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Kremp M, Aberle T, Sock E, Bohl B, Hillgärtner S, Winkler J, Wegner M. Transcription factor Olig2 is a major downstream effector of histone demethylase Phf8 during oligodendroglial development. Glia 2024. [PMID: 38613395 DOI: 10.1002/glia.24538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
The plant homeodomain finger protein Phf8 is a histone demethylase implicated by mutation in mice and humans in neural crest defects and neurodevelopmental disturbances. Considering its widespread expression in cell types of the central nervous system, we set out to determine the role of Phf8 in oligodendroglial cells to clarify whether oligodendroglial defects are a possible contributing factor to Phf8-dependent neurodevelopmental disorders. Using loss- and gain-of-function approaches in oligodendroglial cell lines and primary cell cultures, we show that Phf8 promotes the proliferation of rodent oligodendrocyte progenitor cells and impairs their differentiation to oligodendrocytes. Intriguingly, Phf8 has a strong positive impact on Olig2 expression by acting on several regulatory regions of the gene and changing their histone modification profile. Taking the influence of Olig2 levels on oligodendroglial proliferation and differentiation into account, Olig2 likely acts as an important downstream effector of Phf8 in these cells. In line with such an effector function, ectopic Olig2 expression in Phf8-deficient cells rescues the proliferation defect. Additionally, generation of human oligodendrocytes from induced pluripotent stem cells did not require PHF8 in a system that relies on forced expression of Olig2 during oligodendroglial induction. We conclude that Phf8 may impact nervous system development at least in part through its action in oligodendroglial cells.
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Affiliation(s)
- Marco Kremp
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Tim Aberle
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Elisabeth Sock
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bettina Bohl
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Simone Hillgärtner
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jürgen Winkler
- Abteilung für Molekulare Neurologie, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Wegner
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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2
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Yang Q, Zhang Q, Yi S, Zhang S, Yi S, Zhou X, Qin Z, Chen B, Luo J. Novel germline variants in KMT2C in Chinese patients with Kleefstra syndrome-2. Front Neurol 2024; 15:1340458. [PMID: 38356881 PMCID: PMC10864639 DOI: 10.3389/fneur.2024.1340458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Kleefstra syndrome (KLEFS) refers to a rare inherited neurodevelopmental disorder characterized by intellectual disability (ID), language and motor delays, behavioral abnormalities, abnormal facial appearance, and other variable clinical features. KLEFS is subdivided into two subtypes: Kleefstra syndrome-1 (KLEFS1, OMIM: 610253), caused by a heterozygous microdeletion encompassing the Euchromatic Histone Lysine Methyltransferase 1 (EHMT1) gene on chromosome 9q34.3 or pathogenic variants in the EHMT1 gene, and Kleefstra syndrome-2 (KLEFS2, OMIM: 617768), caused by pathogenic variants in the KMT2C gene. More than 100 cases of KLEFS1 have been reported with pathogenic variants in the EHMT1 gene. However, only 13 patients with KLEFS2 have been reported to date. In the present study, five unrelated Chinese patients were diagnosed with KLEFS2 caused by KMT2C variants through whole-exome sequencing (WES). We identified five different variants of the KMT2C gene in these patients: c.9166C>T (p.Gln3056*), c.9232_9247delCAGCGATCAGAACCGT (p.Gln3078fs*13), c.5068dupA (p.Arg1690fs*10), c.10815_10819delAAGAA (p.Lys3605fs*7), and c.6911_6912insA (p.Met2304fs*8). All five patients had a clinical profile similar to that of patients with KLEFS2. To analyze the correlation between the genotype and phenotype of KLEFS2, we examined 18 variants and their associated phenotypes in 18 patients with KLEFS2. Patients carrying KMT2C variants presented with a wide range of phenotypic defects and an extremely variable phenotype. We concluded that the core phenotypes associated with KMT2C variants were intellectual disability, facial dysmorphisms, language and motor delays, behavioral abnormalities, hypotonia, short stature, and weight loss. Additionally, sex may be one factor influencing the outcome. Our findings expand the phenotypic and genetic spectrum of KLEFS2 and help to clarify the genotype-phenotype correlation.
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Affiliation(s)
- Qi Yang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiang Zhang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Sheng Yi
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shujie Zhang
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shang Yi
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xunzhao Zhou
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Zailong Qin
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Biyan Chen
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Jingsi Luo
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Department of Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Clinical Research Center for Pediatric Diseases, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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3
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Abad C, Robayo MC, Muñiz-Moreno MDM, Bernardi MT, Otero MG, Kosanovic C, Griswold AJ, Pierson TM, Walz K, Young JI. Gatad2b, associated with the neurodevelopmental syndrome GAND, plays a critical role in neurodevelopment and cortical patterning. Transl Psychiatry 2024; 14:33. [PMID: 38238293 PMCID: PMC10796954 DOI: 10.1038/s41398-023-02678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/06/2023] [Accepted: 11/23/2023] [Indexed: 01/22/2024] Open
Abstract
GATAD2B (GATA zinc finger domain containing 2B) variants are associated with the neurodevelopmental syndrome GAND, characterized by intellectual disability (ID), infantile hypotonia, apraxia of speech, epilepsy, macrocephaly and distinct facial features. GATAD2B encodes for a subunit of the Nucleosome Remodeling and Histone Deacetylase (NuRD) complex. NuRD controls transcriptional programs critical for proper neurodevelopment by coupling histone deacetylase with ATP-dependent chromatin remodeling activity. To study mechanisms of pathogenesis for GAND, we characterized a mouse model harboring an inactivating mutation in Gatad2b. Homozygous Gatad2b mutants die perinatally, while haploinsufficient Gatad2b mice exhibit behavioral abnormalities resembling the clinical features of GAND patients. We also observed abnormal cortical patterning, and cellular proportions and cell-specific alterations in the developmental transcriptome in these mice. scRNAseq of embryonic cortex indicated misexpression of genes key for corticogenesis and associated with neurodevelopmental syndromes such as Bcl11b, Nfia and H3f3b and Sox5. These data suggest a crucial role for Gatad2b in brain development.
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Affiliation(s)
- Clemer Abad
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Maria C Robayo
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Maria Del Mar Muñiz-Moreno
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Maria T Bernardi
- IQUIBICEN - CONICET, School of Exact and Natural Sciences - University of Buenos Aires, Buenos Aires, Argentina
| | - Maria G Otero
- The Board of Governors Regenerative Medicine Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Christina Kosanovic
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Tyler Mark Pierson
- The Board of Governors Regenerative Medicine Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
- Guerin Children's, Departments of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA, USA
- Department of Neurology, Cedars Sinai Medical Center, Los Angeles, CA, USA
- The Center for the Undiagnosed Patient, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Katherina Walz
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- IQUIBICEN - CONICET, School of Exact and Natural Sciences - University of Buenos Aires, Buenos Aires, Argentina
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Juan I Young
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA.
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA.
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4
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Valencia AM, Sankar A, van der Sluijs PJ, Satterstrom FK, Fu J, Talkowski ME, Vergano SAS, Santen GWE, Kadoch C. Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders. Nat Genet 2023; 55:1400-1412. [PMID: 37500730 PMCID: PMC10412456 DOI: 10.1038/s41588-023-01451-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
DNA sequencing-based studies of neurodevelopmental disorders (NDDs) have identified a wide range of genetic determinants. However, a comprehensive analysis of these data, in aggregate, has not to date been performed. Here, we find that genes encoding the mammalian SWI/SNF (mSWI/SNF or BAF) family of ATP-dependent chromatin remodeling protein complexes harbor the greatest number of de novo missense and protein-truncating variants among nuclear protein complexes. Non-truncating NDD-associated protein variants predominantly disrupt the cBAF subcomplex and cluster in four key structural regions associated with high disease severity, including mSWI/SNF-nucleosome interfaces, the ATPase-core ARID-armadillo repeat (ARM) module insertion site, the Arp module and DNA-binding domains. Although over 70% of the residues perturbed in NDDs overlap with those mutated in cancer, ~60% of amino acid changes are NDD-specific. These findings provide a foundation to functionally group variants and link complex aberrancies to phenotypic severity, serving as a resource for the chromatin, clinical genetics and neurodevelopment communities.
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Affiliation(s)
- Alfredo M Valencia
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Chemical Biology Program, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Akshay Sankar
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - F Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Jack Fu
- Massachusetts General Hospital, Boston, MA, USA
| | - Michael E Talkowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Samantha A Schrier Vergano
- Children's Hospital of the King's Daughters, Norfolk, Virginia, USA
- Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Cigall Kadoch
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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5
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Rots D, Jakub TE, Keung C, Jackson A, Banka S, Pfundt R, de Vries BBA, van Jaarsveld RH, Hopman SMJ, van Binsbergen E, Valenzuela I, Hempel M, Bierhals T, Kortüm F, Lecoquierre F, Goldenberg A, Hertz JM, Andersen CB, Kibæk M, Prijoles EJ, Stevenson RE, Everman DB, Patterson WG, Meng L, Gijavanekar C, De Dios K, Lakhani S, Levy T, Wagner M, Wieczorek D, Benke PJ, Lopez Garcia MS, Perrier R, Sousa SB, Almeida PM, Simões MJ, Isidor B, Deb W, Schmanski AA, Abdul-Rahman O, Philippe C, Bruel AL, Faivre L, Vitobello A, Thauvin C, Smits JJ, Garavelli L, Caraffi SG, Peluso F, Davis-Keppen L, Platt D, Royer E, Leeuwen L, Sinnema M, Stegmann APA, Stumpel CTRM, Tiller GE, Bosch DGM, Potgieter ST, Joss S, Splitt M, Holden S, Prapa M, Foulds N, Douzgou S, Puura K, Waltes R, Chiocchetti AG, Freitag CM, Satterstrom FK, De Rubeis S, Buxbaum J, Gelb BD, Branko A, Kushima I, Howe J, Scherer SW, Arado A, Baldo C, Patat O, Bénédicte D, Lopergolo D, Santorelli FM, Haack TB, Dufke A, Bertrand M, Falb RJ, Rieß A, Krieg P, Spranger S, Bedeschi MF, Iascone M, Josephi-Taylor S, Roscioli T, Buckley MF, Liebelt J, Dagli AI, Aten E, Hurst ACE, Hicks A, Suri M, Aliu E, Naik S, Sidlow R, Coursimault J, Nicolas G, Küpper H, Petit F, Ibrahim V, Top D, Di Cara F, Louie RJ, Stolerman E, Brunner HG, Vissers LELM, Kramer JM, Kleefstra T. The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder. Am J Hum Genet 2023; 110:963-978. [PMID: 37196654 PMCID: PMC10257005 DOI: 10.1016/j.ajhg.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
De novo variants are a leading cause of neurodevelopmental disorders (NDDs), but because every monogenic NDD is different and usually extremely rare, it remains a major challenge to understand the complete phenotype and genotype spectrum of any morbid gene. According to OMIM, heterozygous variants in KDM6B cause "neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities." Here, by examining the molecular and clinical spectrum of 85 reported individuals with mostly de novo (likely) pathogenic KDM6B variants, we demonstrate that this description is inaccurate and potentially misleading. Cognitive deficits are seen consistently in all individuals, but the overall phenotype is highly variable. Notably, coarse facies and distal skeletal anomalies, as defined by OMIM, are rare in this expanded cohort while other features are unexpectedly common (e.g., hypotonia, psychosis, etc.). Using 3D protein structure analysis and an innovative dual Drosophila gain-of-function assay, we demonstrated a disruptive effect of 11 missense/in-frame indels located in or near the enzymatic JmJC or Zn-containing domain of KDM6B. Consistent with the role of KDM6B in human cognition, we demonstrated a role for the Drosophila KDM6B ortholog in memory and behavior. Taken together, we accurately define the broad clinical spectrum of the KDM6B-related NDD, introduce an innovative functional testing paradigm for the assessment of KDM6B variants, and demonstrate a conserved role for KDM6B in cognition and behavior. Our study demonstrates the critical importance of international collaboration, sharing of clinical data, and rigorous functional analysis of genetic variants to ensure correct disease diagnosis for rare disorders.
