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Ali SM, AlMasri DA, Prada CE, Lin D, Bosley TM, Kozak I. Clinical and ocular abnormalities in DEGCAGS syndrome-Developmental delay with gastrointestinal, cardiovascular, genitourinary, and skeletal abnormalities. Mol Genet Genomic Med 2024; 12:e2329. [PMID: 38014480 PMCID: PMC10767677 DOI: 10.1002/mgg3.2329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 10/24/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
PURPOSE To describe clinical and ocular abnormalities in a case of Developmental Delay with Gastrointestinal, Cardiovascular, Genitourinary, and Skeletal Abnormalities (DEGCAGS syndrome). METHODS A clinical report. CASE DESCRIPTION An infant born to a consanguineous Middle Eastern family who was delivered by cesarean section because of in utero growth restriction, premature labor, and breech presentation. Post-partum medical problems included hypotension, generalized hypotonia, bradycardia, apnea requiring resuscitation and positive pressure ventilation, facial dysmorphia, skeletal malformations, and disorders of the gastrointestinal, immune, urinary, respiratory, cardiac, and visual systems. The family reported that a previous child had severe hypotonia at birth and was given the diagnosis of hypoxic ischemic encephalopathy; that child remains on a ventilator in a chronic care facility. Our patient was found to be homozygous for a novel pathogenic missense variant in theZNF699 zinc finger gene on chromosome 19p13 causing a syndrome known as Developmental Delay with Gastrointestinal, Cardiovascular, Genitourinary, and Skeletal Abnormalities (DEGCAGS syndrome). We review this variable syndrome, including abnormalities of the visual system not described previously. CONCLUSIONS We describe the 15th child to be presumably identified with the DEGCAGS syndrome and the first individual with homozygous missense variants in the ZNF699 gene who had complete clinical examination and detailed retinal imaging.
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Affiliation(s)
- Syed M Ali
- Moorfields Eye Hospital Abu-Dhabi, Abu Dhabi, UAE
- Mohammed Bin Rashed University, Dubai, UAE
- Danat Al Emarat Hospital, Abu Dhabi, UAE
| | | | - Carlos E Prada
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Feinberg School of Medicine of Northwestern University, Chicago, Illinois, USA
| | - Doris Lin
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas M Bosley
- The Neuro-Ophthalmology Division, The Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, USA
| | - Igor Kozak
- Moorfields Eye Hospital Abu-Dhabi, Abu Dhabi, UAE
- Mohammed Bin Rashed University, Dubai, UAE
- Danat Al Emarat Hospital, Abu Dhabi, UAE
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2
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Ward SK, Wadley A, Tsai CHA, Benke PJ, Emrick L, Fisher K, Houck KM, Dai H, Guillen Sacoto MJ, Craigen W, Glaser K, Murdock DR, Rohena L, Diderich KEM, Bruggenwirth HT, Lee B, Bacino C, Burrage LC, Rosenfeld JA. De novo missense variants in ZBTB47 are associated with developmental delays, hypotonia, seizures, gait abnormalities, and variable movement abnormalities. Am J Med Genet A 2024; 194:17-30. [PMID: 37743782 PMCID: PMC11221546 DOI: 10.1002/ajmg.a.63399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023]
Abstract
The collection of known genetic etiologies of neurodevelopmental disorders continues to increase, including several syndromes associated with defects in zinc finger protein transcription factors (ZNFs) that vary in clinical severity from mild learning disabilities and developmental delay to refractory seizures and severe autism spectrum disorder. Here we describe a new neurodevelopmental disorder associated with variants in ZBTB47 (also known as ZNF651), which encodes zinc finger and BTB domain-containing protein 47. Exome sequencing (ES) was performed for five unrelated patients with neurodevelopmental disorders. All five patients are heterozygous for a de novo missense variant in ZBTB47, with p.(Glu680Gly) (c.2039A>G) detected in one patient and p.(Glu477Lys) (c.1429G>A) identified in the other four patients. Both variants impact conserved amino acid residues. Bioinformatic analysis of each variant is consistent with pathogenicity. We present five unrelated patients with de novo missense variants in ZBTB47 and a phenotype characterized by developmental delay with intellectual disability, seizures, hypotonia, gait abnormalities, and variable movement abnormalities. We propose that these variants in ZBTB47 are the basis of a new neurodevelopmental disorder.
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Affiliation(s)
- Scott K Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
- Department of Pediatrics, Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexandrea Wadley
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Chun-Hui Anne Tsai
- Department of Pediatrics, Section of Genetics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Paul J Benke
- Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
| | - Lisa Emrick
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Kristen Fisher
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Kimberly M Houck
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
| | | | - William Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Kimberly Glaser
- Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
- Invitae, San Francisco, California, USA
| | - David R Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
- The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Luis Rohena
- Department of Pediatrics, Division of Medical Genetics, San Antonio Military Medical Center, San Antonio, Texas, USA
- Department of Pediatrics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Hennie T Bruggenwirth
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Carlos Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, Texas, USA
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3
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Christensen MB, Levy AM, Mohammadi NA, Niceta M, Kaiyrzhanov R, Dentici ML, Alam CA, Alesi V, Benoit V, Bhatia KP, Bierhals T, Boßelmann CM, Buratti J, Callewaert B, Ceulemans B, Charles P, De Wachter M, Dehghani M, D'haenens E, Doco-Fenzy M, Geßner M, Gobert C, Guliyeva U, Haack TB, Hammer TB, Heinrich T, Hempel M, Herget T, Hoffmann U, Horvath J, Houlden H, Keren B, Kresge C, Kumps C, Lederer D, Lermine A, Magrinelli F, Maroofian R, Mehrjardi MYV, Moudi M, Müller AJ, Oostra AJ, Pletcher BA, Ros-Pardo D, Samarasekera S, Tartaglia M, Van Schil K, Vogt J, Wassmer E, Winkelmann J, Zaki MS, Zech M, Lerche H, Radio FC, Gomez-Puertas P, Møller RS, Tümer Z. Biallelic variants in ZNF142 lead to a syndromic neurodevelopmental disorder. Clin Genet 2022; 102:98-109. [PMID: 35616059 PMCID: PMC9546172 DOI: 10.1111/cge.14165] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022]
Abstract
Biallelic variants of the gene encoding for the zinc-finger protein 142 (ZNF142) have recently been associated with intellectual disability (ID), speech impairment, seizures, and movement disorders in nine individuals from five families. In this study, we obtained phenotype and genotype information of 26 further individuals from 16 families. Among the 27 different ZNF142 variants identified in the total of 35 individuals only four were missense. Missense variants may give a milder phenotype by changing the local structure of ZF motifs as suggested by protein modelling; but this correlation should be validated in larger cohorts and pathogenicity of the missense variants should be investigated with functional studies. Clinical features of the 35 individuals suggest that biallelic ZNF142 variants lead to a syndromic neurodevelopmental disorder with mild to moderate ID, varying degrees of delay in language and gross motor development, early onset seizures, hypotonia, behavioral features, movement disorders, and facial dysmorphism. The differences in symptom frequencies observed in the unpublished individuals compared to those of published, and recognition of previously underemphasized facial features are likely to be due to the small sizes of the previous cohorts, which underlines the importance of larger cohorts for the phenotype descriptions of rare genetic disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Maria B Christensen
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Amanda M Levy
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Nazanin A Mohammadi
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London, United Kingdom
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy.,Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chadi Al Alam
- Pediatric Neurology department, American center for Psychiatry and Neurology, Abu Dhabi and Al Ain, United Arab Emirates.,Pediatric Neurology department, Haykel Hospital, El Koura, Lebanon
| | - Viola Alesi
- Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian M Boßelmann
- Department of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Julien Buratti
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP- HP, Sorbonne Université, Paris, France
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Berten Ceulemans
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Perrine Charles
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP- HP, Sorbonne Université, Paris, France
| | - Matthias De Wachter
- Department of Pediatric Neurology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Mohammadreza Dehghani
- Medical Genetics Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Erika D'haenens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martine Doco-Fenzy
- SFR CAP SANTE, HMB2 CHU, Reims, France.,CHU de Nantes, service de génétique médicale, Nantes, France
| | - Michaela Geßner
- KfH-Board of Trustees for Dialysis and Kidney Transplantation (KfH-Kuratorium für Dialyse und Nierentransplantation e.V.), Neu Isenburg, Germany
| | - Cyrielle Gobert
- Neuropediatric department, Centre Hospitalier Neurologique William Lennox, Ottignies, Belgium
| | | | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Trine B Hammer
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark
| | - Tilman Heinrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,MVZ Humangenetik und Molekularpathologie GmbH, Rostock, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Judit Horvath
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London, United Kingdom
| | - Boris Keren
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP- HP, Sorbonne Université, Paris, France
| | | | - Candy Kumps
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | | | - Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Institute of Neurology, London, United Kingdom
| | | | - Mahdiyeh Moudi
- Department of Genetics, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Amelie J Müller
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Anna J Oostra
- Neuropediatric department, Ghent University Hospital, Ghent, Belgium.,Centre for Developmental disorders, Ghent, Belgium
| | | | - David Ros-Pardo
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), Madrid, Spain
| | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Kristof Van Schil
- Department of Medical Genetics, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham, United Kingdom
| | - Evangeline Wassmer
- Birmingham Women and Children's Hospital, Birmingham, United Kingdom.,Institute of Health and Neurodevelopment, Aston University, Birmingham, United Kingdom
| | - Juliane Winkelmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt.,Genetics Department, Armed Forces College of Medicine (AFCM), Cairo, Egypt
| | - Michael Zech
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | | | - Paulino Gomez-Puertas
- Molecular Modeling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), Madrid, Spain
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Treatment, The Danish Epilepsy Centre, Dianalund, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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4
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Nielsen MM, Trolle C, Vang S, Hornshøj H, Skakkebaek A, Hedegaard J, Nordentoft I, Pedersen JS, Gravholt CH. Epigenetic and transcriptomic consequences of excess X-chromosome material in 47,XXX syndrome-A comparison with Turner syndrome and 46,XX females. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:279-293. [PMID: 32489015 DOI: 10.1002/ajmg.c.31799] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 01/21/2023]
Abstract
47,XXX (triple X) and Turner syndrome (45,X) are sex chromosomal abnormalities with detrimental effects on health with increased mortality and morbidity. In karyotypical normal females, X-chromosome inactivation balances gene expression between sexes and upregulation of the X chromosome in both sexes maintain stoichiometry with the autosomes. In 47,XXX and Turner syndrome a gene dosage imbalance may ensue from increased or decreased expression from the genes that escape X inactivation, as well as from incomplete X chromosome inactivation in 47,XXX. We aim to study genome-wide DNA-methylation and RNA-expression changes can explain phenotypic traits in 47,XXX syndrome. We compare DNA-methylation and RNA-expression data derived from white blood cells of seven women with 47,XXX syndrome, with data from seven female controls, as well as with seven women with Turner syndrome (45,X). To address these questions, we explored genome-wide DNA-methylation and transcriptome data in blood from seven females with 47,XXX syndrome, seven females with Turner syndrome, and seven karyotypically normal females (46,XX). Based on promoter methylation, we describe a demethylation of six X-chromosomal genes (AMOT, HTR2C, IL1RAPL2, STAG2, TCEANC, ZNF673), increased methylation for GEMIN8, and four differentially methylated autosomal regions related to four genes (SPEG, MUC4, SP6, and ZNF492). We illustrate how these changes seem compensated at the transcriptome level although several genes show differential exon usage. In conclusion, our results suggest an impact of the supernumerary X chromosome in 47,XXX syndrome on the methylation status of selected genes despite an overall comparable expression profile.
