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Grünblatt E, Oneda B, Ekici AB, Ball J, Geissler J, Uebe S, Romanos M, Rauch A, Walitza S. High resolution chromosomal microarray analysis in paediatric obsessive-compulsive disorder. BMC Med Genomics 2017; 10:68. [PMID: 29179725 PMCID: PMC5704537 DOI: 10.1186/s12920-017-0299-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 11/06/2017] [Indexed: 02/16/2023] Open
Abstract
Background Obsessive-Compulsive Disorder (OCD) is a common and chronic disorder in which a person has uncontrollable, reoccurring thoughts and behaviours. It is a complex genetic condition and, in case of early onset (EO), the patients manifest a more severe phenotype, and an increased heritability. Large (>500 kb) copy number variations (CNVs) previously associated with autism and schizophrenia have been reported in OCD. Recently, rare CNVs smaller than 500 kb overlapping risk loci for other neurodevelopmental conditions have also been reported in OCD, stressing the importance of examining CNVs of any size range. The aim of this study was to further investigate the role of rare and small CNVs in the aetiology of EO-OCD. Methods We performed high-resolution chromosomal microarray analysis in 121 paediatric OCD patients and in 124 random controls to identify rare CNVs (>50 kb) which might contribute to EO-OCD. Results The frequencies and the size of the observed rare CNVs in the patients did not differ from the controls. However, we observed a significantly higher frequency of rare CNVs affecting brain related genes, especially deletions, in the patients (OR = 1.98, 95% CI 1.02–3.84; OR = 3.61, 95% CI 1.14–11.41, respectively). Similarly, enrichment-analysis of CNVs gene content, performed with three independent methods, confirmed significant clustering of predefined genes involved in synaptic/brain related functional pathways in the patients but not in the controls. In two patients we detected de-novo CNVs encompassing genes previously associated with different neurodevelopmental disorders (NRXN1, ANKS1B, UHRF1BP1). Conclusions Our results further strengthen the role of small rare CNVs, particularly deletions, as susceptibility factors for paediatric OCD. Electronic supplementary material The online version of this article (10.1186/s12920-017-0299-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Neumünsterallee 9, 8032, Zürich, Switzerland. .,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland. .,Department of Psychiatry, Psychosomatic and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany. .,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland. .,Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Wagistrasse 12, 8952, Schlieren, Switzerland.
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich-Schlieren, Switzerland
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen, Erlangen, Germany
| | - Juliane Ball
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Neumünsterallee 9, 8032, Zürich, Switzerland
| | - Julia Geissler
- Center of Mental Health, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany
| | - Steffen Uebe
- Institute of Human Genetics, University Hospital Erlangen, Erlangen, Germany
| | - Marcel Romanos
- Center of Mental Health, Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Würzburg, Germany
| | - Anita Rauch
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.,Institute of Medical Genetics, University of Zurich, Zurich-Schlieren, Switzerland
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Neumünsterallee 9, 8032, Zürich, Switzerland. .,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland. .,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
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Maduna T, Lelievre V. Neuropeptides shaping the central nervous system development: Spatiotemporal actions of VIP and PACAP through complementary signaling pathways. J Neurosci Res 2016; 94:1472-1487. [PMID: 27717098 DOI: 10.1002/jnr.23915] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/04/2016] [Accepted: 08/15/2016] [Indexed: 01/18/2023]
Abstract
Pituitary adenylate cyclase-activating polypeptide (PACAP) and vasoactive intestinal peptide (VIP) are neuropeptides with wide, complementary, and overlapping distributions in the central and peripheral nervous systems, where they exert important regulatory roles in many physiological processes. VIP and PACAP display a large range of biological cellular targets and functions in the adult nervous system including regulation of neurotransmission and neuroendocrine secretion and neuroprotective and neuroimmune responses. As the main focus of the present review, VIP and PACAP also have been long implicated in nervous system development and maturation through their interaction with the seven transmembrane domain G protein-coupled receptors, PAC1, VPAC1, and VPAC2, initiating multiple signaling pathways. Compared with PAC1, which solely binds PACAP with very high affinity, VPACs exhibit high affinities for both VIP and PACAP but differ from each other because of their pharmacological profile for both natural accessory peptides and synthetic or chimeric molecules, with agonistic and antagonistic properties. Complementary to initial pharmacological studies, transgenic animals lacking these neuropeptides or their receptors have been used to further characterize the neuroanatomical, electrophysiological, and behavioral roles of PACAP and VIP in the developing central nervous system. In this review, we recapitulate the critical steps and processes guiding/driving neurodevelopment in vertebrates and superimposing the potential contribution of PACAP and VIP receptors on the given timeline. We also describe how alterations in VIP/PACAP signaling may contribute to both (neuro)developmental and adult pathologies and suggest that tuning of VIP/PACAP signaling in a spatiotemporal manner may represent a novel avenue for preventive therapies of neurological and psychiatric disorders. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tando Maduna
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique UPR3212, Université de Strasbourg, Strasbourg, France
| | - Vincent Lelievre
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique UPR3212, Université de Strasbourg, Strasbourg, France.