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Affiliation(s)
- Dmitrijs Rots
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | - Taryn E Jakub
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada
| | - Crystal Keung
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada
| | - Adam Jackson
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Rolph Pfundt
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | | | | | - Saskia M J Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Irene Valenzuela
- Hospital Universitari Vall D'Hebron, Clinical and Molecular Genetics Unit, Barcelona, Catalonia, Spain
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Francois Lecoquierre
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Alice Goldenberg
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Jens Michael Hertz
- Odense University Hospital, Department of Clinical Genetics, Odense, Denmark; University of Southern Denmark, Department of Clinical Research, Odense, Denmark
| | | | - Maria Kibæk
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | | | | | | | | | - Linyan Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Charul Gijavanekar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Karl De Dios
- Division of Medical Genetics, Dayton Children's Hospital, Dayton, OH, USA
| | - Shenela Lakhani
- Center for Neurogenetics, Weill Cornell Medicine, Brain and Mind Research Institute, New York, NY, USA
| | - Tess Levy
- Center for Neurogenetics, Weill Cornell Medicine, Brain and Mind Research Institute, New York, NY, USA
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University Munich, Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany; Division of Pediatric Neurology, Department of Pediatrics, Dr. von Hauner Children's Hospital, LMU University Hospital, Munich, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Paul J Benke
- Division of Genetics, Joe DiMaggio Children's Hospital, Hollywood, FL, USA
| | | | - Renee Perrier
- Department of Medical Genetics, Alberta Children's Hospital and Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Sergio B Sousa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Pedro M Almeida
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria José Simões
- CBR Genomics, Cantanhede, Portugal; Genoinseq, Next-Generation Sequencing Unit, Biocant, Cantanhede, Portugal
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France
| | - Wallid Deb
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France
| | - Andrew A Schmanski
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Omar Abdul-Rahman
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Laurence Faivre
- Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - Christel Thauvin
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Dijon, France; Inserm, UMR1231, Equipe GAD, Bâtiment B3, Université de Bourgogne Franche Comté, Dijon Cedex, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Jeroen J Smits
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands
| | - Livia Garavelli
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Stefano G Caraffi
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Francesca Peluso
- Medical Genetics Unit, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Laura Davis-Keppen
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Dylan Platt
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Erin Royer
- University of South Dakota Sanford School of Medicine and Sanford Children's Hospital, Sioux Falls, SD, USA
| | - Lisette Leeuwen
- University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Margje Sinnema
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | - Alexander P A Stegmann
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | - Constance T R M Stumpel
- Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Reproduction, Maastricht, the Netherlands
| | - George E Tiller
- Kaiser Permanente, Department of Genetics, Los Angeles, CA, USA
| | | | | | - Shelagh Joss
- West of Scotland Regional Genetics Service, Laboratory Medicine Building, Queen Elizabeth University Hospital, Glasgow, UK
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetic Medicine, International Centre for Life, Newcastle Upon Tyne NE1 3BZ, UK
| | - Simon Holden
- Department of Clinical Genetics, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Matina Prapa
- Department of Clinical Genetics, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Nicola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton NHS Foundation Trust, Southampton SO16 5YA, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Kaija Puura
- Department of Child Psychiatry, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Regina Waltes
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Goethe-Universität, Frankfurt am Main, Germany
| | - F Kyle Satterstrom
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Silvia De Rubeis
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph Buxbaum
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksic Branko
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan; Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Jennifer Howe
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada
| | - Alessia Arado
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Chiara Baldo
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Olivier Patat
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Demeer Bénédicte
- Service de Génétique Clinique, Centre de référence maladies rares, CHU d'Amiens-site Sud, Amiens, France
| | - Diego Lopergolo
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy; UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero Universitaria Senese, Policlinico Le Scotte, Viale Bracci, 2, 53100 Siena, Italy; IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Pisa, Italy
| | - Filippo M Santorelli
- IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, Pisa, Italy
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Miriam Bertrand
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ruth J Falb
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Angelika Rieß
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Peter Krieg
- Department of Pediatrics, Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | | | | | - Maria Iascone
- Laboratory of Medical Genetics, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Sarah Josephi-Taylor
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Tony Roscioli
- Neuroscience Research Australia, University of New South Wales, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics Laboratory, Sydney, NSW, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW 2031, Australia; Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2031, Australia
| | - Michael F Buckley
- New South Wales Health Pathology Randwick Genomics Laboratory, Sydney, NSW, Australia
| | - Jan Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Aditi I Dagli
- Orlando Health Arnold Palmer Hospital for Children, Division of Genetics, Orlando, FL, USA
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, the Netherlands
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alesha Hicks
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, City Hospital Campus, Nottingham, UK
| | - Ermal Aliu
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Sunil Naik
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Richard Sidlow
- Valley Children's Hospital, Valley Children's Place, Madera, CA 93636, USA
| | - Juliette Coursimault
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Gaël Nicolas
- University Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, 76000 Rouen, France
| | - Hanna Küpper
- Neuropediatric Department, University Hospital Tübingen, Tübingen, Germany
| | - Florence Petit
- Centre Hospitalier Universitaire de Lille, Clinique de Génétique Guy Fontaine, Lille, France
| | - Veyan Ibrahim
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada; Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Deniz Top
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada; Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Francesca Di Cara
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | | | | | - Han G Brunner
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands; Maastricht University Medical Center, Department of Clinical Genetics, Maastricht, the Netherlands
| | | | - Jamie M Kramer
- Dalhousie University, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Halifax, NS, Canada.
| | - Tjitske Kleefstra
- Radboudumc, Department of Human Genetics, Nijmegen, the Netherlands; Center for Neuropsychiatry, Vincent van Gogh, Venray, the Netherlands; Department of Clinical Genetics, ErasmusMC, Rotterdam, the Netherlands.
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6
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Miller WB, Baluška F, Reber AS. A revised central dogma for the 21st century:all biology is cognitive information processing. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023:S0079-6107(23)00057-3. [PMID: 37268025 DOI: 10.1016/j.pbiomolbio.2023.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/28/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023]
Abstract
Crick's Central Dogma has been a foundational aspect of 20th century biology, describing an implicit relationship governing the flow of information in biological systems in biomolecular terms. Accumulating scientific discoveries support the need for a revised Central Dogma to buttress evolutionary biology's still-fledgling migration from a Neodarwinian canon. A reformulated Central Dogma to meet contemporary biology is proposed: all biology is cognitive information processing. Central to this contention is the recognition that life is the self-referential state, instantiated within the cellular form. Self-referential cells act to sustain themselves and to do so, cells must be in consistent harmony with their environment. That consonance is achieved by the continuous assimilation of environmental cues and stresses as information to self-referential observers. All received cellular information must be analyzed to be deployed as cellular problem-solving to maintain homeorhetic equipoise. However, the effective implementation of information is definitively a function of orderly information management. Consequently, effective cellular problem-solving is information processing and management. The epicenter of that cellular information processing is its self-referential internal measurement. All further biological self-organization initiates from this obligate activity. As the internal measurement by cells of information is self-referential by definition, self-reference is biological self-organization, underpinning 21st century Cognition-Based Biology.
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Affiliation(s)
| | | | - Arthur S Reber
- Department of Psychology, University of British Columbia, Vancouver, BC, Canada.
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7
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Ssewanyana D, Knight JA, Matthews SG, Wong J, Khani NA, Lye J, Murphy KE, Foshay K, Okeke J, Lye SJ, Hung RJ. Maternal prenatal psychological distress and vitamin intake with children's neurocognitive development. Pediatr Res 2022; 92:1450-1457. [PMID: 35288638 DOI: 10.1038/s41390-022-02003-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/06/2022] [Accepted: 02/06/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Maternal prenatal psychological distress (PPD) is increasingly linked to sub-optimal child neurodevelopment. Daily intake of prenatal vitamin during pre-conception and early pregnancy may ameliorate the effects of PPD on cognition in the offspring. METHODS PPD was assessed in early (12-16 weeks) and late (28-32 weeks) gestation in the Ontario Birth Study. Prenatal vitamin supplement intake information was collected in early gestation. Child cognition at 4 years was assessed using the NIH Toolbox. Poisson regression was used to investigate associations between PPD and/or prenatal vitamin intake and child cognition. RESULTS Four hundred and eighteen mother-child dyads were assessed. Moderate-severe PPD experienced during early gestation was associated with reduced cognition (adjusted incidence rate ratio (IRRadj) = 3.71, 95% confidence interval (CI): 1.57-8.77, P = 0.003). Daily intake of prenatal vitamins was not associated with cognition (IRRadj = 1.34, 95% CI: 0.73-2.46, P = 0.34). Upon stratification, the experience of mild-severe PPD with daily intake of prenatal vitamins was associated with higher incident rates of suboptimal cognition compared to children of women with daily prenatal vitamin intake without any episode of PPD (IRRadj = 2.88, 95% CI: 1.1-7.4). CONCLUSIONS Moderate-severe PPD in early pregnancy is associated with poor cognition in children and daily intake of prenatal vitamin did not ameliorate this association. IMPACT Our findings expand on existing literature by highlighting that exposure to prenatal psychological distress (PPD), in moderate-to-severe form, in the early stages of pregnancy, can have detrimental effects on the offspring's cognitive development at 4 years. Overall, prenatal vitamin intake did not ameliorate the effects of PPD. Early screening and treatment of prenatal maternal mental illness is crucial.
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Affiliation(s)
- Derrick Ssewanyana
- Alliance for Human Development, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.,Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Julia A Knight
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.,Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Stephen G Matthews
- Alliance for Human Development, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.,Department of Physiology, University of Toronto, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada.,Department of Obstetrics and Gynaecology, Sinai Health System, Toronto, ON, Canada
| | - Jody Wong
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Nadya Adel Khani
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Jennifer Lye
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Kellie E Murphy
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada.,Department of Obstetrics and Gynaecology, Sinai Health System, Toronto, ON, Canada
| | - Kim Foshay
- Department of Obstetrics and Gynaecology, Sinai Health System, Toronto, ON, Canada
| | - Justin Okeke
- Department of Obstetrics and Gynaecology, Sinai Health System, Toronto, ON, Canada
| | - Stephen J Lye
- Alliance for Human Development, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.,Department of Physiology, University of Toronto, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada.,Department of Obstetrics and Gynaecology, Sinai Health System, Toronto, ON, Canada
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada. .,Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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8
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Wilson KD, Porter EG, Garcia BA. Reprogramming of the epigenome in neurodevelopmental disorders. Crit Rev Biochem Mol Biol 2022; 57:73-112. [PMID: 34601997 PMCID: PMC9462920 DOI: 10.1080/10409238.2021.1979457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.
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Affiliation(s)
- Khadija D. Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth G. Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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9
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Michurina A, Sakib MS, Kerimoglu C, Krüger DM, Kaurani L, Islam MR, Joshi PD, Schröder S, Centeno TP, Zhou J, Pradhan R, Cha J, Xu X, Eichele G, Zeisberg EM, Kranz A, Stewart AF, Fischer A. Postnatal expression of the lysine methyltransferase SETD1B is essential for learning and the regulation of neuron-enriched genes. EMBO J 2022; 41:e106459. [PMID: 34806773 PMCID: PMC8724770 DOI: 10.15252/embj.2020106459] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/04/2021] [Accepted: 10/15/2021] [Indexed: 01/04/2023] Open
Abstract
In mammals, histone 3 lysine 4 methylation (H3K4me) is mediated by six different lysine methyltransferases. Among these enzymes, SETD1B (SET domain containing 1b) has been linked to syndromic intellectual disability in human subjects, but its role in the mammalian postnatal brain has not been studied yet. Here, we employ mice deficient for Setd1b in excitatory neurons of the postnatal forebrain, and combine neuron-specific ChIP-seq and RNA-seq approaches to elucidate its role in neuronal gene expression. We observe that Setd1b controls the expression of a set of genes with a broad H3K4me3 peak at their promoters, enriched for neuron-specific genes linked to learning and memory function. Comparative analyses in mice with conditional deletion of Kmt2a and Kmt2b histone methyltransferases show that SETD1B plays a more pronounced and potent role in regulating such genes. Moreover, postnatal loss of Setd1b leads to severe learning impairment, suggesting that SETD1B-dependent regulation of H3K4me levels in postnatal neurons is critical for cognitive function.
