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Bamodu O, Chao TY. Dissecting the functional pleiotropism of lysine demethylase 5B in physiology and pathology. JOURNAL OF CANCER RESEARCH AND PRACTICE 2020. [DOI: 10.4103/jcrp.jcrp_5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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52
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Grzybowski AT, Shah RN, Richter WF, Ruthenburg AJ. Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications. Nat Protoc 2019; 14:3275-3302. [PMID: 31723301 PMCID: PMC7158589 DOI: 10.1038/s41596-019-0218-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/25/2019] [Indexed: 01/20/2023]
Abstract
Chromatin immunoprecipitation coupled to next-generation sequencing (ChIP-seq) has served as the central method for the study of histone modifications for the past decade. In ChIP-seq analyses, antibodies selectively capture nucleosomes bearing a modification of interest and the associated DNA is then mapped to the genome to determine the distribution of the mark. This approach has several important drawbacks: (i) ChIP interpretation necessitates the assumption of perfect antibody specificity, despite growing evidence that this is often not the case. (ii) Common methods for evaluating antibody specificity in other formats have little or no bearing on specificity within a ChIP experiment. (iii) Uncalibrated ChIP is reported as relative enrichment, which is biologically meaningless outside the experimental reference frame defined by a discrete immunoprecipitation (IP), thus preventing facile comparison across experimental conditions or modifications. (iv) Differential library amplification and loading onto next-generation sequencers, as well as computational normalization, can further compromise quantitative relationships that may exist between samples. Consequently, the researcher is presented with a series of potential pitfalls and is blind to nearly all of them. Here we provide a detailed protocol for internally calibrated ChIP (ICeChIP), a method we recently developed to resolve these problems by spike-in of defined nucleosomal standards within a ChIP procedure. This protocol is optimized for specificity and quantitative power, allowing for measurement of antibody specificity and absolute measurement of histone modification density (HMD) at genomic loci on a biologically meaningful scale enabling unambiguous comparisons. We provide guidance on optimal conditions for next-generation sequencing (NGS) and instructions for data analysis. This protocol takes between 17 and 18 h, excluding time for sequencing or bioinformatic analysis. The ICeChIP procedure enables accurate measurement of histone post-translational modifications (PTMs) genome-wide in mammalian cells as well as Drosophila melanogaster and Caenorhabditis elegans, indicating suitability for use in eukaryotic cells more broadly.
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Affiliation(s)
- Adrian T Grzybowski
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Rohan N Shah
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
- Division of the Biological Sciences, Pritzker School of Medicine, The University of Chicago, Chicago, IL, USA
| | - William F Richter
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
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Abstract
PURPOSE OF REVIEW To summarize the molecular and clinical findings of KMT2B-related dystonia (DYT-KMT2B), a newly identified genetic dystonia syndrome. RECENT FINDINGS Since first described in 2016, 66 different KMT2B-affecting variants, encompassing a set of frameshift, nonsense, splice-site, missense, and deletion mutations, have been reported in 76 patients. Most mutations are de novo and expected to mediate epigenetic dysregulation by inducing KMT2B haploinsufficiency. DYT-KMT2B is characterized phenotypically by limb-onset childhood dystonia that tends to spread progressively, resulting in generalized dystonia with cranio-cervical involvement. Co-occuring signs such as intellectual disability are frequently observed. Sustained response to deep brain stimulation (DBS), including restoration of independent ambulation, is seen in 93% (27/29) of patients. DYT-KMT2B is emerging as a prevalent monogenic dystonia. Childhood-onset dystonia presentations should prompt a search for KMT2B mutations, preferentially via next-generation-sequencing and genomic-array technologies, to enable specific counseling and treatment. Prospective multicenter studies are desirable to establish KMT2B mutational status as a DBS outcome predictor.
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Affiliation(s)
- Michael Zech
- Institut für Neurogenomik, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Munich, Neuherberg, Germany.,Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Daniel D Lam
- Institut für Neurogenomik, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Munich, Neuherberg, Germany
| | - Juliane Winkelmann
- Institut für Neurogenomik, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Munich, Neuherberg, Germany. .,Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Munich, Germany. .,Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany. .,Munich Cluster for Systems Neurology, SyNergy, Munich, Germany.
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Li W, Pozzo-Miller L. Dysfunction of the corticostriatal pathway in autism spectrum disorders. J Neurosci Res 2019; 98:2130-2147. [PMID: 31758607 DOI: 10.1002/jnr.24560] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022]
Abstract
The corticostriatal pathway that carries sensory, motor, and limbic information to the striatum plays a critical role in motor control, action selection, and reward. Dysfunction of this pathway is associated with many neurological and psychiatric disorders. Corticostriatal synapses have unique features in their cortical origins and striatal targets. In this review, we first describe axonal growth and synaptogenesis in the corticostriatal pathway during development, and then summarize the current understanding of the molecular bases of synaptic transmission and plasticity at mature corticostriatal synapses. Genes associated with autism spectrum disorder (ASD) have been implicated in axonal growth abnormalities, imbalance of the synaptic excitation/inhibition ratio, and altered long-term synaptic plasticity in the corticostriatal pathway. Here, we review a number of ASD-associated high-confidence genes, including FMR1, KMT2A, GRIN2B, SCN2A, NLGN1, NLGN3, MET, CNTNAP2, FOXP2, TSHZ3, SHANK3, PTEN, CHD8, MECP2, DYRK1A, RELN, FOXP1, SYNGAP1, and NRXN, and discuss their relevance to proper corticostriatal function.
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Affiliation(s)
- Wei Li
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lucas Pozzo-Miller
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, USA
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Wang F, Kang P, Li Z, Niu Q. Role of MLL in the modification of H3K4me3 in aluminium-induced cognitive dysfunction. CHEMOSPHERE 2019; 232:121-129. [PMID: 31152896 DOI: 10.1016/j.chemosphere.2019.05.099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
It is widely accepted that aluminium is neurotoxic; it primarily causes cognitive dysfunction, which has been confirmed in human and animal tissue and cell experiments (Bondy, 2010), but its toxic mechanism has yet to be fully elucidated. Epigenetics is the study of changes in gene expression that may be triggered by both genetic and environmental factors and is independent from changes in the underlying DNA sequence, resulting in a change in phenotype without a change in genotype, which in turn affects how cells read genes. Some findings emphasize the potential significance of histone lysine methylation for orderly brain development and as a molecular toolbox to study chromatin function in vivo and in vitro. The H3K4-specific methyltransferase MLL is essential for hippocampal synaptic plasticity and might be involved in cognitive dysfunction. In the present study, we established that chronic aluminium exposure results in cognitive dysfunction, causing deficits in exploratory behaviour and learning and memory, in a dose- and time-dependent manner. Furthermore, we demonstrated in vivo and in vitro that chronic aluminium exposure reduces expression of histone H3K4 tri-methylation (H3K4me3) and the activity and expression of MLL. Taken together, these results indicate that chronic aluminium exposure may reduce H3K4me3 levels through suppressing activation of MLL, which in turn affects cognitive ability.
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Affiliation(s)
- Fei Wang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Pan Kang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Zhaoyang Li
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Qiao Niu
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China.
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Kerr K, McAneney H, Flanagan C, Maxwell AP, McKnight AJ. Differential methylation as a diagnostic biomarker of rare renal diseases: a systematic review. BMC Nephrol 2019; 20:320. [PMID: 31419951 PMCID: PMC6697952 DOI: 10.1186/s12882-019-1517-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The challenges in diagnosis of rare renal conditions can negatively impact patient prognosis, quality of life and result in significant healthcare costs. Differential methylation is emerging as an important biomarker for rare diseases and should be evaluated for rare renal conditions. METHODS A comprehensive systematic review of methylation and rare renal disorders was conducted by searching the electronic databases MEDLINE, EMBASE, PubMed, Cochrane Library, alongside grey literature from GreyLit and OpenGrey databases, for publications published before September 2018. Additionally, the reference lists of the included papers were searched. Data was extracted and appraised including the primary focus, measurement and methodological rigour of the source. Eligibility criteria were adapted using the inclusion criteria from 'The 100,000 Genomes Project' and The National Registry of Rare Kidney Diseases, with additional focus on methylation. RESULTS Thirteen full text articles were included in the review. Diseases analysed for differential methylation included glomerular disease, IgA nephropathy, ADPKD, rare causes of proteinuria, congenital renal agenesis, and membranous nephropathy. CONCLUSIONS Differential methylation has been observed for several rare renal diseases, highlighting its potential for improving molecular characterisation of these disorders. Further investigation of methylation following a standardised reporting structure is necessary to improve research quality. Multi-omic data will provide insights for improved diagnosis, prognosis and support for individuals living and working with rare renal diseases.
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Affiliation(s)
- Katie Kerr
- Centre for Public Health, Queen's University Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, BT9 7AB, Belfast, Northern Ireland
| | - Helen McAneney
- Centre for Public Health, Queen's University Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, BT9 7AB, Belfast, Northern Ireland
| | - Cheryl Flanagan
- 100,000 Genomes Project Team, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | | | - Amy Jayne McKnight
- Centre for Public Health, Queen's University Belfast, c/o Regional Genetics Centre, Level A, Tower Block, Belfast City Hospital, Lisburn Road, BT9 7AB, Belfast, Northern Ireland.
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57
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Genetic Variation in Long-Range Enhancers. Curr Top Behav Neurosci 2019; 42:35-50. [PMID: 31396896 DOI: 10.1007/7854_2019_110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Cis-regulatory elements (CREs), including insulators, promoters, and enhancers, play critical roles in the establishment and maintenance of normal cellular function. Within each cell, the 3D structure of chromatin is arranged in specific patterns to expose the CREs required for optimal spatiotemporal regulation of gene expression. CREs can act over large distances along the linear genome, facilitated by looping of the intervening chromatin to allow direct interaction between distal regulatory elements and their target genes. A number of pathologies are associated with dysregulation of CRE function, including developmental disorders, cancers, and neuropsychiatric disease. A majority of known neuropsychiatric disease risk loci are noncoding, and increasing evidence suggests that they contribute to disease through disruption of CREs. As such, rather than directly altering the amino acid content of proteins, these variants are instead thought to affect where, when, and to what extent a given gene is expressed. The distances over which CREs can operate often render their target genes difficult to identify. Furthermore, as many risk loci contain multiple variants in high linkage disequilibrium, identification of the causative single nucleotide polymorphism(s) therein is not straightforward. Thus, deciphering the genetic etiology of complex neuropsychiatric disorders presents a significant challenge.
