genetic component with an estimate of more than 1000 genes implicated cataloged in SFARI (Simon′s Foundation Autism Research Initiative) gene database. A significant part of both syndromic and idiopathic autism cases can be attributed to disorders caused by the mechanistic target of rapamycin (mTOR)-dependent translation deregulation. We conducted gene-set analyses and revealed that 606 out of 1053 genes (58%) included in the SFARI Gene database and 179 out of 281 genes (64%) included in the first three categories of the database (“high confidence”, “strong candidate”, and “suggestive evidence”) could be attributed to one of the four groups: 1. FMRP (fragile X mental retardation protein) target genes, 2. mTOR signaling network genes, 3. mTOR-modulated genes, 4. vitamin D3 sensitive genes. The additional gene network analysis revealed 43 new genes and 127 new interactions, so in the whole 222 out of 281 (79%) high scored genes from SFARI Gene database were connected with mTOR signaling activity and/or dependent on vitamin D3 availability directly or indirectly. We hypothesized that genetic and/or environment mTOR hyperactivation, including provocation by vitamin D deficiency, might be a common mechanism controlling the expressivity of most autism predisposition genes and even core symptoms of autism.
Collapse
Affiliation(s)
- Ekaterina A. Trifonova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (A.I.K.); (Z.S.M.); (S.A.L.); (A.V.K.)
- Department of Natural Sciences, Novosibirsk National Research State University, Novosibirsk 630090, Russia
- Correspondence:
| | - Alexandra I. Klimenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (A.I.K.); (Z.S.M.); (S.A.L.); (A.V.K.)
| | - Zakhar S. Mustafin
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (A.I.K.); (Z.S.M.); (S.A.L.); (A.V.K.)
| | - Sergey A. Lashin
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (A.I.K.); (Z.S.M.); (S.A.L.); (A.V.K.)
- Department of Natural Sciences, Novosibirsk National Research State University, Novosibirsk 630090, Russia
| | - Alex V. Kochetov
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (A.I.K.); (Z.S.M.); (S.A.L.); (A.V.K.)
- Department of Natural Sciences, Novosibirsk National Research State University, Novosibirsk 630090, Russia
| |
Collapse
|
35
|
Xu Z, Chen Y, Chen Y. Spatiotemporal Regulation of Rho GTPases in Neuronal Migration. Cells 2019; 8:cells8060568. [PMID: 31185627 PMCID: PMC6627650 DOI: 10.3390/cells8060568] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/01/2019] [Accepted: 06/04/2019] [Indexed: 12/17/2022] Open
Abstract
Neuronal migration is essential for the orchestration of brain development and involves several contiguous steps: interkinetic nuclear movement (INM), multipolar–bipolar transition, locomotion, and translocation. Growing evidence suggests that Rho GTPases, including RhoA, Rac, Cdc42, and the atypical Rnd members, play critical roles in neuronal migration by regulating both actin and microtubule cytoskeletal components. This review focuses on the spatiotemporal-specific regulation of Rho GTPases as well as their regulators and effectors in distinct steps during the neuronal migration process. Their roles in bridging extracellular signals and cytoskeletal dynamics to provide optimal structural support to the migrating neurons will also be discussed.
Collapse
Affiliation(s)
- Zhenyan Xu
- The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, Guangdong, China.
| | - Yuewen Chen
- The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, Guangdong, China.
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen 518057, Guangdong, China.
| | - Yu Chen
- The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, Guangdong, China.
- Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, HKUST Shenzhen Research Institute, Shenzhen 518057, Guangdong, China.
| |
Collapse
|
36
|
Niftullayev S, Lamarche-Vane N. Regulators of Rho GTPases in the Nervous System: Molecular Implication in Axon Guidance and Neurological Disorders. Int J Mol Sci 2019; 20:E1497. [PMID: 30934641 PMCID: PMC6471118 DOI: 10.3390/ijms20061497] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/18/2019] [Indexed: 12/11/2022] Open
Abstract
One of the fundamental steps during development of the nervous system is the formation of proper connections between neurons and their target cells-a process called neural wiring, failure of which causes neurological disorders ranging from autism to Down's syndrome. Axons navigate through the complex environment of a developing embryo toward their targets, which can be far away from their cell bodies. Successful implementation of neuronal wiring, which is crucial for fulfillment of all behavioral functions, is achieved through an intimate interplay between axon guidance and neural activity. In this review, our focus will be on axon pathfinding and the implication of some of its downstream molecular components in neurological disorders. More precisely, we will talk about axon guidance and the molecules implicated in this process. After, we will briefly review the Rho family of small GTPases, their regulators, and their involvement in downstream signaling pathways of the axon guidance cues/receptor complexes. We will then proceed to the final and main part of this review, where we will thoroughly comment on the implication of the regulators for Rho GTPases-GEFs (Guanine nucleotide Exchange Factors) and GAPs (GTPase-activating Proteins)-in neurological diseases and disorders.
Collapse
Affiliation(s)
- Sadig Niftullayev
- Cancer Research Program, Research Institute of the MUHC, Montreal, QC H4A 3J1, Canada.