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Affiliation(s)
- Alexandra Michurina
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - M Sadman Sakib
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Cemil Kerimoglu
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Dennis Manfred Krüger
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Lalit Kaurani
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Md Rezaul Islam
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Parth Devesh Joshi
- Department for Gene and BehaviorMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Sophie Schröder
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Tonatiuh Pena Centeno
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Jiayin Zhou
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Ranjit Pradhan
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Julia Cha
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Xingbo Xu
- Department of Cardiology and PneumologyUniversity Medical Center of GöttingenGeorg‐August UniversityGöttingenGermany
- German Centre for Cardiovascular Research (DZHK)Partner Site GöttingenGöttingenGermany
| | - Gregor Eichele
- Department for Gene and BehaviorMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Elisabeth M Zeisberg
- Department of Cardiology and PneumologyUniversity Medical Center of GöttingenGeorg‐August UniversityGöttingenGermany
- German Centre for Cardiovascular Research (DZHK)Partner Site GöttingenGöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGermany
| | - Andrea Kranz
- Biotechnology CenterCenter for Molecular and Cellular BioengineeringDresden University of TechnologyDresdenGermany
| | - A Francis Stewart
- Biotechnology CenterCenter for Molecular and Cellular BioengineeringDresden University of TechnologyDresdenGermany
- Max‐Planck‐Institute for Cell Biology and GeneticsDresdenGermany
| | - André Fischer
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGermany
- Department of Psychiatry and PsychotherapyUniversity Medical Center GöttingenGöttingenGermany
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10
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Ciptasari U, van Bokhoven H. The phenomenal epigenome in neurodevelopmental disorders. Hum Mol Genet 2021; 29:R42-R50. [PMID: 32766754 PMCID: PMC7530535 DOI: 10.1093/hmg/ddaa175] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Disruption of chromatin structure due to epimutations is a leading genetic etiology of neurodevelopmental disorders, collectively known as chromatinopathies. We show that there is an increasing level of convergence from the high diversity of genes that are affected by mutations to the molecular networks and pathways involving the respective proteins, the disrupted cellular and subcellular processes, and their consequence for higher order cellular network function. This convergence is ultimately reflected by specific phenotypic features shared across the various chromatinopathies. Based on these observations, we propose that the commonly disrupted molecular and cellular anomalies might provide a rational target for the development of symptomatic interventions for defined groups of genetically distinct neurodevelopmental disorders.
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Affiliation(s)
- Ummi Ciptasari
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands.,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
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11
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Janowski M, Milewska M, Zare P, Pękowska A. Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue. Pharmaceuticals (Basel) 2021; 14:765. [PMID: 34451862 PMCID: PMC8399958 DOI: 10.3390/ph14080765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/26/2022] Open
Abstract
Neurological disorders (NDs) comprise a heterogeneous group of conditions that affect the function of the nervous system. Often incurable, NDs have profound and detrimental consequences on the affected individuals' lives. NDs have complex etiologies but commonly feature altered gene expression and dysfunctions of the essential chromatin-modifying factors. Hence, compounds that target DNA and histone modification pathways, the so-called epidrugs, constitute promising tools to treat NDs. Yet, targeting the entire epigenome might reveal insufficient to modify a chosen gene expression or even unnecessary and detrimental to the patients' health. New technologies hold a promise to expand the clinical toolkit in the fight against NDs. (Epi)genome engineering using designer nucleases, including CRISPR-Cas9 and TALENs, can potentially help restore the correct gene expression patterns by targeting a defined gene or pathway, both genetically and epigenetically, with minimal off-target activity. Here, we review the implication of epigenetic machinery in NDs. We outline syndromes caused by mutations in chromatin-modifying enzymes and discuss the functional consequences of mutations in regulatory DNA in NDs. We review the approaches that allow modifying the (epi)genome, including tools based on TALENs and CRISPR-Cas9 technologies, and we highlight how these new strategies could potentially change clinical practices in the treatment of NDs.
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Affiliation(s)
| | | | | | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur Street, 02-093 Warsaw, Poland; (M.J.); (M.M.); (P.Z.)
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12
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Truncating SRCAP variants outside the Floating-Harbor syndrome locus cause a distinct neurodevelopmental disorder with a specific DNA methylation signature. Am J Hum Genet 2021; 108:1053-1068. [PMID: 33909990 PMCID: PMC8206150 DOI: 10.1016/j.ajhg.2021.04.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/31/2021] [Indexed: 02/08/2023] Open
Abstract
Truncating variants in exons 33 and 34 of the SNF2-related CREBBP activator protein (SRCAP) gene cause the neurodevelopmental disorder (NDD) Floating-Harbor syndrome (FLHS), characterized by short stature, speech delay, and facial dysmorphism. Here, we present a cohort of 33 individuals with clinical features distinct from FLHS and truncating (mostly de novo) SRCAP variants either proximal (n = 28) or distal (n = 5) to the FLHS locus. Detailed clinical characterization of the proximal SRCAP individuals identified shared characteristics: developmental delay with or without intellectual disability, behavioral and psychiatric problems, non-specific facial features, musculoskeletal issues, and hypotonia. Because FLHS is known to be associated with a unique set of DNA methylation (DNAm) changes in blood, a DNAm signature, we investigated whether there was a distinct signature associated with our affected individuals. A machine-learning model, based on the FLHS DNAm signature, negatively classified all our tested subjects. Comparing proximal variants with typically developing controls, we identified a DNAm signature distinct from the FLHS signature. Based on the DNAm and clinical data, we refer to the condition as “non-FLHS SRCAP-related NDD.” All five distal variants classified negatively using the FLHS DNAm model while two classified positively using the proximal model. This suggests divergent pathogenicity of these variants, though clinically the distal group presented with NDD, similar to the proximal SRCAP group. In summary, for SRCAP, there is a clear relationship between variant location, DNAm profile, and clinical phenotype. These results highlight the power of combined epigenetic, molecular, and clinical studies to identify and characterize genotype-epigenotype-phenotype correlations.
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13
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Mustafin RN, Kazantseva AV, Enikeeva RF, Malykh SB, Khusnutdinova EK. Longitudinal genetic studies of cognitive characteristics. Vavilovskii Zhurnal Genet Selektsii 2021; 24:87-95. [PMID: 33659785 PMCID: PMC7716536 DOI: 10.18699/vj20.599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The present review describes longitudinal studies of cognitive traits and functions determining the causes of their variations and their possible correction to prevent cognitive impairment. The present study reviews the involvement of such environmental factors as nutrition, prenatal maternal stress, social isolation and others in cognitive functioning. The role of epigenetic factors in the implementation of environmental effects in cognitive characteristics is revealed. Considering the epigenome significance, several studies were focused on the design of substances affecting methylation and histone modification, which can be used for the treatment of cognitive disorders. The appropriate correction of epigenetic factors related to environmental differences in cognitive abilities requires to determine the mechanisms of chromatin modifications and variations in DNA methylation. Transposons representing stress-sensitive DNA elements appeared to mediate the environmental influence on epigenetic modifications. They can explain the mechanism of transgenerational transfer of information on cognitive abilities. Recently, large-scale meta-analyses based on the results of studies, which identified genetic associations with various cognitive traits, were carried out. As a result, the role of genes actively expressed in the brain, such as BDNF, COMT, CADM2, CYP2D6, APBA1, CHRNA7, PDE1C, PDE4B, and PDE4D in cognitive abilities was revealed. The association between cognitive functioning and genes, which have been previously involved in developing psychiatric disorders (MEF2C, CYP2D6, FAM109B, SEPT3, NAGA, TCF20, NDUFA6 genes), was revealed, thus indicating the role of the similar mechanisms of genetic and neural networks in both normal cognition and cognitive impairment. An important role in both processes belongs to common epigenetic factors. The genes involved in DNA methylation (DNMT1, DNMT3B, and FTO), histone modifications (CREBBP, CUL4B, EHMT1, EP300, EZH2, HLCS, HUWE1, KAT6B, KMT2A, KMT2D, KMT2C, NSD1, WHSC1, and UBE2A) and chromatin remodeling (ACTB, ARID1A, ARID1B, ATRX, CHD2, CHD7, CHD8, SMARCA2, SMARCA4, SMARCB1, SMARCE1, SRCAP, and SS18L1) are associated with increased risk of psychiatric diseases with cognitive deficiency together with normal cognitive functioning. The data on the correlation between transgenerational epigenetic inheritance of cognitive abilities and the insert of transposable elements in intergenic regions is discussed. Transposons regulate genes functioning in the brain due to the processing of their transcripts into non-coding RNAs. The content, quantity and arrangement of transposable elements in human genome, which do not affect changes in nucleotide sequences of protein encoding genes, but affect their expression, can be transmitted to the next generation.
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Affiliation(s)
| | - A V Kazantseva
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - R F Enikeeva
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - S B Malykh
- Psychological Institute of the Russian Academy of Education, Moscow, Russia M.V. Lomonosov Moscow State University, Laboratory of psychology of professions and conflicts, Moscow, Russia
| | - E K Khusnutdinova
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia M.V. Lomonosov Moscow State University, Laboratory of psychology of professions and conflicts, Moscow, Russia
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14
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Legrand A, Iftimovici A, Khayachi A, Chaumette B. Epigenetics in bipolar disorder: a critical review of the literature. Psychiatr Genet 2021; 31:1-12. [PMID: 33290382 DOI: 10.1097/ypg.0000000000000267] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Bipolar disorder (BD) is a chronic, disabling disease characterised by alternate mood episodes, switching through depressive and manic/hypomanic phases. Mood stabilizers, in particular lithium salts, constitute the cornerstone of the treatment in the acute phase as well as for the prevention of recurrences. The pathophysiology of BD and the mechanisms of action of mood stabilizers remain largely unknown but several pieces of evidence point to gene x environment interactions. Epigenetics, defined as the regulation of gene expression without genetic changes, could be the molecular substrate of these interactions. In this literature review, we summarize the main epigenetic findings associated with BD and response to mood stabilizers. METHODS We searched PubMed, and Embase databases and classified the articles depending on the epigenetic mechanisms (DNA methylation, histone modifications and non-coding RNAs). RESULTS We present the different epigenetic modifications associated with BD or with mood-stabilizers. The major reported mechanisms were DNA methylation, histone methylation and acetylation, and non-coding RNAs. Overall, the assessments are poorly harmonized and the results are more limited than in other psychiatric disorders (e.g. schizophrenia). However, the nature of BD and its treatment offer excellent opportunities for epigenetic research: clear impact of environmental factors, clinical variation between manic or depressive episodes resulting in possible identification of state and traits biomarkers, documented impact of mood-stabilizers on the epigenome. CONCLUSION Epigenetic is a growing and promising field in BD that may shed light on its pathophysiology or be useful as biomarkers of response to mood-stabilizer.
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Affiliation(s)
- Adrien Legrand
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris
| | - Anton Iftimovici
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris
- Neurospin, CEA, Gif-sur-Yvette, France
| | - Anouar Khayachi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Canada
| | - Boris Chaumette
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Paris
- GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France
- Department of Psychiatry, McGill University, Montreal, Canada
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15
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Distinct Pathogenic Genes Causing Intellectual Disability and Autism Exhibit a Common Neuronal Network Hyperactivity Phenotype. Cell Rep 2021; 30:173-186.e6. [PMID: 31914384 DOI: 10.1016/j.celrep.2019.12.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/15/2019] [Accepted: 11/27/2019] [Indexed: 01/31/2023] Open
Abstract
Pathogenic mutations in either one of the epigenetic modifiers EHMT1, MBD5, MLL3, or SMARCB1 have been identified to be causative for Kleefstra syndrome spectrum (KSS), a neurodevelopmental disorder with clinical features of both intellectual disability (ID) and autism spectrum disorder (ASD). To understand how these variants lead to the phenotypic convergence in KSS, we employ a loss-of-function approach to assess neuronal network development at the molecular, single-cell, and network activity level. KSS-gene-deficient neuronal networks all develop into hyperactive networks with altered network organization and excitatory-inhibitory balance. Interestingly, even though transcriptional data reveal distinct regulatory mechanisms, KSS target genes share similar functions in regulating neuronal excitability and synaptic function, several of which are associated with ID and ASD. Our results show that KSS genes mainly converge at the level of neuronal network communication, providing insights into the pathophysiology of KSS and phenotypically congruent disorders.
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16
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Siu MT, Goodman SJ, Yellan I, Butcher DT, Jangjoo M, Grafodatskaya D, Rajendram R, Lou Y, Zhang R, Zhao C, Nicolson R, Georgiades S, Szatmari P, Scherer SW, Roberts W, Anagnostou E, Weksberg R. DNA Methylation of the Oxytocin Receptor Across Neurodevelopmental Disorders. J Autism Dev Disord 2021; 51:3610-3623. [PMID: 33394241 DOI: 10.1007/s10803-020-04792-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 12/24/2022]
Abstract
Many neurodevelopmental disorders (NDDs) share common learning and behavioural impairments, as well as features such as dysregulation of the oxytocin hormone. Here, we examined DNA methylation (DNAm) in the 1st intron of the oxytocin receptor gene, OXTR, in patients with autism spectrum (ASD), attention deficit and hyperactivity (ADHD) and obsessive compulsive (OCD) disorders. DNAm of OXTR was assessed for cohorts of ASD (blood), ADHD (saliva), OCD (saliva), which uncovered sex-specific DNAm differences compared to neurotypical, tissue-matched controls. Individuals with ASD or ADHD exhibiting extreme DNAm values had lower IQ and more social problems, respectively, than those with DNAm within normative ranges. This suggests that OXTR DNAm patterns are altered across NDDs and may be correlated with common clinical outcomes.