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Affiliation(s)
| | - Christian Trolle
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Endocrinology and Internal Medicine and Medical Research Laboratories, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Hornshøj
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Anne Skakkebaek
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Jakob Hedegaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Claus Højbjerg Gravholt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Endocrinology and Internal Medicine and Medical Research Laboratories, Aarhus University Hospital, Aarhus, Denmark
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5
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Exome sequencing revealed a novel homozygous METTL23 gene mutation leading to familial mild intellectual disability with dysmorphic features. Eur J Med Genet 2020; 63:103951. [PMID: 32439618 DOI: 10.1016/j.ejmg.2020.103951] [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: 10/09/2018] [Revised: 03/06/2020] [Accepted: 05/09/2020] [Indexed: 11/21/2022]
Abstract
BACKGROUND Genetic factors represent a considerable part of the etiologies of intellectual disability; however, the identification of causal genetic anomaly has long been complicated by the great clinical and genetic heterogeneity of this type of disease. With advances in next-generation sequencing technologies and functional studies, the identification of genes involved in intellectual development has led to more accurate diagnostics and better understanding of the underlying biological pathways. CASE REPORT We report on the case of two Moroccan siblings presenting mild intellectual disability with minimal dysmorphic features in which whole exome sequencing analysis revealed homozygous mutation in the METTL23 gene. Mutations in this gene have been reported to cause autosomal recessive mild intellectual disability but the association with dysmorphic features remains controversial. CONCLUSION Hereby, we highlight the similarity of the dysmorphic traits and the characteristic facial features in patients with METTL23-related intellectual disability, suggesting the consideration of a distinct clinical entity associating mild intellectual deficiency with specific facial dysmorphy for an efficient diagnosis orientation and a better phenotype-genotype correlation in intellectual disability disorders.
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6
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Al-Naama N, Mackeh R, Kino T. C 2H 2-Type Zinc Finger Proteins in Brain Development, Neurodevelopmental, and Other Neuropsychiatric Disorders: Systematic Literature-Based Analysis. Front Neurol 2020; 11:32. [PMID: 32117005 PMCID: PMC7034409 DOI: 10.3389/fneur.2020.00032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/10/2020] [Indexed: 12/15/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are multifaceted pathologic conditions manifested with intellectual disability, autistic features, psychiatric problems, motor dysfunction, and/or genetic/chromosomal abnormalities. They are associated with skewed neurogenesis and brain development, in part through dysfunction of the neural stem cells (NSCs) where abnormal transcriptional regulation on key genes play significant roles. Recent accumulated evidence highlights C2H2-type zinc finger proteins (C2H2-ZNFs), the largest transcription factor family in humans, as important targets for the pathologic processes associated with NDDs. In this review, we identified their significant accumulation (74 C2H2-ZNFs: ~10% of all human member proteins) in brain physiology and pathology. Specifically, we discuss their physiologic contribution to brain development, particularly focusing on their actions in NSCs. We then explain their pathologic implications in various forms of NDDs, such as morphological brain abnormalities, intellectual disabilities, and psychiatric disorders. We found an important tendency that poly-ZNFs and KRAB-ZNFs tend to be involved in the diseases that compromise gross brain structure and human-specific higher-order functions, respectively. This may be consistent with their characteristic appearance in the course of species evolution and corresponding contribution to these brain activities.
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Affiliation(s)
- Njoud Al-Naama
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Rafah Mackeh
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
| | - Tomoshige Kino
- Laboratory of Molecular and Genomic Endocrinology, Division of Translational Medicine, Sidra Medicine, Doha, Qatar
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7
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Zhang L, Yu M, Xu H, Wei X, Liu Y, Huang C, Chen H, Guo Z. RNA sequencing revealed the abnormal transcriptional profile in cloned bovine embryos. Int J Biol Macromol 2020; 150:492-500. [PMID: 32035150 DOI: 10.1016/j.ijbiomac.2020.02.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/04/2020] [Accepted: 02/04/2020] [Indexed: 12/11/2022]
Abstract
Somatic cell nuclear transfer (SCNT) has potential applications in agriculture and biomedicine, but the efficiency of cloning is still low. In this study, the transcriptional profiles in cloned and fertilized embryos were measured and compared by RNA sequencing. The 2-cell embryos were detected to identify the earliest transcriptional differences between embryos derived through IVF and SCNT. As a result, 364 genes showed decreased expression in cloned 2-cell embryos and were enriched in "intracellular protein transport" and "ubiquitin mediated proteolysis". In blastocysts, 593 genes showed decreased expression in cloned blastocysts and were enriched in "RNA binding", "nucleotide binding", "embryo development", and "adherens junction". We identified 14 development related genes that were not activated in the cloned embryos. Then, 68 and 245 long non-coding RNAs were recognized abnormally expressed in cloned 2-cell embryos and cloned blastocysts, respectively. Furthermore, we found that incomplete RNA-editing occurred in cloned embryos and might be caused by decreased ADAR expression. In conclusion, our study revealed the abnormal transcripts and deficient RNA-editing sites in cloned embryos and provided new data for further mechanistic studies of somatic nuclear reprogramming.
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Affiliation(s)
- Lei Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Mengying Yu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Hongyu Xu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Xing Wei
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Yingxiang Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Chenyang Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Huanhuan Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling, China; Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, Yangling, Shaanxi Province 712100, China.
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8
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Le Gall J, Nizon M, Pichon O, Andrieux J, Audebert-Bellanger S, Baron S, Beneteau C, Bilan F, Boute O, Busa T, Cormier-Daire V, Ferec C, Fradin M, Gilbert-Dussardier B, Jaillard S, Jønch A, Martin-Coignard D, Mercier S, Moutton S, Rooryck C, Schaefer E, Vincent M, Sanlaville D, Le Caignec C, Jacquemont S, David A, Isidor B. Sex chromosome aneuploidies and copy-number variants: a further explanation for neurodevelopmental prognosis variability? Eur J Hum Genet 2017; 25:930-934. [PMID: 28612834 PMCID: PMC5567159 DOI: 10.1038/ejhg.2017.93] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 01/19/2023] Open
Abstract
Sex chromosome aneuploidies (SCA) is a group of conditions in which individuals have an abnormal number of sex chromosomes. SCA, such as Klinefelter's syndrome, XYY syndrome, and Triple X syndrome are associated with a large range of neurological outcome. Another genetic event such as another cytogenetic abnormality may explain a part of this variable expressivity. In this study, we have recruited fourteen patients with intellectual disability or developmental delay carrying SCA associated with a copy-number variant (CNV). In our cohort (four patients 47,XXY, four patients 47,XXX, and six patients 47,XYY), seven patients were carrying a pathogenic CNV, two a likely pathogenic CNV and five a variant of uncertain significance. Our analysis suggests that CNV might be considered as an additional independent genetic factor for intellectual disability and developmental delay for patients with SCA and neurodevelopmental disorder.
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Affiliation(s)
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | | | - Joris Andrieux
- Laboratoire de Génétique Médicale, CHRU Lille, Lille, France
| | | | - Sabine Baron
- Service d’endocrinologie Pédiatrique, CHU Nantes, Nantes, France
| | | | - Frédéric Bilan
- Service de Génétique, CHU Poitiers, France; EA 3808 Université Poitiers, France
| | - Odile Boute
- Génétique Médicale, CHRU Lille, Lille, France
| | - Tiffany Busa
- Génétique Médicale, CHU Timone Enfants, AP-HM, Marseille, France
| | | | - Claude Ferec
- Laboratoire de Génétique Moléculaire et d'histocompatibilité, CHU Brest, Brest, France
| | | | | | | | - Aia Jønch
- Service de Génétique Médicale, CHU Vaudois, Lausanne, Switzerland
| | | | - Sandra Mercier
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | | | | | - Elise Schaefer
- Service de Génétique Médicale, CHU Strasbourg, Strasbourg, France
| | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | | | | | | | - Albert David
- Service de Génétique Médicale, CHU Nantes, Nantes, France
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9
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McCusker CD, Athippozhy A, Diaz-Castillo C, Fowlkes C, Gardiner DM, Voss SR. Positional plasticity in regenerating Amybstoma mexicanum limbs is associated with cell proliferation and pathways of cellular differentiation. BMC DEVELOPMENTAL BIOLOGY 2015; 15:45. [PMID: 26597593 PMCID: PMC4657325 DOI: 10.1186/s12861-015-0095-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/16/2015] [Indexed: 01/07/2023]
Abstract
Background The endogenous ability to dedifferentiate, re-pattern, and re-differentiate adult cells to repair or replace damaged or missing structures is exclusive to only a few tetrapod species. The Mexican axolotl is one example of these species, having the capacity to regenerate multiple adult structures including their limbs by generating a group of progenitor cells, known as the blastema, which acquire pattern and differentiate into the missing tissues. The formation of a limb regenerate is dependent on cells in the connective tissues that retain memory of their original position in the limb, and use this information to generate the pattern of the missing structure. Observations from recent and historic studies suggest that blastema cells vary in their potential to pattern distal structures during the regeneration process; some cells are plastic and can be reprogrammed to obtain new positional information while others are stable. Our previous studies showed that positional information has temporal and spatial components of variation; early bud (EB) and apical late bud (LB) blastema cells are plastic while basal-LB cells are stable. To identify the potential cellular and molecular basis of this variation, we compared these three cell populations using histological and transcriptional approaches. Results Histologically, the basal-LB sample showed greater tissue organization than the EB and apical-LB samples. We also observed that cell proliferation was more abundant in EB and apical-LB tissue when compared to basal-LB and mature stump tissue. Lastly, we found that genes associated with cellular differentiation were expressed more highly in the basal-LB samples. Conclusions Our results characterize histological and transcriptional differences between EB and apical-LB tissue compared to basal-LB tissue. Combined with our results from a previous study, we hypothesize that the stability of positional information is associated with tissue organization, cell proliferation, and pathways of cellular differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12861-015-0095-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Antony Athippozhy
- Department of Biology, Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40506, USA.
| | - Carlos Diaz-Castillo
- Department of Developmental and Cellular Biology, University of California, Irvine, CA, 92602, USA.
| | - Charless Fowlkes
- Donald Bren School of Information and Computer Science, University of California, Irvine, CA, 92602, USA.
| | - David M Gardiner
- Department of Developmental and Cellular Biology, University of California, Irvine, CA, 92602, USA.
| | - S Randal Voss
- Department of Biology, Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40506, USA.