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58
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O'Donnell-Luria AH, Pais LS, Faundes V, Wood JC, Sveden A, Luria V, Abou Jamra R, Accogli A, Amburgey K, Anderlid BM, Azzarello-Burri S, Basinger AA, Bianchini C, Bird LM, Buchert R, Carre W, Ceulemans S, Charles P, Cox H, Culliton L, Currò A, Demurger F, Dowling JJ, Duban-Bedu B, Dubourg C, Eiset SE, Escobar LF, Ferrarini A, Haack TB, Hashim M, Heide S, Helbig KL, Helbig I, Heredia R, Héron D, Isidor B, Jonasson AR, Joset P, Keren B, Kok F, Kroes HY, Lavillaureix A, Lu X, Maas SM, Maegawa GHB, Marcelis CLM, Mark PR, Masruha MR, McLaughlin HM, McWalter K, Melchinger EU, Mercimek-Andrews S, Nava C, Pendziwiat M, Person R, Ramelli GP, Ramos LLP, Rauch A, Reavey C, Renieri A, Rieß A, Sanchez-Valle A, Sattar S, Saunders C, Schwarz N, Smol T, Srour M, Steindl K, Syrbe S, Taylor JC, Telegrafi A, Thiffault I, Trauner DA, van der Linden H, van Koningsbruggen S, Villard L, Vogel I, Vogt J, Weber YG, Wentzensen IM, Widjaja E, Zak J, Baxter S, Banka S, Rodan LH. Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy. Am J Hum Genet 2019; 104:1210-1222. [PMID: 31079897 PMCID: PMC6556837 DOI: 10.1016/j.ajhg.2019.03.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/21/2019] [Indexed: 01/22/2023] Open
Abstract
We delineate a KMT2E-related neurodevelopmental disorder on the basis of 38 individuals in 36 families. This study includes 31 distinct heterozygous variants in KMT2E (28 ascertained from Matchmaker Exchange and three previously reported), and four individuals with chromosome 7q22.2-22.23 microdeletions encompassing KMT2E (one previously reported). Almost all variants occurred de novo, and most were truncating. Most affected individuals with protein-truncating variants presented with mild intellectual disability. One-quarter of individuals met criteria for autism. Additional common features include macrocephaly, hypotonia, functional gastrointestinal abnormalities, and a subtle facial gestalt. Epilepsy was present in about one-fifth of individuals with truncating variants and was responsive to treatment with anti-epileptic medications in almost all. More than 70% of the individuals were male, and expressivity was variable by sex; epilepsy was more common in females and autism more common in males. The four individuals with microdeletions encompassing KMT2E generally presented similarly to those with truncating variants, but the degree of developmental delay was greater. The group of four individuals with missense variants in KMT2E presented with the most severe developmental delays. Epilepsy was present in all individuals with missense variants, often manifesting as treatment-resistant infantile epileptic encephalopathy. Microcephaly was also common in this group. Haploinsufficiency versus gain-of-function or dominant-negative effects specific to these missense variants in KMT2E might explain this divergence in phenotype, but requires independent validation. Disruptive variants in KMT2E are an under-recognized cause of neurodevelopmental abnormalities.
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Affiliation(s)
- Anne H O'Donnell-Luria
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Víctor Faundes
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Jordan C Wood
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Abigail Sveden
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Victor Luria
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Andrea Accogli
- Department of Pediatrics, Department of Neurology and Neurosurgery, McGill University, Montreal, QC H4A 3J1, Quebec, Canada; Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica Scienze Materno-Infantili, Università degli studi di Genova, 16126 Genova, Italy; IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Kimberly Amburgey
- Division of Neurology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto M5G 1X8, ON, Canada
| | - Britt Marie Anderlid
- Department of Molecular Medicine and Surgery, Centre for Molecular Medicine, Karolinska Institutet, Stockholm 17176, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Silvia Azzarello-Burri
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich CH-8952, Switzerland; Neuroscience Center Zurich, University of Zurich and Eidgenössische Technische Hochschule, Zurich 8057, Switzerland
| | - Alice A Basinger
- Genetics, Cook Children's Physician Network, Fort Worth, TX 76104, USA
| | - Claudia Bianchini
- Pediatric Neurology, Neurogenetics, and Neurobiology Unit and Laboratories, Neuroscience Department, Meyer Children's Hospital, University of Florence, 50139 Florence, Italy
| | - Lynne M Bird
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA; Division of Genetics, Rady Children's Hospital of San Diego, San Diego, CA 92123, USA
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen 72076, Germany
| | - Wilfrid Carre
- Laboratoire de Génétique Moléculaire et Génomique, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France
| | - Sophia Ceulemans
- Division of Genetics, Rady Children's Hospital of San Diego, San Diego, CA 92123, USA
| | - Perrine Charles
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75013, France; Groupe de Recherche Clinique Déficience Intellectuelle et Autisme, Sorbonne University, Paris 75006, France
| | - Helen Cox
- West Midlands Regional Clinical Genetics Service, Birmingham Women's and Children's Hospital, National Health Service Foundation Trust, Birmingham B15 2TG, UK; Birmingham Health Partners, Birmingham Women's and Children's Hospital, National Health Service Foundation Trust, Birmingham B15 2TG, UK
| | - Lisa Culliton
- Department of Neurology, Children's Mercy Hospital and Clinics, Kansas City, MO 64108, USA
| | - Aurora Currò
- Medical Genetics, University of Siena, 53100 Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy
| | - Florence Demurger
- Service de Génétique Clinique, Centre de Référence Maladies Rares Centre Labellisé Anomalies du Développement-Ouest, Centre Hospitalier Universitaire de Rennes, 35033 Rennes, France
| | - James J Dowling
- Division of Neurology, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto M5G 1X8, ON, Canada
| | - Benedicte Duban-Bedu
- Centre de Génétique Chromosomique, Groupement des Hôpitaux de l'Institut Catholique de Lille Hôpital Saint Vincent de Paul, 59020 Lille, France; Faculté de médecine de l'Université Catholoique de Lille, 59800 Lille, France
| | - Christèle Dubourg
- Laboratoire de Génétique Moléculaire et Génomique, Centre Hospitalier Universitaire de Rennes, Rennes 35033, France
| | - Saga Elise Eiset
- Department of Clinical Genetics, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Luis F Escobar
- St. Vincent's Children's Hospital, Indianapolis, IN 46260, USA
| | - Alessandra Ferrarini
- Medical Genetic Unit, Italian Hospital of Lugano, Lugano, Switzerland; Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen 72076, Germany
| | - Mona Hashim
- Oxford National Institute for Health Research Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Solveig Heide
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75013, France; Groupe de Recherche Clinique Déficience Intellectuelle et Autisme, Sorbonne University, Paris 75006, France
| | - Katherine L Helbig
- Division of Neurology and Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- Division of Neurology and Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104 USA; Department of Neuropediatrics, University Medical Center, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | | | - Delphine Héron
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75013, France; Groupe de Recherche Clinique Déficience Intellectuelle et Autisme, Sorbonne University, Paris 75006, France
| | - Bertrand Isidor
- Service de Génétique Médicale, Hôpital Hôtel-Dieu, Centre Hospitalier Universitaire de Nantes, 44093 Nantes, France
| | - Amy R Jonasson
- Division of Genetics and Metabolism, Department of Pediatrics, University of Florida, FL 32610, USA
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich CH-8952, Switzerland; Neuroscience Center Zurich, University of Zurich and Eidgenössische Technische Hochschule, Zurich 8057, Switzerland
| | - Boris Keren
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75013, France; Groupe de Recherche Clinique Déficience Intellectuelle et Autisme, Sorbonne University, Paris 75006, France
| | - Fernando Kok
- Mendelics Genomic Analysis, Sao Paulo 04013, Brazil
| | - Hester Y Kroes
- Department of Medical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, Netherlands
| | - Alinoë Lavillaureix
- Service de Génétique Clinique, Centre de Référence Maladies Rares Centre Labellisé Anomalies du Développement-Ouest, Centre Hospitalier Universitaire de Rennes, 35033 Rennes, France
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Saskia M Maas
- Department of Clinical Genetics, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Gustavo H B Maegawa
- Division of Genetics and Metabolism, Department of Pediatrics, University of Florida, FL 32610, USA
| | - Carlo L M Marcelis
- Department of Clinical Genetics, Radboud University Medical Centre, 6525 GA Nijmegen, the Netherlands
| | - Paul R Mark
- Division of Medical Genetics and Genomics, Spectrum Health, Grand Rapids, MI 49544, USA
| | - Marcelo R Masruha
- Department of Neurology and Neurosurgery, Universidade de Federal de São Paulo, São Paulo 04023, Brazil
| | | | | | - Esther U Melchinger
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen 72076, Germany
| | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Caroline Nava
- Department of Genetics, Centre de Référence Déficiences Intellectuelles de Causes Rares, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75013, France; Groupe de Recherche Clinique Déficience Intellectuelle et Autisme, Sorbonne University, Paris 75006, France
| | - Manuela Pendziwiat
- Department of Neuropediatrics, University Medical Center, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | | | - Gian Paolo Ramelli
- Neuropediatric Unit, Pediatric Department of Southern Switzerland, San Giovanni Hospital, 6500 Bellinzona, Switzerland
| | | | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich CH-8952, Switzerland; Neuroscience Center Zurich, University of Zurich and Eidgenössische Technische Hochschule, Zurich 8057, Switzerland; Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases, University of Zurich, CH-8006 Zurich, Switzerland
| | | | - Alessandra Renieri
- Medical Genetics, University of Siena, 53100 Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy
| | - Angelika Rieß
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen 72076, Germany
| | - Amarilis Sanchez-Valle
- Department of Pediatrics, Division of Genetics and Metabolism, University of South Florida, Tampa, FL 33606, USA
| | - Shifteh Sattar
- Section of Pediatric Neurology, Rady Children's Hospital, San Diego, CA 92123, USA; Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Carol Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, Kansas City, MO 64108, USA; School of Medicine, University of Missouri, Kansas City, MO 64108, USA
| | - Niklas Schwarz
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Thomas Smol
- EA7364 Rares du Developpement Embryonnaire et du Metabolisme, Institut de Genetique Medicale, Centre Hospitalier Universitaire de Lille, University of Lille, F-59000 Lille, France
| | - Myriam Srour
- Department of Pediatrics, Department of Neurology and Neurosurgery, McGill University, Montreal, QC H4A 3J1, Quebec, Canada
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich CH-8952, Switzerland; Neuroscience Center Zurich, University of Zurich and Eidgenössische Technische Hochschule, Zurich 8057, Switzerland
| | - Steffen Syrbe
- Division of Child Neurology and Inherited Metabolic Diseases, Department of General Paediatrics, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Jenny C Taylor
- Oxford National Institute for Health Research Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | - Isabelle Thiffault
- School of Medicine, University of Missouri, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Hospital and Clinics, Kansas City, MO 64108, USA
| | - Doris A Trauner
- Section of Pediatric Neurology, Rady Children's Hospital, San Diego, CA 92123, USA; Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Helio van der Linden
- Pediatric Neurology and Neurophysiology, Instituto de Neurologia de Goiania, Goiania 74210, Brazil
| | - Silvana van Koningsbruggen
- Department of Clinical Genetics, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Laurent Villard
- Department of Medical Genetics, Assistance Publique - Hôpitaux de Marseille, Hôpital d'Enfants de La Timone, 13005 Marseille, France; Marseille Medical Genetics Center, Aix Marseille Univ, Inserm, U1251, Marseille, France
| | - Ida Vogel
- Department of Clinical Genetics, Aarhus University Hospital, 8200 Aarhus, Denmark; Center for Fetal Diagnostics, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Julie Vogt
- West Midlands Regional Clinical Genetics Service, Birmingham Women's and Children's Hospital, National Health Service Foundation Trust, Birmingham B15 2TG, UK; Birmingham Health Partners, Birmingham Women's and Children's Hospital, National Health Service Foundation Trust, Birmingham B15 2TG, UK
| | - Yvonne G Weber
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany; Department for Neurosurgery, University of Tübingen, 72076 Tübingen, Germany
| | | | - Elysa Widjaja
- Department of Diagnostic Imaging, Hospital for Sick Children, University of Toronto, Toronto, M5G 1X8, ON, Canada
| | - Jaroslav Zak
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Samantha Baxter
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University National Health Service Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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59
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Yabuta S, Shidoji Y. Cytoplasmic translocation of nuclear LSD1 ( KDM1A) in human hepatoma cells is induced by its inhibitors. Hepat Oncol 2019; 6:HEP13. [PMID: 31205679 PMCID: PMC6566134 DOI: 10.2217/hep-2018-0008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Aim Histone-modifiable lysine-specific demethylase-1 (LSD1/KDM1A) is an oncoprotein upregulated in cancers, including hepatoma. We previously reported that the hepatoma-preventive geranylgeranoic acid (GGA) inhibits KDM1A at the same IC50 as that of the clinically used tranylcypromine. Here, we report that these inhibitors induce the cytoplasmic translocation of nuclear KDM1A in a human hepatoma-derived cell line. Methods & results Immunofluorescence studies revealed that KDM1A was cytoplasmically localized in HuH-7 cells 3 h after GGA or tranylcypromine addition. However, GGA did not affect the subcellular localization of another histone lysine-specific demethylase, KDM5A. This suggests that GGA-induced translocation is KDM1A specific. Conclusion These data demonstrate, for the first time, that KDM1A inhibitors specifically induce the cytoplasmic translocation of nuclear KDM1A.