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Affiliation(s)
- Michelle T Siu
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah J Goodman
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Isaac Yellan
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Darci T Butcher
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Maryam Jangjoo
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Daria Grafodatskaya
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Rageen Rajendram
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Youliang Lou
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Rujun Zhang
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Chunhua Zhao
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Rob Nicolson
- Department of Psychiatry, University of Western Ontario, London, ON, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Peter Szatmari
- The Margaret and Wallace McCain Centre for Child, Youth & Family Mental Health and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Wendy Roberts
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada.,Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, 555 University Ave, Toronto, ON, M5G 1X8, Canada. .,Institute of Medical Science, School of Graduate Studies, University of Toronto, Toronto, ON, Canada.
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17
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Mustafin RN, Kazantseva AV, Malykh SB, Khusnutdinova EK. Genetic Mechanisms of Cognitive Development. RUSS J GENET+ 2020. [DOI: 10.1134/s102279542007011x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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ODLURO syndrome: personal experience and review of the literature. Radiol Med 2020; 126:316-322. [DOI: 10.1007/s11547-020-01255-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/05/2020] [Indexed: 12/20/2022]
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19
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Di Fede E, Massa V, Augello B, Squeo G, Scarano E, Perri AM, Fischetto R, Causio FA, Zampino G, Piccione M, Curridori E, Mazza T, Castellana S, Larizza L, Ghelma F, Colombo EA, Gandini MC, Castori M, Merla G, Milani D, Gervasini C. Expanding the phenotype associated to KMT2A variants: overlapping clinical signs between Wiedemann-Steiner and Rubinstein-Taybi syndromes. Eur J Hum Genet 2020; 29:88-98. [PMID: 32641752 PMCID: PMC7852672 DOI: 10.1038/s41431-020-0679-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/03/2020] [Accepted: 06/23/2020] [Indexed: 12/16/2022] Open
Abstract
Lysine-specific methyltransferase 2A (KMT2A) is responsible for methylation of histone H3 (K4H3me) and contributes to chromatin remodeling, acting as "writer" of the epigenetic machinery. Mutations in KMT2A were first reported in Wiedemann-Steiner syndrome (WDSTS). More recently, KMT2A variants have been described in probands with a specific clinical diagnosis comprised in the so-called chromatinopathies. Such conditions, including WDSTS, are a group of overlapping disorders caused by mutations in genes coding for the epigenetic machinery. Among them, Rubinstein-Taybi syndrome (RSTS) is mainly caused by heterozygous pathogenic variants in CREBBP or EP300. In this work, we used next generation sequencing (either by custom-made panel or by whole exome) to identify alternative causative genes in individuals with a RSTS-like phenotype negative to CREBBP and EP300 mutational screening. In six patients we identified different novel unreported variants in KMT2A gene. The identified variants are de novo in at least four out of six tested individuals and all of them display some typical RSTS phenotypic features but also WDSTS specific signs. This study reinforces the concept that germline variants affecting the epigenetic machinery lead to a shared molecular effect (alteration of the chromatin state) determining superimposable clinical conditions.
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Affiliation(s)
- Elisabetta Di Fede
- Genetica Medica e Biologia Applicata, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Valentina Massa
- Genetica Medica e Biologia Applicata, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy.,"Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milano, Italy
| | - Bartolomeo Augello
- Unità di Genetica Medica, IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Gabriella Squeo
- Unità di Genetica Medica, IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Emanuela Scarano
- Ambulatorio di Malattie Rare, Sindromologia ed Auxologia U.O. Pediatria AOU S.Orsola-Malpighi, Bologna, Italy
| | - Anna Maria Perri
- Ambulatorio di Malattie Rare, Sindromologia ed Auxologia U.O. Pediatria AOU S.Orsola-Malpighi, Bologna, Italy
| | - Rita Fischetto
- U.O.C. Malattie Metaboliche Genetica Medica, PO Giovanni XXIII, AOU Policlinico Consorziale, Bari, Italy
| | - Francesco Andrea Causio
- U.O.C. Malattie Metaboliche Genetica Medica, PO Giovanni XXIII, AOU Policlinico Consorziale, Bari, Italy
| | - Giuseppe Zampino
- Centro Malattie Rare e Difetti Congeniti, Fondazione Policlinico Universitario A. Gemelli, Università Cattolica, Roma, Italy
| | - Maria Piccione
- Dipartimento di scienze per la promozione della salute e la cura della madre e del bambino "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Elena Curridori
- Dipartimento di clinica pediatrica e malattie rare, Ospedale pediatrico Antonio Cao, Cagliari, Italy
| | - Tommaso Mazza
- Unit of Bioinformatics IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Unit of Bioinformatics IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Lidia Larizza
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Filippo Ghelma
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Elisa Adele Colombo
- Genetica Medica e Biologia Applicata, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Maria Chiara Gandini
- Genetica Medica e Biologia Applicata, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Marco Castori
- Unità di Genetica Medica, IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Giuseppe Merla
- Unità di Genetica Medica, IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Donatella Milani
- UOSD Pediatria ad alta intensità di cura, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milano, Milano, Italy
| | - Cristina Gervasini
- Genetica Medica e Biologia Applicata, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy. .,"Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milano, Italy.
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20
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Coneys R, Wood IC. Alzheimer's disease: the potential of epigenetic treatments and current clinical candidates. Neurodegener Dis Manag 2020; 10:543-558. [PMID: 32552286 DOI: 10.2217/nmt-2019-0034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease is a progressive and fatal neurodegenerative disease affecting 50 million people worldwide, characterized by memory loss and neuronal degeneration. Current treatments have limited efficacy and there is no cure. Alzheimer's is likely caused by a combination of factors, providing several potential therapeutic targets. One area of interest is the epigenetic regulation of gene expression within the brain. Epigenetic marks, including DNA methylation and histone modifications, show consistent changes with age and in those with Alzheimer's. Some epigenetic regulation has been linked to disease pathology and progression and are the focus of current research. Epigenetic regulators might make promising therapeutic targets yet challenges need to be overcome to generate an efficacious drug lacking deleterious side effects.
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Affiliation(s)
- Rachel Coneys
- Leonard Wolfson Experimental Neurology Centre, Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Ian C Wood
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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21
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Schut EHS, Alonso A, Smits S, Khamassi M, Samanta A, Negwer M, Kasri NN, Navarro Lobato I, Genzel L. The Object Space Task reveals increased expression of cumulative memory in a mouse model of Kleefstra syndrome. Neurobiol Learn Mem 2020; 173:107265. [PMID: 32531423 DOI: 10.1016/j.nlm.2020.107265] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/06/2020] [Accepted: 05/30/2020] [Indexed: 11/27/2022]
Abstract
Kleefstra syndrome is a disorder caused by a mutation in the EHMT1 gene characterized in humans by general developmental delay, mild to severe intellectual disability and autism. Here, we characterized cumulative memory in the Ehmt1+/- mouse model using the Object Space Task. We combined conventional behavioral analysis with automated analysis by deep-learning networks, a session-based computational learning model, and a trial-based classifier. Ehmt1+/- mice showed more anxiety-like features and generally explored objects less, but the difference decreased over time. Interestingly, when analyzing memory-specific exploration, Ehmt1+/- show increased expression of cumulative memory, but a deficit in a more simple, control memory condition. Using our automatic classifier to differentiate between genotypes, we found that cumulative memory features are better suited for classification than general exploration differences. Thus, detailed behavioral classification with the Object Space Task produced a more detailed behavioral phenotype of the Ehmt1+/- mouse model.
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Affiliation(s)
- Evelien H S Schut
- Donders Institute for Brain Cognition and Behaviour, Radboud University, Nijmegen, Netherlands; Department of Human Genetics and Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, Netherlands
| | - Alejandra Alonso
- Donders Institute for Brain Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Steven Smits
- Donders Institute for Brain Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Mehdi Khamassi
- Institute of Intelligent Systems and Robotics, Sorbonne Université, CNRS, Paris, France
| | - Anumita Samanta
- Donders Institute for Brain Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Moritz Negwer
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, Netherlands
| | - Irene Navarro Lobato
- Donders Institute for Brain Cognition and Behaviour, Radboud University, Nijmegen, Netherlands
| | - Lisa Genzel
- Donders Institute for Brain Cognition and Behaviour, Radboud University, Nijmegen, Netherlands; Department of Human Genetics and Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB Nijmegen, Netherlands.
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22
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Squeo GM, Augello B, Massa V, Milani D, Colombo EA, Mazza T, Castellana S, Piccione M, Maitz S, Petracca A, Prontera P, Accadia M, Della Monica M, Di Giacomo MC, Melis D, Selicorni A, Giglio S, Fischetto R, Di Fede E, Malerba N, Russo M, Castori M, Gervasini C, Merla G. Customised next-generation sequencing multigene panel to screen a large cohort of individuals with chromatin-related disorder. J Med Genet 2020; 57:760-768. [PMID: 32170002 DOI: 10.1136/jmedgenet-2019-106724] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND The regulation of the chromatin state by epigenetic mechanisms plays a central role in gene expression, cell function, and maintenance of cell identity. Hereditary disorders of chromatin regulation are a group of conditions caused by abnormalities of the various components of the epigenetic machinery, namely writers, erasers, readers, and chromatin remodelers. Although neurological dysfunction is almost ubiquitous in these disorders, the constellation of additional features characterizing many of these genes and the emerging clinical overlap among them indicate the existence of a community of syndromes. The introduction of high-throughput next generation sequencing (NGS) methods for testing multiple genes simultaneously is a logical step for the implementation of diagnostics of these disorders. METHODS We screened a heterogeneous cohort of 263 index patients by an NGS-targeted panel, containing 68 genes associated with more than 40 OMIM entries affecting chromatin function. RESULTS This strategy allowed us to identify clinically relevant variants in 87 patients (32%), including 30 for which an alternative clinical diagnosis was proposed after sequencing analysis and clinical re-evaluation. CONCLUSION Our findings indicate that this approach is effective not only in disorders with locus heterogeneity, but also in order to anticipate unexpected misdiagnoses due to clinical overlap among cognate disorders. Finally, this work highlights the utility of a prompt diagnosis in such a clinically and genetically heterogeneous group of disorders that we propose to group under the umbrella term of chromatinopathies.
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Affiliation(s)
- Gabriella Maria Squeo
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Bartolomeo Augello
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Valentina Massa
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Donatella Milani
- UOSD Pediatria ad alta intensità di cura, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Adele Colombo
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Maria Piccione
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Antonio Petracca
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital "Cardinale G. Panico", Tricase, Italy
| | - Matteo Della Monica
- Medical Genetics Unit, Cardarelli Hospital, Largo A Cardarelli, Napoli, Italy
| | | | - Daniela Melis
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Angelo Selicorni
- Pediatric Department, ASST Lariana, Sant'Anna General Hospital, Como, Italy
| | - Sabrina Giglio
- Department of Biomedical, Experimental and Clinical Sciences 'Mario Serio', Medical Genetics Unit, University Hospital Meyer, Firenze, Italy
| | - Rita Fischetto
- Metabolic Diseases, Clinical Genetics and Diabetology Unit, Paediatric Hospital Giovanni XXIII, Bari, Italy
| | - Elisabetta Di Fede
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Natascia Malerba
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Matteo Russo
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Marco Castori
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Cristina Gervasini
- Dipartimento di Scienze della Salute, Universita degli Studi di Milano Dipartimento di Scienze della Salute, Milano, Italy
| | - Giuseppe Merla
- Division of Medical Genetics, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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23
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Aygun D, Bjornsson HT. Clinical epigenetics: a primer for the practitioner. Dev Med Child Neurol 2020; 62:192-200. [PMID: 31749156 DOI: 10.1111/dmcn.14398] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/01/2019] [Indexed: 12/12/2022]
Abstract
Disruption of epigenetic modifications and the factors that maintain these modifications is rapidly emerging as a cause of developmental disorders. Here we summarize some of the major principles of epigenetics including how epigenetic modifications are: (1) normally reset in the germ line, (2) form an additional layer of interindividual variation, (3) are environmentally sensitive, and (4) change over time in humans. We also briefly discuss the disruption of growth and intellect associated with the Mendelian disorders of the epigenetic machinery and the classical imprinting disorders (such as Beckwith-Wiedemann syndrome, Silver-Russell syndrome, Prader-Willi syndrome, and Angelman syndrome), as well as suggesting some diagnostic considerations for the clinicians taking care of these patients. Finally, we discuss novel therapeutic strategies targeting epigenetic modifications, which may offer a safe alternative to up and coming genome editing strategies for the treatment of genetic diseases. This review provides a starting point for clinicians interested in epigenetics and the role epigenetic disruption plays in human disease. WHAT THIS PAPER ADDS: Clinicians are introduced to four main principles of epigenetics. Clinical features of imprinting disorders and Mendelian disorders of epigenetic machinery are presented.