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10
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Calvel P, Kusz-Zamelczyk K, Makrythanasis P, Janecki D, Borel C, Conne B, Vannier A, Béna F, Gimelli S, Fichna P, Antonarakis SE, Nef S, Jaruzelska J. A Case of Wiedemann-Steiner Syndrome Associated with a 46,XY Disorder of Sexual Development and Gonadal Dysgenesis. Sex Dev 2015; 9:289-95. [DOI: 10.1159/000441512] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2015] [Indexed: 11/19/2022] Open
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11
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Gulkovskyi RV, Chernushyn SY, Kravchenko SA, Livshits LA. ZNF527 gene rs386809049 analysis in population of ukraine. CYTOL GENET+ 2015. [DOI: 10.3103/s0095452715040040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Vander Pluym JH, O'Sullivan J, Andrew G, Bolduc FV. Genomic characterization of chromosome 8 pericentric trisomy. Clin Case Rep 2015; 3:570-7. [PMID: 26273445 PMCID: PMC4527799 DOI: 10.1002/ccr3.234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/29/2015] [Indexed: 11/10/2022] Open
Abstract
We present a patient with trisomy 8p11.21q11.21 associated with language, gross motor, fine motor, and cognitive delay. Furthermore, using array-based comparative genomic hybridization, we identify the specific genes duplicated in our patient.
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Affiliation(s)
- Juliana H Vander Pluym
- Division of Pediatric Neuroscience, Stollery Children Hospital, University of Alberta Edmonton, Alberta, Canada
| | - Julia O'Sullivan
- Division of Pediatric Neuroscience, Stollery Children Hospital, University of Alberta Edmonton, Alberta, Canada
| | - Gail Andrew
- Division of Neurodevelopmental and Neuromotor Pediatrics, University of Alberta Edmonton, Alberta, Canada
| | - Francois V Bolduc
- Division of Pediatric Neuroscience, Stollery Children Hospital, University of Alberta Edmonton, Alberta, Canada ; Neuroscience and Mental Health Institute, University of Alberta Edmonton, Alberta, Canada
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13
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Melo JB, Estevinho A, Saraiva J, Ramos L, Carreira IM. Cutis Aplasia as a clinical hallmark for the syndrome associated with 19q13.11 deletion: the possible role for UBA2 gene. Mol Cytogenet 2015; 8:21. [PMID: 25883683 PMCID: PMC4399573 DOI: 10.1186/s13039-015-0123-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/25/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wide genome screening through array comparative genomic hybridization made possible the recognition of the novel 19q13.11 deletion syndrome. There are very few cases reported with this deletion, but clinically this condition seems to be recognizable by pre and postnatal growth retardation, microcephaly, developmental delay/intellectual disabilities, speech disturbance, hypospadias (in males) and signs of ectodermal dysplasia and cutis aplasia over the posterior occiput. RESULTS Using oligoarray CGH, a 4.6 Mb deletion in 19q13.11q13.12 was detected in a 23 year old female patient that presented clinical features previously associated with 19q13.11 deletion. CONCLUSIONS Our work reinforces the idea that a region encompassing four zinc finger genes is likely to be responsible for the syndrome, and that the difference in minor clinical manifestation depends on the genes present outside the minimal overlapping region proposed for this syndrome. We also review all cases described in the literature and discuss the correlation between haploinsufficiency of UBA2 gene and cutis aplasia present in the majority of the patients reported, and its importance as a clinical hallmark of 19q13.11 deletion syndrome, when associated with more common features like developmental delay, microcephaly, speech disturbance and hypospadias in males.
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Affiliation(s)
- Joana B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal ; CIMAGO - Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal ; CNC - IBILI - Center of Neurosciences - Institute for Biomedical Imaging and Life Sciences, Coimbra, Portugal
| | - Alexandra Estevinho
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal ; CIMAGO - Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Jorge Saraiva
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal ; University Clinic of Pediatrics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Lina Ramos
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Isabel M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal ; CIMAGO - Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal ; CNC - IBILI - Center of Neurosciences - Institute for Biomedical Imaging and Life Sciences, Coimbra, Portugal
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14
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Diagnostic Yield of Chromosomal Microarray Analysis in a Cohort of Patients with Autism Spectrum Disorders from a Highly Consanguineous Population. J Autism Dev Disord 2015; 45:2323-8. [DOI: 10.1007/s10803-015-2394-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Agha Z, Iqbal Z, Azam M, Ayub H, Vissers LELM, Gilissen C, Ali SHB, Riaz M, Veltman JA, Pfundt R, van Bokhoven H, Qamar R. Exome sequencing identifies three novel candidate genes implicated in intellectual disability. PLoS One 2014; 9:e112687. [PMID: 25405613 PMCID: PMC4236113 DOI: 10.1371/journal.pone.0112687] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/10/2014] [Indexed: 01/07/2023] Open
Abstract
Intellectual disability (ID) is a major health problem mostly with an unknown etiology. Recently exome sequencing of individuals with ID identified novel genes implicated in the disease. Therefore the purpose of the present study was to identify the genetic cause of ID in one syndromic and two non-syndromic Pakistani families. Whole exome of three ID probands was sequenced. Missense variations in two plausible novel genes implicated in autosomal recessive ID were identified: lysine (K)-specific methyltransferase 2B (KMT2B), zinc finger protein 589 (ZNF589), as well as hedgehog acyltransferase (HHAT) with a de novo mutation with autosomal dominant mode of inheritance. The KMT2B recessive variant is the first report of recessive Kleefstra syndrome-like phenotype. Identification of plausible causative mutations for two recessive and a dominant type of ID, in genes not previously implicated in disease, underscores the large genetic heterogeneity of ID. These results also support the viewpoint that large number of ID genes converge on limited number of common networks i.e. ZNF589 belongs to KRAB-domain zinc-finger proteins previously implicated in ID, HHAT is predicted to affect sonic hedgehog, which is involved in several disorders with ID, KMT2B associated with syndromic ID fits the epigenetic module underlying the Kleefstra syndromic spectrum. The association of these novel genes in three different Pakistani ID families highlights the importance of screening these genes in more families with similar phenotypes from different populations to confirm the involvement of these genes in pathogenesis of ID.
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Affiliation(s)
- Zehra Agha
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan
| | - Zafar Iqbal
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Maleeha Azam
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Humaira Ayub
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Lisenka E. L. M. Vissers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Syeda Hafiza Benish Ali
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Moeen Riaz
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Joris A. Veltman
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Cognitive Neurosciences, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- * E-mail: (HvB); (RQ)
| | - Raheel Qamar
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
- Department of Biochemistry, Al-Nafees Medical College & Hospital, Isra University, Islamabad, Pakistan
- * E-mail: (HvB); (RQ)
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16
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Reiff RE, Ali BR, Baron B, Yu TW, Ben-Salem S, Coulter ME, Schubert CR, Hill RS, Akawi NA, Al-Younes B, Kaya N, Evrony GD, Al-Saffar M, Felie JM, Partlow JN, Sunu CM, Schembri-Wismayer P, Alkuraya FS, Meyer BF, Walsh CA, Al-Gazali L, Mochida GH. METTL23, a transcriptional partner of GABPA, is essential for human cognition. Hum Mol Genet 2014; 23:3456-66. [PMID: 24501276 PMCID: PMC4049305 DOI: 10.1093/hmg/ddu054] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/12/2013] [Accepted: 01/31/2014] [Indexed: 02/06/2023] Open
Abstract
Whereas many genes associated with intellectual disability (ID) encode synaptic proteins, transcriptional defects leading to ID are less well understood. We studied a large, consanguineous pedigree of Arab origin with seven members affected with ID and mild dysmorphic features. Homozygosity mapping and linkage analysis identified a candidate region on chromosome 17 with a maximum multipoint logarithm of odds score of 6.01. Targeted high-throughput sequencing of the exons in the candidate region identified a homozygous 4-bp deletion (c.169_172delCACT) in the METTL23 (methyltransferase like 23) gene, which is predicted to result in a frameshift and premature truncation (p.His57Valfs*11). Overexpressed METTL23 protein localized to both nucleus and cytoplasm, and physically interacted with GABPA (GA-binding protein transcription factor, alpha subunit). GABP, of which GABPA is a component, is known to regulate the expression of genes such as THPO (thrombopoietin) and ATP5B (ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide) and is implicated in a wide variety of important cellular functions. Overexpression of METTL23 resulted in increased transcriptional activity at the THPO promoter, whereas knockdown of METTL23 with siRNA resulted in decreased expression of ATP5B, thus revealing the importance of METTL23 as a regulator of GABPA function. The METTL23 mutation highlights a new transcriptional pathway underlying human intellectual function.