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Affiliation(s)
- Suemi Yabuta
- Molecular & Cellular Biology, Graduate School of Human Health Science, University of Nagasaki, 1-1-1 Academy Hills, Nagayo, Nagasaki 851-2195, Japan
| | - Yoshihiro Shidoji
- Molecular & Cellular Biology, Graduate School of Human Health Science, University of Nagasaki, 1-1-1 Academy Hills, Nagayo, Nagasaki 851-2195, Japan
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60
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Gusev FE, Reshetov DA, Mitchell AC, Andreeva TV, Dincer A, Grigorenko AP, Fedonin G, Halene T, Aliseychik M, Goltsov AY, Solovyev V, Brizgalov L, Filippova E, Weng Z, Akbarian S, Rogaev EI. Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons. FASEB J 2019; 33:8161-8173. [PMID: 30970224 DOI: 10.1096/fj.201802646r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human prefrontal cortex (PFC) is associated with broad individual variabilities in functions linked to personality, social behaviors, and cognitive functions. The phenotype variabilities associated with brain functions can be caused by genetic or epigenetic factors. The interactions between these factors in human subjects is, as of yet, poorly understood. The heterogeneity of cerebral tissue, consisting of neuronal and nonneuronal cells, complicates the comparative analysis of gene activities in brain specimens. To approach the underlying neurogenomic determinants, we performed a deep analysis of open chromatin-associated histone methylation in PFC neurons sorted from multiple human individuals in conjunction with whole-genome and transcriptome sequencing. Integrative analyses produced novel unannotated neuronal genes and revealed individual-specific chromatin "blueprints" of neurons that, in part, relate to genetic background. Surprisingly, we observed gender-dependent epigenetic signals, implying that gender may contribute to the chromatin variabilities in neurons. Finally, we found epigenetic, allele-specific activation of the testis-specific gene nucleoporin 210 like (NUP210L) in brain in some individuals, which we link to a genetic variant occurring in <3% of the human population. Recently, the NUP210L locus has been associated with intelligence and mathematics ability. Our findings highlight the significance of epigenetic-genetic footprinting for exploring neurologic function in a subject-specific manner.-Gusev, F. E., Reshetov, D. A., Mitchell, A. C., Andreeva, T. V., Dincer, A., Grigorenko, A. P., Fedonin, G., Halene, T., Aliseychik, M., Goltsov, A. Y., Solovyev, V., Brizgalov, L., Filippova, E., Weng, Z., Akbarian, S., Rogaev, E. I. Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons.
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Affiliation(s)
- Fedor E Gusev
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Denis A Reshetov
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Amanda C Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tatiana V Andreeva
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Aslihan Dincer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anastasia P Grigorenko
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Gennady Fedonin
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia
| | - Tobias Halene
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Maria Aliseychik
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andrey Y Goltsov
- Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia
| | - Victor Solovyev
- Department of Cell Biology, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Leonid Brizgalov
- Center of Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena Filippova
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Zhiping Weng
- Department of Cell Biology, Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
| | - Schahram Akbarian
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Evgeny I Rogaev
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Human Genetics and Genomics, Laboratory of Evolutionary Genomics, Vavilov Institute of General Genetics of Russian Academy of Science, Moscow, Russia.,Center for Genetics and Genetic Technologies, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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61
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Rowe EM, Xing V, Biggar KK. Lysine methylation: Implications in neurodegenerative disease. Brain Res 2019; 1707:164-171. [DOI: 10.1016/j.brainres.2018.11.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/13/2018] [Accepted: 11/18/2018] [Indexed: 12/14/2022]
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62
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Collins BE, Greer CB, Coleman BC, Sweatt JD. Histone H3 lysine K4 methylation and its role in learning and memory. Epigenetics Chromatin 2019; 12:7. [PMID: 30616667 PMCID: PMC6322263 DOI: 10.1186/s13072-018-0251-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023] Open
Abstract
Epigenetic modifications such as histone methylation permit change in chromatin structure without accompanying change in the underlying genomic sequence. A number of studies in animal models have shown that dysregulation of various components of the epigenetic machinery causes cognitive deficits at the behavioral level, suggesting that proper epigenetic control is necessary for the fundamental processes of learning and memory. Histone H3 lysine K4 (H3K4) methylation comprises one component of such epigenetic control, and global levels of this mark are increased in the hippocampus during memory formation. Modifiers of H3K4 methylation are needed for memory formation, shown through animal studies, and many of the same modifiers are mutated in human cognitive diseases. Indeed, all of the known H3K4 methyltransferases and four of the known six H3K4 demethylases have been associated with impaired cognition in a neurologic or psychiatric disorder. Cognitive impairment in such patients often manifests as intellectual disability, consistent with a role for H3K4 methylation in learning and memory. As a modification quintessentially, but not exclusively, associated with transcriptional activity, H3K4 methylation provides unique insights into the regulatory complexity of writing, reading, and erasing chromatin marks within an activated neuron. The following review will discuss H3K4 methylation and connect it to transcriptional events required for learning and memory within the developed nervous system. This will include an initial discussion of the most recent advances in the developing methodology to analyze H3K4 methylation, namely mass spectrometry and deep sequencing, as well as how these methods can be applied to more deeply understand the biology of this mark in the brain. We will then introduce the core enzymatic machinery mediating addition and removal of H3K4 methylation marks and the resulting epigenetic signatures of these marks throughout the neuronal genome. We next foray into the brain, discussing changes in H3K4 methylation marks within the hippocampus during memory formation and retrieval, as well as the behavioral correlates of H3K4 methyltransferase deficiency in this region. Finally, we discuss the human cognitive diseases connected to each H3K4 methylation modulator and summarize advances in developing drugs to target them.
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Affiliation(s)
- Bridget E Collins
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - Celeste B Greer
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - Benjamin C Coleman
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - J David Sweatt
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA.
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63
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Adolescent exposure to Δ 9-tetrahydrocannabinol alters the transcriptional trajectory and dendritic architecture of prefrontal pyramidal neurons. Mol Psychiatry 2019; 24:588-600. [PMID: 30283037 PMCID: PMC6430678 DOI: 10.1038/s41380-018-0243-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 07/25/2018] [Accepted: 08/08/2018] [Indexed: 12/21/2022]
Abstract
Neuronal circuits within the prefrontal cortex (PFC) mediate higher cognitive functions and emotional regulation that are disrupted in psychiatric disorders. The PFC undergoes significant maturation during adolescence, a period when cannabis use in humans has been linked to subsequent vulnerability to psychiatric disorders such as addiction and schizophrenia. Here, we investigated in a rat model the effects of adolescent exposure to Δ9-tetrahydrocannabinol (THC), a psychoactive component of cannabis, on the morphological architecture and transcriptional profile of layer III pyramidal neurons-using cell type- and layer-specific high-resolution microscopy, laser capture microdissection and next-generation RNA-sequencing. The results confirmed known normal expansions in basal dendritic arborization and dendritic spine pruning during the transition from late adolescence to early adulthood that were accompanied by differential expression of gene networks associated with neurodevelopment in control animals. In contrast, THC exposure disrupted the normal developmental process by inducing premature pruning of dendritic spines and allostatic atrophy of dendritic arborization in early adulthood. Surprisingly, there was minimal overlap of the developmental transcriptomes between THC- and vehicle-exposed rats. THC altered functional gene networks related to cell morphogenesis, dendritic development, and cytoskeleton organization. Marked developmental network disturbances were evident for epigenetic regulators with enhanced co-expression of chromatin- and dendrite-related genes in THC-treated animals. Dysregulated PFC co-expression networks common to both the THC-treated animals and patients with schizophrenia were enriched for cytoskeletal and neurite development. Overall, adolescent THC exposure altered the morphological and transcriptional trajectory of PFC pyramidal neurons, which could enhance vulnerability to psychiatric disorders.
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64
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Matthews AM, Blydt-Hansen I, Al-Jabri B, Andersen J, Tarailo-Graovac M, Price M, Selby K, Demos M, Connolly M, Drögemoller B, Shyr C, Mwenifumbo J, Elliott AM, Lee J, Ghani A, Stöckler S, Salvarinova R, Vallance H, Sinclair G, Ross CJ, Wasserman WW, McKinnon ML, Horvath GA, Goez H, van Karnebeek CD. Atypical cerebral palsy: genomics analysis enables precision medicine. Genet Med 2018; 21:1621-1628. [DOI: 10.1038/s41436-018-0376-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/08/2018] [Indexed: 11/09/2022] Open
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65
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García-Cabezas MÁ, Barbas H, Zikopoulos B. Parallel Development of Chromatin Patterns, Neuron Morphology, and Connections: Potential for Disruption in Autism. Front Neuroanat 2018; 12:70. [PMID: 30174592 PMCID: PMC6107687 DOI: 10.3389/fnana.2018.00070] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/30/2018] [Indexed: 12/27/2022] Open
Abstract
The phenotype of neurons and their connections depend on complex genetic and epigenetic processes that regulate the expression of genes in the nucleus during development and throughout life. Here we examined the distribution of nuclear chromatin patters in relation to the epigenetic landscape, phenotype and connections of neurons with a focus on the primate cerebral cortex. We show that nuclear patterns of chromatin in cortical neurons are related to neuron size and cortical connections. Moreover, we point to evidence that reveals an orderly sequence of events during development, linking chromatin and gene expression patterns, neuron morphology, function, and connections across cortical areas and layers. Based on this synthesis, we posit that systematic studies of changes in chromatin patterns and epigenetic marks across cortical areas will provide novel insights on the development and evolution of cortical networks, and their disruption in connectivity disorders of developmental origin, like autism. Achieving this requires embedding and interpreting genetic, transcriptional, and epigenetic studies within a framework that takes into consideration distinct types of neurons, local circuit interactions, and interareal pathways. These features vary systematically across cortical areas in parallel with laminar structure and are differentially affected in disorders. Finally, based on evidence that autism-associated genetic polymorphisms are especially prominent in excitatory neurons and connectivity disruption affects mostly limbic cortices, we employ this systematic approach to propose novel, targeted studies of projection neurons in limbic areas to elucidate the emergence and time-course of developmental disruptions in autism.