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Affiliation(s)
- Deniz Aygun
- School of Arts and Sciences, Tufts University, Medford, MA, USA
| | - Hans T Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, Baltimore, MD, USA.,Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA.,Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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24
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Tejada MI, Ibarluzea N. Non-syndromic X linked intellectual disability: Current knowledge in light of the recent advances in molecular and functional studies. Clin Genet 2020; 97:677-687. [PMID: 31898314 DOI: 10.1111/cge.13698] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/09/2019] [Accepted: 12/24/2019] [Indexed: 12/23/2022]
Abstract
Since the discovery of the FMR1 gene and the clinical and molecular characterization of Fragile X Syndrome in 1991, more than 141 genes have been identified in the X-chromosome in these 28 years thanks to applying continuously evolving molecular techniques to X-linked intellectual disability (XLID) families. In the past decade, array comparative genomic hybridization and next generation sequencing technologies have accelerated gene discovery exponentially. Classically, XLID has been subdivided in syndromic intellectual disability (S-XLID)-where intellectual disability (ID) is always associated with other recognizable physical and/or neurological features-and non-specific or non-syndromic intellectual disability (NS-XLID) where the only common feature is ID. Nevertheless, new advances on the study of these entities have showed that this classification is not always clear-cut because distinct variants in several of these XLID genes can result in S-XLID as well as in NS-XLID. This review focuses on the current knowledge on the XLID genes involved in non-syndromic forms, with the emphasis on their pathogenic mechanism, thus allowing the possibility to elucidate why some of them can give both syndromic and non-syndromic phenotypes.
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Affiliation(s)
- María Isabel Tejada
- Genetics Service, Cruces University Hospital, Osakidetza Basque Health Service, Barakaldo, Spain.,Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain.,Clinical Group, Centre for Biomedical Research on Rare Diseases (CIBERER), Valencia, Spain
| | - Nekane Ibarluzea
- Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain.,Clinical Group, Centre for Biomedical Research on Rare Diseases (CIBERER), Valencia, Spain
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25
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Neuronal network dysfunction in a model for Kleefstra syndrome mediated by enhanced NMDAR signaling. Nat Commun 2019; 10:4928. [PMID: 31666522 PMCID: PMC6821803 DOI: 10.1038/s41467-019-12947-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 10/10/2019] [Indexed: 12/24/2022] Open
Abstract
Kleefstra syndrome (KS) is a neurodevelopmental disorder caused by mutations in the histone methyltransferase EHMT1. To study the impact of decreased EHMT1 function in human cells, we generated excitatory cortical neurons from induced pluripotent stem (iPS) cells derived from KS patients. Neuronal networks of patient-derived cells exhibit network bursting with a reduced rate, longer duration, and increased temporal irregularity compared to control networks. We show that these changes are mediated by upregulation of NMDA receptor (NMDAR) subunit 1 correlating with reduced deposition of the repressive H3K9me2 mark, the catalytic product of EHMT1, at the GRIN1 promoter. In mice EHMT1 deficiency leads to similar neuronal network impairments with increased NMDAR function. Finally, we rescue the KS patient-derived neuronal network phenotypes by pharmacological inhibition of NMDARs. Summarized, we demonstrate a direct link between EHMT1 deficiency and NMDAR hyperfunction in human neurons, providing a potential basis for more targeted therapeutic approaches for KS.
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Cytrynbaum C, Choufani S, Weksberg R. Epigenetic signatures in overgrowth syndromes: Translational opportunities. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:491-501. [PMID: 31828978 DOI: 10.1002/ajmg.c.31745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/04/2019] [Accepted: 09/12/2019] [Indexed: 12/21/2022]
Abstract
In recent years, numerous overgrowth syndromes have been found to be caused by pathogenic DNA sequence variants in "epigenes," genes that encode proteins that function in epigenetic regulation. Epigenetic marks, including DNA methylation (DNAm), histone modifications and chromatin conformation, have emerged as a vital genome-wide regulatory mechanism that modulate the transcriptome temporally and spatially to drive normal developmental and cellular processes. Evidence suggests that epigenetic marks are layered and engage in crosstalk, in that disruptions of any one component of the epigenetic machinery impact the others. This interdependence of epigenetic marks underpins the recent identification of gene-specific DNAm signatures for a variety of disorders caused by pathogenic variants in epigenes. Here, we discuss the power of DNAm signatures with respect to furthering our understanding of disease pathophysiology, enhancing the efficacy of molecular diagnostics and identifying new targets for therapeutics of overgrowth syndromes. These findings highlight the promise of the field of epigenomics to provide unprecedented insights into disease mechanisms generating a host of opportunities to advance precision medicine.
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Affiliation(s)
- Cheryl Cytrynbaum
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario
| | - Sanaa Choufani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario.,Department of Pediatrics, University of Toronto, Toronto, Ontario.,Institute of Medical Science, University of Toronto, Toronto, Ontario
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Bi-allelic Variants in METTL5 Cause Autosomal-Recessive Intellectual Disability and Microcephaly. Am J Hum Genet 2019; 105:869-878. [PMID: 31564433 DOI: 10.1016/j.ajhg.2019.09.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/04/2019] [Indexed: 02/01/2023] Open
Abstract
Intellectual disability (ID) is a genetically and clinically heterogeneous disorder, characterized by limited cognitive abilities and impaired adaptive behaviors. In recent years, exome sequencing (ES) has been instrumental in deciphering the genetic etiology of ID. Here, through ES of a large cohort of individuals with ID, we identified two bi-allelic frameshift variants in METTL5, c.344_345delGA (p.Arg115Asnfs∗19) and c.571_572delAA (p.Lys191Valfs∗10), in families of Pakistani and Yemenite origin. Both of these variants were segregating with moderate to severe ID, microcephaly, and various facial dysmorphisms, in an autosomal-recessive fashion. METTL5 is a member of the methyltransferase-like protein family, which encompasses proteins with a seven-beta-strand methyltransferase domain. We found METTL5 expression in various substructures of rodent and human brains and METTL5 protein to be enriched in the nucleus and synapses of the hippocampal neurons. Functional studies of these truncating variants in transiently transfected orthologous cells and cultured hippocampal rat neurons revealed no effect on the localization of METTL5 but alter its level of expression. Our in silico analysis and 3D modeling simulation predict disruption of METTL5 function by both variants. Finally, mettl5 knockdown in zebrafish resulted in microcephaly, recapitulating the human phenotype. This study provides evidence that biallelic variants in METTL5 cause ID and microcephaly in humans and highlights the essential role of METTL5 in brain development and neuronal function.
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La Rovere M, Franzago M, Stuppia L. Epigenetics and Neurological Disorders in ART. Int J Mol Sci 2019; 20:ijms20174169. [PMID: 31454921 PMCID: PMC6747212 DOI: 10.3390/ijms20174169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022] Open
Abstract
About 1–4% of children are currently generated by Assisted Reproductive Technologies (ART) in developed countries. These babies show only a slightly increased risk of neonatal malformations. However, follow-up studies have suggested a higher susceptibility to multifactorial, adult onset disorders like obesity, diabetes and cardiovascular diseases in ART offspring. It has been suggested that these conditions could be the consequence of epigenetic, alterations, due to artificial manipulations of gametes and embryos potentially able to alter epigenetic stability during zygote reprogramming. In the last years, epigenetic alterations have been invoked as a possible cause of increased risk of neurological disorders, but at present the link between epigenetic modifications and long-term effects in terms of neurological diseases in ART children remains unclear, due to the short follow up limiting retrospective studies. In this review, we summarize the current knowledge about neurological disorders promoted by epigenetics alterations in ART. Based on data currently available, it is possible to conclude that little, if any, evidence of an increased risk of neurological disorders in ART conceived children is provided. Most important, the large majority of reports appears to be limited to epidemiological studies, not providing any experimental evidence about epigenetic modifications responsible for an increased risk.
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Affiliation(s)
- Marina La Rovere
- Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences, "G. d'Annunzio" University, 66100 Chieti-Pescara, Italy
| | - Marica Franzago
- Department of Medicine and Aging, School of Medicine and Health Sciences, "G. d'Annunzio" University, 66100 Chieti-Pescara, Italy
- Aging Center Studies-Translational Medicine (CeSI-Met), "G. d'Annunzio" University, 66100 Chieti-Pescara, Italy
| | - Liborio Stuppia
- Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences, "G. d'Annunzio" University, 66100 Chieti-Pescara, Italy.
- Aging Center Studies-Translational Medicine (CeSI-Met), "G. d'Annunzio" University, 66100 Chieti-Pescara, Italy.
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Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment. Neurobiol Dis 2019; 132:104583. [PMID: 31445158 DOI: 10.1016/j.nbd.2019.104583] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 07/31/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023] Open
Abstract
Dravet syndrome (DS) is an early onset refractory epilepsy typically caused by de novo heterozygous variants in SCN1A encoding the α-subunit of the neuronal sodium channel Nav1.1. The syndrome is characterized by age-related progression of seizures, cognitive decline and movement disorders. We hypothesized that the distinct neurodevelopmental features in DS are caused by the disruption of molecular pathways in Nav1.1 haploinsufficient cells resulting in perturbed neural differentiation and maturation. Here, we established DS-patient and control induced pluripotent stem cell derived neural progenitor cells (iPSC NPC) and GABAergic inter-neuronal (iPSC GABA) cells. The DS-patient iPSC GABA cells showed a shift in sodium current activation and a perturbed response to induced oxidative stress. Transcriptome analysis revealed specific dysregulations of genes for chromatin structure, mitotic progression, neural plasticity and excitability in DS-patient iPSC NPCs and DS-patient iPSC GABA cells versus controls. The transcription factors FOXM1 and E2F1, positive regulators of the disrupted pathways for histone modification and cell cycle regulation, were markedly up-regulated in DS-iPSC GABA lines. Our study highlights transcriptional changes and disrupted pathways of chromatin remodeling in Nav1.1 haploinsufficient GABAergic cells, providing a molecular framework that overlaps with that of neurodevelopmental disorders and other epilepsies.
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Abstract
The epigenetic control of gene expression could be affected by addition and/or removal of post-translational modifications such as phosphorylation, acetylation and methylation of histone proteins, as well as methylation of DNA (5-methylation on cytosines). Misregulation of these modifications is associated with altered gene expression, resulting in various disease conditions. G9a belongs to the protein lysine methyltransferases that specifically methylates the K9 residue of histone H3, leading to suppression of several tumor suppressor genes. In this review, G9a functions, role in various diseases, structural biology aspects for inhibitor design, structure-activity relationship among the reported inhibitors are discussed which could aid in the design and development of potent G9a inhibitors for cancer treatment in the future.