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B2, Canada.
| | - Nathalie Lamarche-Vane
- Cancer Research Program, Research Institute of the MUHC, Montreal, QC H4A 3J1, Canada.
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 2B2, Canada.
| |
Collapse
|
37
|
Kukimoto-Niino M, Tsuda K, Ihara K, Mishima-Tsumagari C, Honda K, Ohsawa N, Shirouzu M. Structural Basis for the Dual Substrate Specificity of DOCK7 Guanine Nucleotide Exchange Factor. Structure 2019; 27:741-748.e3. [PMID: 30853411 DOI: 10.1016/j.str.2019.02.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/18/2018] [Accepted: 02/04/2019] [Indexed: 11/15/2022]
Abstract
The Dedicator Of CytoKinesis (DOCK) family of atypical guanine nucleotide exchange factors activates the Rho family GTPases Rac and/or Cdc42 through DOCK homology region 2 (DHR-2). Previous structural analyses of the DHR-2 domains of DOCK2 and DOCK9 have shown that they preferentially bind Rac1 and Cdc42, respectively; however, the molecular mechanism by which DHR-2 distinguishes between these GTPases is unclear. Here we report the crystal structure of the Cdc42-bound form of the DOCK7 DHR-2 domain showing dual specificity for Rac1 and Cdc42. The structure revealed increased substrate tolerance of DOCK7 at the interfaces with switch 1 and residue 56 of Cdc42. Furthermore, molecular dynamics simulations showed a closed-to-open conformational change in the DOCK7 DHR-2 domain between the Cdc42- and Rac1-bound states by lobe B displacement. Our results suggest that lobe B acts as a sensor for identifying different switch 1 conformations and explain how DOCK7 recognizes both Rac1 and Cdc42.
Collapse
Affiliation(s)
- Mutsuko Kukimoto-Niino
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
| | - Kengo Tsuda
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Kentaro Ihara
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Chiemi Mishima-Tsumagari
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Honda
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Noboru Ohsawa
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan.
| |
Collapse
|
38
|
Capkova P, Srovnal J, Capkova Z, Staffova K, Becvarova V, Trkova M, Adamova K, Santava A, Curtisova V, Hajduch M, Prochazka M. MLPA is a practical and complementary alternative to CMA for diagnostic testing in patients with autism spectrum disorders and identifying new candidate CNVs associated with autism. PeerJ 2019; 6:e6183. [PMID: 30647996 PMCID: PMC6330045 DOI: 10.7717/peerj.6183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 11/28/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a complex heterogeneous developmental disease with a significant genetic background that is frequently caused by rare copy number variants (CNVs). Microarray-based whole-genome approaches for CNV detection are widely accepted. However, the clinical significance of most CNV is poorly understood, so results obtained using such methods are sometimes ambiguous. We therefore evaluated a targeted approach based on multiplex ligation-dependent probe amplification (MLPA) using selected probemixes to detect clinically relevant variants for diagnostic testing of ASD patients. We compare the reliability and efficiency of this test to those of chromosomal microarray analysis (CMA) and other tests available to our laboratory. In addition, we identify new candidate genes for ASD identified in a cohort of ASD-diagnosed patients. METHOD We describe the use of MLPA, CMA, and karyotyping to detect CNV in 92 ASD patients and evaluate their clinical significance. RESULT Pathogenic and likely pathogenic mutations were identified by CMA in eight (8.07% of the studied cohort) and 12 (13.04%) ASD patients, respectively, and in eight (8.07%) and four (4.35%) patients, respectively, by MLPA. The detected mutations include the 22q13.3 deletion, which was attributed to ring chromosome 22 formation based on karyotyping. CMA revealed a total of 91 rare CNV in 55 patients: eight pathogenic, 15 designated variants of unknown significance (VOUS)-likely pathogenic, 10 VOUS-uncertain, and 58 VOUS-likely benign or benign. MLPA revealed 18 CNV in 18 individuals: eight pathogenic, four designated as VOUS-likely pathogenic, and six designated as VOUS-likely benign/benign. Rare CNVs were detected in 17 (58.62%) out of 29 females and 38 (60.32%) out of 63 males in the cohort. Two genes, DOCK8 and PARK2, were found to be overlapped by CNV designated pathogenic, VOUS-likely pathogenic, or VOUS-uncertain in multiple patients. Moreover, the studied ASD cohort exhibited significant (p < 0.05) enrichment of duplications encompassing DOCK8. CONCLUSION Multiplex ligation-dependent probe amplification and CMA yielded concordant results for 12 patients bearing CNV designated pathogenic or VOUS-likely pathogenic. Unambiguous diagnoses were achieved for eight patients (corresponding to 8.7% of the total studied population) by both MLPA and CMA, for one (1.09%) patient by karyotyping, and for one (1.09%) patient by FRAXA testing. MLPA and CMA thus achieved identical reliability with respect to clinically relevant findings. As such, MLPA could be useful as a fast and inexpensive test in patients with syndromic autism. The detection rate of potentially pathogenic variants (VOUS-likely pathogenic) achieved by CMA was higher than that for MLPA (13.04% vs. 4.35%). However, there was no corresponding difference in the rate of unambiguous diagnoses of ASD patients. In addition, the results obtained suggest that DOCK8 may play a role in the etiology of ASD.