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Ayhan Y, McFarland R, Pletnikov MV. Animal models of gene-environment interaction in schizophrenia: A dimensional perspective. Prog Neurobiol 2015; 136:1-27. [PMID: 26510407 DOI: 10.1016/j.pneurobio.2015.10.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 09/07/2015] [Accepted: 10/22/2015] [Indexed: 12/12/2022]
Abstract
Schizophrenia has long been considered as a disorder with multifactorial origins. Recent discoveries have advanced our understanding of the genetic architecture of the disease. However, even with the increase of identified risk variants, heritability estimates suggest an important contribution of non-genetic factors. Various environmental risk factors have been proposed to play a role in the etiopathogenesis of schizophrenia. These include season of birth, maternal infections, obstetric complications, adverse events at early childhood, and drug abuse. Despite the progress in identification of genetic and environmental risk factors, we still have a limited understanding of the mechanisms whereby gene-environment interactions (G × E) operate in schizophrenia and psychoses at large. In this review we provide a critical analysis of current animal models of G × E relevant to psychotic disorders and propose that dimensional perspective will advance our understanding of the complex mechanisms of these disorders.
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Affiliation(s)
- Yavuz Ayhan
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, USA; Hacettepe University Faculty of Medicine, Department of Psychiatry, Turkey
| | - Ross McFarland
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, USA; Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, USA
| | - Mikhail V Pletnikov
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, USA; Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, USA; Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, USA; Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, USA.
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4
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Shen S, Gehlert DR, Collier DA. PACAP and PAC1 receptor in brain development and behavior. Neuropeptides 2013; 47:421-30. [PMID: 24220567 DOI: 10.1016/j.npep.2013.10.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 10/12/2013] [Accepted: 10/13/2013] [Indexed: 10/26/2022]
Abstract
Pituitary adenylate cyclase-activating polypeptide (PACAP) and vasoactive intestinal peptide (VIP) act through three class B G-protein coupled receptors, PAC1, VPAC1 and VPAC2, initiating multiple signaling pathways. In addition to natural peptides ligands, a number of synthetic peptides and a small molecular antagonist have been generated. Genetically modified animals have been produced for the neuropeptides and receptors. Neuroanatomical, electrophysiological, behavioral and pharmacological characterization of the mutants and transgenic mice uncovered diverse roles of PACAP-PAC1-VAPC2 signaling in peripheral tissues and in the central nervous system. Human genetic studies suggest that the PACAP-PAC1-VPAC2 signaling can be associated with psychiatric illness via mechanisms of not only loss-of-function, but also gain-of-function. For example, a duplication of chromosome 7q36.3 (encoding the VPAC2 receptor) was shown to be associated with schizophrenia, and high levels of PACAP-PAC1 signaling are associated with posttraumatic stress disorder. Whereas knockout animals are appropriate to address loss-of-function of human genetics, transgenic mice overexpressing human transgenes in native environment using artificial chromosomes are particularly valuable and essential to address the consequences of gain-of-function. This review focuses on role of PACAP and PAC1 receptor in brain development, behavior of animals and potential implication in human neurodevelopmental disorders. It also encourages keeping an open mind that alterations of VIP/PACAP signaling may associate with psychiatric illness without overt neuroanatomic changes, and that tuning of VIP/PACAP signaling may represent a novel avenue for the treatment of the psychiatric illness.
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Affiliation(s)
- Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, National University of Ireland (NUI) Galway, Galway, Ireland.
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Faraone SV, Seidman LJ, Buka S, Goldstein JM, Lyons M, Kremen WS, Glatt SJ. Festschrift celebrating the career of Ming T. Tsuang. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:551-8. [PMID: 24132890 DOI: 10.1002/ajmg.b.32194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 07/23/2013] [Indexed: 01/25/2023]
Affiliation(s)
- Stephen V Faraone
- Departments of Psychiatry and of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, New York
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6
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Mura G, Petretto DR, Bhat KM, Carta MG. Schizophrenia: from epidemiology to rehabilitation. Clin Pract Epidemiol Ment Health 2012; 8:52-66. [PMID: 22962559 PMCID: PMC3434422 DOI: 10.2174/1745017901208010052] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Revised: 12/26/2011] [Accepted: 01/01/2012] [Indexed: 12/27/2022]
Abstract
Purpose/Objective: We discuss recent evidences about schizophrenia (frequency, onset, course, risk factors and genetics) and their influences to some epidemiological myths about schizophrenia diffuse between psychiatric and psychopathology clinicians. The scope is to evaluate if the new acquisitions may change the rehabilitation approaches to schizophrenia modifying the balance about the neurodevelopmental hypothesis of schizophrenia accepting that the cognitive deficits are produced by errors during the normal development of the brain (neurodevelopmental hypothesis) that remains stable in the course of illness and the neurodegenerative hypothesis according of which they derived from a degenerative process that goes on inexorably. Research Method/Design: A review of the literature about epidemiology of schizophrenia has been performed and the contributions of some of these evidence to neurodevelopmental hypothesis and to rehabilitation has been described. Results: It cannot be definitively concluded for or against the neurodevelopmental or degenerative hypothesis, but efforts in understanding basis of schizophrenia must go on. Until now, rehabilitation programs are based on the vulnerability-stress model: supposing an early deficit that go on stable during the life under favorable circumstances. So, rehabilitation approaches (as neuro-cognitive approaches, social skill training, cognitive-emotional training) are focused on the individual and micro-group coping skills, aiming to help people with schizophrenia to cope with environmental stress factors. Conclusions/Implications: Coping of cognitive deficits in schizophrenia may represents the starting-point for further research on schizophrenia, cohort studies and randomized trials are necessary to defined the range of effectiveness and the outcome of the treatments.