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Affiliation(s)
- Rachel E Reiff
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences
| | - Byron Baron
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, Msida MSD2080, Malta
| | - Timothy W Yu
- Division of Genetics and Genomics, Department of Medicine Department of Pediatrics Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA Program in Medical and Population Genetics, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Salma Ben-Salem
- Department of Pathology, College of Medicine and Health Sciences
| | - Michael E Coulter
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Christian R Schubert
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics Research Laboratory of Electronics and Department of Electrical Engineering and Computer Science, Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Nadia A Akawi
- Department of Pathology, College of Medicine and Health Sciences
| | - Banan Al-Younes
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Gilad D Evrony
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Program in Biological and Biomedical Sciences and
| | - Muna Al-Saffar
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al-Ain, United Arab Emirates
| | - Jillian M Felie
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jennifer N Partlow
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christine M Sunu
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pierre Schembri-Wismayer
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, Msida MSD2080, Malta
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics Department of Neurology, Harvard Medical School, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al-Ain, United Arab Emirates
| | - Ganeshwaran H Mochida
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Department of Pediatrics Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
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17
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Kambouris M, Maroun RC, Ben-Omran T, Al-Sarraj Y, Errafii K, Ali R, Boulos H, Curmi PA, El-Shanti H. Mutations in zinc finger 407 [ZNF407] cause a unique autosomal recessive cognitive impairment syndrome. Orphanet J Rare Dis 2014; 9:80. [PMID: 24907849 PMCID: PMC4070100 DOI: 10.1186/1750-1172-9-80] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 05/29/2014] [Indexed: 01/14/2023] Open
Abstract
Background A consanguineous Arab family is affected by an apparently novel autosomal recessive disorder characterized by cognitive impairment, failure-to-thrive, hypotonia and dysmorphic features including bilateral ptosis and epicanthic folds, synophrys, midface hypoplasia, downturned mouth corners, thin upper vermillion border and prominent ears, bilateral 5th finger camptodactyly, bilateral short 4th metatarsal bones, and limited knee mobility bilaterally. Methods The family was studied by homozygosity mapping, candidate gene mutation screening and whole Exome Next Generation Sequencing of a single affected member to identify the offending gene and mutation. The mutated gene product was studied by structural bioinformatics methods. Results A damaging c.C5054G mutation affecting an evolutionary highly conserved amino acid p.S1685W was identified in the ZNF407 gene at 18q23. The Serine to Tryptophane mutation affects two of the three ZNF407 isoforms and is located in the last third of the protein, in a linker peptide adjoining two zinc-finger domains. Structural analyses of this mutation shows disruption of an H-bond that locks the relative spatial position of the two fingers, leading to a higher flexibility of the linker and thus to a decreased probability of binding to the target DNA sequence essentially eliminating the functionality of downstream domains and interfering with the expression of various genes under ZNF407 control during fetal brain development. Conclusions ZNF407 is a transcription factor with an essential role in brain development. When specific and limited in number homozygosity intervals exist that harbor the offending gene in consanguineous families, Whole Exome Sequencing of a single affected individual is an efficient approach to gene mapping and mutation identification.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hatem El-Shanti
- Qatar Biomedical Research Institute, Medical Genetics Center, 69 Lusail Street, West Bay Area, P,O, Box: 33123, Doha, Qatar.
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18
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Schuurs-Hoeijmakers JHM, Vulto-van Silfhout AT, Vissers LELM, van de Vondervoort IIGM, van Bon BWM, de Ligt J, Gilissen C, Hehir-Kwa JY, Neveling K, del Rosario M, Hira G, Reitano S, Vitello A, Failla P, Greco D, Fichera M, Galesi O, Kleefstra T, Greally MT, Ockeloen CW, Willemsen MH, Bongers EMHF, Janssen IM, Pfundt R, Veltman JA, Romano C, Willemsen MA, van Bokhoven H, Brunner HG, de Vries BBA, de Brouwer APM. Identification of pathogenic gene variants in small families with intellectually disabled siblings by exome sequencing. J Med Genet 2013; 50:802-11. [PMID: 24123876 DOI: 10.1136/jmedgenet-2013-101644] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Intellectual disability (ID) is a common neurodevelopmental disorder affecting 1-3% of the general population. Mutations in more than 10% of all human genes are considered to be involved in this disorder, although the majority of these genes are still unknown. OBJECTIVES We investigated 19 small non-consanguineous families with two to five affected siblings in order to identify pathogenic gene variants in known, novel and potential ID candidate genes. Non-consanguineous families have been largely ignored in gene identification studies as small family size precludes prior mapping of the genetic defect. METHODS AND RESULTS Using exome sequencing, we identified pathogenic mutations in three genes, DDHD2, SLC6A8, and SLC9A6, of which the latter two have previously been implicated in X-linked ID phenotypes. In addition, we identified potentially pathogenic mutations in BCORL1 on the X-chromosome and in MCM3AP, PTPRT, SYNE1, and ZNF528 on autosomes. CONCLUSIONS We show that potentially pathogenic gene variants can be identified in small, non-consanguineous families with as few as two affected siblings, thus emphasising their value in the identification of syndromic and non-syndromic ID genes.
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19
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Parkel S, Lopez-Atalaya JP, Barco A. Histone H3 lysine methylation in cognition and intellectual disability disorders. Learn Mem 2013; 20:570-9. [PMID: 24045506 DOI: 10.1101/lm.029363.112] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Recent research indicates that epigenetic mechanisms and, in particular, the post-translational modification (PTM) of histones may contribute to memory encoding and storage. Among the dozens of possible histone PTMs, the methylation/demethylation of lysines in the N-terminal tail of histone H3 exhibits particularly strong links with cognitive abilities. First, the persistence and tight association with distinct transcriptional states of the gene make these modifications particularly suitable for being part of the molecular underpinnings of memory storage. Second, correlative evidence indicates that the methylation/demethylation of lysines in histone H3 is actively regulated during memory processes. Third, several enzymes regulating these PTMs are associated with intellectual disability disorders. We review here these three lines of evidence and discuss the potential role of epigenetic mechanisms centered on the methylation of lysine residues on histone H3 in neuroplasticity and neurodevelopmental disorders associated with intellectual disability.
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Affiliation(s)
- Sven Parkel
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant 03550, Alicante, Spain
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20
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Willemsen M, Kleefstra T. Making headway with genetic diagnostics of intellectual disabilities. Clin Genet 2013; 85:101-10. [DOI: 10.1111/cge.12244] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/24/2013] [Accepted: 07/24/2013] [Indexed: 01/31/2023]
Affiliation(s)
- M.H. Willemsen
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen The Netherlands
| | - T. Kleefstra
- Department of Human Genetics; Radboud University Medical Centre; Nijmegen The Netherlands
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21
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Piton A, Redin C, Mandel JL. XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing. Am J Hum Genet 2013; 93:368-83. [PMID: 23871722 DOI: 10.1016/j.ajhg.2013.06.013] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 05/29/2013] [Accepted: 06/08/2013] [Indexed: 12/30/2022] Open
Abstract
Because of the unbalanced sex ratio (1.3-1.4 to 1) observed in intellectual disability (ID) and the identification of large ID-affected families showing X-linked segregation, much attention has been focused on the genetics of X-linked ID (XLID). Mutations causing monogenic XLID have now been reported in over 100 genes, most of which are commonly included in XLID diagnostic gene panels. Nonetheless, the boundary between true mutations and rare non-disease-causing variants often remains elusive. The sequencing of a large number of control X chromosomes, required for avoiding false-positive results, was not systematically possible in the past. Such information is now available thanks to large-scale sequencing projects such as the National Heart, Lung, and Blood (NHLBI) Exome Sequencing Project, which provides variation information on 10,563 X chromosomes from the general population. We used this NHLBI cohort to systematically reassess the implication of 106 genes proposed to be involved in monogenic forms of XLID. We particularly question the implication in XLID of ten of them (AGTR2, MAGT1, ZNF674, SRPX2, ATP6AP2, ARHGEF6, NXF5, ZCCHC12, ZNF41, and ZNF81), in which truncating variants or previously published mutations are observed at a relatively high frequency within this cohort. We also highlight 15 other genes (CCDC22, CLIC2, CNKSR2, FRMPD4, HCFC1, IGBP1, KIAA2022, KLF8, MAOA, NAA10, NLGN3, RPL10, SHROOM4, ZDHHC15, and ZNF261) for which replication studies are warranted. We propose that similar reassessment of reported mutations (and genes) with the use of data from large-scale human exome sequencing would be relevant for a wide range of other genetic diseases.
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Affiliation(s)
- Amélie Piton
- Department of Translational Medicine and Neurogenetics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7104, Institut National de la Santé et de la Recherche Médicale Unité 964, University of Strasbourg, 67404 Illkirch Cedex, France; Chaire de Génétique Humaine, Collège de France, 75231 Paris Cedex 05, France.
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Ganesamoorthy D, Bruno DL, McGillivray G, Norris F, White SM, Adroub S, Amor DJ, Yeung A, Oertel R, Pertile MD, Ngo C, Arvaj AR, Walker S, Charan P, Palma-Dias R, Woodrow N, Slater HR. Meeting the challenge of interpreting high-resolution single nucleotide polymorphism array data in prenatal diagnosis: does increased diagnostic power outweigh the dilemma of rare variants? BJOG 2013; 120:594-606. [PMID: 23332022 DOI: 10.1111/1471-0528.12150] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2012] [Indexed: 01/14/2023]
Abstract
OBJECTIVE Several studies have already shown the superiority of chromosomal microarray analysis (CMA) compared with conventional karyotyping for prenatal investigation of fetal ultrasound abnormality. This study used very high-resolution single nucleotide polymorphism (SNP) arrays to determine the impact on detection rates of all clinical categories of copy number variations (CNVs), and address the issue of interpreting and communicating findings of uncertain or unknown clinical significance, which are to be expected at higher frequency when using very high-resolution CMA. DESIGN Prospective validation study. SETTING Tertiary clinical genetics centre. POPULATION Women referred for further investigation of fetal ultrasound anomaly. METHODS We prospectively tested 104 prenatal samples using both conventional karyotyping and high-resolution arrays. MAIN OUTCOME MEASURES The detection rates for each clinical category of CNV. RESULTS Unequivocal pathogenic CNVs were found in six cases, including one with uniparental disomy (paternal UPD 14). A further four cases had a 'likely pathogenic' finding. Overall, CMA improved the detection of 'pathogenic' and 'likely pathogenic' abnormalities from 2.9% (3/104) to 9.6% (10/104). CNVs of 'unknown' clinical significance that presented interpretational difficulties beyond results from parental investigations were detected in 6.7% (7/104) of samples. CONCLUSIONS Increased detection sensitivity appears to be the main benefit of high-resolution CMA. Despite this, in this cohort there was no significant benefit in terms of improving detection of small pathogenic CNVs. A potential disadvantage is the high detection rate of CNVs of 'unknown' clinical significance. These findings emphasise the importance of establishing an evidence-based policy for the interpretation and reporting of CNVs, and the need to provide appropriate pre- and post-test counselling.