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31
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Nixon KC, Rousseau J, Stone MH, Sarikahya M, Ehresmann S, Mizuno S, Matsumoto N, Miyake N, Baralle D, McKee S, Izumi K, Ritter AL, Heide S, Héron D, Depienne C, Titheradge H, Kramer JM, Campeau PM, Campeau PM. A Syndromic Neurodevelopmental Disorder Caused by Mutations in SMARCD1, a Core SWI/SNF Subunit Needed for Context-Dependent Neuronal Gene Regulation in Flies. Am J Hum Genet 2019; 104:596-610. [PMID: 30879640 DOI: 10.1016/j.ajhg.2019.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
Mutations in several genes encoding components of the SWI/SNF chromatin remodeling complex cause neurodevelopmental disorders (NDDs). Here, we report on five individuals with mutations in SMARCD1; the individuals present with developmental delay, intellectual disability, hypotonia, feeding difficulties, and small hands and feet. Trio exome sequencing proved the mutations to be de novo in four of the five individuals. Mutations in other SWI/SNF components cause Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, or other syndromic and non-syndromic NDDs. Although the individuals presented here have dysmorphisms and some clinical overlap with these syndromes, they lack their typical facial dysmorphisms. To gain insight into the function of SMARCD1 in neurons, we investigated the Drosophila ortholog Bap60 in postmitotic memory-forming neurons of the adult Drosophila mushroom body (MB). Targeted knockdown of Bap60 in the MB of adult flies causes defects in long-term memory. Mushroom-body-specific transcriptome analysis revealed that Bap60 is required for context-dependent expression of genes involved in neuron function and development in juvenile flies when synaptic connections are actively being formed in response to experience. Taken together, we identify an NDD caused by SMARCD1 mutations and establish a role for the SMARCD1 ortholog Bap60 in the regulation of neurodevelopmental genes during a critical time window of juvenile adult brain development when neuronal circuits that are required for learning and memory are formed.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Philippe M Campeau
- Centre Hospitalier Universitaire Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, University of Montreal, Montreal, QC H4A 3J1, Canada.
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Lewis CR, Henderson-Smith A, Breitenstein RS, Sowards HA, Piras IS, Huentelman MJ, Doane LD, Lemery-Chalfant K. Dopaminergic gene methylation is associated with cognitive performance in a childhood monozygotic twin study. Epigenetics 2019; 14:310-323. [PMID: 30806146 DOI: 10.1080/15592294.2019.1583032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Individual differences in cognitive function are due to a combination of heritable and non-heritable factors. A large body of evidence from clinical, cognitive, and pharmacological neuroscience implicates dopaminergic gene variants as modulators of cognitive functions. Neuroepigenetic studies demonstrate environmental factors also influence complex phenotypes by affecting gene expression regulation. To evaluate the mechanism of environmental influence on cognitive abilities, we examined if epigenetic regulation of dopaminergic genes plays a role in cognition. Using a DNA methylation profiling microarray, we used a monozygotic (MZ) twin difference design to evaluate if co-twin differences in methylation of CpG sites near six dopaminergic genes predicted differences in response inhibition and memory performance. Studying MZ twins allows us to assess if environmentally driven differences in methylation affect differences in phenotype while controlling for the influence of genotype and shared family environment. Response inhibition was assessed with the flanker task and short-term and working memory were assessed with digit span recall. We found MZ co-twin differences in DRD4 gene methylation predicted differences in short-term memory. MZ differences in COMT, DBH, DAT1, DRD1, and DRD2 gene methylation predicted differences in response inhibition. Taken together, findings suggest methylation status of dopaminergic genes may influence cognitive functions in a dissociable manner. Our results highlight the importance of the epigenome and environment, over and above the influence of genotype, in supporting complex cognitive functions.
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Affiliation(s)
- Candace R Lewis
- a Neurogenomics Division , Translational Genomics Research Institute , Phoenix , AZ , USA.,b Psychology Department , Arizona State University , Tempe , AZ , USA
| | | | | | - Hayley A Sowards
- b Psychology Department , Arizona State University , Tempe , AZ , USA
| | - Ignazio S Piras
- a Neurogenomics Division , Translational Genomics Research Institute , Phoenix , AZ , USA
| | - Matthew J Huentelman
- a Neurogenomics Division , Translational Genomics Research Institute , Phoenix , AZ , USA
| | - Leah D Doane
- b Psychology Department , Arizona State University , Tempe , AZ , USA
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Liester MB, Sullivan EE. A review of epigenetics in human consciousness. COGENT PSYCHOLOGY 2019. [DOI: 10.1080/23311908.2019.1668222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Mitchell B. Liester
- Department of Psychiatry, University of Colorado School of Medicine, P.O. Box 302 153 N. Washington Street, Suite 103, Monument, CO 80132, USA
| | - Erin E. Sullivan
- Computer Science, University of Oklahoma, P.O. Box 302, Monument, CO 80132, USA
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Affiliation(s)
- Andre Fischer
- Department for Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany.
- Department for Systems Medicine and Brain Diseases, German Center for Neurodegenerative Diseases (DZNE) site Göttingen, Göttingen, Germany.
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Seo S, Mathison A, Grzenda A, Podratz J, Calvo E, Brimijoin S, Windebank A, Iovanna J, Lomberk G, Urrutia R. Mechanisms Underlying the Regulation of HP1γ by the NGF-PKA Signaling Pathway. Sci Rep 2018; 8:15077. [PMID: 30305677 PMCID: PMC6180112 DOI: 10.1038/s41598-018-33475-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/19/2018] [Indexed: 02/08/2023] Open
Abstract
Heterochromatin protein 1 γ (HP1γ) is a well-known chromatin protein, which regulates gene silencing during the execution of processes associated with embryogenesis, organ maturation, and cell differentiation. We find that, in vivo, the levels of HP1γ are downregulated during nervous system development. Similar results are recapitulated in vitro during nerve growth factor (NGF)-induced neuronal cell differentiation in PC12 cells. Mechanistically, our experiments demonstrate that in differentiating PC12 cells, NGF treatment decreases the association of HP1γ to silent heterochromatin, leads to phosphorylation of this protein at S83 via protein kinase A (PKA), and ultimately results in its degradation. Genome-wide experiments, using gain-of-function (overexpression) and loss-of-function (RNAi) paradigms, demonstrate that changing the level of HP1γ impacts on PC12 differentiation, at least in part, through gene networks involved in this process. Hence, inactivation of HP1γ by different post-translational mechanisms, including reduced heterochromatin association, phosphorylation, and degradation, is necessary for neuronal cell differentiation to occur. Indeed, we show that the increase of HP1γ levels has the reverse effect, namely antagonizing neuronal cell differentiation, supporting that this protein acts as a barrier for this process. Thus, these results describe the regulation and participation of HP1γ in a novel membrane-to-nucleus pathway, through NGF-PKA signaling, which is involved in NGF-induced neuronal cell differentiation.
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Affiliation(s)
- Seungmae Seo
- Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Angela Mathison
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA
| | - Adrienne Grzenda
- University of California, Los Angeles, Psychiatry Residency Program, Los Angeles, CA, USA
| | - Jewel Podratz
- Department of Neuroscience, Mayo Clinic, Rochester, MN, USA
| | - Ezequiel Calvo
- Centre Génomique du Centre de Recherche du CHUL Research Center, Ville de Québec, Quebec, Canada
| | - Stephen Brimijoin
- Department of Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | | | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix Marseille Université, Marseille, France
| | - Gwen Lomberk
- Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA. .,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA.
| | - Raul Urrutia
- Genomic Sciences and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, WI, USA. .,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA.
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Nature versus nurture in the spectrum of rheumatic diseases: Classification of spondyloarthritis as autoimmune or autoinflammatory. Autoimmun Rev 2018; 17:935-941. [PMID: 30005857 DOI: 10.1016/j.autrev.2018.04.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 04/10/2018] [Indexed: 02/08/2023]
Abstract
Spondyloarthritides (SpA) include inflammatory joint diseases with various clinical phenotypes that may also include the axial skeleton and/or entheses. SpA include psoriatic arthritis, reactive arthritis, enteropathic arthritis and ankylosing spondylitis; the latter is frequently associated with extra-articular manifestations, such as uveitis, psoriasis, and inflammatory bowel disease. SpA are associated with the HLA-B27 allele and recognize T cells as key pathogenetic players. In contrast to other rheumatic diseases, SpA affect women and men equally and are not associated with detectable serum autoantibodies. In addition, but opposite to rheumatoid arthritis, SpA are responsive to treatment regimens including IL-23 or IL-17-targeting biologics, yet are virtually unresponsive to steroid treatment. Based on these differences with prototypical autoimmune diseases, such as rheumatoid arthritis or connective tissue diseases, SpA may be better classified among autoinflammatory diseases, with a predominant innate immunity involvement. This would rank SpA closer to gouty arthritis and periodic fevers in the spectrum of rheumatic diseases, as opposed to autoimmune-predominant diseases. We herein provide available literature on risk factors associated with SpA in support of this hypothesis with a specific focus on genetic and environmental factors.
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Linda K, Fiuza C, Nadif Kasri N. The promise of induced pluripotent stem cells for neurodevelopmental disorders. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:382-391. [PMID: 29128445 DOI: 10.1016/j.pnpbp.2017.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/30/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022]
Abstract
A major challenge in clinical genetics and medicine is represented by genetically and phenotypically highly diverse neurodevelopmental disorders, like for example intellectual disability and autism. Intellectual disability is characterized by substantial limitations in cognitive function and adaptive behaviour. At the cellular level, this is reflected by deficits in synaptic structure and plasticity and therefore has been coined as a synaptic disorder or "synaptopathy". In this review, we summarize the findings from recent studies in which iPSCs have been used to model specific neurodevelopmental syndromes, including Fragile X syndrome, Rett syndrome, Williams-Beuren syndrome and Phelan-McDermid syndrome. We discuss what we have learned from these studies and what key issues need to be addressed to move the field forward.
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Affiliation(s)
- Katrin Linda
- Department of Human Genetics, Department of Cognitive Neuroscience, Radboudumc, 6500 HB, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands
| | - Carol Fiuza
- Department of Human Genetics, Department of Cognitive Neuroscience, Radboudumc, 6500 HB, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Department of Cognitive Neuroscience, Radboudumc, 6500 HB, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands.
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Larizza L, Finelli P. Developmental disorders with intellectual disability driven by chromatin dysregulation: Clinical overlaps and molecular mechanisms. Clin Genet 2018; 95:231-240. [DOI: 10.1111/cge.13365] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/28/2018] [Accepted: 04/14/2018] [Indexed: 12/30/2022]
Affiliation(s)
- L. Larizza
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
| | - P. Finelli
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
- Department of Medical Biotechnology and Translational Medicine; Università degli Studi di Milano; Milan Italy
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39
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Stevens SJ, van der Schoot V, Leduc MS, Rinne T, Lalani SR, Weiss MM, van Hagen JM, Lachmeijer AM, Stockler-Ipsiroglu SG, Lehman A, Brunner HG. De novo mutations in the SET
nuclear proto-oncogene, encoding a component of the inhibitor of histone acetyltransferases (INHAT) complex in patients with nonsyndromic intellectual disability. Hum Mutat 2018; 39:1014-1023. [DOI: 10.1002/humu.23541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/12/2018] [Accepted: 04/20/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Servi J.C. Stevens
- Department of Clinical Genetics; Maastricht University Medical Centre; Maastricht the Netherlands
| | - Vyne van der Schoot
- Department of Clinical Genetics; Maastricht University Medical Centre; Maastricht the Netherlands
| | - Magalie S. Leduc
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
- Baylor Genetics; Houston Texas USA
| | - Tuula Rinne
- Department of Genetics; Radboud University Medical Centre; Nijmegen the Netherlands
| | - Seema R. Lalani
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | - Marjan M. Weiss
- Department of Clinical Genetics; VU University Medical Centre; Amsterdam the Netherlands
| | - Johanna M. van Hagen
- Department of Clinical Genetics; VU University Medical Centre; Amsterdam the Netherlands
| | | | | | - Anna Lehman
- Department of Medical Genetics; British Columbia Children's Hospital; Vancouver Canada
| | - Han G Brunner
- Department of Clinical Genetics; Maastricht University Medical Centre; Maastricht the Netherlands
- Department of Genetics; Radboud University Medical Centre; Nijmegen the Netherlands
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40
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Qureshi IA, Mehler MF. Epigenetic mechanisms underlying nervous system diseases. HANDBOOK OF CLINICAL NEUROLOGY 2018; 147:43-58. [PMID: 29325627 DOI: 10.1016/b978-0-444-63233-3.00005-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing. These mechanisms are intimately involved in executing fundamental genomic programs, including gene transcription, posttranscriptional RNA processing and transport, translation, X-chromosome inactivation, genomic imprinting, retrotransposon regulation, DNA replication, and DNA repair and the maintenance of genomic stability. For the nervous system, epigenetics offers a novel and robust framework for explaining how brain development and aging occur, neural cellular diversity is generated, synaptic and neural network connectivity and plasticity are mediated, and complex cognitive and behavioral phenotypes are inherited transgenerationally. Epigenetic factors and processes are, not surprisingly, implicated in nervous system disease pathophysiology through several emerging paradigms - mutations and genetic variation in genes encoding epigenetic factors; impairments in epigenetic factor expression, localization, and function; epigenetic mechanisms modulating disease-associated factors and pathways; and the presence of deregulated epigenetic profiles in central and peripheral tissues.