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Affiliation(s)
- Gioia Mura
- Consultation Liaison Psychiatric Unit at the University Hospital of Cagliari, University of Cagliari and AOU Cagliari - Italy
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7
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Ng MYM, Levinson DF, Faraone SV, Suarez BK, DeLisi LE, Arinami T, Riley B, Paunio T, Pulver AE, Irmansyah, Holmans PA, Escamilla M, Wildenauer DB, Williams NM, Laurent C, Mowry BJ, Brzustowicz LM, Maziade M, Sklar P, Garver DL, Abecasis GR, Lerer B, Fallin MD, Gurling HMD, Gejman PV, Lindholm E, Moises HW, Byerley W, Wijsman EM, Forabosco P, Tsuang MT, Hwu HG, Okazaki Y, Kendler KS, Wormley B, Fanous A, Walsh D, O’Neill FA, Peltonen L, Nestadt G, Lasseter VK, Liang KY, Papadimitriou GM, Dikeos DG, Schwab SG, Owen MJ, O’Donovan MC, Norton N, Hare E, Raventos H, Nicolini H, Albus M, Maier W, Nimgaonkar VL, Terenius L, Mallet J, Jay M, Godard S, Nertney D, Alexander M, Crowe RR, Silverman JM, Bassett AS, Roy MA, Mérette C, Pato CN, Pato MT, Roos JL, Kohn Y, Amann-Zalcenstein D, Kalsi G, McQuillin A, Curtis D, Brynjolfson J, Sigmundsson T, Petursson H, Sanders AR, Duan J, Jazin E, Myles-Worsley M, Karayiorgou M, Lewis CM. Meta-analysis of 32 genome-wide linkage studies of schizophrenia. Mol Psychiatry 2009; 14:774-85. [PMID: 19349958 PMCID: PMC2715392 DOI: 10.1038/mp.2008.135] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Accepted: 11/11/2008] [Indexed: 02/07/2023]
Abstract
A genome scan meta-analysis (GSMA) was carried out on 32 independent genome-wide linkage scan analyses that included 3255 pedigrees with 7413 genotyped cases affected with schizophrenia (SCZ) or related disorders. The primary GSMA divided the autosomes into 120 bins, rank-ordered the bins within each study according to the most positive linkage result in each bin, summed these ranks (weighted for study size) for each bin across studies and determined the empirical probability of a given summed rank (P(SR)) by simulation. Suggestive evidence for linkage was observed in two single bins, on chromosomes 5q (142-168 Mb) and 2q (103-134 Mb). Genome-wide evidence for linkage was detected on chromosome 2q (119-152 Mb) when bin boundaries were shifted to the middle of the previous bins. The primary analysis met empirical criteria for 'aggregate' genome-wide significance, indicating that some or all of 10 bins are likely to contain loci linked to SCZ, including regions of chromosomes 1, 2q, 3q, 4q, 5q, 8p and 10q. In a secondary analysis of 22 studies of European-ancestry samples, suggestive evidence for linkage was observed on chromosome 8p (16-33 Mb). Although the newer genome-wide association methodology has greater power to detect weak associations to single common DNA sequence variants, linkage analysis can detect diverse genetic effects that segregate in families, including multiple rare variants within one locus or several weakly associated loci in the same region. Therefore, the regions supported by this meta-analysis deserve close attention in future studies.
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Affiliation(s)
- MYM Ng
- King’s College London, Department of Medical and Molecular Genetics, London, UK
| | - DF Levinson
- Department of Psychiatry, Stanford University, Stanford, CA, USA
| | - SV Faraone
- Departments of Psychiatry and of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - BK Suarez
- Washington University in St Louis, St Louis, MO, USA
| | - LE DeLisi
- Department of Psychiatry, The New York University Langone Medical Center, New York, NY, USA
- Nathan S Kline Institute for Psychiatric Research, Orangeburg, NY, USA
| | - T Arinami
- Department of Medical Genetics, University of Tsukuba, Tsukuba, Japan
| | - B Riley
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - T Paunio
- National Public Health Institute, Helsinki, Finland
- Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland
| | - AE Pulver
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Irmansyah
- Department of Psychiatry, University of Indonesia, Jakarta, Indonesia
| | - PA Holmans
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - M Escamilla
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - DB Wildenauer
- Center for Clinical Research in Neuropsychiatry, School of Psychiatry and Clinical Neurosciences, University of Western Australia, Perth, WA, Australia
| | - NM Williams
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - C Laurent
- Department of Child Psychiatry, Université Pierre et Marie Curie and Hôpital de la Pitiè-Salpêtrière, Paris, France
| | - BJ Mowry
- Queensland Centre for Mental Health Research and University of Queensland, Brisbane, QLD, Australia
| | - LM Brzustowicz
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - M Maziade
- Department of Psychiatry, Laval University & Centre de recherche Université Laval Robert-Giffard, Québec, QC, Canada
| | - P Sklar
- Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - DL Garver
- VA Medical Center, Asheville, NC, USA
| | - GR Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - B Lerer
- Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - MD Fallin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - HMD Gurling
- Department of Mental Health Sciences, University College London, London, UK
| | - PV Gejman
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute and Northwestern University, Evanston, IL, USA
| | - E Lindholm
- Department of Development & Genetics, Uppsala University, Uppsala, Sweden
| | | | - W Byerley
- University of California, San Francisco, CA, USA
| | - EM Wijsman
- Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, USA
| | - P Forabosco
- King’s College London, Department of Medical and Molecular Genetics, London, UK
| | - MT Tsuang
- Center for Behavioral Genomics and Department of Psychiatry, University of California, San Diego, CA, USA