Collapse
Affiliation(s)
- Pavlina Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Josef Srovnal
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Zuzana Capkova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Katerina Staffova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | | | | | - Katerina Adamova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Alena Santava
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Vaclava Curtisova
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Martin Prochazka
- Department of Medical Genetics, University Hospital Olomouc, Olomouc, Czech Republic
| |
Collapse
|
39
|
Structure of BAI1/ELMO2 complex reveals an action mechanism of adhesion GPCRs via ELMO family scaffolds. Nat Commun 2019; 10:51. [PMID: 30604775 PMCID: PMC6318265 DOI: 10.1038/s41467-018-07938-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/30/2018] [Indexed: 12/28/2022] Open
Abstract
The brain-specific angiogenesis inhibitor (BAI) subfamily of adhesion G protein-coupled receptors (aGPCRs) plays crucial roles in diverse cellular processes including phagocytosis, myoblast fusion, and synaptic development through the ELMO/DOCK/Rac signaling pathway, although the underlying molecular mechanism is not well understood. Here, we demonstrate that an evolutionarily conserved fragment located in the C-terminal cytoplasmic tail of BAI-aGPCRs is specifically recognized by the RBD-ARR-ELMO (RAE) supramodule of the ELMO family scaffolds. The crystal structures of ELMO2-RAE and its complex with BAI1 uncover the molecular basis of BAI/ELMO interactions. Based on the complex structure we identify aGPCR-GPR128 as another upstream receptor for the ELMO family scaffolds, most likely with a recognition mode similar to that of BAI/ELMO interactions. Finally, we map disease-causing mutations of BAI and ELMO and analyze their effects on complex formation.
Collapse
|
40
|
Ganesh S, Ahmed P. H, Nadella RK, More RP, Seshadri M, Viswanath B, Rao M, Jain S, Mukherjee O. Exome sequencing in families with severe mental illness identifies novel and rare variants in genes implicated in Mendelian neuropsychiatric syndromes. Psychiatry Clin Neurosci 2019; 73:11-19. [PMID: 30367527 PMCID: PMC7380025 DOI: 10.1111/pcn.12788] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/08/2018] [Accepted: 10/11/2018] [Indexed: 12/14/2022]
Abstract
AIM Severe mental illnesses (SMI), such as bipolar disorder and schizophrenia, are highly heritable, and have a complex pattern of inheritance. Genome-wide association studies detect a part of the heritability, which can be attributed to common genetic variation. Examination of rare variants with next-generation sequencing may add to the understanding of the genetic architecture of SMI. METHODS We analyzed 32 ill subjects from eight multiplex families and 33 healthy individuals using whole-exome sequencing. Prioritized variants were selected by a three-step filtering process, which included: deleteriousness by five in silico algorithms; sharing within families by affected individuals; rarity in South Asian sample estimated using the Exome Aggregation Consortium data; and complete absence of these variants in control individuals from the same gene pool. RESULTS We identified 42 rare, non-synonymous deleterious variants (~5 per pedigree) in this study. None of the variants were shared across families, indicating a 'private' mutational profile. Twenty (47.6%) of the variant harboring genes were previously reported to contribute to the risk of diverse neuropsychiatric syndromes, nine (21.4%) of which were of Mendelian inheritance. These included genes carrying novel deleterious variants, such as the GRM1 gene implicated in spinocerebellar ataxia 44 and the NIPBL gene implicated in Cornelia de Lange syndrome. CONCLUSION Next-generation sequencing approaches in family-based studies are useful to identify novel and rare variants in genes for complex disorders like SMI. The findings of the study suggest a potential phenotypic burden of rare variants in Mendelian disease genes, indicating pleiotropic effects in the etiology of SMI.