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Affiliation(s)
- Miguel Á García-Cabezas
- Neural Systems Laboratory, Department of Health Sciences, Boston University, Boston, MA, United States
| | - Helen Barbas
- Neural Systems Laboratory, Department of Health Sciences, Boston University, Boston, MA, United States.,Graduate Program in Neuroscience, Boston University, Boston, MA, United States
| | - Basilis Zikopoulos
- Graduate Program in Neuroscience, Boston University, Boston, MA, United States.,Human Systems Neuroscience Laboratory, Department of Health Sciences, Boston University, Boston, MA, United States
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66
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Symmank J, Bayer C, Schmidt C, Hahn A, Pensold D, Zimmer-Bensch G. DNMT1 modulates interneuron morphology by regulating Pak6 expression through crosstalk with histone modifications. Epigenetics 2018; 13:536-556. [PMID: 29912614 DOI: 10.1080/15592294.2018.1475980] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epigenetic mechanisms of gene regulation, including DNA methylation and histone modifications, call increasing attention in the context of development and human health. Thereby, interactions between DNA methylating enzymes and histone modifications tremendously multiply the spectrum of potential regulatory functions. Epigenetic networks are critically involved in the establishment and functionality of neuronal circuits that are composed of gamma-aminobutyric acid (GABA)-positive inhibitory interneurons and excitatory principal neurons in the cerebral cortex. We recently reported a crucial role of the DNA methyltransferase 1 (DNMT1) during the migration of immature POA-derived cortical interneurons by promoting the migratory morphology through repression of Pak6. However, the DNMT1-dependent regulation of Pak6 expression appeared to occur independently of direct DNA methylation. Here, we show that in addition to its DNA methylating activity, DNMT1 can act on gene transcription by modulating permissive H3K4 and repressive H3K27 trimethylation in developing inhibitory interneurons, similar to what was found in other cell types. In particular, the transcriptional control of Pak6, interactions of DNMT1 with the Polycomb-repressor complex 2 (PCR2) core enzyme EZH2, mediating repressive H3K27 trimethylations at regulatory regions of the Pak6 gene locus. Similar to what was observed upon Dnmt1 depletion, inhibition of EZH2 caused elevated Pak6 expression levels accompanied by increased morphological complexity, which was rescued by siRNA-mediated downregulation of Pak6 expression. Together, our data emphasise the relevance of DNMT1-dependent crosstalk with histone tail methylation for transcriptional control of genes like Pak6 required for proper cortical interneuron migration.
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Affiliation(s)
- Judit Symmank
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Cathrin Bayer
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Christiane Schmidt
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Anne Hahn
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Daniel Pensold
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Geraldine Zimmer-Bensch
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany.,b Institute for Biology II , Division of Functional Epigenetics in the Animal Model, RWTH Aachen University , Aachen , Germany
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67
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CUL4B promotes the pathology of adjuvant-induced arthritis in rats through the canonical Wnt signaling. J Mol Med (Berl) 2018; 96:495-511. [DOI: 10.1007/s00109-018-1635-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 02/07/2018] [Accepted: 03/22/2018] [Indexed: 12/19/2022]
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68
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KMT2A and KMT2B Mediate Memory Function by Affecting Distinct Genomic Regions. Cell Rep 2018; 20:538-548. [PMID: 28723559 DOI: 10.1016/j.celrep.2017.06.072] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 04/09/2017] [Accepted: 06/23/2017] [Indexed: 11/23/2022] Open
Abstract
Kmt2a and Kmt2b are H3K4 methyltransferases of the Set1/Trithorax class. We have recently shown the importance of Kmt2b for learning and memory. Here, we report that Kmt2a is also important in memory formation. We compare the decrease in H3K4 methylation and de-regulation of gene expression in hippocampal neurons of mice with knockdown of either Kmt2a or Kmt2b. Kmt2a and Kmt2b control largely distinct genomic regions and different molecular pathways linked to neuronal plasticity. Finally, we show that the decrease in H3K4 methylation resulting from Kmt2a knockdown partially recapitulates the pattern previously reported in CK-p25 mice, a model for neurodegeneration and memory impairment. Our findings point to the distinct functions of even closely related histone-modifying enzymes and provide essential insight for the development of more efficient and specific epigenetic therapies against brain diseases.
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69
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Večeřa J, Bártová E, Krejčí J, Legartová S, Komůrková D, Rudá-Kučerová J, Štark T, Dražanová E, Kašpárek T, Šulcová A, Dekker FJ, Szymanski W, Seiser C, Weitzer G, Mechoulam R, Micale V, Kozubek S. HDAC1 and HDAC3 underlie dynamic H3K9 acetylation during embryonic neurogenesis and in schizophrenia-like animals. J Cell Physiol 2018; 233:530-548. [PMID: 28300292 PMCID: PMC7615847 DOI: 10.1002/jcp.25914] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 03/14/2017] [Indexed: 12/21/2022]
Abstract
Although histone acetylation is one of the most widely studied epigenetic modifications, there is still a lack of information regarding how the acetylome is regulated during brain development and pathophysiological processes. We demonstrate that the embryonic brain (E15) is characterized by an increase in H3K9 acetylation as well as decreases in the levels of HDAC1 and HDAC3. Moreover, experimental induction of H3K9 hyperacetylation led to the overexpression of NCAM in the embryonic cortex and depletion of Sox2 in the subventricular ependyma, which mimicked the differentiation processes. Inducing differentiation in HDAC1-deficient mouse ESCs resulted in early H3K9 deacetylation, Sox2 downregulation, and enhanced astrogliogenesis, whereas neuro-differentiation was almost suppressed. Neuro-differentiation of (wt) ESCs was characterized by H3K9 hyperacetylation that was associated with HDAC1 and HDAC3 depletion. Conversely, the hippocampi of schizophrenia-like animals showed H3K9 deacetylation that was regulated by an increase in both HDAC1 and HDAC3. The hippocampi of schizophrenia-like brains that were treated with the cannabinoid receptor-1 inverse antagonist AM251 expressed H3K9ac at the level observed in normal brains. Together, the results indicate that co-regulation of H3K9ac by HDAC1 and HDAC3 is important to both embryonic brain development and neuro-differentiation as well as the pathophysiology of a schizophrenia-like phenotype.
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MESH Headings
- Acetylation
- Animals
- Antipsychotic Agents/pharmacology
- Brain/drug effects
- Brain/embryology
- Brain/enzymology
- Brain/pathology
- Cannabinoid Receptor Antagonists/pharmacology
- Disease Models, Animal
- Epigenesis, Genetic
- Gene Expression Regulation, Developmental
- Gestational Age
- Histone Deacetylase 1/antagonists & inhibitors
- Histone Deacetylase 1/genetics
- Histone Deacetylase 1/metabolism
- Histone Deacetylase Inhibitors/pharmacology
- Histone Deacetylases/genetics
- Histone Deacetylases/metabolism
- Histones/metabolism
- Methylazoxymethanol Acetate
- Mice, Inbred C57BL
- Neural Cell Adhesion Molecules/genetics
- Neural Cell Adhesion Molecules/metabolism
- Neurogenesis/drug effects
- Neurons/drug effects
- Neurons/enzymology
- Neurons/pathology
- Protein Processing, Post-Translational
- Rats, Sprague-Dawley
- Receptor, Cannabinoid, CB1/antagonists & inhibitors
- Receptor, Cannabinoid, CB1/metabolism
- SOXB1 Transcription Factors/genetics
- SOXB1 Transcription Factors/metabolism
- Schizophrenia/chemically induced
- Schizophrenia/drug therapy
- Schizophrenia/enzymology
- Schizophrenia/genetics
- Signal Transduction
- Time Factors
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Affiliation(s)
- Josef Večeřa
- Faculty of Science, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Eva Bártová
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno, Czech Republic
| | - Jana Krejčí
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno, Czech Republic
| | - Soňa Legartová
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno, Czech Republic
| | - Denisa Komůrková
- Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Brno, Czech Republic
| | - Jana Rudá-Kučerová
- Faculty of Medicine, Department of Pharmacology, Masaryk University, Brno, Czech Republic
| | - Tibor Štark
- Faculty of Medicine, Department of Pharmacology, Masaryk University, Brno, Czech Republic
| | - Eva Dražanová
- Faculty of Medicine, Department of Pharmacology, Masaryk University, Brno, Czech Republic
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Brno, Czech Republic
| | - Tomáš Kašpárek
- Behavioral and Social Neuroscience Group, CEITEC—Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Alexandra Šulcová
- Behavioral and Social Neuroscience Group, CEITEC—Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Frank J. Dekker
- Chemical and Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands
| | - Wiktor Szymanski
- Department of Radiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Christian Seiser
- Max F. Perutz Laboratories, Vienna Biocenter (VBC), Vienna, Austria
| | - Georg Weitzer
- Max F. Perutz Laboratories, Vienna Biocenter (VBC), Vienna, Austria
| | - Raphael Mechoulam
- Faculty of Medicine, Institute for Drug Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vincenzo Micale
- Behavioral and Social Neuroscience Group, CEITEC—Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, School of Medicine, University of Catania, Catania, Italy
| | - Stanislav Kozubek
- Faculty of Science, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
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Kyzar EJ, Zhang H, Sakharkar AJ, Pandey SC. Adolescent alcohol exposure alters lysine demethylase 1 (LSD1) expression and histone methylation in the amygdala during adulthood. Addict Biol 2017; 22:1191-1204. [PMID: 27183824 DOI: 10.1111/adb.12404] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/27/2022]
Abstract
Alcohol exposure in adolescence is an important risk factor for the development of alcoholism in adulthood. Epigenetic processes are implicated in the persistence of adolescent alcohol exposure-related changes, specifically in the amygdala. We investigated the role of histone methylation mechanisms in the persistent effects of adolescent intermittent ethanol (AIE) exposure in adulthood. Adolescent rats were exposed to 2 g/kg ethanol (2 days on/off) or intermittent n-saline (AIS) during postnatal days (PND) 28-41 and used for behavioral and epigenetic studies. We found that AIE exposure caused a long-lasting decrease in mRNA and protein levels of lysine demethylase 1(Lsd1) and mRNA levels of Lsd1 + 8a (a neuron-specific splice variant) in specific amygdaloid structures compared with AIS-exposed rats when measured at adulthood. Interestingly, AIE increased histone H3 lysine 9 dimethylation (H3K9me2) levels in the central nucleus of the amygdala (CeA) and medial nucleus of the amygdala (MeA) in adulthood without producing any change in H3K4me2 protein levels. Acute ethanol challenge (2 g/kg) in adulthood attenuated anxiety-like behaviors and the decrease in Lsd1 + 8a mRNA levels in the amygdala induced by AIE. AIE caused an increase in H3K9me2 occupancy at the brain-derived neurotrophic factor exon IV promoter in the amygdala that returned to baseline after acute ethanol challenge in adulthood. These results indicate that AIE specifically modulates epizymes involved in H3K9 dimethylation in the amygdala in adulthood, which are possibly responsible for AIE-induced chromatin remodeling and adult psychopathology such as anxiety.