- Harvard Institute of Psychiatric Epidemiology & Genetics, Boston, MA, USA
| | - H-G Hwu
- National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Y Okazaki
- Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
| | - KS Kendler
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - B Wormley
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - A Fanous
- Washington VA Medical Center, Washington, DC, USA
- Department of Psychiatry, Georgetown University Medical Center, Virginia Commonwealth University, Richmond, VA, USA
| | - D Walsh
- The Health Research Board, Dublin, Ireland
| | - FA O’Neill
- Department of Psychiatry, Queens University, Belfast, Northern Ireland
| | - L Peltonen
- Department of Molecular Medicine, National Public Health Institute, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
- The Broad Institute, MIT, Boston, MA, USA
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - G Nestadt
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - VK Lasseter
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - KY Liang
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - GM Papadimitriou
- 1st Department of Psychiatry, University of Athens Medical School, and University Mental Health Research Institute, Athens, Greece
| | - DG Dikeos
- 1st Department of Psychiatry, University of Athens Medical School, and University Mental Health Research Institute, Athens, Greece
| | - SG Schwab
- Western Australian Institute for Medical Research, University of Western Australia, Perth, WA, Australia
- School of Psychiatry and Clinical Neurosciences, University of Western Australia, Perth, WA, Australia
- School of Medicine and Pharmacology, University of Western Australia, Perth, WA, Australia
| | - MJ Owen
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - MC O’Donovan
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - N Norton
- Department of Psychological Medicine, School of Medicine, Cardiff University, Cardiff, UK
| | - E Hare
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - H Raventos
- School of Biology and CIBCM, University of Costa Rica, San Jose, Costa Rica
| | - H Nicolini
- Carracci Medical Group and Universidad Autonoma de la Ciudad de Mexico, Mexico City, Mexico
| | - M Albus
- State Mental Hospital, Haar, Germany
| | - W Maier
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | - VL Nimgaonkar
- Departments of Psychiatry and Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - L Terenius
- Department of Clinical Neuroscience, Karolinska Hospital, Stockholm, Sweden
| | - J Mallet
- Laboratoire de Génétique Moléculaire de la Neurotransmission et des Processus Neurodégénératifs, Centre National de la Recherche Scientifique, Hôpital de la Pitié Salpêtrière, Paris, France
| | - M Jay
- Department of Child Psychiatry, Université Pierre et Marie Curie and Hôpital de la Pitiè-Salpêtrière, Paris, France
| | - S Godard
- INSERM, Institut de Myologie, Hôpital de la Pitiè-Salpêtrière, Paris, France
| | - D Nertney
- Queensland Centre for Mental Health Research and University of Queensland, Brisbane, QLD, Australia
| | - M Alexander
- Department of Psychiatry, Stanford University, Stanford, CA, USA
| | - RR Crowe
- Department of Psychiatry, The University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - JM Silverman
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - AS Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - M-A Roy
- Department of Psychiatry, Laval University & Centre de recherche Université Laval Robert-Giffard, Québec, QC, Canada
| | - C Mérette
- Department of Psychiatry, Laval University & Centre de recherche Université Laval Robert-Giffard, Québec, QC, Canada
| | - CN Pato
- Center for Genomic Psychiatry, University of Southern California, Los Angeles, CA, USA
| | - MT Pato
- Center for Genomic Psychiatry, University of Southern California, Los Angeles, CA, USA
| | - J Louw Roos
- Department of Psychiatry, University of Pretoria, Weskoppies Hospital, Pretoria, Republic of South Africa
| | - Y Kohn
- Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - D Amann-Zalcenstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - G Kalsi
- Department of Mental Health Sciences, University College London, London, UK
| | - A McQuillin
- Department of Mental Health Sciences, University College London, London, UK
| | - D Curtis
- Department of Psychological Medicine, St Bartholomew’s and Royal London School of Medicine and Dentistry, London, UK
| | - J Brynjolfson
- Department of Psychiatry, General Hospital, Reykjavik, Iceland
| | - T Sigmundsson
- Department of Psychiatry, General Hospital, Reykjavik, Iceland
| | - H Petursson
- Department of Psychiatry, General Hospital, Reykjavik, Iceland
| | - AR Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute and Northwestern University, Evanston, IL, USA
| | - J Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem Research Institute and Northwestern University, Evanston, IL, USA
| | - E Jazin
- Department of Development & Genetics, Uppsala University, Uppsala, Sweden
| | - M Myles-Worsley
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - M Karayiorgou
- Departments of Psychiatry and Genetics & Development, Columbia University Medical Center, New York, NY, USA
| | - CM Lewis
- King’s College London, Department of Medical and Molecular Genetics, London, UK
- King’s College London, MRC SGDP Centre, Institute of Psychiatry, London, UK
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Wiener HW, Klei L, Irvin MD, Perry RT, Aliyu MH, Allen TB, Bradford LD, Calkins ME, Devlin B, Edwards N, Gur RE, Gur RC, Kwentus J, Lyons PD, McEvoy JP, Nasrallah HA, Nimgaonkar VL, O'Jile J, Santos AB, Savage RM, Go RCP. Linkage analysis of schizophrenia in African-American families. Schizophr Res 2009; 109:70-9. [PMID: 19264455 PMCID: PMC2721327 DOI: 10.1016/j.schres.2009.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 02/04/2009] [Accepted: 02/08/2009] [Indexed: 12/12/2022]