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Affiliation(s)
- D Ganesamoorthy
- VCGS Cytogenetics Laboratory, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
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23
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Lo-Castro A, Brancati F, Digilio MC, Garaci FG, Bollero P, Alfieri P, Curatolo P. Neurobehavioral phenotype observed in KBG syndrome caused by ANKRD11 mutations. Am J Med Genet B Neuropsychiatr Genet 2013. [PMID: 23184435 DOI: 10.1002/ajmg.b.32113] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
KBG syndrome is a rare disease characterized by typical facial dysmorphism, macrodontia of upper central incisors, skeletal abnormalities, and developmental delay. Recently, mutations in ANKRD11 gene have been identified in a subset of patients with KBG syndrome, while a contiguous gene deletion syndrome involving 16q24.3 region (including ANKRD11) was delineated in patients with facial dysmorphism, autism, intellectual disability, and brain abnormalities. Although numerous evidences point to a central causative role of ANKRD11 in the neurologic features of these patients, their neurocognitive and behavior phenotypes are still poorly characterized. Herein, we report the complete neurological and psychiatric features observed in two patients with KBG syndrome due to ANKRD11 mutations. Both patients show intellectual disabilities, severe impairment in communication skills, deficits in several aspects of executive functions and working memory and anxious traits. Their features are compared with those of previously reported patients with KBG syndrome aiding in the delineation of neurocognitive phenotype associated to ANKRD11 mutations.
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Affiliation(s)
- Adriana Lo-Castro
- Department of Neuroscience, Child Neurology and Psychiatry Unit, Tor Vergata University Hospital, Rome, Italy
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24
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Ren CM, Liang Y, Wei F, Zhang YN, Zhong SQ, Gu H, Dong XS, Huang YY, Ke H, Son XM, Tang D, Chen Z. Balanced translocation t(3;18)(p13;q22.3) and points mutation in the ZNF407 gene detected in patients with both moderate non-syndromic intellectual disability and autism. Biochim Biophys Acta Mol Basis Dis 2012. [PMID: 23195952 DOI: 10.1016/j.bbadis.2012.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Intellectual disability (ID) is a common disease. While the etiology remains incompletely understood, genetic defects are a major contributor, which include mutations in genes encoding zinc finger proteins. These proteins modulate gene expression via binding to DNA. Consistent with this knowledge, we report here the identification of mutations in the ZNF407 gene in ID/autistic patients. In our study of an ID patient with autism, a reciprocal translocation 46,XY,t(3;18)(p13;q22.3) was detected. By using FISH and long-range PCR approaches, we have precisely mapped the breakpoints associated with this translocation in a gene-free region in chromosome 3 and in the third intron of the ZNF407 gene in chromosome18. The latter reduces ZNF407 expression. Consistent with this observation, in our subsequent investigation of 105 ID/autism patients with similar clinical presentations, two missense mutations Y460C and P1195A were identified. These mutations cause non-conservative amino acid substitutions in the linker regions between individual finger structures. In line with the linker regions being critical for the integrity of zinc finger motifs, both mutations may result in loss of ZNF407 function. Taken together, we demonstrate that mutations in the ZNF407 gene contribute to the pathogenesis of a group of ID patients with autism.
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Affiliation(s)
- Cong-mian Ren
- Department of Medical Genetics, Sun Yat-sen University, Guangzhou, People's Republic of China
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25
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Willemsen MH, de Leeuw N, de Brouwer AP, Pfundt R, Hehir-Kwa JY, Yntema HG, Nillesen WM, de Vries BB, van Bokhoven H, Kleefstra T. Interpretation of clinical relevance of X-chromosome copy number variations identified in a large cohort of individuals with cognitive disorders and/or congenital anomalies. Eur J Med Genet 2012; 55:586-98. [DOI: 10.1016/j.ejmg.2012.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 05/05/2012] [Accepted: 05/05/2012] [Indexed: 01/01/2023]
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26
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Ferreira SI, Matoso E, Venâncio M, Saraiva J, Melo JB, Carreira IM. Critical region in 2q31.2q32.3 deletion syndrome: Report of two phenotypically distinct patients, one with an additional deletion in Alagille syndrome region. Mol Cytogenet 2012; 5:25. [PMID: 22550961 PMCID: PMC3460744 DOI: 10.1186/1755-8166-5-25] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 04/17/2012] [Indexed: 12/04/2022] Open
Abstract
Background Standard cytogenetic analysis has revealed to date more than 30 reported cases presenting interstitial deletions involving region 2q31-q32, but with poorly defined breakpoints. After the postulation of 2q31.2q32.3 deletion as a clinically recognizable disorder, more patients were reported with a critical region proposed and candidate genes pointed out. Results We report two female patients with de novo chromosome 2 cytogenetically visible deletions, one of them with an additional de novo deletion in chromosome 20p12.2p12.3. Patient I presents a 16.8 Mb deletion in 2q31.2q32.3 while patient II presents a smaller deletion of 7 Mb in 2q32.1q32.3, entirely contained within patient I deleted region, and a second 4 Mb deletion in Alagille syndrome region. Patient I clearly manifests symptoms associated with the 2q31.2q32.3 deletion syndrome, like the muscular phenotype and behavioral problems, while patient II phenotype is compatible with the 20p12 deletion since she manifests problems at the cardiac level, without significant dysmorphisms and an apparently normal psychomotor development. Conclusions Whereas Alagille syndrome is a well characterized condition mainly caused by haploinsufficiency of JAG1 gene, with manifestations that can range from slight clinical findings to major symptoms in different domains, the 2q31.2q32.3 deletion syndrome is still being delineated. The occurrence of both imbalances in reported patient II would be expected to cause a more severe phenotype compared to the individual phenotype associated with each imbalance, which is not the case, since there are no manifestations due to the 2q32 deletion. This, together with the fact that patient I deleted region overlaps previously reported cases and patient II deletion is outside this common region, reinforces the existence of a critical region in 2q31.3q32.1, between 181 to 185 Mb, responsible for the clinical phenotype.
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Affiliation(s)
- Susana Isabel Ferreira
- Laboratório de Citogenética e Genómica - Faculty of Medicine, University of Coimbra, Coimbra, Portugal.
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27
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Meda SA, Narayanan B, Liu J, Perrone-Bizzozero NI, Stevens MC, Calhoun VD, Glahn DC, Shen L, Risacher SL, Saykin AJ, Pearlson GD. A large scale multivariate parallel ICA method reveals novel imaging-genetic relationships for Alzheimer's disease in the ADNI cohort. Neuroimage 2012; 60:1608-21. [PMID: 22245343 DOI: 10.1016/j.neuroimage.2011.12.076] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 12/16/2011] [Accepted: 12/19/2011] [Indexed: 11/16/2022] Open
Abstract
The underlying genetic etiology of late onset Alzheimer's disease (LOAD) remains largely unknown, likely due to its polygenic architecture and a lack of sophisticated analytic methods to evaluate complex genotype-phenotype models. The aim of the current study was to overcome these limitations in a bi-multivariate fashion by linking intermediate magnetic resonance imaging (MRI) phenotypes with a genome-wide sample of common single nucleotide polymorphism (SNP) variants. We compared associations between 94 different brain regions of interest derived from structural MRI scans and 533,872 genome-wide SNPs using a novel multivariate statistical procedure, parallel-independent component analysis, in a large, national multi-center subject cohort. The study included 209 elderly healthy controls, 367 subjects with amnestic mild cognitive impairment and 181 with mild, early-stage LOAD, all of them Caucasian adults, from the Alzheimer's Disease Neuroimaging Initiative cohort. Imaging was performed on comparable 1.5 T scanners at over 50 sites in the USA/Canada. Four primary "genetic components" were associated significantly with a single structural network including all regions involved neuropathologically in LOAD. Pathway analysis suggested that each component included several genes already known to contribute to LOAD risk (e.g. APOE4) or involved in pathologic processes contributing to the disorder, including inflammation, diabetes, obesity and cardiovascular disease. In addition significant novel genes identified included ZNF673, VPS13, SLC9A7, ATP5G2 and SHROOM2. Unlike conventional analyses, this multivariate approach identified distinct groups of genes that are plausibly linked in physiologic pathways, perhaps epistatically. Further, the study exemplifies the value of this novel approach to explore large-scale data sets involving high-dimensional gene and endophenotype data.
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Affiliation(s)
- Shashwath A Meda
- Olin Neuropsychiatric Research Center, Hartford Hospital/IOL, Hartford, CT 06106, USA.
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28
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Delphin N, Hanein S, Taie LF, Zanlonghi X, Bonneau D, Moisan JP, Boyle C, Nitschke P, Pruvost S, Bonnefont JP, Munnich A, Roche O, Kaplan J, Rozet JM. Intellectual disability associated with retinal dystrophy in the Xp11.3 deletion syndrome: ZNF674 on trial. Guilty or innocent? Eur J Hum Genet 2011; 20:352-6. [PMID: 22126752 DOI: 10.1038/ejhg.2011.217] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
X-linked retinal dystrophies (XLRD) are listed among the most severe RD owing to their early onset, leading to significant visual loss before the age of 30. One-third of XLRD are accounted for by RP2 mutations at the Xp11.23 locus. Deletions of ca. 1.2 Mb in the Xp11.3-p11.23 region have been previously reported in two independent families segregating XLRD with intellectual disability (ID). Although the RD was ascribed to the deletion of RP2, the ID was suggested to be accounted for by the loss of ZNF674, which mutations were independently reported to account for isolated XLID. Here, we report deletions in the Xp11.3-p11.23 region responsible for the loss of ZNF674 in two unrelated families segregating XLRD, but no ID, identified by chromosomal microarray analysis. These findings question the responsibility of ZNF674 deletions in ID associated with X-linked retinal dystrophy.
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Affiliation(s)
- Nathalie Delphin
- INSERM U781 - Department of Genetics/Fondation IMAGINE and Paris Descartes University, CHU Necker Enfants Malades, Paris, France
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29
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Biparental inheritance of chromosomal abnormalities in male twins with non-syndromic mental retardation. Eur J Med Genet 2011; 54:e383-8. [PMID: 21426945 DOI: 10.1016/j.ejmg.2011.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Accepted: 03/14/2011] [Indexed: 01/22/2023]
Abstract
In a monozygotic twin couple with mental retardation (MR), we identified a maternally inherited inversion and a paternally inherited translocation: 46,XY,inv(10)(p11.2q21.2)mat,t(9;18)(p22;q21.1)pat. The maternally inherited inv(10) was a benign variant without any apparent phenotypical implications. The translocation breakpoint at 9p was within a cluster of interferon α genes and the 18q21 breakpoint truncated ZBTB7C (zinc finger and BTB containing 7C gene). In addition, analyses with array-CGH revealed a 931 kb maternally inherited deletion on chromosome 8q22 as well as an 875 kb maternally inherited duplication on 5p14. The deletion encompasses the RIM2 (Rab3A-interacting molecule 2), FZD6 (Frizzled homolog 6) and BAALC (Brain and Acute Leukemia Gene, Cytoplasmic) genes and the duplication includes the 5' end of the CDH9 (cadherin 9) gene. Exome sequencing did not reveal any additional mutations that could explain the MR phenotype. The protein products of the above mentioned genes are involved in different aspects of brain development and/or maintenance of the neurons which suggest that accumulation of genetic defects segregating from both parents might be the basis of MR in the twins. This hypothesis was further supported by protein interaction analysis.