Collapse
Affiliation(s)
- Suhas Ganesh
- Department of PsychiatryNational Institute of Mental Health and NeurosciencesBengaluruIndia
- Department of Psychiatry, Schizophrenia Neuropharmacology Research Group at YaleYale UniversityConnecticutUSA
| | | | - Ravi K. Nadella
- Department of PsychiatryNational Institute of Mental Health and NeurosciencesBengaluruIndia
| | - Ravi P. More
- National Centre for Biological SciencesBengaluruIndia
| | - Manasa Seshadri
- Department of PsychiatryNational Institute of Mental Health and NeurosciencesBengaluruIndia
| | - Biju Viswanath
- Department of PsychiatryNational Institute of Mental Health and NeurosciencesBengaluruIndia
| | - Mahendra Rao
- Centre for Brain Development and RepairInstitute for Stem Cell Biology and Regenerative MedicineBengaluruIndia
| | - Sanjeev Jain
- Department of PsychiatryNational Institute of Mental Health and NeurosciencesBengaluruIndia
| | - Odity Mukherjee
- Centre for Brain Development and RepairInstitute for Stem Cell Biology and Regenerative MedicineBengaluruIndia
| |
Collapse
|
41
|
The Small Yeast GTPase Rho5 and Its Dimeric GEF Dck1/Lmo1 Respond to Glucose Starvation. Int J Mol Sci 2018; 19:ijms19082186. [PMID: 30049968 PMCID: PMC6121567 DOI: 10.3390/ijms19082186] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/21/2018] [Accepted: 07/23/2018] [Indexed: 12/25/2022] Open
Abstract
Rho5 is a small GTPase of Saccharomyces cerevisiae and a homolog of mammalian Rac1. The latter regulates glucose metabolism and actin cytoskeleton dynamics, and its misregulation causes cancer and a variety of other diseases. In yeast, Rho5 has been implicated in different signal transduction pathways, governing cell wall integrity and the responses to high medium osmolarity and oxidative stress. It has also been proposed to affect mitophagy and apoptosis. Here, we demonstrate that Rho5 rapidly relocates from the plasma membrane to mitochondria upon glucose starvation, mediated by its dimeric GDP/GTP exchange factor (GEF) Dck1/Lmo1. A function in response to glucose availability is also suggested by synthetic genetic phenotypes of a rho5 deletion with gpr1, gpa2, and sch9 null mutants. On the other hand, the role of mammalian Rac1 in regulating the action cytoskeleton does not seem to be strongly conserved in S. cerevisiae Rho5. We propose that Rho5 serves as a central hub in integrating various stress conditions, including a crosstalk with the cAMP/PKA (cyclic AMP activating protein kinase A) and Sch9 branches of glucose signaling pathways.
Collapse
|
42
|
Tang CS, Zhuang X, Lam WY, Ngan ESW, Hsu JS, Michelle YU, Man-Ting SO, Cherny SS, Ngo ND, Sham PC, Tam PK, Garcia-Barcelo MM. Uncovering the genetic lesions underlying the most severe form of Hirschsprung disease by whole-genome sequencing. Eur J Hum Genet 2018; 26:818-826. [PMID: 29483666 PMCID: PMC5974185 DOI: 10.1038/s41431-018-0129-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 02/02/2018] [Accepted: 02/13/2018] [Indexed: 11/08/2022] Open
Abstract
Hirschsprung disease (HSCR) is a complex birth defect characterized by the lack of ganglion cells along a variable length of the distal intestine. A large proportion of HSCR patients remain genetically unexplained. We applied whole-genome sequencing (WGS) on 9 trios where the probands are sporadically affected with the most severe form of the disorder and harbor no coding sequence variants affecting the function of known HSCR genes. We found de novo protein-altering variants in three intolerant to change genes-CCT2, VASH1, and CYP26A1-for which a plausible link with the enteric nervous system (ENS) exists. De novo single-nucleotide and indel variants were present in introns and non-coding neighboring regions of ENS-related genes, including NRG1 and ERBB4. Joint analysis with those inherited rare variants found under recessive and/or digenic models revealed both patient-unique and shared genetic features where rare variants were found to be enriched in the extracellular matrix-receptor (ECM-receptor) pathway (p = 3.4 × 10-11). Delineation of the genetic profile of each patient might help finding common grounds that could lead to the discovery of shared molecules that could be used as drug targets for the currently ongoing cell therapy effort which aims at providing an alternative to the surgical treatment.
Collapse
Affiliation(s)
- Clara Sm Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong, Hong Kong
| | - Xuehan Zhuang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wai-Yee Lam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Elly Sau-Wai Ngan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jacob Shujui Hsu
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Y U Michelle
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - S O Man-Ting
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Stacey S Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Pak C Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Paul Kh Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
- Dr. Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong, Hong Kong
| | - Maria-Mercè Garcia-Barcelo
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong.
| |
Collapse
|
43
|
Ayana R, Singh S, Pati S. Deconvolution of Human Brain Cell Type Transcriptomes Unraveled Microglia-Specific Potential Biomarkers. Front Neurol 2018; 9:266. [PMID: 29755398 PMCID: PMC5932158 DOI: 10.3389/fneur.2018.00266] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/05/2018] [Indexed: 12/19/2022] Open
Abstract
Microglial cells form a context-dependent network of brain immunoeffector cells. Despite their indispensable roles, unresolved questions exist around biomarker discovery relevant to their cellular localization, self-renewing potential, and brain developmental dynamics. To resolve the existent gap in the annotation of candidate biomarkers, we conducted a meta-analysis of brain cells using available high-throughput data sets for deciphering microglia-specific expression profiles. We have identified 3,290 significant genes specific to microglia and further selected the top 20 dysregulated genes on the basis of p-value and log2FC. To this list, we added 7 known microglia-specific markers making the candidate list comprising 27 genes for further downstream analyses. Next, we established a connectome of these potential markers with their putative protein partners, which demonstrated strong associations of upregulated genes like Dedicator of cytokinesis 2 (DOCK2) with early/mature microglial markers such as Sphingosine kinase 1 (SPHK1), CD68, and CD45. To elucidate their respective brain anatomical location, we deconvoluted the BrainSpan Atlas expression data. This analysis showed high expression of the majority of candidate genes in microglia-dense regions (Amygdala, Hippocampus, Striatum) in the postnatal brain. Furthermore, to decipher their localized expression across brain ages, we constructed a developmental dynamics map (DDM) comprising extensive gene expression profiles throughout prenatal to postnatal stages, which resulted in the discovery of novel microglia-specific gene signatures. One of the interesting readout from DDM is that all the microglia-dense regions exhibit dynamic regulation of few genes at 37 post conception week (pcw), the transition period between pre- and postnatal stages. To validate these findings and correlate them as potential biomarkers, we analyzed the expression of corresponding proteins in hESC-derived human microglia precursors. The cultured microglial precursors showed expression of Pentraxin 3 (PTX3) and SPHK1 as well as several known markers like CD68, Allograft inflammatory factor 1 (AIF1/IBA1). In summary, this study has furnished critical insights into microglia dynamics across human brain ages and cataloged potential transcriptomic fingerprints that can be further exploited for designing novel neurotherapeutics.