Abstract
While many studies have sought a window into the genetics of schizophrenia, few have focused on African-American families. An exception is the Project among African-Americans to Explore Risks for Schizophrenia (PAARTNERS), which seeks to identify novel and known risk variation for schizophrenia by genetic analyses of African-American families. We report a linkage study of diagnostic status in 217 African-American families using the Illumina Linkage Panel. Due to assumed incomplete and time-dependent penetrance, we performed linkage analysis using two different treatments of diagnosis: (1) treating both affected and unaffected individuals as informative for linkage (using the program SIBPAL) and (2) treating only affected individuals as informative (using the program MERLIN). We also explore three definitions of affected status: narrowly defined schizophrenia; one broadened to include schizoaffective disorder; and another including all diagnoses indicating psychosis. Several regions show a decrease in the evidence for linkage as the definition broadens 8q22.1 (rs911, 99.26 cM; SIBPAL p-value [p] goes from 0.006 to 0.02), 16q24.3 (rs1006547, 130.48 cM; p from 0.00095 to 0.0085), and 20q13.2 (rs1022689, 81.73 cM; p from 0.00015 to 0.032). One region shows a substantial increase in evidence for linkage, 11p15.2 (rs722317, 24.27 cM; p from 0.0022 to 0.0000003); MERLIN results support the significance of the SIBPAL results (p=0.00001). Our linkage results overlap two broad, previously-reported linkage regions: 8p23.3-p12 found in studies sampling largely families of European ancestry; and 11p11.2-q22.3 reported by a study of African-American families. These results should prove quite useful for uncovering loci affecting risk for schizophrenia.
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Affiliation(s)
- H W Wiener
- University of Alabama at Birmingham, School of Public Health, Dept. of Epidemiology, 1665 University Blvd., RPHB, Birmingham, AL 35294-0022, USA.
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9
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Bassett AS, Marshall CR, Lionel AC, Chow EWC, Scherer SW. Copy number variations and risk for schizophrenia in 22q11.2 deletion syndrome. Hum Mol Genet 2008; 17:4045-53. [PMID: 18806272 PMCID: PMC2638574 DOI: 10.1093/hmg/ddn307] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
22q11.2 Deletion Syndrome (22q11.2DS) is a common microdeletion syndrome with congenital and late-onset features. Testing for the genomic content of copy number variations (CNVs) may help elucidate the 22q11.2 deletion mechanism and the variable clinical expression of the syndrome including the high (25%) risk for schizophrenia. We used genome-wide microarrays to assess CNV content and the parental origin of 22q11.2 deletions in a cohort of 100 adults with 22q11.2DS (44 with schizophrenia) and controls. 22q11.2DS subjects with schizophrenia failed to exhibit de novo CNVs or any excess of novel inherited CNVs outside the 22q11.2 region. There were no significant effects of parental origin of the 22q11.2 deletion, deletion length, parental age or family history on expression of schizophrenia. There was no evidence for a general increase of de novo CNVs in 22q11.2DS. A novel finding was the relative paucity of males with de novo 22q11.2 deletions of paternal origin (P = 0.019). The Y chromosome may play a mediating role in the mechanism of 22q11.2 deletion events during spermatogenesis, resulting in the previously observed excess of maternal de novo 22q11.2 deletions. Hemizygosity of the 22q11.2 region appears to be the major CNV-related risk factor for schizophrenia in 22q11.2DS. The results reinforce the need for further efforts to identify specific molecular mechanisms underlying this expression and to identify the 1% of patients with schizophrenia who carry 22q11.2 deletions.
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Affiliation(s)
- Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada.
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10
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Takahashi S, Cui YH, Han YH, Fagerness JA, Galloway B, Shen YC, Kojima T, Uchiyama M, Faraone SV, Tsuang MT. Association of SNPs and haplotypes in APOL1, 2 and 4 with schizophrenia. Schizophr Res 2008; 104:153-64. [PMID: 18632255 PMCID: PMC3736834 DOI: 10.1016/j.schres.2008.05.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Revised: 05/16/2008] [Accepted: 05/22/2008] [Indexed: 12/23/2022]
Abstract
Prior work found the APOL1, 2 and 4 genes, located on chromosome 22q12.3-q13.1, to be upregulated in brains of schizophrenic patients. We performed a family-based association study using 130 SNPs tagging the APOL gene family (APOL1-6). The subjects were 112 African-American (AA), 114 European-American (EA), 109 Chinese (Ch) and 42 Japanese (Jp) families with schizophrenia (377 families, 1161 genotyped members and 647 genotyped affected in total). Seven SNPs had p-values<0.05 in the APOL1, 2 and 4 regions for the AA, EA and combined (AA and EA) samples. In the AA sample, two SNPs, rs9610449 and rs6000200 showed low p-values; and a haplotype which comprised these two SNPs yielded a p-value of 0.00029 using the global test (GT) and the allele specific test (AST). The two SNPs and the haplotype were associated with risk for schizophrenia in African-Americans. In the combined (AA and EA) sample, two SNPs, rs2003813 and rs2157249 showed low p-values; and a three SNP haplotype including these two SNPs was significant using the GT (p=0.0013) and the AST (p=0.000090). The association of this haplotype with schizophrenia was significant for the entire (AA, EA, Ch and Jp) sample using the GT (p=0.00054) and the AST (p=0.00011). Although our study is not definitive, it suggests that the APOL genes should be more extensively studied in schizophrenia.