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30
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Betancur C. Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting. Brain Res 2010; 1380:42-77. [PMID: 21129364 DOI: 10.1016/j.brainres.2010.11.078] [Citation(s) in RCA: 578] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/22/2010] [Accepted: 11/23/2010] [Indexed: 12/31/2022]
Abstract
There is increasing evidence that autism spectrum disorders (ASDs) can arise from rare highly penetrant mutations and genomic imbalances. The rare nature of these variants, and the often differing orbits of clinical and research geneticists, can make it difficult to fully appreciate the extent to which we have made progress in understanding the genetic etiology of autism. In fact, there is a persistent view in the autism research community that there are only a modest number of autism loci known. We carried out an exhaustive review of the clinical genetics and research genetics literature in an attempt to collate all genes and recurrent genomic imbalances that have been implicated in the etiology of ASD. We provide data on 103 disease genes and 44 genomic loci reported in subjects with ASD or autistic behavior. These genes and loci have all been causally implicated in intellectual disability, indicating that these two neurodevelopmental disorders share common genetic bases. A genetic overlap between ASD and epilepsy is also apparent in many cases. Taken together, these findings clearly show that autism is not a single clinical entity but a behavioral manifestation of tens or perhaps hundreds of genetic and genomic disorders. Increased recognition of the etiological heterogeneity of ASD will greatly expand the number of target genes for neurobiological investigations and thereby provide additional avenues for the development of pathway-based pharmacotherapy. Finally, the data provide strong support for high-resolution DNA microarrays as well as whole-exome and whole-genome sequencing as critical approaches for identifying the genetic causes of ASDs.
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31
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Filges I, Röthlisberger B, Blattner A, Boesch N, Demougin P, Wenzel F, Huber AR, Heinimann K, Weber P, Miny P. Deletion in Xp22.11: PTCHD1 is a candidate gene for X-linked intellectual disability with or without autism. Clin Genet 2010; 79:79-85. [PMID: 21091464 DOI: 10.1111/j.1399-0004.2010.01590.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Submicroscopic chromosomal anomalies play an important role in the aetiology of intellectual disability (ID) and have been shown to account for up to 10% of non-syndromic forms. We present a family with two affected boys compatible with X-linked inheritance of a phenotype of severe neurodevelopmental disorder co-segregating with a deletion in Xp22.11 exclusively containing the PTCHD1 gene. Although the exact function of this gene is unknown to date, the structural overlap of its encoded patched domain-containing protein 1, the transmembrane protein involved in the sonic hedgehog pathway, and its expression in human cortex and cerebellum as well as in mice and drosophila brain suggests a causative role of its nullisomy in the developmental phenotype of our family. Our findings support the recent notions that PTCHD1 may play a role in X-linked intellectual disability (XLID) and autism disorders.
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Affiliation(s)
- I Filges
- Division of Medical Genetics, University Children's Hospital and Department of Biomedicine, Römergasse 8,Basel, Switzerland.
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32
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Cocchella A, Malacarne M, Forzano F, Marciano C, Pierluigi M, Perroni L, Faravelli F, Di Maria E. The refinement of the critical region for the 2q31.2q32.3 deletion syndrome indicates candidate genes for mental retardation and speech impairment. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:1342-6. [PMID: 20552675 DOI: 10.1002/ajmg.b.31107] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Current literature provides more than 30 patients with interstitial deletions in chromosome 2q31q33. Only a few of them were studied using high-resolution methods. Among these, two patients had presented with a particular consistence of some clinical features associated to a deletion between bands q31.2 and q32.3 of chromosome 2. This clinical pattern, labeled as "2q31.2q32.3 syndrome," consists of multiple dysmorphisms, developmental delay, mental retardation and behavioural disturbances. We report an adult female patient with a 4.4 Mb deletion in the 2q31.2q32.3 region, showing facial dysmorphisms, mental retardation and absence of speech. The region overlaps with the deletion found in the two cases previously reported. The critical region points to a few genes, namely NEUROD1, ZNF804A, PDE1A, and ITGA4, which are good candidates to explain the cognitive and behavioural phenotype, as well as the severe speech impairment associated with the 2q31.2q32.3 deletion.
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33
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Lagali PS, Corcoran CP, Picketts DJ. Hippocampus development and function: role of epigenetic factors and implications for cognitive disease. Clin Genet 2010; 78:321-33. [DOI: 10.1111/j.1399-0004.2010.01503.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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34
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Ramaswamy V, Castillo M, Bolduc FV. Developmental disability: duplication of zinc finger transcription factors 673 and 674. Pediatr Neurol 2010; 43:209-12. [PMID: 20691945 DOI: 10.1016/j.pediatrneurol.2010.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 12/10/2009] [Accepted: 04/26/2010] [Indexed: 01/30/2023]
Abstract
The past decade has witnessed a tremendous increase in our ability to identify precise genetic etiologies of developmental delay and intellectual disability. Mutations in various transcription factors were found in patients with intellectual disability. Specifically, the importance of a subgroup of transcription factors containing zinc finger motifs have been increasingly recognized in developmental delay and intellectual disability. We present a patient with intellectual disability in whom the duplication of two genes, ZNF673 and ZNF674, was identified through array-based comparative genomic hybridization. Our report reinforces the role of zinc finger transcription factors in cognitive development. Furthermore, it illustrates that not only deletions, but duplications, can cause developmental delay and intellectual disability.
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Affiliation(s)
- Vijay Ramaswamy
- Division of Pediatric Neurology, University of Alberta, Edmonton, Alberta, Canada
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35
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Maestrini E, Pagnamenta AT, Lamb JA, Bacchelli E, Sykes NH, Sousa I, Toma C, Barnby G, Butler H, Winchester L, Scerri TS, Minopoli F, Reichert J, Cai G, Buxbaum JD, Korvatska O, Schellenberg GD, Dawson G, Bildt AD, Minderaa RB, Mulder EJ, Morris AP, Bailey AJ, Monaco AP. High-density SNP association study and copy number variation analysis of the AUTS1 and AUTS5 loci implicate the IMMP2L-DOCK4 gene region in autism susceptibility. Mol Psychiatry 2010; 15:954-68. [PMID: 19401682 PMCID: PMC2934739 DOI: 10.1038/mp.2009.34] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 02/19/2009] [Accepted: 04/02/2009] [Indexed: 01/02/2023]
Abstract
Autism spectrum disorders are a group of highly heritable neurodevelopmental disorders with a complex genetic etiology. The International Molecular Genetic Study of Autism Consortium previously identified linkage loci on chromosomes 7 and 2, termed AUTS1 and AUTS5, respectively. In this study, we performed a high-density association analysis in AUTS1 and AUTS5, testing more than 3000 single nucleotide polymorphisms (SNPs) in all known genes in each region, as well as SNPs in non-genic highly conserved sequences. SNP genotype data were also used to investigate copy number variation within these regions. The study sample consisted of 127 and 126 families, showing linkage to the AUTS1 and AUTS5 regions, respectively, and 188 gender-matched controls. Further investigation of the strongest association results was conducted in an independent European family sample containing 390 affected individuals. Association and copy number variant analysis highlighted several genes that warrant further investigation, including IMMP2L and DOCK4 on chromosome 7. Evidence for the involvement of DOCK4 in autism susceptibility was supported by independent replication of association at rs2217262 and the finding of a deletion segregating in a sib-pair family.
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Affiliation(s)
- E Maestrini
- Department of Biology, University of Bologna, Bologna, Italy
| | - A T Pagnamenta
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - J A Lamb
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, UK
| | - E Bacchelli
- Department of Biology, University of Bologna, Bologna, Italy
| | - N H Sykes
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - I Sousa
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - C Toma
- Department of Biology, University of Bologna, Bologna, Italy
| | - G Barnby
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - H Butler
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - L Winchester
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - T S Scerri
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - F Minopoli
- Department of Biology, University of Bologna, Bologna, Italy
| | - J Reichert
- Department of Psychiatry, Seaver Autism Research Center, Mount Sinai School of Medicine, New York, NY, USA
| | - G Cai
- Department of Psychiatry, Seaver Autism Research Center, Mount Sinai School of Medicine, New York, NY, USA
| | - J D Buxbaum
- Department of Psychiatry, Seaver Autism Research Center, Mount Sinai School of Medicine, New York, NY, USA
| | - O Korvatska
- Geriatric Research Education and Clinical Centre, Veterans Affairs Puget Sound Health Care System, Seattle Division, Seattle, WA, USA
| | - G D Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - G Dawson
- Autism Speaks, New York, NY, USA
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - A de Bildt
- Department of Psychiatry, Child and Adolescent Psychiatry, University Medical Center Groningen, Groningen, The Netherlands
| | - R B Minderaa
- Department of Psychiatry, Child and Adolescent Psychiatry, University Medical Center Groningen, Groningen, The Netherlands
| | - E J Mulder
- Department of Psychiatry, Child and Adolescent Psychiatry, University Medical Center Groningen, Groningen, The Netherlands
| | - A P Morris
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - A J Bailey
- University Department of Psychiatry, Warneford Hospital, Oxford, UK
| | - A P Monaco
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - IMGSAC12
- Department of Biology, University of Bologna, Bologna, Italy
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, UK
- Department of Psychiatry, Seaver Autism Research Center, Mount Sinai School of Medicine, New York, NY, USA
- Geriatric Research Education and Clinical Centre, Veterans Affairs Puget Sound Health Care System, Seattle Division, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Autism Speaks, New York, NY, USA
- Department of Psychology, University of Washington, Seattle, WA, USA
- Department of Psychiatry, Child and Adolescent Psychiatry, University Medical Center Groningen, Groningen, The Netherlands
- University Department of Psychiatry, Warneford Hospital, Oxford, UK
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36
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Kaufman L, Ayub M, Vincent JB. The genetic basis of non-syndromic intellectual disability: a review. J Neurodev Disord 2010; 2:182-209. [PMID: 21124998 PMCID: PMC2974911 DOI: 10.1007/s11689-010-9055-2] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 06/25/2010] [Indexed: 11/06/2022] Open
Abstract
Intellectual disability (ID), also referred to as mental retardation (MR), is frequently the result of genetic mutation. Where ID is present together with additional clinical symptoms or physical anomalies, there is often sufficient information available for the diagnosing physician to identify a known syndrome, which may then educe the identification of the causative defect. However, where co-morbid features are absent, narrowing down a specific gene can only be done by ‘brute force’ using the latest molecular genetic techniques. Here we attempt to provide a systematic review of genetic causes of cases of ID where no other symptoms or co-morbid features are present, or non-syndromic ID. We attempt to summarize commonalities between the genes and the molecular pathways of their encoded proteins. Since ID is a common feature of autism, and conversely autistic features are frequently present in individuals with ID, we also look at possible overlaps in genetic etiology with non-syndromic ID.