Collapse
Affiliation(s)
- R Ayana
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Lucknow, India
| | - Shailja Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Lucknow, India.,Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Soumya Pati
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Lucknow, India
| |
Collapse
|
44
|
Li X, Jiang M, Chen D, Xu B, Wang R, Chu Y, Wang W, Zhou L, Lei Z, Nie Y, Fan D, Shang Y, Wu K, Liang J. miR-148b-3p inhibits gastric cancer metastasis by inhibiting the Dock6/Rac1/Cdc42 axis. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:71. [PMID: 29587866 PMCID: PMC5872400 DOI: 10.1186/s13046-018-0729-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/08/2018] [Indexed: 12/19/2022]
Abstract
Background Our previous work showed that some Rho GTPases, including Rho, Rac1 and Cdc42, play critical roles in gastric cancer (GC); however, how they are regulated in GC remains largely unknown. In this study, we aimed to investigate the roles and molecular mechanisms of Dock6, an atypical Rho guanine nucleotide exchange factor (GEF), in GC metastasis. Methods The expression levels of Dock6 and miR-148b-3p in GC tissues and paired nontumor tissues were determined by immunohistochemistry (IHC) and in situ hybridization (ISH), respectively. The correlation between Dock6/miR-148b-3p expression and the overall survival of GC patients was calculated by the Kaplan-Meier method and log-rank test. The roles of Dock6 and miR-148b-3p in GC were investigated by in vitro and in vivo functional studies. Rac1 and Cdc42 activation was investigated by GST pull-down assays. The inhibition of Dock6 transcription by miR-148b-3p was determined by luciferase reporter assays. Results A significant increase in Dock6 expression was found in GC tissues compared with nontumor tissues, and its positive expression was associated with lymph node metastasis and a higher TNM stage. Patients with positive Dock6 expression exhibited shorter overall survival periods than patients with negative Dock6 expression. Dock6 promoted GC migration and invasion by increasing the activation of Rac1 and Cdc42. miR-148b-3p expression was negatively correlated with Dock6 expression in GC, and it decreased the motility of GC cells by inhibiting the Dock6/Rac1/Cdc42 axis. Conclusions Dock6 was over-expressed in GC tissues, and its positive expression was associated with GC metastasis and indicated poor prognosis of GC patients. Targeting of Dock6 by miR-148b-3p could activate Rac1 and Cdc42, directly affecting the motility of GC cells. Targeting the Dock6-Rac1/Cdc42 axis could serve as a new therapeutic strategy for GC treatment. Electronic supplementary material The online version of this article (10.1186/s13046-018-0729-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xiaowei Li
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China
| | - Mingzuo Jiang
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China
| | - Di Chen
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China
| | - Bing Xu
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China.,Department of Gastroenterology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, 710004, China
| | - Rui Wang
- National-Local Joint Engineering Research Center of Biodiagnostics & Biotheraphy, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710032, China
| | - Yi Chu
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China
| | - Weijie Wang
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China
| | - Lin Zhou
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Zhijie Lei
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China
| | - Yulong Shang
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China.
| | - Kaichun Wu
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China.
| | - Jie Liang
- State Key Laboratory of Cancer Biology & National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Road, Xi'an, Shaanxi, 710032, China.