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Affiliation(s)
- Evan J. Kyzar
- Center for Alcohol Research in Epigenetics, Department of Psychiatry; University of Illinois at Chicago; Chicago IL USA
- Jesse Brown Veterans Affairs Medical Center; Chicago IL USA
| | - Huaibo Zhang
- Center for Alcohol Research in Epigenetics, Department of Psychiatry; University of Illinois at Chicago; Chicago IL USA
- Jesse Brown Veterans Affairs Medical Center; Chicago IL USA
| | - Amul J. Sakharkar
- Center for Alcohol Research in Epigenetics, Department of Psychiatry; University of Illinois at Chicago; Chicago IL USA
- Jesse Brown Veterans Affairs Medical Center; Chicago IL USA
| | - Subhash C. Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry; University of Illinois at Chicago; Chicago IL USA
- Jesse Brown Veterans Affairs Medical Center; Chicago IL USA
- Department of Anatomy and Cell Biology; University of Illinois at Chicago; Chicago IL USA
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71
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Maciukiewicz M, Marshe VS, Tiwari AK, Fonseka TM, Freeman N, Kennedy JL, Rotzinger S, Foster JA, Kennedy SH, Müller DJ. Genome-wide association studies of placebo and duloxetine response in major depressive disorder. THE PHARMACOGENOMICS JOURNAL 2017; 18:406-412. [PMID: 28696415 DOI: 10.1038/tpj.2017.29] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/01/2017] [Accepted: 03/16/2017] [Indexed: 12/28/2022]
Abstract
We investigated variants associated with treatment response in depressed patients treated with either the antidepressant duloxetine or placebo using a genome-wide approach. Our sample (N=391) included individuals aged 18-75 years, diagnosed with major depressive disorder and treated with either duloxetine or placebo for up to 8 weeks. We conducted genome-wide associations for treatment response as operationalized by percentage change in Montgomery-Åsberg Depression Rating Scale score from baseline, as well as mixed models analyses across five time points. In the placebo-treated subsample (N=205), we observed a genome-wide association with rs76767803 (β=0.69, P=1.25 × 10-8) upstream of STAC1. STAC1 rs76767803 was also associated with response using mixed model analysis (χ2=3.95; P=0.001). In the duloxetine-treated subsample (N=186), we observed suggestive associations with ZNF385D (rs4261893; β=-0.46, P=1.55 × 10-5), NCAM1 (rs2303377; β=0.45, P=1.76 × 10-5) and MLL5 (rs117986340; β=0.91, P=3.04 × 10-5). Our findings suggest that a variant upstream of STAC1 is associated with placebo response, which might have implications for treatment optimization, clinical trial design and drug development.
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Affiliation(s)
- M Maciukiewicz
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - V S Marshe
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - A K Tiwari
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - T M Fonseka
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Department of Psychiatry, University Health Network, Toronto, ON, Canada.,Department of Psychiatry, St. Michael's Hospital, Toronto, ON, Canada
| | - N Freeman
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - J L Kennedy
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - S Rotzinger
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University Health Network, Toronto, ON, Canada
| | - J A Foster
- Department of Psychiatry and Behavioral Neurosciences, McMaster University, Hamilton, ON, Canada
| | - S H Kennedy
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University Health Network, Toronto, ON, Canada.,Department of Psychiatry, St. Michael's Hospital, Toronto, ON, Canada
| | - D J Müller
- Pharmacogenetic Research Clinic, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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72
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Bondar N, Bryzgalov L, Ershov N, Gusev F, Reshetnikov V, Avgustinovich D, Tenditnik M, Rogaev E, Merkulova T. Molecular Adaptations to Social Defeat Stress and Induced Depression in Mice. Mol Neurobiol 2017; 55:3394-3407. [DOI: 10.1007/s12035-017-0586-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 04/28/2017] [Indexed: 12/31/2022]
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73
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Le Hellard S, Wang Y, Witoelar A, Zuber V, Bettella F, Hugdahl K, Espeseth T, Steen VM, Melle I, Desikan R, Schork AJ, Thompson WK, Dale AM, Djurovic S, Andreassen OA. Identification of Gene Loci That Overlap Between Schizophrenia and Educational Attainment. Schizophr Bull 2017; 43:654-664. [PMID: 27338279 PMCID: PMC5463752 DOI: 10.1093/schbul/sbw085] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
There is evidence for genetic overlap between cognitive abilities and schizophrenia (SCZ), and genome-wide association studies (GWAS) demonstrate that both SCZ and general cognitive abilities have a strong polygenic component with many single-nucleotide polymorphisms (SNPs) each with a small effect. Here we investigated the shared genetic architecture between SCZ and educational attainment, which is regarded as a "proxy phenotype" for cognitive abilities, but may also reflect other traits. We applied a conditional false discovery rate (condFDR) method to GWAS of SCZ (n = 82 315), college completion ("College," n = 95 427), and years of education ("EduYears," n = 101 069). Variants associated with College or EduYears showed enrichment of association with SCZ, demonstrating polygenic overlap. This was confirmed by an increased replication rate in SCZ. By applying a condFDR threshold <0.01, we identified 18 genomic loci associated with SCZ after conditioning on College and 15 loci associated with SCZ after conditioning on EduYears. Ten of these loci overlapped. Using conjunctional FDR, we identified 10 loci shared between SCZ and College, and 29 loci shared between SCZ and EduYears. The majority of these loci had effects in opposite directions. Our results provide evidence for polygenic overlap between SCZ and educational attainment, and identify novel pleiotropic loci. Other studies have reported genetic overlap between SCZ and cognition, or SCZ and educational attainment, with negative correlation. Importantly, our methods enable identification of bi-directional effects, which highlight the complex relationship between SCZ and educational attainment, and support polygenic mechanisms underlying both cognitive dysfunction and creativity in SCZ.
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Affiliation(s)
- Stéphanie Le Hellard
- NORMENT—KG Jebsen Centre, Department of Clinical Science, University of Bergen, Bergen, Norway;,Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Yunpeng Wang
- NORMENT—KG Jebsen Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway;,NORMENT—KG Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway;,Multimodal Imaging Lab, University of California at San Diego, La Jolla, CA;,Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Aree Witoelar
- NORMENT—KG Jebsen Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway;,NORMENT—KG Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Verena Zuber
- NORMENT—KG Jebsen Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway;,NORMENT—KG Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway;,NCMM, University of Oslo, Oslo, Norway
| | - Francesco Bettella
- NORMENT—KG Jebsen Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway;,NORMENT—KG Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Kenneth Hugdahl
- NORMENT, Department of Biological and Medical Psychology, University of Bergen, Bergen, Norway;,Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Thomas Espeseth
- NORMENT—KG Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway;,Department of Psychology, University of Oslo, Oslo, Norway
| | - Vidar M. Steen
- NORMENT—KG Jebsen Centre, Department of Clinical Science, University of Bergen, Bergen, Norway;,Dr Einar Martens Research Group for Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Ingrid Melle
- NORMENT—KG Jebsen Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway;,NORMENT—KG Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Rahul Desikan
- Multimodal Imaging Lab, University of California at San Diego, La Jolla, CA;,Department of Radiology, University of California at San Diego, La Jolla, CA
| | - Andrew J. Schork
- Multimodal Imaging Lab, University of California at San Diego, La Jolla, CA;,Department of Cognitive Science, University of California San Diego, La Jolla, CA
| | - Wesley K. Thompson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA
| | - Anders M. Dale
- Multimodal Imaging Lab, University of California at San Diego, La Jolla, CA;,Department of Cognitive Science, University of California San Diego, La Jolla, CA;,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Srdjan Djurovic
- NORMENT—KG Jebsen Centre, Department of Clinical Science, University of Bergen, Bergen, Norway;,NORMENT—KG Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway;,Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Ole A. Andreassen
- NORMENT—KG Jebsen Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway;,NORMENT—KG Jebsen Centre, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway;,Multimodal Imaging Lab, University of California at San Diego, La Jolla, CA
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74
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Primetime for Learning Genes. Genes (Basel) 2017; 8:genes8020069. [PMID: 28208656 PMCID: PMC5333058 DOI: 10.3390/genes8020069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/27/2017] [Accepted: 02/08/2017] [Indexed: 01/06/2023] Open
Abstract
Learning genes in mature neurons are uniquely suited to respond rapidly to specific environmental stimuli. Expression of individual learning genes, therefore, requires regulatory mechanisms that have the flexibility to respond with transcriptional activation or repression to select appropriate physiological and behavioral responses. Among the mechanisms that equip genes to respond adaptively are bivalent domains. These are specific histone modifications localized to gene promoters that are characteristic of both gene activation and repression, and have been studied primarily for developmental genes in embryonic stem cells. In this review, studies of the epigenetic regulation of learning genes in neurons, particularly the brain-derived neurotrophic factor gene (BDNF), by methylation/demethylation and chromatin modifications in the context of learning and memory will be highlighted. Because of the unique function of learning genes in the mature brain, it is proposed that bivalent domains are a characteristic feature of the chromatin landscape surrounding their promoters. This allows them to be “poised” for rapid response to activate or repress gene expression depending on environmental stimuli.
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75
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Mutations in the histone methyltransferase gene KMT2B cause complex early-onset dystonia. Nat Genet 2016; 49:223-237. [PMID: 27992417 DOI: 10.1038/ng.3740] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 11/14/2016] [Indexed: 02/08/2023]
Abstract
Histone lysine methylation, mediated by mixed-lineage leukemia (MLL) proteins, is now known to be critical in the regulation of gene expression, genomic stability, cell cycle and nuclear architecture. Despite MLL proteins being postulated as essential for normal development, little is known about the specific functions of the different MLL lysine methyltransferases. Here we report heterozygous variants in the gene KMT2B (also known as MLL4) in 27 unrelated individuals with a complex progressive childhood-onset dystonia, often associated with a typical facial appearance and characteristic brain magnetic resonance imaging findings. Over time, the majority of affected individuals developed prominent cervical, cranial and laryngeal dystonia. Marked clinical benefit, including the restoration of independent ambulation in some cases, was observed following deep brain stimulation (DBS). These findings highlight a clinically recognizable and potentially treatable form of genetic dystonia, demonstrating the crucial role of KMT2B in the physiological control of voluntary movement.
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76
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Shen EY, Jiang Y, Javidfar B, Kassim B, Loh YHE, Ma Q, Mitchell AC, Pothula V, Stewart AF, Ernst P, Yao WD, Martin G, Shen L, Jakovcevski M, Akbarian S. Neuronal Deletion of Kmt2a/Mll1 Histone Methyltransferase in Ventral Striatum is Associated with Defective Spike-Timing-Dependent Striatal Synaptic Plasticity, Altered Response to Dopaminergic Drugs, and Increased Anxiety. Neuropsychopharmacology 2016; 41:3103-3113. [PMID: 27485686 PMCID: PMC5101561 DOI: 10.1038/npp.2016.144] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 12/27/2022]
Abstract
Lysine (K) methyltransferase 2a (Kmt2a) and other regulators of H3 lysine 4 methylation, a histone modification enriched at promoters and enhancers, are widely expressed throughout the brain, but molecular and cellular phenotypes in subcortical areas remain poorly explored. We report that Kmt2a conditional deletion in postnatal forebrain is associated with excessive nocturnal activity and with absent or blunted responses to stimulant and dopaminergic agonist drugs, in conjunction with near-complete loss of spike-timing-dependent long-term potentiation in medium spiny neurons (MSNs). Selective ablation of Kmt2a, but not the ortholog Kmt2b, in adult ventral striatum/nucleus accumbens neurons markedly increased anxiety scores in multiple behavioral paradigms. Striatal transcriptome sequencing in adult mutants identified 262 Kmt2a-sensitive genes, mostly downregulated in Kmt2a-deficient mice. Transcriptional repression includes the 5-Htr2a serotonin receptor, strongly associated with anxiety- and depression-related disorders in human and animal models. Consistent with the role of Kmt2a in promoting gene expression, the transcriptional regulators Bahcc1, Isl1, and Sp9 were downregulated and affected by H3K4 promoter hypomethylation. Therefore, Kmt2a regulates synaptic plasticity in striatal neurons and provides an epigenetic drug target for anxiety and dopamine-mediated behaviors.