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Huang S, Wu S, Ding J, Lin J, Wei L, Gu J, He X. MicroRNA-181a modulates gene expression of zinc finger family members by directly targeting their coding regions. Nucleic Acids Res 2010; 38:7211-8. [PMID: 20591824 PMCID: PMC2978345 DOI: 10.1093/nar/gkq564] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small endogenous, non-coding RNAs that specifically bind to the 3' untranslated region (3'UTR) of target genes in animals. However, some recent studies have demonstrated that miRNAs also target the coding regions of mammalian genes. Here, we show that miRNA-181a downregulates the expression of a large number of zinc finger genes (ZNFs). Bioinformatics analysis revealed that these ZNFs contain many miR-181a seed-matched sites within their coding sequences (CDS). In particular, miR-181a 8-mer-matched sequences were mostly localized to the regions coding for the ZNF C2H2 domain. A series of reporter assays confirmed that miR-181a inhibits the expression of ZNFs by directly targeting their CDS. These inhibitory effects might be due to the multiple target sites located within the ZNF genes. In conclusion, our findings indicate that some miRNA species may regulate gene family by targeting their coding regions, thus providing an important and novel perspective for decoding the complex mechanism of miRNA/mRNA interplay.
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Affiliation(s)
- Shenglin Huang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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38
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CAMOS, a nonprogressive, autosomal recessive, congenital cerebellar ataxia, is caused by a mutant zinc-finger protein, ZNF592. Eur J Hum Genet 2010; 18:1107-13. [PMID: 20531441 DOI: 10.1038/ejhg.2010.82] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
CAMOS (Cerebellar Ataxia with Mental retardation, Optic atrophy and Skin abnormalities) is a rare autosomal recessive syndrome characterized by a nonprogressive congenital cerebellar ataxia associated with mental retardation, optic atrophy, and skin abnormalities. Using homozygosity mapping in a large inbred Lebanese Druze family, we previously reported the mapping of the disease gene at chromosome 15q24-q26 to a 3.6-cM interval between markers D15S206 and D15S199. Screening of candidate genes lying in this region led to the identification of a homozygous p.Gly1046Arg missense mutation in ZNF592, in all five affected individuals of the family. ZNF592 encodes a 1267-amino-acid zinc-finger (ZnF) protein, and the mutation, located within the eleventh ZnF, is predicted to affect the DNA-binding properties of ZNF592. Although the precise role of ZNF592 remains to be determined, our results suggest that ZNF592 is implicated in a complex developmental pathway, and that the mutation is likely to disturb the highly orchestrated regulation of genes during cerebellar development, by either disrupting interactions with target DNA or with a partner protein.
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39
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Lugtenberg D, Zangrande-Vieira L, Kirchhoff M, Whibley AC, Oudakker AR, Kjaergaard S, Vianna-Morgante AM, Kleefstra T, Ruiter M, Jehee FS, Ullmann R, Schwartz CE, Stratton M, Raymond FL, Veltman JA, Vrijenhoek T, Pfundt R, Schuurs-Hoeijmakers JHM, Hehir-Kwa JY, Froyen G, Chelly J, Ropers HH, Moraine C, Gècz J, Knijnenburg J, Kant SG, Hamel BCJ, Rosenberg C, van Bokhoven H, de Brouwer APM. Recurrent deletion of ZNF630 at Xp11.23 is not associated with mental retardation. Am J Med Genet A 2010; 152A:638-45. [PMID: 20186789 DOI: 10.1002/ajmg.a.33292] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
ZNF630 is a member of the primate-specific Xp11 zinc finger gene cluster that consists of six closely related genes, of which ZNF41, ZNF81, and ZNF674 have been shown to be involved in mental retardation. This suggests that mutations of ZNF630 might influence cognitive function. Here, we detected 12 ZNF630 deletions in a total of 1,562 male patients with mental retardation from Brazil, USA, Australia, and Europe. The breakpoints were analyzed in 10 families, and in all cases they were located within two segmental duplications that share more than 99% sequence identity, indicating that the deletions resulted from non-allelic homologous recombination. In 2,121 healthy male controls, 10 ZNF630 deletions were identified. In total, there was a 1.6-fold higher frequency of this deletion in males with mental retardation as compared to controls, but this increase was not statistically significant (P-value = 0.174). Conversely, a 1.9-fold lower frequency of ZNF630 duplications was observed in patients, which was not significant either (P-value = 0.163). These data do not show that ZNF630 deletions or duplications are associated with mental retardation.
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Affiliation(s)
- Dorien Lugtenberg
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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40
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Willemsen MH, Fernandez BA, Bacino CA, Gerkes E, de Brouwer APM, Pfundt R, Sikkema-Raddatz B, Scherer SW, Marshall CR, Potocki L, van Bokhoven H, Kleefstra T. Identification of ANKRD11 and ZNF778 as candidate genes for autism and variable cognitive impairment in the novel 16q24.3 microdeletion syndrome. Eur J Hum Genet 2010; 18:429-35. [PMID: 19920853 PMCID: PMC2987261 DOI: 10.1038/ejhg.2009.192] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 09/02/2009] [Accepted: 09/22/2009] [Indexed: 11/09/2022] Open
Abstract
The clinical use of array comparative genomic hybridization in the evaluation of patients with multiple congenital anomalies and/or mental retardation has recently led to the discovery of a number of novel microdeletion and microduplication syndromes. We present four male patients with overlapping molecularly defined de novo microdeletions of 16q24.3. The clinical features observed in these patients include facial dysmorphisms comprising prominent forehead, large ears, smooth philtrum, pointed chin and wide mouth, variable cognitive impairment, autism spectrum disorder, structural anomalies of the brain, seizures and neonatal thrombocytopenia. Although deletions vary in size, the common region of overlap is only 90 kb and comprises two known genes, Ankyrin Repeat Domain 11 (ANKRD11) (MIM 611192) and Zinc Finger 778 (ZNF778), and is located approximately 10 kb distally to Cadherin 15 (CDH15) (MIM 114019). This region is not found as a copy number variation in controls. We propose that these patients represent a novel and distinctive microdeletion syndrome, characterized by autism spectrum disorder, variable cognitive impairment, facial dysmorphisms and brain abnormalities. We suggest that haploinsufficiency of ANKRD11 and/or ZNF778 contribute to this phenotype and speculate that further investigation of non-deletion patients who have features suggestive of this 16q24.3 microdeletion syndrome might uncover other mutations in one or both of these genes.
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Affiliation(s)
- Marjolein H Willemsen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, PO Box 9101, Nijmegen 6500 HB, The Netherlands.
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41
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Lorenz P, Dietmann S, Wilhelm T, Koczan D, Autran S, Gad S, Wen G, Ding G, Li Y, Rousseau-Merck MF, Thiesen HJ. The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues. BMC Genomics 2010; 11:206. [PMID: 20346131 PMCID: PMC2865497 DOI: 10.1186/1471-2164-11-206] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 03/26/2010] [Indexed: 11/17/2022] Open
Abstract
Background Expansion of multi-C2H2 domain zinc finger (ZNF) genes, including the Krüppel-associated box (KRAB) subfamily, paralleled the evolution of tetrapodes, particularly in mammalian lineages. Advances in their cataloging and characterization suggest that the functions of the KRAB-ZNF gene family contributed to mammalian speciation. Results Here, we characterized the human 8q24.3 ZNF cluster on the genomic, the phylogenetic, the structural and the transcriptome level. Six (ZNF7, ZNF34, ZNF250, ZNF251, ZNF252, ZNF517) of the seven locus members contain exons encoding KRAB domains, one (ZNF16) does not. They form a paralog group in which the encoded KRAB and ZNF protein domains generally share more similarities with each other than with other members of the human ZNF superfamily. The closest relatives with respect to their DNA-binding domain were ZNF7 and ZNF251. The analysis of orthologs in therian mammalian species revealed strong conservation and purifying selection of the KRAB-A and zinc finger domains. These findings underscore structural/functional constraints during evolution. Gene losses in the murine lineage (ZNF16, ZNF34, ZNF252, ZNF517) and potential protein truncations in primates (ZNF252) illustrate ongoing speciation processes. Tissue expression profiling by quantitative real-time PCR showed similar but distinct patterns for all tested ZNF genes with the most prominent expression in fetal brain. Based on accompanying expression signatures in twenty-six other human tissues ZNF34 and ZNF250 revealed the closest expression profiles. Together, the 8q24.3 ZNF genes can be assigned to a cerebellum, a testis or a prostate/thyroid subgroup. These results are consistent with potential functions of the ZNF genes in morphogenesis and differentiation. Promoter regions of the seven 8q24.3 ZNF genes display common characteristics like missing TATA-box, CpG island-association and transcription factor binding site (TFBS) modules. Common TFBS modules partly explain the observed expression pattern similarities. Conclusions The ZNF genes at human 8q24.3 form a relatively old mammalian paralog group conserved in eutherian mammals for at least 130 million years. The members persisted after initial duplications by undergoing subfunctionalizations in their expression patterns and target site recognition. KRAB-ZNF mediated repression of transcription might have shaped organogenesis in mammalian ontogeny.