| |
Collapse
|
45
|
Sun Y, Ye L, Zheng Y, Yang Z. Identification of crucial genes associated with Parkinson's disease using microarray data. Mol Med Rep 2017; 17:3775-3782. [PMID: 29257331 DOI: 10.3892/mmr.2017.8305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 02/23/2017] [Indexed: 11/06/2022] Open
Abstract
The present study aimed to examine potential crucial genes associated with Parkinson's disease (PD) in addition to the interactions and regulators of these genes. The chip data (GSE7621) were obtained from the Gene Expression Omnibus and standardized using the robust multi‑array average in the Affy package of R software. The differentially expressed genes (DEGs) were then screened using the Samr package with a false discovery rate (FDR) <0.05 and |log2 fold change (FC)|>1. Crucial PD‑associated genes were predicted using the Genetic Association Database in the Database for Annotation, Visualization and Integrated Discovery and sequence alignment. Furthermore, transcription factors (TFs) of the crucial PD‑associated genes were predicted, and protein‑protein interactions (PPIs) between the crucial PD‑associated genes were analyzed using the Search Tool for the Retrieval of Interacting Genes/Proteins. Additionally, another dataset of PD was used to validate the expression of crucial PD‑associated genes. A total of 670 DEGs (398 upregulated and 272 downregulated genes) were identified in the PD samples. Of these, 10 DEGs enriched in pathways associated with the nervous system were predicted to be crucial in PD, including C‑X‑C chemokine receptor type 4 (CXCR4), deleted in colorectal cancer (DCC) and NCL adaptor protein 2 (NCK2). All 10 genes were associated with neuron development and differentiation. They were simultaneously modulated by multiple TFs, including GATA, E2F and E4 promoter‑binding protein 4. The PPI networks showed that DCC and CXCR4 were hub proteins. The DCC‑netrin 1‑roundabout guidance receptor 2‑slit guidance ligand 1 interaction pathway, and several genes, including TOX high mobility group box family member 4, kinase insert domain receptor and zymogen granule protein 16B, which interacted with CXCR4, were novel findings. Additionally, CXCR4 and NCK2 were upregulated in another dataset (GSE8397) of PD. These genes, interactions of proteins and TFs may be important in the progression of PD.
Collapse
Affiliation(s)
- Yongqi Sun
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Linlin Ye
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yonghui Zheng
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Zichao Yang
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| |
Collapse
|
46
|
Lee SH, Chiu YC, Li YH, Lin CC, Hou HA, Chou WC, Tien HF. High expression of dedicator of cytokinesis 1 ( DOCK1) confers poor prognosis in acute myeloid leukemia. Oncotarget 2017; 8:72250-72259. [PMID: 29069784 PMCID: PMC5641127 DOI: 10.18632/oncotarget.19706] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022] Open
Abstract
DOCK family genes encode evolutionarily conserved guanine nucleotide exchange factors for Rho GTPase involving multiple biological functions. Yet the patterns and prognostic significance of their expression in acute myeloid leukemia (AML) remain unexplored. Here we analyzed the expression patterns of 11 DOCK family genes in AML cells based on the array data of 347 patients from our cohort and several other published datasets. We further focused on the implications of the expression of DOCK1 since it was the only one in DOCK family to be associated with survival. Physiological functions and biological pathways associated with DOCK1 were identified using bioinformatics approaches. With a median follow up of 57 months, higher DOCK1 expression was associated with shorter disease free and overall survival. The finding could be validated by two independent cohorts. Multivariate analysis showed higher DOCK1 expression as a strong independent unfavorable prognostic factor. Higher DOCK1 expression was closely associated with older age, higher platelet and peripheral blast counts, intermediate-risk cytogenetics, FLT3-ITD, MLL-PTD and mutations in PTPN11, NPM1, RUNX1, ASXL1 and DNMT3A. Functional enrichment analysis suggested the association of DOCK1 overexpression with several key physiological pathways including cell proliferation, motility, and chemotaxis. Therefore, we suggested that AML with higher DOCK1 expression showed characteristic clinical and biological features. DOCK1 expression is an important prognostic marker and a potential therapeutic target for the treatment of AML. Studies in large prospective cohorts are necessary to confirm our findings. Further mechanistic studies to delineate the role of DOCK1 in the leukemogenesis are warranted.
Collapse
Affiliation(s)
- Sze-Hwei Lee
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Chiao Chiu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Yi-Hung Li
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Chin Lin
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsin-An Hou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Chien Chou
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hwei-Fang Tien
- Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| |
Collapse
|
47
|
Liu X, Guo Z, Liu W, Sun W, Ma C. Differential proteome analysis of hippocampus and temporal cortex using label-free based 2D-LC-MS/MS. J Proteomics 2017. [PMID: 28627465 DOI: 10.1016/j.jprot.2017.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hippocampus and temporal cortex are important brain regions, which play distinct, but complimentary roles in mediating learning and memory. Herein, we utilized label-free differential proteome strategy to explore function of normal human hippocampus and temporal cortex in learning and memory. As a result, a total of 5529 and 5702 proteins were identified in hippocampus and temporal cortex, respectively, 516 of which were significantly differential expressed, with abundance span 5 orders of magnitudes. Pathways analysis showed that temporal cortex was involved in growth of axons growth and synapse density regulation, through which could regulate long-term potentiation and long-term retention of trace memory. Hippocampus was involved in regulation of cell survival and cell viability, and regulates neurons proliferation by actin dynamics changes, through which involved in both short-term memory and long-term memory. Four selected differential proteins were further validated by Western blot and immunohistochemistry. For the first time, we identified proteins and associated pathways of hippocampus and temporal cortex in human cognition process using proteomic strategy, which would provide references for generating corresponding insights in hippocampus and temporal cortex-related cognitive function. The original data files can be downloaded at http://211.102.209.254/page/PSV023.html;?url=1489542083729AFHp (password: kYxh). SIGNIFICANCE This study explored the potential molecular mechanism of hippocampus and temporal cortex in human cognition function using proteomics strategy, which will offer a baseline reference for further cognitive disorders study and reveal insights into physiology of temporal cortex and hippocampus.