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Affiliation(s)
| | - Yan Jiang
- Department of Psychiatry, New York, NY, USA
| | | | | | - Yong-Hwee E Loh
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY, USA
| | - Qi Ma
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | | | | | | | - Patricia Ernst
- University of Colorado School of Medicine, Department of Pediatrics, Aurora, CO, USA
| | - Wei-Dong Yao
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Gilles Martin
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Li Shen
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, New York, NY, USA
| | - Mira Jakovcevski
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany,Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Kraepelinstrasse 2, 80804 Munich, Germany, Tel: +49 89 30622 643, E-mail:
| | - Schahram Akbarian
- Department of Psychiatry, New York, NY, USA,Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, Floor 9 Room 105, 1470 Madison Avenue, New York, NY 10029, USA, Tel: +1 212 824 8984, E-mail:
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77
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Zech M, Boesch S, Maier EM, Borggraefe I, Vill K, Laccone F, Pilshofer V, Ceballos-Baumann A, Alhaddad B, Berutti R, Poewe W, Haack TB, Haslinger B, Strom TM, Winkelmann J. Haploinsufficiency of KMT2B, Encoding the Lysine-Specific Histone Methyltransferase 2B, Results in Early-Onset Generalized Dystonia. Am J Hum Genet 2016; 99:1377-1387. [PMID: 27839873 DOI: 10.1016/j.ajhg.2016.10.010] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 10/25/2016] [Indexed: 12/26/2022] Open
Abstract
Early-onset generalized dystonia represents the severest form of dystonia, a hyperkinetic movement disorder defined by involuntary twisting postures. Although frequently transmitted as a single-gene trait, the molecular basis of dystonia remains largely obscure. By whole-exome sequencing a parent-offspring trio in an Austrian kindred affected by non-familial early-onset generalized dystonia, we identified a dominant de novo frameshift mutation, c.6406delC (p.Leu2136Serfs∗17), in KMT2B, encoding a lysine-specific methyltransferase involved in transcriptional regulation via post-translational modification of histones. Whole-exome-sequencing-based exploration of a further 30 German-Austrian individuals with early-onset generalized dystonia uncovered another three deleterious mutations in KMT2B-one de novo nonsense mutation (c.1633C>T [p.Arg545∗]), one de novo essential splice-site mutation (c.7050-2A>G [p.Phe2321Serfs∗93]), and one inherited nonsense mutation (c.2428C>T [p.Gln810∗]) co-segregating with dystonia in a three-generation kindred. Each of the four mutations was predicted to mediate a loss-of-function effect by introducing a premature termination codon. Suggestive of haploinsufficiency, we found significantly decreased total mRNA levels of KMT2B in mutant fibroblasts. The phenotype of individuals with KMT2B loss-of-function mutations was dominated by childhood lower-limb-onset generalized dystonia, and the family harboring c.2428C>T (p.Gln810∗) showed variable expressivity. In most cases, dystonic symptoms were accompanied by heterogeneous non-motor features. Independent support for pathogenicity of the mutations comes from the observation of high rates of dystonic presentations in KMT2B-involving microdeletion syndromes. Our findings thus establish generalized dystonia as the human phenotype associated with haploinsufficiency of KMT2B. Moreover, we provide evidence for a causative role of disordered histone modification, chromatin states, and transcriptional deregulation in dystonia pathogenesis.
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Affiliation(s)
- Michael Zech
- Institut für Neurogenomik, Helmholtz Zentrum München, 85764 Munich, Germany; Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Sylvia Boesch
- Department of Neurology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Esther M Maier
- Dr. von Haunersches Kinderspital, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Ingo Borggraefe
- Dr. von Haunersches Kinderspital, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Katharina Vill
- Dr. von Haunersches Kinderspital, Ludwig-Maximilians-Universität München, 80337 Munich, Germany
| | - Franco Laccone
- Institute of Medical Genetics, Medical School of Vienna, 1090 Vienna, Austria
| | | | - Andres Ceballos-Baumann
- Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany; Schön Klinik München Schwabing, 80804 Munich, Germany
| | - Bader Alhaddad
- Institut für Humangenetik, Technische Universität München, 81675 Munich, Germany
| | - Riccardo Berutti
- Institut für Humangenetik, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Werner Poewe
- Department of Neurology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Tobias B Haack
- Institut für Humangenetik, Technische Universität München, 81675 Munich, Germany; Institut für Humangenetik, Helmholtz Zentrum München, 85764 Munich, Germany; Devision of Molecular Genetics, Universitätsklinikum Tübingen, 72076 Tübingen, Germany
| | - Bernhard Haslinger
- Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Tim M Strom
- Institut für Humangenetik, Technische Universität München, 81675 Munich, Germany; Institut für Humangenetik, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Juliane Winkelmann
- Institut für Neurogenomik, Helmholtz Zentrum München, 85764 Munich, Germany; Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany; Institut für Humangenetik, Technische Universität München, 81675 Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, 81377 Munich, Germany.
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78
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Ricq EL, Hooker JM, Haggarty SJ. Toward development of epigenetic drugs for central nervous system disorders: Modulating neuroplasticity via H3K4 methylation. Psychiatry Clin Neurosci 2016; 70:536-550. [PMID: 27485392 PMCID: PMC5764164 DOI: 10.1111/pcn.12426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2016] [Indexed: 12/19/2022]
Abstract
The mammalian brain dynamically activates or silences gene programs in response to environmental input and developmental cues. This neuroplasticity is controlled by signaling pathways that modify the activity, localization, and/or expression of transcriptional-regulatory enzymes in combination with alterations in chromatin structure in the nucleus. Consistent with this key neurobiological role, disruptions in the fine-tuning of epigenetic and transcriptional regulation have emerged as a recurrent theme in studies of the genetics of neurodevelopmental and neuropsychiatric disorders. Furthermore, environmental factors have been implicated in the increased risk of heterogeneous, multifactorial, neuropsychiatric disorders via epigenetic mechanisms. Aberrant epigenetic regulation of gene expression thus provides an attractive unifying model for understanding the complex risk architecture of mental illness. Here, we review emerging genetic evidence implicating dysregulation of histone lysine methylation in neuropsychiatric disease and outline advancements in small-molecule probes targeting this chromatin modification. The emerging field of neuroepigenetic research is poised to provide insight into the biochemical basis of genetic risk for diverse neuropsychiatric disorders and to develop the highly selective chemical tools and imaging agents necessary to dissect dynamic transcriptional-regulatory mechanisms in the nervous system. On the basis of these findings, continued advances may lead to the validation of novel, disease-modifying therapeutic targets for a range of disorders with aberrant chromatin-mediated neuroplasticity.
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Affiliation(s)
- Emily L. Ricq
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
- Chemical Neurobiology Laboratory, Center for Human Genetic Research, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jacob M. Hooker
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory, Center for Human Genetic Research, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
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79
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Saur T, Cohen BM, Ma Q, Babb SM, Buttner EA, Yao WD. Acute and chronic effects of clozapine on cholinergic transmission in cultured mouse superior cervical ganglion neurons. J Neurogenet 2016; 30:297-305. [PMID: 27627024 PMCID: PMC6061957 DOI: 10.1080/01677063.2016.1229779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 08/18/2016] [Accepted: 08/24/2016] [Indexed: 10/21/2022]
Abstract
Cholinergic dysfunction contributes to cognitive deficits in schizophrenia. The atypical antipsychotic clozapine improves cognition in patients with schizophrenia, possibly through modulation of the cholinergic system. However, little is known about specific underlying mechanisms. We investigated the acute and chronic effects of clozapine on cholinergic synaptic transmission in cultured superior cervical ganglion (SCG) neurons. Spontaneous excitatory postsynaptic currents (sEPSCs) were detected and were reversibly inhibited by the nicotinic receptor antagonist d-tubocurarine, confirming that the synaptic responses were primarily mediated by nicotinic receptors. Bath application of clozapine at therapeutic concentrations rapidly and reversely inhibited both the amplitude and frequency of sEPSCs in a concentration-dependent manner, without changing either rise or decay time, suggesting that clozapine effects have both presynaptic and postsynaptic origins. The acute effects of clozapine on sEPSCs were recapitulated by chronic treatment of SCG cultures with similar concentrations of clozapine, as clozapine treatment for 4 d reduced the frequency and amplitude of sEPSCs without affecting their kinetics. Cell survival analysis indicated that SCG neuron cell counts after chronic clozapine treatment were comparable to the control group. These results demonstrate that therapeutic concentrations of clozapine suppress nicotinic synaptic transmission in SCG cholinergic synapses, a simple in vitro preparation of cholinergic transmission.
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Affiliation(s)
- Taixiang Saur
- a McLean Hospital/Harvard Medical School , Belmont , MA , USA
| | - Bruce M Cohen
- a McLean Hospital/Harvard Medical School , Belmont , MA , USA
| | - Qi Ma
- b New England Primate Research Center, Harvard Medical School , Southborough , MA , USA
| | - Suzann M Babb
- a McLean Hospital/Harvard Medical School , Belmont , MA , USA
| | - Edgar A Buttner
- a McLean Hospital/Harvard Medical School , Belmont , MA , USA
| | - Wei-Dong Yao
- b New England Primate Research Center, Harvard Medical School , Southborough , MA , USA
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80
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Yue W, Cheng W, Liu Z, Tang Y, Lu T, Zhang D, Tang M, Huang Y. Genome-wide DNA methylation analysis in obsessive-compulsive disorder patients. Sci Rep 2016; 6:31333. [PMID: 27527274 PMCID: PMC4985637 DOI: 10.1038/srep31333] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/18/2016] [Indexed: 11/09/2022] Open
Abstract
Literatures have suggested that not only genetic but also environmental factors, interactively accounted for susceptibility of obsessive-compulsive disorder (OCD). DNA methylation may regulate expression of genes as the heritable epigenetic modification. The examination for genome-wide DNA methylation was performed on blood samples from 65 patients with OCD, as well as 96 healthy control subjects. The DNA methylation was examined at over 485,000 CpG sites using the Illumina Infinium Human Methylation450 BeadChip. As a result, 8,417 probes corresponding to 2,190 unique genes were found to be differentially methylated between OCD and healthy control subjects. Of those genes, 4,013 loci were located in CpG islands and 2,478 were in promoter regions. These included BCYRN1, BCOR, FGF13, HLA-DRB1, ARX, etc., which have previously been reported to be associated with OCD. Pathway analyses indicated that regulation of actin cytoskeleton, cell adhesion molecules (CAMs), actin binding, transcription regulator activity, and other pathways might be further associated with risk of OCD. Unsupervised clustering analysis of the top 3,000 most variable probes revealed two distinct groups with significantly more people with OCD in cluster one compared with controls (67.74% of cases v.s. 27.13% of controls, Chi-square = 26.011, df = 1, P = 3.41E-07). These results strongly suggested that differential DNA methylation might play an important role in etiology of OCD.