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Affiliation(s)
- Sakae Takahashi
- Division of Psychiatry, Department of Psychiatry, Nihon University, School of Medicine, Tokyo, Japan
| | - Yu-hu Cui
- Institute of Mental Health, Peking University, Peking, China
| | - Yong-hua Han
- Institute of Mental Health, Peking University, Peking, China
| | - Jesen A. Fagerness
- Department of Psychiatry, Harvard Medical School, and Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Brian Galloway
- Department of Psychiatry, Harvard Medical School, and Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Yu-cun Shen
- Institute of Mental Health, Peking University, Peking, China
| | - Takuya Kojima
- Division of Psychiatry, Department of Psychiatry, Nihon University, School of Medicine, Tokyo, Japan
| | - Makoto Uchiyama
- Division of Psychiatry, Department of Psychiatry, Nihon University, School of Medicine, Tokyo, Japan
| | - Stephen V. Faraone
- Departments of Psychiatry and of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Ming T. Tsuang
- Department of Psychiatry, Harvard Medical School, Massachusetts Mental Health Center, Boston, MA, USA,Department of Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA,Harvard Institute of Psychiatric Epidemiology and Genetics, Boston, MA, USA,Department of Epidemiology, Harvard School of Public Health, Boston, MA,University of California, San Diego, CA, USA
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11
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Karoutzou G, Emrich HM, Dietrich DE. The myelin-pathogenesis puzzle in schizophrenia: a literature review. Mol Psychiatry 2008; 13:245-60. [PMID: 17925796 DOI: 10.1038/sj.mp.4002096] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Schizophrenia is a serious and disabling mental disorder with symptoms such as auditory hallucinations, disordered thinking and delusions, avolition, anhedonia, blunted affect and apathy. In this review article we seek to present the current scientific findings from linkage studies and susceptible genes and the pathophysiology of white matter in schizophrenia. The article has been reviewed in two parts. The first part deals with the linkage studies and susceptible genes in schizophrenia in order to have a clear-cut picture of the involvement of chromosomes and their genes in schizophrenia. The genetic linkage results seem to be replicated in some cases but in others are not. From these results, we cannot draw a fine map to a single locus or gene, leading to the conclusion that schizophrenia is not caused by a single factor/gene. In the second part of the article we present the oligodendrocyte-related genes that are associated with schizophrenia, as we hypothesize a potential role of oligodendrocyte-related genes in the pathology of the disorder.
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Affiliation(s)
- G Karoutzou
- Department of Clinical Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
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12
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Chavarría-Siles I, Walss-Bass C, Quezada P, Dassori A, Contreras S, Medina R, Ramírez M, Armas R, Salazar R, Leach RJ, Raventos H, Escamilla MA. TGFB-induced factor (TGIF): a candidate gene for psychosis on chromosome 18p. Mol Psychiatry 2007; 12:1033-41. [PMID: 17440433 DOI: 10.1038/sj.mp.4001997] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Schizophrenia (SC) and bipolar disorder (BP) share many clinical features, among them psychosis. We previously identified a putative gene locus for psychosis on chromosome 18p in a sample from the Central Valley of Costa Rica (CVCR) population. The present study replicated the association to a specific allele of microsatellite marker D18S63 on 18p11.3, using a newly collected sample from the CVCR. A combined analysis of both samples, plus additional subjects, showed that this specific allele on D18S63, which lies within an intron on the TGFB-induced factor (TGIF) gene, is strongly associated (P-value=0.0005) with psychosis. Eleven additional SNP markers, spanning five genes in the region, were analyzed in the combined sample from the CVCR. Only the four SNPs within the TGIF gene were in strong linkage disequilibrium with D18S63 (D'=1.00). A specific haplotype for all five markers within the TGIF gene showed evidence of association (P-value=0.011) to psychosis. A second, distinct haplotype, containing a newly identified nonsynonymous polymorphism in exon 5 of the TGIF gene, showed a nonsignificant trend towards association to psychosis (P-value=0.077). TGIF is involved in neurodevelopment, neuron survival and controls the expression of dopamine receptors. Altogether, our results point to the possible involvement of TGIF in the pathophysiology of psychotic disorders in the CVCR population.