Collapse
Affiliation(s)
- Xiaoyan Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Zhengguang Guo
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wei Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wei Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
| | - Chao Ma
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
| |
Collapse
|
48
|
Tang J, Fan Y, Li H, Xiang Q, Zhang DF, Li Z, He Y, Liao Y, Wang Y, He F, Zhang F, Shugart YY, Liu C, Tang Y, Chan RCK, Wang CY, Yao YG, Chen X. Whole-genome sequencing of monozygotic twins discordant for schizophrenia indicates multiple genetic risk factors for schizophrenia. J Genet Genomics 2017. [PMID: 28645778 DOI: 10.1016/j.jgg.2017.05.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Schizophrenia is a common disorder with a high heritability, but its genetic architecture is still elusive. We implemented whole-genome sequencing (WGS) analysis of 8 families with monozygotic (MZ) twin pairs discordant for schizophrenia to assess potential association of de novo mutations (DNMs) or inherited variants with susceptibility to schizophrenia. Eight non-synonymous DNMs (including one splicing site) were identified and shared by twins, which were either located in previously reported schizophrenia risk genes (p.V24689I mutation in TTN, p.S2506T mutation in GCN1L1, IVS3+1G > T in DOCK1) or had a benign to damaging effect according to in silico prediction analysis. By searching the inherited rare damaging or loss-of-function (LOF) variants and common susceptible alleles from three classes of schizophrenia candidate genes, we were able to distill genetic alterations in several schizophrenia risk genes, including GAD1, PLXNA2, RELN and FEZ1. Four inherited copy number variations (CNVs; including a large deletion at 16p13.11) implicated for schizophrenia were identified in four families, respectively. Most of families carried both missense DNMs and inherited risk variants, which might suggest that DNMs, inherited rare damaging variants and common risk alleles together conferred to schizophrenia susceptibility. Our results support that schizophrenia is caused by a combination of multiple genetic factors, with each DNM/variant showing a relatively small effect size.
Collapse
Affiliation(s)
- Jinsong Tang
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yu Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China
| | - Hong Li
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China; Department of Psychiatry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Qun Xiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China
| | - Zongchang Li
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Ying He
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yanhui Liao
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Ya Wang
- Neuropsychology and Applied Cognitive Neuroscience Laboratory, and CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fan He
- Beijing Key Laboratory of Mental Disorders, Department of Psychiatry, Beijing Anding Hospital, and Center of Schizophrenia, Beijing Institute for Brain Disorders and Laboratory of Brain Disorders of the Ministry of Science and Technology, Capital Medical University, Beijing 100088, China
| | - Fengyu Zhang
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yin Yao Shugart
- Unit on Statistical Genomics, Intramural Research Programs, National Institute of Mental Health, NIH, Bethesda 20892, USA
| | - Chunyu Liu
- Institute of Human Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yanqing Tang
- Department of Psychiatry, The First Affiliated Hospital of China Medical University, Shenyang 110122, China.
| | - Raymond C K Chan
- Neuropsychology and Applied Cognitive Neuroscience Laboratory, and CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Chuan-Yue Wang
- Beijing Key Laboratory of Mental Disorders, Department of Psychiatry, Beijing Anding Hospital, and Center of Schizophrenia, Beijing Institute for Brain Disorders and Laboratory of Brain Disorders of the Ministry of Science and Technology, Capital Medical University, Beijing 100088, China.
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Xiaogang Chen
- Institute of Mental Health, National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatry, and Key Laboratory of Psychiatry and Mental Health of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha 410011, China.
| |
Collapse
|
49
|
Blazejczyk M, Macias M, Korostynski M, Firkowska M, Piechota M, Skalecka A, Tempes A, Koscielny A, Urbanska M, Przewlocki R, Jaworski J. Kainic Acid Induces mTORC1-Dependent Expression of Elmo1 in Hippocampal Neurons. Mol Neurobiol 2017; 54:2562-2578. [PMID: 26993296 PMCID: PMC5390005 DOI: 10.1007/s12035-016-9821-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/29/2016] [Indexed: 12/24/2022]
Abstract
Epileptogenesis is a process triggered by initial environmental or genetic factors that result in epilepsy and may continue during disease progression. Important parts of this process include changes in transcriptome and the pathological rewiring of neuronal circuits that involves changes in neuronal morphology. Mammalian/mechanistic target of rapamycin (mTOR) is upregulated by proconvulsive drugs, e.g., kainic acid, and is needed for progression of epileptogenesis, but molecular aspects of its contribution are not fully understood. Since mTOR can modulate transcription, we tested if rapamycin, an mTOR complex 1 inhibitor, affects kainic acid-evoked transcriptome changes. Using microarray technology, we showed that rapamycin inhibits the kainic acid-induced expression of multiple functionally heterogeneous genes. We further focused on engulfment and cell motility 1 (Elmo1), which is a modulator of actin dynamics and therefore could contribute to pathological rewiring of neuronal circuits during epileptogenesis. We showed that prolonged overexpression of Elmo1 in cultured hippocampal neurons increased axonal growth, decreased dendritic spine density, and affected their shape. In conclusion, data presented herein show that increased mTORC1 activity in response to kainic acid has no global effect on gene expression. Instead, our findings suggest that mTORC1 inhibition may affect development of epilepsy, by modulating expression of specific subset of genes, including Elmo1, and point to a potential role for Elmo1 in morphological changes that accompany epileptogenesis.