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Affiliation(s)
- Weihua Yue
- Peking University Sixth Hospital &Institute of Mental Health, Beijing 100191, China.,National Clinical Research Center for Mental Disorders &Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing 100191, China
| | - Weiqiu Cheng
- Peking University Sixth Hospital &Institute of Mental Health, Beijing 100191, China.,National Clinical Research Center for Mental Disorders &Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing 100191, China
| | - Zhaorui Liu
- Peking University Sixth Hospital &Institute of Mental Health, Beijing 100191, China.,National Clinical Research Center for Mental Disorders &Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing 100191, China
| | - Yi Tang
- Peking University Sixth Hospital &Institute of Mental Health, Beijing 100191, China.,National Clinical Research Center for Mental Disorders &Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing 100191, China.,Department of Mental Health, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Tianlan Lu
- Peking University Sixth Hospital &Institute of Mental Health, Beijing 100191, China.,National Clinical Research Center for Mental Disorders &Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing 100191, China
| | - Dai Zhang
- Peking University Sixth Hospital &Institute of Mental Health, Beijing 100191, China.,National Clinical Research Center for Mental Disorders &Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing 100191, China.,Peking-Tsinghua Center for Life Sciences/PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Muni Tang
- Guangzhou Psychiatry Hospital, Guangzhou, 510080, China
| | - Yueqin Huang
- Peking University Sixth Hospital &Institute of Mental Health, Beijing 100191, China.,National Clinical Research Center for Mental Disorders &Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing 100191, China
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81
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Horton JR, Liu X, Gale M, Wu L, Shanks JR, Zhang X, Webber PJ, Bell JSK, Kales SC, Mott BT, Rai G, Jansen DJ, Henderson MJ, Urban DJ, Hall MD, Simeonov A, Maloney DJ, Johns MA, Fu H, Jadhav A, Vertino PM, Yan Q, Cheng X. Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds. Cell Chem Biol 2016; 23:769-781. [PMID: 27427228 PMCID: PMC4958579 DOI: 10.1016/j.chembiol.2016.06.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/15/2016] [Accepted: 06/04/2016] [Indexed: 12/12/2022]
Abstract
The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases removes methyl groups from methylated lysine 4 of histone H3. Accumulating evidence supports a role for KDM5 family members as oncogenic drivers. We compare the in vitro inhibitory properties and binding affinity of ten diverse compounds with all four family members, and present the crystal structures of the KDM5A-linked Jumonji domain in complex with eight of these inhibitors in the presence of Mn(II). All eight inhibitors structurally examined occupy the binding site of α-ketoglutarate, but differ in their specific binding interactions, including the number of ligands involved in metal coordination. We also observed inhibitor-induced conformational changes in KDM5A, particularly those residues involved in the binding of α-ketoglutarate, the anticipated peptide substrate, and intramolecular interactions. We discuss how particular chemical moieties contribute to inhibitor potency and suggest strategies that might be utilized in the successful design of selective and potent epigenetic inhibitors.
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Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Xu Liu
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Molly Gale
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lizhen Wu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - John R Shanks
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Philip J Webber
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA
| | - Joshua S K Bell
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Bryan T Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Daniel J Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Daniel J Urban
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Margaret A Johns
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Paula M Vertino
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA.
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82
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Wei G, Deng X, Agarwal S, Iwase S, Disteche C, Xu J. Patient Mutations of the Intellectual Disability Gene KDM5C Downregulate Netrin G2 and Suppress Neurite Growth in Neuro2a Cells. J Mol Neurosci 2016; 60:33-45. [PMID: 27421841 DOI: 10.1007/s12031-016-0770-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 05/13/2016] [Indexed: 12/11/2022]
Abstract
The X-linked lysine (K)-specific demethylase 5C (KDM5C) gene plays an important role in brain development and behavior. It encodes a histone demethylase that is involved in gene regulation in neuronal differentiation and morphogenesis. When mutated, it causes neuropsychiatric symptoms, such as intellectual disability, delayed language development, epilepsy, and impulsivity. To better understand how the patient mutations affect neuronal development, we expressed KDM5C mutants in Neuro2a cells, a mouse neuroblastoma cell line. Retinoic acid (RA)-induced neurite growth was suppressed by the mutation KDM5C (Y751C) , KDM5C (H514A) , and KDM5C (F642L) , but not KDM5C (D87G) or KDM5C (A388P) . RNA-seq analysis indicated an upregulation of genes important for neuronal development, such as Ntng2, Enah, Gas1, Slit2, and Dscam, in response to the RA treatment in control Neuro2a cells transfected with GFP or wild-type KDM5C. In contrast, in cells transfected with KDM5C (Y751C) , these genes were not upregulated by RA. Ntng2 was downregulated in cells with KDM5C mutations, concordant with the lower levels of H3K4 methylation at its promoter. Moreover, knocking down Ntng2 in control Neuro2a cells led to the phenotype of short neurites similar to that of cells with KDM5C (Y751C) , whereas Ntng2 overexpression in the mutant cells rescued the morphological phenotype. These findings provide new insight into the pathogenesis of phenotypes associated with KDM5C mutations.
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Affiliation(s)
- Gengze Wei
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, USA
| | - Xinxian Deng
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Saurabh Agarwal
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI, USA
| | | | - Jun Xu
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, USA.
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83
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Lumish HS, Wynn J, Devinsky O, Chung WK. Brief Report: SETD2 Mutation in a Child with Autism, Intellectual Disabilities and Epilepsy. J Autism Dev Disord 2016; 45:3764-70. [PMID: 26084711 DOI: 10.1007/s10803-015-2484-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Whole exome sequencing (WES) has been utilized with increasing frequency to identify mutations underlying rare diseases. Autism spectrum disorders (ASD) and intellectual disability (ID) are genetically heterogeneous, and novel genes for these disorders are rapidly being identified, making these disorders ideal candidates for WES. Here we report a 17-year-old girl with ASD, developmental delay, ID, seizures, Chiari I malformation, macrocephaly, and short stature. She was found by WES to have a de novo c.2028delT (P677LfsX19) mutation in the SET domain-containing protein 2 (SETD2) gene, predicted to be gene-damaging. This case offers evidence for the potential the role of SETD2 in ASD and ID and provides further detail about the phenotypic manifestations of mutations in SETD2.
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Affiliation(s)
- Heidi S Lumish
- College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Orrin Devinsky
- Department of Neurology, Psychiatry, and Neurosurgery, NYU Langone Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University, 1150 St. Nicholas Avenue, Room 620, New York, NY, 10032, USA.
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84
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Histone Lysine Methylation in TGF-β1 Mediated p21 Gene Expression in Rat Mesangial Cells. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6927234. [PMID: 27247942 PMCID: PMC4876202 DOI: 10.1155/2016/6927234] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/11/2016] [Indexed: 01/11/2023]
Abstract
Transforming growth factor beta1- (TGF-β1-) induced p21-dependent mesangial cell (MC) hypertrophy plays a key role in the pathogenesis of chronic renal diseases including diabetic nephropathy (DN). Increasing evidence demonstrated the role of posttranscriptional modifications (PTMs) in the event; however, the precise regulatory mechanism of histone lysine methylation remains largely unknown. Here, we examined the roles of both histone H3 lysine 4 and lysine 9 methylations (H3K4me/H3K9me) in TGF-β1 induced p21 gene expression in rat mesangial cells (RMCs). Our results indicated that TGF-β1 upregulated the expression of p21 gene in RMCs, which was positively correlated with the increased chromatin marks associated with active genes (H3K4me1/H3K4me2/H3K4me3) and negatively correlated with the decreased levels of repressive marks (H3K9me2/H3K9me3) at p21 gene promoter. TGF-β1 also elevated the recruitment of the H3K4 methyltransferase (HMT) SET7/9 to the p21 gene promoter. SET7/9 gene silencing with small interfering RNAs (siRNAs) significantly abolished the TGF-β1 induced p21 gene expression. Taken together, these results reveal the key role of histone H3Kme in TGF-β1 mediated p21 gene expression in RMC, partly through HMT SET7/9 occupancy, suggesting H3Kme and SET7/9 may be potential renoprotective agents in managing chronic renal diseases.
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85
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Pilotto S, Speranzini V, Marabelli C, Rusconi F, Toffolo E, Grillo B, Battaglioli E, Mattevi A. LSD1/KDM1A mutations associated to a newly described form of intellectual disability impair demethylase activity and binding to transcription factors. Hum Mol Genet 2016; 25:2578-2587. [PMID: 27094131 DOI: 10.1093/hmg/ddw120] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/30/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023] Open
Abstract
Genetic diseases often lead to rare and severe syndromes and the identification of the genetic and protein alterations responsible for the pathogenesis is essential to understand both the physiological and pathological role of the gene product. Recently, de novo variants have been mapped on the gene encoding for the lysine-specific histone demethylase 1 (LSD1)/lysine(K)-specific histone demethylase 1A in three patients characterized by a new genetic disorder. We have analyzed the effects of these pathological mutations on the structure, stability and activity of LSD1 using both in vitro and cellular approaches. The three mutations (Glu403Lys, Asp580Gly and Tyr785His) affect active-site residues and lead to a partial impairment of catalytic activity. They also differentially perturb the ability of LSD1 to engage transcription factors that orchestrate key developmental programs. Moreover, cellular data indicate a decrease in the protein cellular half-life. Taken together, these results demonstrate the relevance of LSD1 in gene regulation and how even moderate alterations in its stability, catalytic activity and binding properties can strongly affect organism development. This depicts a perturbed interplay of catalytic and non-catalytic processes at the origin of the pathology.
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Affiliation(s)
- Simona Pilotto
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Valentina Speranzini
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Chiara Marabelli
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Francesco Rusconi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20133 Milano, Italy
| | - Emanuela Toffolo
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20133 Milano, Italy
| | - Barbara Grillo
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20133 Milano, Italy
| | - Elena Battaglioli
- Department of Medical Biotechnology and Translational Medicine, University of Milan, 20133 Milano, Italy .,CNR, Institute of Neuroscience, 20129 Milano, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
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86
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Paděrová J, Holubová A, Simandlová M, Puchmajerová A, Vlčková M, Malíková M, Pourová R, Vejvalková S, Havlovicová M, Šenkeříková M, Ptáková N, Drábová J, Geryk J, Maver A, Křepelová A, Macek M. Molecular genetic analysis in 14 Czech Kabuki syndrome patients is confirming the utility of phenotypic scoring. Clin Genet 2016; 90:230-7. [DOI: 10.1111/cge.12754] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/30/2016] [Accepted: 02/01/2016] [Indexed: 01/17/2023]
Affiliation(s)
- J. Paděrová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - A. Holubová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Simandlová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - A. Puchmajerová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Vlčková
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Malíková
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - R. Pourová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - S. Vejvalková
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Havlovicová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Šenkeříková
- Department of Medical Genetics; Charles University Prague-Faculty of Medicine and University Hospital Hradec Králové; Hradec Králové Czech Republic
| | - N. Ptáková
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - J. Drábová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - J. Geryk
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - A. Maver
- Department of Obstetrics & Gynecology, Centre for Mendelian Genomics, Clinical Institute of Medical Genetics; University Medical Centre Ljubljana; Ljubljana Slovenia
| | - A. Křepelová
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
| | - M. Macek
- Department of Biology and Medical Genetics; Charles University Prague-2 Faculty of Medicine and University Hospital Motol; Prague Czech Republic
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87
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Mariani L, Lussi YC, Vandamme J, Riveiro A, Salcini AE. The H3K4me3/2 histone demethylase RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1. Development 2016; 143:851-63. [PMID: 26811384 DOI: 10.1242/dev.132985] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/16/2016] [Indexed: 12/25/2022]
Abstract
The dynamic regulation of histone modifications is important for modulating transcriptional programs during development. Aberrant H3K4 methylation is associated with neurological disorders, but how the levels and the recognition of this modification affect specific neuronal processes is unclear. Here, we show that RBR-2, the sole homolog of the KDM5 family of H3K4me3/2 demethylases in Caenorhabditis elegans, ensures correct axon guidance by controlling the expression of the actin regulator wsp-1. Loss of rbr-2 results in increased levels of H3K4me3 at the transcriptional start site of wsp-1, with concomitant higher wsp-1 expression responsible for defective axon guidance. In agreement, overexpression of WSP-1 mimics rbr-2 loss, and its depletion restores normal axon guidance in rbr-2 mutants. NURF-1, an H3K4me3-binding protein and member of the chromatin-remodeling complex NURF, is required for promoting aberrant wsp-1 transcription in rbr-2 mutants and its ablation restores wild-type expression of wsp-1 and axon guidance. Thus, our results establish a precise role for epigenetic regulation in neuronal development by demonstrating a functional link between RBR-2 activity, H3K4me3 levels, the NURF complex and the expression of WSP-1.