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Affiliation(s)
- I Chavarría-Siles
- Psychiatric Genetics Research Center, Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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13
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Cameron DB, Galas L, Jiang Y, Raoult E, Vaudry D, Komuro H. Cerebellar cortical-layer-specific control of neuronal migration by pituitary adenylate cyclase-activating polypeptide. Neuroscience 2007; 146:697-712. [PMID: 17383102 PMCID: PMC1951536 DOI: 10.1016/j.neuroscience.2007.02.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Revised: 01/30/2007] [Accepted: 02/04/2007] [Indexed: 12/21/2022]
Abstract
Migration of immature neurons is essential for forming the cortical layers and nuclei. Impairment of migration results in aberrant neuronal cytoarchitecture, which leads to various neurological disorders. Neurons alter the mode, tempo and rate of migration when they translocate through different cortical layers, but little is known about the mechanisms underlying this process. Here we show that endogenous pituitary adenylate cyclase-activating polypeptide (PACAP) has short-term and cortical-layer-specific effects on granule cell migration in the early postnatal mouse cerebellum. Application of exogenous PACAP significantly slowed the migration of isolated granule cells and shortened the leading process in the microexplant cultures of the postnatal day (P)0-3 cerebella. Interestingly, in the cerebellar slices of P10 mice, application of exogenous PACAP significantly inhibited granule cell migration in the external granular layer (EGL) and molecular layer (ML), but failed to alter the movement in the Purkinje cell layer (PCL) and internal granular layer (IGL). In contrast, application of PACAP antagonist accelerated granule cell migration in the PCL, but did not change the movement in the EGL, ML and IGL. Inhibition of the cAMP signaling and the activity of phospholipase C significantly reduced the effects of exogenous PACAP on granule cell migration. The PACAP action on granule cell migration was transient, and lasted for approximately 2 h. The duration of PACAP action on granule cell migration was determined by the desensitization of its receptors and prolonged by inhibiting the protein kinase C. Endogenous PACAP was present sporadically in the bottom of the ML, intensively in the PCL, and throughout the IGL. Collectively, these results indicated that PACAP acts on granule cell migration as "a brake (stop signal) for cell movement." Furthermore, these results suggest that endogenous PACAP slows granule cell migration when the cells enter the PACAP-rich PCL, and 2 h later the desensitization of PACAP receptors allows the cells to accelerate the rate of migration and to actively move within the PACAP-rich IGL. Therefore, endogenous PACAP may provide a cue that regulates granule cell migration in a cerebellar cortical-layer-specific manner.
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Affiliation(s)
- D. Bryant Cameron
- Department of Neurosciences, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
| | - Ludovic Galas
- European Institute for Peptide Research (IFRMP 23), Laboratory of Cellular and Molecular Neuroendocrinology, Institute National de la Sante et de la Recherche Medicale U-413, University of Rouen, Mont-Saint-Aignan, France 76821
| | - Yulan Jiang
- Department of Neurosciences, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
| | - Emilie Raoult
- European Institute for Peptide Research (IFRMP 23), Laboratory of Cellular and Molecular Neuroendocrinology, Institute National de la Sante et de la Recherche Medicale U-413, University of Rouen, Mont-Saint-Aignan, France 76821
| | - David Vaudry
- European Institute for Peptide Research (IFRMP 23), Laboratory of Cellular and Molecular Neuroendocrinology, Institute National de la Sante et de la Recherche Medicale U-413, University of Rouen, Mont-Saint-Aignan, France 76821
| | - Hitoshi Komuro
- Department of Neurosciences, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
- Department of Molecular Medicine, The Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio 44195, USA
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14
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Escamilla MA, Ontiveros A, Nicolini H, Raventos H, Mendoza R, Medina R, Munoz R, Levinson D, Peralta JM, Dassori A, Almasy L. A genome-wide scan for schizophrenia and psychosis susceptibility loci in families of Mexican and Central American ancestry. Am J Med Genet B Neuropsychiatr Genet 2007; 144B:193-9. [PMID: 17044102 DOI: 10.1002/ajmg.b.30411] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Schizophrenia is a complex psychiatric disorder, likely to be caused in part by multiple genes. In this study, linkage analyses were performed to identify chromosomal regions most likely to be associated with schizophrenia and psychosis in multiplex families of Mexican and Central American origin. Four hundred and fifty-nine individuals from 99 families, containing at least two siblings with hospital diagnoses of schizophrenia or schizoaffective disorder, were genotyped. Four hundred and four microsatellite markers were genotyped for all individuals and multipoint non-parametric linkage analyses were performed using broad (any psychosis) and narrow (schizophrenia and schizoaffective disorder) models. Under the broad model, three chromosomal regions (1pter-p36, 5q35, and 18p11) exhibited evidence of linkage with non-parametric lod (NPL) scores greater than 2.7 (equivalent to empirical P values of less than 0.001) with the peak multipoint NPL = 3.42 (empirical P value = 0.00003), meeting genomewide evidence for significant linkage in the 1pter-p36 region. Under the narrow model, the same three loci showed (non-significant) evidence of linkage. These linkage findings (1pter-p36, 18p11, and 5q35) highlight where genes for psychosis and schizophrenia are most likely to be found in persons of Mexican and Central American ancestry, and correspond to recent linkages of schizophrenia or psychosis in other populations which were formed in part from emigrants from the Spanish empire of the 15th and 16th centuries.
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Affiliation(s)
- M A Escamilla
- Department of Psychiatry, University of Texas Health Science Center at San Antonio (UTHSCSA), San Antonio, Texas, 78229-3900, USA.