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Affiliation(s)
- Irfan A Qureshi
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine; Institute for Brain Disorders and Neural Regeneration; Departments of Neurology, Neuroscience, Psychiatry and Behavioral Sciences and Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Mark F Mehler
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine; Institute for Brain Disorders and Neural Regeneration; Departments of Neurology, Neuroscience, Psychiatry and Behavioral Sciences; Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities; Einstein Cancer Center; Ruth L. and David S. Gottesman Stem Cell Institute; and Center for Epigenomics and Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, United States.
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41
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Goodwin LR, Picketts DJ. The role of ISWI chromatin remodeling complexes in brain development and neurodevelopmental disorders. Mol Cell Neurosci 2017; 87:55-64. [PMID: 29249292 DOI: 10.1016/j.mcn.2017.10.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/04/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022] Open
Abstract
The mammalian ISWI (Imitation Switch) genes SMARCA1 and SMARCA5 encode the ATP-dependent chromatin remodeling proteins SNF2L and SNF2H. The ISWI proteins interact with BAZ (bromodomain adjacent to PHD zinc finger) domain containing proteins to generate eight distinct remodeling complexes. ISWI complex-mediated nucleosome positioning within genes and gene regulatory elements is proving important for the transition from a committed progenitor state to a differentiated cell state. Genetic studies have implicated the involvement of many ATP-dependent chromatin remodeling proteins in neurodevelopmental disorders (NDDs), including SMARCA1. Here we review the characterization of mice inactivated for ISWI and their interacting proteins, as it pertains to brain development and disease. A better understanding of chromatin dynamics during neural development is a prerequisite to understanding disease pathologies and the development of therapeutics for these complex disorders.
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Affiliation(s)
- Laura R Goodwin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
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42
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Epigenetic Etiology of Intellectual Disability. J Neurosci 2017; 37:10773-10782. [PMID: 29118205 DOI: 10.1523/jneurosci.1840-17.2017] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/26/2017] [Accepted: 09/26/2017] [Indexed: 12/31/2022] Open
Abstract
Intellectual disability (ID) is a prevailing neurodevelopmental condition associated with impaired cognitive and adaptive behaviors. Many chromatin-modifying enzymes and other epigenetic regulators have been genetically associated with ID disorders (IDDs). Here we review how alterations in the function of histone modifiers, chromatin remodelers, and methyl-DNA binding proteins contribute to neurodevelopmental defects and altered brain plasticity. We also discuss how progress in human genetics has led to the generation of mouse models that unveil the molecular etiology of ID, and outline the direction in which this field is moving to identify therapeutic strategies for IDDs. Importantly, because the chromatin regulators linked to IDDs often target common downstream genes and cellular processes, the impact of research in individual syndromes goes well beyond each syndrome and can also contribute to the understanding and therapy of other IDDs. Furthermore, the investigation of these disorders helps us to understand the role of chromatin regulators in brain development, plasticity, and gene expression, thereby answering fundamental questions in neurobiology.
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Koemans TS, Kleefstra T, Chubak MC, Stone MH, Reijnders MRF, de Munnik S, Willemsen MH, Fenckova M, Stumpel CTRM, Bok LA, Sifuentes Saenz M, Byerly KA, Baughn LB, Stegmann APA, Pfundt R, Zhou H, van Bokhoven H, Schenck A, Kramer JM. Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder. PLoS Genet 2017; 13:e1006864. [PMID: 29069077 PMCID: PMC5656305 DOI: 10.1371/journal.pgen.1006864] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/10/2017] [Indexed: 11/18/2022] Open
Abstract
Kleefstra syndrome, caused by haploinsufficiency of euchromatin histone methyltransferase 1 (EHMT1), is characterized by intellectual disability (ID), autism spectrum disorder (ASD), characteristic facial dysmorphisms, and other variable clinical features. In addition to EHMT1 mutations, de novo variants were reported in four additional genes (MBD5, SMARCB1, NR1I3, and KMT2C), in single individuals with clinical characteristics overlapping Kleefstra syndrome. Here, we present a novel cohort of five patients with de novo loss of function mutations affecting the histone methyltransferase KMT2C. Our clinical data delineates the KMT2C phenotypic spectrum and reinforces the phenotypic overlap with Kleefstra syndrome and other related ID disorders. To elucidate the common molecular basis of the neuropathology associated with mutations in KMT2C and EHMT1, we characterized the role of the Drosophila KMT2C ortholog, trithorax related (trr), in the nervous system. Similar to the Drosophila EHMT1 ortholog, G9a, trr is required in the mushroom body for short term memory. Trr ChIP-seq identified 3371 binding sites, mainly in the promoter of genes involved in neuronal processes. Transcriptional profiling of pan-neuronal trr knockdown and G9a null mutant fly heads identified 613 and 1123 misregulated genes, respectively. These gene sets show a significant overlap and are associated with nearly identical gene ontology enrichments. The majority of the observed biological convergence is derived from predicted indirect target genes. However, trr and G9a also have common direct targets, including the Drosophila ortholog of Arc (Arc1), a key regulator of synaptic plasticity. Our data highlight the clinical and molecular convergence between the KMT2 and EHMT protein families, which may contribute to a molecular network underlying a larger group of ID/ASD-related disorders. Neurodevelopmental disorders (NDDs) like intellectual disability (ID) and autism spectrum disorder (ASD) present an enormous challenge to affected individuals, their families, and society. Understanding the mechanisms underlying NDDs may lead to the development of targeted therapeutics, but this is complicated by the great clinical and genetic heterogeneity seen in patients. Mutations in hundreds of genes have been implicated in NDDs, giving rise to diverse clinical presentations. However, evidence suggests that many of these genes lie in common biological pathways, and mutations in genes that are involved in similar biological functions give rise to more similar clinical phenotypes. Here, we define a novel ID disorder with comorbid ASD (ID/ASD) caused by mutations in KMT2C. This disorder is defined by clinical features that overlap with a group of other disorders, including Kleefstra syndrome, which is caused by EHMT1 mutations. In the fruit fly, we show that the KMT2 and EHMT protein families regulate a highly converging set of biological processes. Both EHMT1 and KMT2C encode histone methyltransferases, which regulate gene transcription by modifying chromatin structure. Further understanding of the common gene regulatory networks associated with this group of ID- and ASD-related disorders may lead to the identification of novel therapeutic targets.
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Affiliation(s)
- Tom S. Koemans
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, The Netherlands
| | - Melissa C. Chubak
- Department of Biology, Faculty of Science, Western University, London, Ontario, Canada
| | - Max H. Stone
- Department of Biology, Faculty of Science, Western University, London, Ontario, Canada
- Division of Genetics and Development, Children’s Health Research Institute, London, Ontario, Canada
| | - Margot R. F. Reijnders
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, The Netherlands
| | - Sonja de Munnik
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, The Netherlands
| | - Marjolein H. Willemsen
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, The Netherlands
| | - Michaela Fenckova
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, The Netherlands
| | - Connie T. R. M. Stumpel
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Levinus A. Bok
- Department of Pediatrics, Máxima Medical Centre, Veldhoven, The Netherlands
| | | | - Kyna A. Byerly
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Linda B. Baughn
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Alexander P. A. Stegmann
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, The Netherlands
| | - Huiqing Zhou
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Molecular Developmental Biology, Radboud University, Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, The Netherlands
| | - Annette Schenck
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, Nijmegen, The Netherlands
- * E-mail: (AS); (JMK)
| | - Jamie M. Kramer
- Department of Biology, Faculty of Science, Western University, London, Ontario, Canada
- Division of Genetics and Development, Children’s Health Research Institute, London, Ontario, Canada
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- * E-mail: (AS); (JMK)
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44
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Scandaglia M, Lopez-Atalaya JP, Medrano-Fernandez A, Lopez-Cascales MT, Del Blanco B, Lipinski M, Benito E, Olivares R, Iwase S, Shi Y, Barco A. Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons. Cell Rep 2017; 21:47-59. [PMID: 28978483 PMCID: PMC5679733 DOI: 10.1016/j.celrep.2017.09.014] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/29/2017] [Accepted: 09/04/2017] [Indexed: 12/17/2022] Open
Abstract
During development, chromatin-modifying enzymes regulate both the timely establishment of cell-type-specific gene programs and the coordinated repression of alternative cell fates. To dissect the role of one such enzyme, the intellectual-disability-linked lysine demethylase 5C (Kdm5c), in the developing and adult brain, we conducted parallel behavioral, transcriptomic, and epigenomic studies in Kdm5c-null and forebrain-restricted inducible knockout mice. Together, genomic analyses and functional assays demonstrate that Kdm5c plays a critical role as a repressor responsible for the developmental silencing of germline genes during cellular differentiation and in fine-tuning activity-regulated enhancers during neuronal maturation. Although the importance of these functions declines after birth, Kdm5c retains an important genome surveillance role preventing the incorrect activation of non-neuronal and cryptic promoters in adult neurons.
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Affiliation(s)
- Marilyn Scandaglia
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Jose P Lopez-Atalaya
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Alejandro Medrano-Fernandez
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Maria T Lopez-Cascales
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Beatriz Del Blanco
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Michal Lipinski
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Eva Benito
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Roman Olivares
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, 5815 Medical Science II, Ann Arbor, MI 48109, USA
| | - Yang Shi
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Angel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Molecular Neurobiology and Neuropathology Unit, Av. Santiago Ramón y Cajal s/n, Sant Joan d'Alacant, 03550 Alicante, Spain.
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45
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Arguinano AA, Naderi E, Ndiaye NC, Stathopoulou M, Dadé S, Alizadeh B, Visvikis-Siest S. IL6R haplotype rs4845625*T/rs4537545*C is a risk factor for simultaneously high CRP, LDL and ApoB levels. Genes Immun 2017; 18:163-169. [PMID: 28769070 DOI: 10.1038/gene.2017.16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/10/2017] [Accepted: 06/22/2017] [Indexed: 11/09/2022]
Abstract
Interleukin 6 receptor (IL-6R), mediating IL-6's biological functions, plays an important role in different diseases such as diabetes, obesity and cardio-vascular diseases. In this study, we investigated the effects of two single nucleotide polymorphisms (SNPs), within the IL-6R loci, previously associated with C-reactive protein (CRP) and coronary heart diseases risk, and with controversial effects on lipids traits: SNP rs4845625 and SNP rs4537545. The results showed that both investigated SNPs were antagonistically related with CRP levels; the minor rs4845625*T allele was associated with increased CRP levels (P-value=0.011), while the minor rs4537545*T allele was associated with decreased CRP levels (P-value=0.009). Interestingly, the minor rs4845625*T allele was significantly associated with higher low-density lipoprotein cholesterol (LDL-C) and ApoB levels (P=0.007 and P=0.009 respectively). Haplotype analysis showed that the TC haplotype, having the minor rs4845625*T allele, was related simultaneously with increased levels of CRP, LDL-C and ApoB levels, thus could be considered as a risk factor. Our investigation detects for the first time an independent effect of rs4845625 on LDL-C and ApoB traits, explaining an important range of those traits variability (3.49 and 5.57% respectively). Our findings might be of high clinical significance in pharmacogenomics studies of tocilizumab for which IL-6R is target.