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Affiliation(s)
- Luca Mariani
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Yvonne C Lussi
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Julien Vandamme
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Alba Riveiro
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
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88
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Li X, Li C, Li X, Cui P, Li Q, Guo Q, Han H, Liu S, Sun G. Involvement of Histone Lysine Methylation in p21 Gene Expression in Rat Kidney In Vivo and Rat Mesangial Cells In Vitro under Diabetic Conditions. J Diabetes Res 2016; 2016:3853242. [PMID: 27652271 PMCID: PMC5019898 DOI: 10.1155/2016/3853242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 07/27/2016] [Indexed: 01/21/2023] Open
Abstract
Diabetic nephropathy (DN), a common complication associated with type 1 and type 2 diabetes mellitus (DM), characterized by glomerular mesangial expansion, inflammation, accumulation of extracellular matrix (ECM) protein, and hypertrophy, is the major cause of end-stage renal disease (ESRD). Increasing evidence suggested that p21-dependent glomerular and mesangial cell (MC) hypertrophy play key roles in the pathogenesis of DN. Recently, posttranscriptional modifications (PTMs) have uncovered novel molecular mechanisms involved in DN. However, precise regulatory mechanism of histone lysine methylation (HKme) mediating p21 related hypertrophy associated with DN is not clear. We evaluated the roles of HKme and histone methyltransferase (HMT) SET7/9 in p21 gene expression in glomeruli of diabetic rats and in high glucose- (HG-) treated rat mesangial cells (RMCs). p21 gene expression was upregulated in diabetic rats glomeruli; chromatin immunoprecipitation (ChIP) assays showed decreased histone H3-lysine9-dimethylation (H3K9me2) accompanied with enhanced histone H3-lysine4-methylation (H3K4me1/3) and SET7/9 occupancies at the p21 promoter. HG-treated RMCs exhibited increased p21 mRNA, H3K4me level, SET7/9 recruitment, and inverse H3K9me, which were reversed by TGF-β1 antibody. These data uncovered key roles of H3Kme and SET7/9 responsible for p21 gene expression in vivo and in vitro under diabetic conditions and confirmed preventive effect of TGF-β1 antibody on DN.
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Affiliation(s)
- Xiangjun Li
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Science, Jilin University, Changchun, Jilin 130021, China
| | - Chaoyuan Li
- Department of Nephrology, 2nd Hospital of Jilin University, Changchun, Jilin 130041, China
| | - Xiaoxia Li
- Department of Nephrology, 2nd Hospital of Jilin University, Changchun, Jilin 130041, China
| | - Peihe Cui
- Department of Nephrology, 2nd Hospital of Jilin University, Changchun, Jilin 130041, China
| | - Qifeng Li
- Department of Nephrology, 2nd Hospital of Jilin University, Changchun, Jilin 130041, China
| | - Qiaoyan Guo
- Department of Nephrology, 2nd Hospital of Jilin University, Changchun, Jilin 130041, China
| | - Hongbo Han
- Department of Endocrinology, 208th Hospital of Chinese PLA, Changchun, Jilin 130062, China
| | - Shujun Liu
- Department of Nephrology, 2nd Hospital of Jilin University, Changchun, Jilin 130041, China
| | - Guangdong Sun
- Department of Nephrology, 2nd Hospital of Jilin University, Changchun, Jilin 130041, China
- *Guangdong Sun:
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89
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Vallianatos CN, Iwase S. Disrupted intricacy of histone H3K4 methylation in neurodevelopmental disorders. Epigenomics 2015; 7:503-19. [PMID: 26077434 DOI: 10.2217/epi.15.1] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Methylation of histone H3 lysine 4 (H3K4me) is an intricately regulated posttranslational modification, which is broadly associated with enhancers and promoters of actively transcribed genomic loci. Recent advances in next-generation sequencing have identified a number of H3K4me regulators mutated in neurodevelopmental disorders including intellectual disabilities, autism spectrum disorders, and schizophrenia. Here, we aim to summarize the molecular function of H3K4me-regulating enzymes in brain development and function. We describe four H3K4me methyltransferases (KMT2A, KMT2C, KMT2D, KMT2F), four demethylases (KDM1A, KDM5A, KDM5B, KDM5C), and two reader proteins (PHF21A, PHF8) mutated in neurodevelopmental disorders. Understanding the role of these chromatin regulators in the development and maintenance of neural connections will advance therapeutic opportunities for prevention and treatment of these lifelong neurodevelopmental disorders.
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Affiliation(s)
- Christina N Vallianatos
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA.,Predoctoral Training Program in Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
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90
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Neuronal Kmt2a/Mll1 histone methyltransferase is essential for prefrontal synaptic plasticity and working memory. J Neurosci 2015; 35:5097-108. [PMID: 25834037 DOI: 10.1523/jneurosci.3004-14.2015] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Neuronal histone H3-lysine 4 methylation landscapes are defined by sharp peaks at gene promoters and other cis-regulatory sequences, but molecular and cellular phenotypes after neuron-specific deletion of H3K4 methyl-regulators remain largely unexplored. We report that neuronal ablation of the H3K4-specific methyltransferase, Kmt2a/Mixed-lineage leukemia 1 (Mll1), in mouse postnatal forebrain and adult prefrontal cortex (PFC) is associated with increased anxiety and robust cognitive deficits without locomotor dysfunction. In contrast, only mild behavioral phenotypes were observed after ablation of the Mll1 ortholog Kmt2b/Mll2 in PFC. Impaired working memory after Kmt2a/Mll1 ablation in PFC neurons was associated with loss of training-induced transient waves of Arc immediate early gene expression critical for synaptic plasticity. Medial prefrontal layer V pyramidal neurons, a major output relay of the cortex, demonstrated severely impaired synaptic facilitation and temporal summation, two forms of short-term plasticity essential for working memory. Chromatin immunoprecipitation followed by deep sequencing in Mll1-deficient cortical neurons revealed downregulated expression and loss of the transcriptional mark, trimethyl-H3K4, at <50 loci, including the homeodomain transcription factor Meis2. Small RNA-mediated Meis2 knockdown in PFC was associated with working memory defects similar to those elicited by Mll1 deletion. Therefore, mature prefrontal neurons critically depend on maintenance of Mll1-regulated H3K4 methylation at a subset of genes with an essential role in cognition and emotion.
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Shen EY, Jiang Y, Mao W, Futai K, Hock H, Akbarian S. Cognition and mood-related behaviors in L3mbtl1 null mutant mice. PLoS One 2015; 10:e0121252. [PMID: 25849281 PMCID: PMC4388653 DOI: 10.1371/journal.pone.0121252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/31/2015] [Indexed: 01/22/2023] Open
Abstract
Alterations in histone lysine methylation and epigenetic regulators of gene expression could play a role in the neurobiology and treatment of patients diagnosed with mood spectrum disorder, including depression and anxiety. Mutations and altered expression of various lysine methyltransferases (KMTs) and demethylases (KDMs) have been linked to changes in motivational and emotional behaviors in preclinical model systems. However, it is not known whether regulators operating downstream of histone lysine methylation could affect mood-related behavior. Malignant Brain Tumor (MBT) domain 'chromatin reader' proteins bind to methylated histone lysine residues and associate with chromatin remodeling complexes to facilitate or repress gene expression. MBT proteins, including the founding member, L3mbtl1, maintain high levels of expression in neurons of the mature brain. Here, we exposed L3mbtl1 null mutant mice to a wide range of tests exploring cognition and mood-relevant behaviors at baseline and in the context of social isolation, as a stressor to elicit depression-related behavior in susceptible mice. L3mbtl1 loss-of-function was associated with significant decreases in depression and and anxiety in some of the behavioral paradigms. This was not associated with a more generalized neurological dysfunction because cognition and memory remained unaltered in comparison to controls. These findings warrant further investigations on the role of MBT chromatin reader proteins in the context of emotional and affective behaviors.
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Affiliation(s)
- Erica Y. Shen
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, United States of America
| | - Yan Jiang
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, United States of America
| | - Wenjie Mao
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, 01604, United States of America
| | - Kensuke Futai
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, 01604, United States of America
| | - Hanno Hock
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts, 02114, United States of America
| | - Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, United States of America
- * E-mail:
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Wakabayashi K, Mori F, Kakita A, Takahashi H, Utsumi J, Sasaki H. Analysis of microRNA from archived formalin-fixed paraffin-embedded specimens of amyotrophic lateral sclerosis. Acta Neuropathol Commun 2014; 2:173. [PMID: 25497327 PMCID: PMC4279903 DOI: 10.1186/s40478-014-0173-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/01/2014] [Indexed: 12/13/2022] Open
Abstract
Background MicroRNAs (miRNAs) are noncoding small RNAs that regulate gene expression. This study investigated whether formalin-fixed paraffin-embedded (FFPE) specimens from postmortem cases of neurodegenerative disorders would be suitable for miRNA profiling. Results Ten FFPE samples from 6 cases of amyotrophic lateral sclerosis (ALS) and 4 neurologically normal controls were selected for miRNA analysis on the basis of the following criteria for RNA quality: (i) a postmortem interval of less than 6 hours, (ii) a formalin fixation time of less than 4 weeks, (iii) an RNA yield per sample of more than 500 ng, and (iv) sufficient quality of the RNA agarose gel image. An overall RNA extraction success rate was 46.2%. For ALS, a total of 364 miRNAs were identified in the motor cortex, 91 being up-regulated and 233 down-regulated. Target genes were predicted using miRNA bioinformatics software, and the data applied to ontology analysis. This indicated that one of the miRNAs up-regulated in ALS (miR-338-3p) had already been identified in leukocytes, serum, cerebrospinal fluid and frozen spinal cord from ALS patients. Conclusion Although analysis was possible for just under half of the specimens examined, we were able to show that informative miRNA data can be derived from archived FFPE samples from postmortem cases of neurodegenerative disorders. Electronic supplementary material The online version of this article (doi:10.1186/s40478-014-0173-z) contains supplementary material, which is available to authorized users.
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Edelstein L, Smythies J, Noble D. Introduction. Philos Trans R Soc Lond B Biol Sci 2014; 369:rstb.2013.0501. [PMID: 25135962 DOI: 10.1098/rstb.2013.0501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - John Smythies
- Integrative Neuroscience Program, Center for Brain and Cognition, Department of Psychology, University of California San Diego, La Jolla, CA 92093, USA Department of Psychiatry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Denis Noble
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
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