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15
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Lang B, Song B, Davidson W, MacKenzie A, Smith N, McCaig CD, Harmar AJ, Shen S. Expression of the human PAC1 receptor leads to dose-dependent hydrocephalus-related abnormalities in mice. J Clin Invest 2006; 116:1924-34. [PMID: 16823490 PMCID: PMC1483148 DOI: 10.1172/jci27597] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Accepted: 04/25/2006] [Indexed: 01/16/2023] Open
Abstract
Hydrocephalus is a common and potentially devastating birth defect affecting the CNS, and its relationship with G protein-coupled receptors (GPCRs) is unknown. We have expressed 2, 4, or 6 copies of a GPCR--the human PAC1 receptor with a 130-kb transgene in the mouse nervous system in a pattern closely resembling that of the endogenous gene. Consistent with PAC1 actions, PKA and PKC activity were elevated in the brains of Tg mice. Remarkably, Tg mice developed dose-dependent hydrocephalus-like characteristics, including enlarged third and lateral ventricles and reduced cerebral cortex, corpus callosum, and subcommissural organ (SCO). Neuronal proliferation and apoptosis were implicated in hydrocephalus, and we observed significantly reduced neuronal proliferation and massively increased neuronal apoptosis in the developing cortex and SCO of Tg embryos, while neurite outgrowth and neuronal migration in vitro remain uncompromised. Ventricular ependymal cilia are crucial for directing cerebrospinal fluid flow, and ependyma of Tg mice exhibited disrupted cilia with increased phospho-CREB immunoreactivity. These data demonstrate that altered neuronal proliferation/apoptosis and disrupted ependymal cilia are the main factors contributing to hydrocephalus in PAC1-overexpressing mice. This is the first report to our knowledge demonstrating that misregulation of GPCRs can be involved in hydrocephalus-related neurodevelopmental disorders.
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Affiliation(s)
- Bing Lang
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom.
Ultrasound Department, Aberdeen Maternity Hospital, Grampian University Hospitals NHS Trust, Aberdeen, United Kingdom.
Centre for Neuroscience Research, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Bing Song
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom.
Ultrasound Department, Aberdeen Maternity Hospital, Grampian University Hospitals NHS Trust, Aberdeen, United Kingdom.
Centre for Neuroscience Research, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy Davidson
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom.
Ultrasound Department, Aberdeen Maternity Hospital, Grampian University Hospitals NHS Trust, Aberdeen, United Kingdom.
Centre for Neuroscience Research, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Alastair MacKenzie
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom.
Ultrasound Department, Aberdeen Maternity Hospital, Grampian University Hospitals NHS Trust, Aberdeen, United Kingdom.
Centre for Neuroscience Research, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Norman Smith
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom.
Ultrasound Department, Aberdeen Maternity Hospital, Grampian University Hospitals NHS Trust, Aberdeen, United Kingdom.
Centre for Neuroscience Research, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Colin D. McCaig
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom.
Ultrasound Department, Aberdeen Maternity Hospital, Grampian University Hospitals NHS Trust, Aberdeen, United Kingdom.
Centre for Neuroscience Research, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Anthony J. Harmar
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom.
Ultrasound Department, Aberdeen Maternity Hospital, Grampian University Hospitals NHS Trust, Aberdeen, United Kingdom.
Centre for Neuroscience Research, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sanbing Shen
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom.
Ultrasound Department, Aberdeen Maternity Hospital, Grampian University Hospitals NHS Trust, Aberdeen, United Kingdom.
Centre for Neuroscience Research, School of Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
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16
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Wigginton JE, Abecasis GR. An evaluation of the replicate pool method: quick estimation of genome-wide linkage peak p-values. Genet Epidemiol 2006; 30:320-32. [PMID: 16832873 DOI: 10.1002/gepi.20147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The calculation of empirical p-values for genome-wide non-parametric linkage tests continues to present significant computational challenges for many complex disease mapping studies. The gold standard approach is to use gene dropping to simulate null genome scans. Unfortunately, this approach is too computationally expensive for many data sets of interest. An alternative, more efficient method for sampling null genome scans is to pre-calculate pools of family-specific statistics and then resample from these replicate pools to generate "pseudo-replicate" genome scans. In this study, we use simulations to explore properties of the replicate pool p-value estimator pRP and show that it provides an excellent approximation to the traditional gene-dropping estimator for significantly less computational effort. While the computational efficiency of the replicate pool estimator is noticeable in almost all data sets, by applying the replicate pool method to several previously characterized data sets we show that savings in computational effort can be especially significant (on the order of 10,000-fold or more) when one or more large families are analyzed. We also estimate replicate pool p-values for the schizophrenia data described by Abecasis et al. and show that pRP closely approximates gene-drop p-values for all linkage peaks reported for this study. Lastly, we expand upon Song et al.'s previous work by deriving a conservative estimator of the variance for PRP that can easily be computed in practical settings. We have implemented the replicate pool method along with our variance estimator in a new program called Pseudo, which is the first widely available automated implementation of the replicate pool method.
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Affiliation(s)
- Janis E Wigginton
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA.
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17
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Skol AD, Xiao R, Boehnke M. An algorithm to construct genetically similar subsets of families with the use of self-reported ethnicity information. Am J Hum Genet 2005; 77:346-54. [PMID: 16080111 PMCID: PMC1226201 DOI: 10.1086/432961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 06/15/2005] [Indexed: 01/05/2023] Open
Abstract
We present a simple algorithm that uses self-reported ethnicity information, pedigree structure, and affection status to group families into genetically more homogeneous subsets. This algorithm should prove useful to researchers who wish to perform genetic analyses on more-homogeneous subsets when they suspect that ignoring heterogeneity could lead to false-positive results or loss of power. We applied our algorithm to the self-reported ethnicity information of 159 families from the Veterans Affairs Cooperative Study of schizophrenia. We compared these estimates of population membership with those obtained using the program structure in an analysis of 378 microsatellite markers. We found excellent concordance between family classifications determined using self-reported ethnicity information and our algorithm and those determined using genetic marker data and structure; 158 of the 159 families had concordant classifications. In addition, the degree of admixture estimated using our algorithm and self-reported ethnicity information correlated well with that predicted using the genotype information.
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Affiliation(s)
- Andrew D Skol
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109-2029, USA.
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