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Affiliation(s)
- A A Arguinano
- INSERM UMR U1122; IGE-PCV 'Interactions Gène-Environnement en Physiopathologie Cardio-vasculaire', Faculté de Pharmacie, Université de Lorraine, Nancy, France
| | - E Naderi
- INSERM UMR U1122; IGE-PCV 'Interactions Gène-Environnement en Physiopathologie Cardio-vasculaire', Faculté de Pharmacie, Université de Lorraine, Nancy, France.,Department of Epidemiology, University Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - N C Ndiaye
- INSERM UMR U1122; IGE-PCV 'Interactions Gène-Environnement en Physiopathologie Cardio-vasculaire', Faculté de Pharmacie, Université de Lorraine, Nancy, France
| | - M Stathopoulou
- INSERM UMR U1122; IGE-PCV 'Interactions Gène-Environnement en Physiopathologie Cardio-vasculaire', Faculté de Pharmacie, Université de Lorraine, Nancy, France
| | - S Dadé
- INSERM UMR U1122; IGE-PCV 'Interactions Gène-Environnement en Physiopathologie Cardio-vasculaire', Faculté de Pharmacie, Université de Lorraine, Nancy, France
| | - B Alizadeh
- INSERM UMR U1122; IGE-PCV 'Interactions Gène-Environnement en Physiopathologie Cardio-vasculaire', Faculté de Pharmacie, Université de Lorraine, Nancy, France.,Department of Epidemiology, University Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - S Visvikis-Siest
- INSERM UMR U1122; IGE-PCV 'Interactions Gène-Environnement en Physiopathologie Cardio-vasculaire', Faculté de Pharmacie, Université de Lorraine, Nancy, France.,Department of Internal Medicine and Geriatrics, CHU Technopôle Nancy-Brabois, Rue du Morvan, Vandoeuvre-lès-Nancy, France
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46
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Chaumette B, Kebir O, Krebs MO. [Genetics and epigenetics of schizophrenia and other psychoses]. Biol Aujourdhui 2017; 211:69-82. [PMID: 28682228 DOI: 10.1051/jbio/2017015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Indexed: 06/07/2023]
Abstract
Schizophrenia and other psychoses are categorical psychiatric diagnoses corresponding to frequent and heterogeneous disorders. Their physiopathology still remains largely unknown despite numerous recent advances. In particular, the last decade has identified different types of genetic variants, thanks to emergence of high-throughput methods. These methods allow both the identification of rare variants with a large effect such as punctual mutations or copy-number variants and the identification of frequent variants with a limited effect such as polymorphisms. Many impacted genes have been identified showing a very high genetic heterogeneity of psychoses. These genes are overrepresented in synaptic and neurotransmission pathways. Only a small fraction of psychoses could be easily explained by genetics but this screening in clinical practice is important as it can lead to therapeutic challenge or genetic counselling. Nowadays, it is clear that the pathophysiology of the psychoses can only be understood by an integrative approach taking into account the interaction between genes and environment. This interaction could be mediated by the epigenome defined as the modification of gene expression without changes in DNA sequence. Epigenome is stable but could be modified by environmental factors. Several epigenetic mechanisms have been studied in psychosis, in particular the DNA methylation, the modification of histones and the microRNA. All of these mechanisms are under regulation by genetic factors and variants in these epigenetic-involved genes and cofactors have been also associated with schizophrenia. Thus, pathophysiology of psychosis is complex and morestudiesare needed before definitive conclusions. Altogether, the recent advances in the genetics and epigenetics of psychosis are promising and could open the way to a recategorization of these disorders as well as the identification of new therapeutic targets.
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Affiliation(s)
- Boris Chaumette
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Oussama Kebir
- INSERM, U894, Laboratoire "Physiopathologie des maladies psychiatriques", Centre de Psychiatrie et Neurosciences, Université Paris Descartes, Sorbonne Paris Cité, 102-108 rue de la Santé, 75014 Paris, France Institut de Psychiatrie-GDR 3557, Centre Hospitalier Sainte-Anne, Paris, France
| | - Marie-Odile Krebs
- INSERM, U894, Laboratoire "Physiopathologie des maladies psychiatriques", Centre de Psychiatrie et Neurosciences, Université Paris Descartes, Sorbonne Paris Cité, 102-108 rue de la Santé, 75014 Paris, France Institut de Psychiatrie-GDR 3557, Centre Hospitalier Sainte-Anne, Paris, France
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47
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Mastrototaro G, Zaghi M, Sessa A. Epigenetic Mistakes in Neurodevelopmental Disorders. J Mol Neurosci 2017; 61:590-602. [DOI: 10.1007/s12031-017-0900-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/15/2017] [Indexed: 12/28/2022]
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48
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Whitton L, Cosgrove D, Clarkson C, Harold D, Kendall K, Richards A, Mantripragada K, Owen MJ, O'Donovan MC, Walters J, Hartmann A, Konte B, Rujescu D, Gill M, Corvin A, Rea S, Donohoe G, Morris DW. Cognitive analysis of schizophrenia risk genes that function as epigenetic regulators of gene expression. Am J Med Genet B Neuropsychiatr Genet 2016; 171:1170-1179. [PMID: 27762073 DOI: 10.1002/ajmg.b.32503] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 09/27/2016] [Indexed: 12/13/2022]
Abstract
Epigenetic mechanisms are an important heritable and dynamic means of regulating various genomic functions, including gene expression, to orchestrate brain development, adult neurogenesis, and synaptic plasticity. These processes when perturbed are thought to contribute to schizophrenia pathophysiology. A core feature of schizophrenia is cognitive dysfunction. For genetic disorders where cognitive impairment is more severe such as intellectual disability, there are a disproportionally high number of genes involved in the epigenetic regulation of gene transcription. Evidence now supports some shared genetic aetiology between schizophrenia and intellectual disability. GWAS have identified 108 chromosomal regions associated with schizophrenia risk that span 350 genes. This study identified genes mapping to those loci that have epigenetic functions, and tested the risk alleles defining those loci for association with cognitive deficits. We developed a list of 350 genes with epigenetic functions and cross-referenced this with the GWAS loci. This identified eight candidate genes: BCL11B, CHD7, EP300, EPC2, GATAD2A, KDM3B, RERE, SATB2. Using a dataset of Irish psychosis cases and controls (n = 1235), the schizophrenia risk SNPs at these loci were tested for effects on IQ, working memory, episodic memory, and attention. Strongest associations were for rs6984242 with both measures of IQ (P = 0.001) and episodic memory (P = 0.007). We link rs6984242 to CHD7 via a long range eQTL. These associations were not replicated in independent samples. Our study highlights that a number of genes mapping to risk loci for schizophrenia may function as epigenetic regulators of gene expression but further studies are required to establish a role for these genes in cognition. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Laura Whitton
- Cognitive Genetics and Cognitive Therapy Group, Neuroimaging, Cognition and Genomics (NICOG) Centre and NCBES Galway Neuroscience Centre, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
| | - Donna Cosgrove
- Cognitive Genetics and Cognitive Therapy Group, Neuroimaging, Cognition and Genomics (NICOG) Centre and NCBES Galway Neuroscience Centre, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
| | - Christopher Clarkson
- Centre for Chromosome Biology, Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
| | - Denise Harold
- Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine and Discipline of Psychiatry, Trinity College Dublin, Dublin, Ireland.,School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Kimberley Kendall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Alex Richards
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Kiran Mantripragada
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - James Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Betina Konte
- Department of Psychiatry, University of Halle, Halle, Germany
| | - Dan Rujescu
- Department of Psychiatry, University of Halle, Halle, Germany
| | | | - Michael Gill
- Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine and Discipline of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | - Aiden Corvin
- Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine and Discipline of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | - Stephen Rea
- Centre for Chromosome Biology, Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
| | - Gary Donohoe
- Cognitive Genetics and Cognitive Therapy Group, Neuroimaging, Cognition and Genomics (NICOG) Centre and NCBES Galway Neuroscience Centre, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
| | - Derek W Morris
- Cognitive Genetics and Cognitive Therapy Group, Neuroimaging, Cognition and Genomics (NICOG) Centre and NCBES Galway Neuroscience Centre, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
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49
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Bart Martens M, Frega M, Classen J, Epping L, Bijvank E, Benevento M, van Bokhoven H, Tiesinga P, Schubert D, Nadif Kasri N. Euchromatin histone methyltransferase 1 regulates cortical neuronal network development. Sci Rep 2016; 6:35756. [PMID: 27767173 PMCID: PMC5073331 DOI: 10.1038/srep35756] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/05/2016] [Indexed: 12/12/2022] Open
Abstract
Heterozygous mutations or deletions in the human Euchromatin histone methyltransferase 1 (EHMT1) gene cause Kleefstra syndrome, a neurodevelopmental disorder that is characterized by autistic-like features and severe intellectual disability (ID). Neurodevelopmental disorders including ID and autism may be related to deficits in activity-dependent wiring of brain circuits during development. Although Kleefstra syndrome has been associated with dendritic and synaptic defects in mice and Drosophila, little is known about the role of EHMT1 in the development of cortical neuronal networks. Here we used micro-electrode arrays and whole-cell patch-clamp recordings to investigate the impact of EHMT1 deficiency at the network and single cell level. We show that EHMT1 deficiency impaired neural network activity during the transition from uncorrelated background action potential firing to synchronized network bursting. Spontaneous bursting and excitatory synaptic currents were transiently reduced, whereas miniature excitatory postsynaptic currents were not affected. Finally, we show that loss of function of EHMT1 ultimately resulted in less regular network bursting patterns later in development. These data suggest that the developmental impairments observed in EHMT1-deficient networks may result in a temporal misalignment between activity-dependent developmental processes thereby contributing to the pathophysiology of Kleefstra syndrome.
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Affiliation(s)
- Marijn Bart Martens
- Department of Neuroinformatics, Radboud University Nijmegen, Faculty of Science, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Monica Frega
- Donders Institute for Brain, Cognition and Behaviour, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboudumc, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Jessica Classen
- Donders Institute for Brain, Cognition and Behaviour, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboudumc, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Lisa Epping
- Department of Neuroinformatics, Radboud University Nijmegen, Faculty of Science, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Elske Bijvank
- Donders Institute for Brain, Cognition and Behaviour, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboudumc, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Marco Benevento
- Donders Institute for Brain, Cognition and Behaviour, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboudumc, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Donders Institute for Brain, Cognition and Behaviour, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboudumc, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Paul Tiesinga
- Department of Neuroinformatics, Radboud University Nijmegen, Faculty of Science, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Dirk Schubert
- Donders Institute for Brain, Cognition and Behaviour, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboudumc, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
| | - Nael Nadif Kasri
- Donders Institute for Brain, Cognition and Behaviour, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
- Department of Cognitive Neuroscience, Radboudumc, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, P.O. Box 9101, 6500 HB, Nijmegen, the Netherlands
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50
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Witteveen JS, Willemsen MH, Dombroski TCD, van Bakel NHM, Nillesen WM, van Hulten JA, Jansen EJR, Verkaik D, Veenstra-Knol HE, van Ravenswaaij-Arts CMA, Wassink-Ruiter JSK, Vincent M, David A, Le Caignec C, Schieving J, Gilissen C, Foulds N, Rump P, Strom T, Cremer K, Zink AM, Engels H, de Munnik SA, Visser JE, Brunner HG, Martens GJM, Pfundt R, Kleefstra T, Kolk SM. Haploinsufficiency of MeCP2-interacting transcriptional co-repressor SIN3A causes mild intellectual disability by affecting the development of cortical integrity. Nat Genet 2016; 48:877-87. [PMID: 27399968 DOI: 10.1038/ng.3619] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 06/15/2016] [Indexed: 12/13/2022]
Abstract
Numerous genes are associated with neurodevelopmental disorders such as intellectual disability and autism spectrum disorder (ASD), but their dysfunction is often poorly characterized. Here we identified dominant mutations in the gene encoding the transcriptional repressor and MeCP2 interactor switch-insensitive 3 family member A (SIN3A; chromosome 15q24.2) in individuals who, in addition to mild intellectual disability and ASD, share striking features, including facial dysmorphisms, microcephaly and short stature. This phenotype is highly related to that of individuals with atypical 15q24 microdeletions, linking SIN3A to this microdeletion syndrome. Brain magnetic resonance imaging showed subtle abnormalities, including corpus callosum hypoplasia and ventriculomegaly. Intriguingly, in vivo functional knockdown of Sin3a led to reduced cortical neurogenesis, altered neuronal identity and aberrant corticocortical projections in the developing mouse brain. Together, our data establish that haploinsufficiency of SIN3A is associated with mild syndromic intellectual disability and that SIN3A can be considered to be a key transcriptional regulator of cortical brain development.
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Affiliation(s)
- Josefine S Witteveen
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Thaís C D Dombroski
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Nick H M van Bakel
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Willy M Nillesen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Josephus A van Hulten
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Eric J R Jansen
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Dave Verkaik
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | | | - Marie Vincent
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, Nantes, France
| | - Albert David
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, Nantes, France
| | - Cedric Le Caignec
- Centre Hospitalier Universitaire de Nantes, Service de Génétique Médicale, Nantes, France.,Laboratoire de Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Faculté de Médecine, INSERM UMRS 957, Nantes, France
| | - Jolanda Schieving
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Nicola Foulds
- Wessex Clinical Genetics Services, University Hospital Southampton National Health Service Foundation Trust, Princess Anne Hospital, Southampton, UK.,Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Patrick Rump
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tim Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Sonja A de Munnik
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Jasper E Visser
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Neurology, Amphia Hospital Breda, Berda, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Gerard J M Martens
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Nijmegen, the Netherlands
| | - Sharon M Kolk
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, the Netherlands
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