Collapse
Affiliation(s)
- Magdalena Blazejczyk
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena St., 02-109, Warsaw, Poland.
| | - Matylda Macias
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena St., 02-109, Warsaw, Poland
| | - Michal Korostynski
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna St, 31-343, Krakow, Poland
| | - Marcelina Firkowska
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena St., 02-109, Warsaw, Poland
| | - Marcin Piechota
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna St, 31-343, Krakow, Poland
| | - Agnieszka Skalecka
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena St., 02-109, Warsaw, Poland
| | - Aleksandra Tempes
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena St., 02-109, Warsaw, Poland
| | - Alicja Koscielny
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena St., 02-109, Warsaw, Poland
| | - Malgorzata Urbanska
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena St., 02-109, Warsaw, Poland
| | - Ryszard Przewlocki
- Institute of Pharmacology, Polish Academy of Sciences, 12 Smetna St, 31-343, Krakow, Poland
| | - Jacek Jaworski
- International Institute of Molecular and Cell Biology, 4 Ks. Trojdena St., 02-109, Warsaw, Poland.
| |
Collapse
|
50
|
Valente TS, Baldi F, Sant’Anna AC, Albuquerque LG, Paranhos da Costa MJR. Genome-Wide Association Study between Single Nucleotide Polymorphisms and Flight Speed in Nellore Cattle. PLoS One 2016; 11:e0156956. [PMID: 27300296 PMCID: PMC4907449 DOI: 10.1371/journal.pone.0156956] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 05/23/2016] [Indexed: 12/17/2022] Open
Abstract
Introduction Cattle temperament is an important factor that affects the profitability of beef cattle enterprises, due to its relationship with productivity traits, animal welfare and labor safety. Temperament is a complex phenotype often assessed by measuring a series of behavioral traits, which result from the effects of multiple environmental and genetic factors, and their interactions. The aims of this study were to perform a genome-wide association study and detect genomic regions, potential candidate genes and their biological mechanisms underlying temperament, measured by flight speed (FS) test in Nellore cattle. Materials and Methods The genome-wide association study (GWAS) was performed using a single-step procedure (ssGBLUP) which combined simultaneously all 16,600 phenotypes from genotyped and non-genotyped animals, full pedigree information of 162,645 animals and 1,384 genotyped animals in one step. The animals were genotyped with High Density Bovine SNP BeadChip which contains 777,962 SNP markers. After quality control (QC) a total of 455,374 SNPs remained. Results Heritability estimated for FS was 0.21 ± 0.02. Consecutive SNPs explaining 1% or more of the total additive genetic variance were considered as windows associated with FS. Nine candidate regions located on eight different Bos taurus chromosomes (BTA) (1 at 73 Mb, 2 at 65 Mb, 5 at 22 Mb and 119 Mb, 9 at 98 Mb, 11 at 67 Mb, 15 at 16 Mb, 17 at 63 Kb, and 26 at 47 Mb) were identified. The candidate genes identified in these regions were NCKAP5 (BTA2), PARK2 (BTA9), ANTXR1 (BTA11), GUCY1A2 (BTA15), CPE (BTA17) and DOCK1 (BTA26). Among these genes PARK2, GUCY1A2, CPE and DOCK1 are related to dopaminergic system, memory formation, biosynthesis of peptide hormone and neurotransmitter and brain development, respectively. Conclusions Our findings allowed us to identify nine genomic regions (SNP windows) associated with beef cattle temperament, measured by FS test. Within these windows, six promising candidate genes and their biological functions were identified. These results may contribute to a better comprehension into the genetic control of temperament expression in Nellore cattle.
Collapse
Affiliation(s)
- Tiago Silva Valente
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de Acesso Professor Paulo Donato Castellane, Jaboticabal, SP 14.884-900, Brazil
| | - Fernando Baldi
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de Acesso Professor Paulo Donato Castellane, Jaboticabal, SP 14.884-900, Brazil
| | - Aline Cristina Sant’Anna
- Universidade Federal de Juiz de Fora (UFJF), Instituto de Ciências Biológicas, Departamento de Zoologia, Rua José Lourenço Kelmer, Juiz de Fora, MG 36.036-900, Brazil
| | - Lucia Galvão Albuquerque
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de Acesso Professor Paulo Donato Castellane, Jaboticabal, SP 14.884-900, Brazil
| | - Mateus José Rodrigues Paranhos da Costa
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de Acesso Professor Paulo Donato Castellane, Jaboticabal, SP 14.884-900, Brazil
- * E-mail:
| |
Collapse
|