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Affiliation(s)
- Peter Lorenz
- Institute of Immunology, University of Rostock, Schillingallee 70, 18055 Rostock, Germany
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42
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Kleine-Kohlbrecher D, Christensen J, Vandamme J, Abarrategui I, Bak M, Tommerup N, Shi X, Gozani O, Rappsilber J, Salcini AE, Helin K. A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation. Mol Cell 2010; 38:165-78. [PMID: 20346720 PMCID: PMC2989439 DOI: 10.1016/j.molcel.2010.03.002] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Revised: 02/07/2010] [Accepted: 03/09/2010] [Indexed: 01/15/2023]
Abstract
X-linked mental retardation (XLMR) is an inherited disorder that mostly affects males and is caused by mutations in genes located on the X chromosome. Here, we show that the XLMR protein PHF8 and a C. elegans homolog F29B9.2 catalyze demethylation of di- and monomethylated lysine 9 of histone H3 (H3K9me2/me1). The PHD domain of PHF8 binds to H3K4me3 and colocalizes with H3K4me3 at transcription initiation sites. Furthermore, PHF8 interacts with another XMLR protein, ZNF711, which binds to a subset of PHF8 target genes, including the XLMR gene JARID1C. Of interest, the C. elegans PHF8 homolog is highly expressed in neurons, and mutant animals show impaired locomotion. Taken together, our results functionally link the XLMR gene PHF8 to two other XLMR genes, ZNF711 and JARID1C, indicating that MR genes may be functionally linked in pathways, causing the complex phenotypes observed in patients developing MR.
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Affiliation(s)
- Daniela Kleine-Kohlbrecher
- Biotech Research and Innovation Centre (BRIC), Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
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43
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van Bokhoven H, Kramer JM. Disruption of the epigenetic code: an emerging mechanism in mental retardation. Neurobiol Dis 2010; 39:3-12. [PMID: 20304068 DOI: 10.1016/j.nbd.2010.03.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 03/10/2010] [Accepted: 03/12/2010] [Indexed: 01/18/2023] Open
Abstract
Mental retardation (MR) is a highly diverse group of cognitive disorders. Gene defects account for about half of all patients and mutations causative for impaired cognition have been identified in more than 400 genes. While there are numerous genetic defects underlying MR, a more limited number of pathways is emerging whose disruption appears to be shared by groups of MR genes. One of these common pathways is composed of MR genes that encode regulators of chromatin structure and of chromatin-mediated transcription regulation. Already more than 20 "epigenetic MR genes" have been identified and this number is likely to increase in the coming years when deep sequencing of exomes and genomes will become commonplace. Prominent examples of epigenetic MR genes include the methyl CpG-binding protein MECP2 and the CREB binding protein, CBP. Interestingly, several epigenetic MR proteins have been found to interact directly with one another or act together in complexes that regulate the local chromatin structure at target genes. Thus, it appears that the functions of individual epigenetic MR proteins converge onto similar biological processes that are crucial to neuronal processes. The next challenge will be to gain more insight into patterns of altered DNA methylation and histone modifications that are caused by epigenetic gene mutations and how these will disrupt the brain-specific expression of target genes. Such research may reveal that a wide variety of mutations in the genetic code result in a more limited number of disruptions to the epigenetic code. If so, this will provide a rationale for therapeutic strategies.
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Affiliation(s)
- Hans van Bokhoven
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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44
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Zou YS, Milunsky JM. Developmental disability and hypomelanosis of Ito in a female with 7.3 Mb de novo duplication of Xp11.3-p11.4 and random X inactivation. Am J Med Genet A 2010; 149A:2573-7. [PMID: 19876908 DOI: 10.1002/ajmg.a.33066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ying S Zou
- Center for Human Genetics, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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45
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Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proc Natl Acad Sci U S A 2009; 106:22358-63. [PMID: 20007773 DOI: 10.1073/pnas.0911376106] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Humans differ from other primates by marked differences in cognitive abilities and a significantly larger brain. These differences correlate with metabolic changes, as evidenced by the relative up-regulation of energy-related genes and metabolites in human brain. While the mechanisms underlying these evolutionary changes have not been elucidated, altered activities of key transcription factors (TFs) could play a pivotal role. To assess this possibility, we analyzed microarray data from five tissues from humans and chimpanzees. We identified 90 TF genes with significantly different expression levels in human and chimpanzee brain among which the rapidly evolving KRAB-zinc finger genes are markedly over-represented. The differentially expressed TFs cluster within a robust regulatory network consisting of two distinct but interlinked modules, one strongly associated with energy metabolism functions, and the other with transcription, vesicular transport, and ubiquitination. Our results suggest that concerted changes in a relatively small number of interacting TFs may coordinate major gene expression differences in human and chimpanzee brain.
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46
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Bashiardes S, Kousoulidou L, van Bokhoven H, Ropers HH, Chelly J, Moraine C, de Brouwer APM, Van Esch H, Froyen G, Patsalis PC. A new chromosome x exon-specific microarray platform for screening of patients with X-linked disorders. J Mol Diagn 2009; 11:562-8. [PMID: 19779134 DOI: 10.2353/jmoldx.2009.090086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Recent studies and advances in high-density oligonucleotide arrays have shown that microdeletions and microduplications occur at a high frequency in the human genome, causing various genetic conditions including mental retardation. Thus far little is known about the pathways leading to this disease, and implementation of microarrays is hampered by their increasing cost and complexity, underlining the need for new diagnostic tools. The aim of this study was to introduce a new targeted platform called "chromosome X exon-specific array" and to apply this new platform to screening of 20 families (including one blind positive control) with suspected X-linked mental retardation, to identify new causative X-linked mental retardation genes. The new microarray contains of 21,939 oligonucleotides covering 92.9% of all exons of all genes on chromosome X. Patient screening resulted in successful identification of the blind positive control included in the sample of 20 families, and one of the remaining 19 families was found to carry a 1.78-kilobase deletion involving all exons of pseudogene BRAF2. The BRAF2 deletion segregated in the family and was not found in 200 normal male samples, and no copy number variations are reported in this region. Further studies and focused investigation of X-linked disorders have the potential to reveal the molecular basis of human genetic pathological conditions that are caused by copy-number changes in chromosome X genes.
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Affiliation(s)
- Stavros Bashiardes
- Cyprus Institute of Neurology and Genetics, PO Box 23462, 1683 Nicosia, Cyprus
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47
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Gécz J, Shoubridge C, Corbett M. The genetic landscape of intellectual disability arising from chromosome X. Trends Genet 2009; 25:308-16. [PMID: 19556021 DOI: 10.1016/j.tig.2009.05.002] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 05/14/2009] [Accepted: 05/14/2009] [Indexed: 01/07/2023]
Abstract
X-linked mental retardation (XLMR) or intellectual disability (ID) is a common, clinically complex and genetically heterogeneous disease arising from many mutations along the X chromosome. It affects between 1/600-1/1000 males and a substantial number of females. Research during the past decade has identified >90 different XLMR genes, affecting a wide range of cellular processes. Many more genes remain uncharacterized, especially for the non-syndromic XLMR forms. Currently, approximately 11% of X-chromosome genes are implicated in XLMR; however, apart from a few notable exceptions, most contribute individually to <0.1% of the total landscape, which arguably remains only about half complete. There remain many hills to climb and valleys to cross before the ID landscape is fully triangulated.
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Affiliation(s)
- Jozef Gécz
- Molecular Pathology, SA Pathology at Women's and Children's Hospital, North Adelaide, SA 5006, Australia
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48
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Emerson RO, Thomas JH. Adaptive evolution in zinc finger transcription factors. PLoS Genet 2009; 5:e1000325. [PMID: 19119423 PMCID: PMC2604467 DOI: 10.1371/journal.pgen.1000325] [Citation(s) in RCA: 220] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Accepted: 12/02/2008] [Indexed: 01/10/2023] Open
Abstract
The majority of human genes are conserved among mammals, but some gene families have undergone extensive expansion in particular lineages. Here, we present an evolutionary analysis of one such gene family, the poly–zinc-finger (poly-ZF) genes. The human genome encodes approximately 700 members of the poly-ZF family of putative transcriptional repressors, many of which have associated KRAB, SCAN, or BTB domains. Analysis of the gene family across the tree of life indicates that the gene family arose from a small ancestral group of eukaryotic zinc-finger transcription factors through many repeated gene duplications accompanied by functional divergence. The ancestral gene family has probably expanded independently in several lineages, including mammals and some fishes. Investigation of adaptive evolution among recent paralogs using dN/dS analysis indicates that a major component of the selective pressure acting on these genes has been positive selection to change their DNA-binding specificity. These results suggest that the poly-ZF genes are a major source of new transcriptional repression activity in humans and other primates. Gene families, arising by the repeated duplication and diversification of existing genes, are a pervasive feature of the genomes of higher organisms. In this study, we analyze the evolutionary history of one of the largest gene families in humans, the poly–zinc-finger genes. Each poly–zinc-finger gene is thought to act by regulating the expression levels of one or more other genes, but the ultimate function and purpose of most poly–zinc-finger genes is unknown. We have found that the poly–zinc-finger gene family has been growing rapidly in many lineages including the human lineage, and that evolution has favored the creation of new poly–zinc-finger genes that have different DNA targets than the genes from which they were derived. These results suggest that the emergence of new and different poly–zinc-finger genes has probably been important in the evolution of humans and many other animal species.
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Affiliation(s)
- Ryan O. Emerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - James H. Thomas
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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49
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Genes and pathways differentially expressed in the brains of Fxr2 knockout mice. Neurobiol Dis 2008; 32:510-20. [PMID: 18930145 DOI: 10.1016/j.nbd.2008.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 07/26/2008] [Accepted: 09/09/2008] [Indexed: 11/20/2022] Open
Abstract
Fragile X syndrome is a common inherited form of mental retardation and originates from the absence of expression of the FMR1 gene. This gene and its two homologues, FXR1 and FXR2, encode for a family of fragile X related (FXR) proteins with similar tissue distribution, together with sequence and functional homology. Based on these characteristics, it has been suggested that these proteins might partly complement one another. To unravel the function of Fxr2 protein, the expression pattern of 12,588 genes was studied in the brains of wild-type and Fxr2 knockout mice, an animal model which shows behavioral abnormalities partly similar to those observed in Fmr1-knockout mice. By genome expression profiling and stringent significance tests we identify genes and gene groups de-regulated in the brains of Fxr2 knockout mice. Differential expression of candidate genes was validated by real-time PCR, in situ hybridization, immunohistochemistry and western blot analysis. A number of differentially expressed genes associated with the Fxr2 phenotype have been previously involved in other memory or cognitive disorders.
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50
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Genetic and epigenetic defects in mental retardation. Int J Biochem Cell Biol 2008; 41:96-107. [PMID: 18765296 DOI: 10.1016/j.biocel.2008.08.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Revised: 08/06/2008] [Accepted: 08/07/2008] [Indexed: 11/23/2022]
Abstract
Mental retardation (MR) is a highly diverse group of cognitive disorders. The high incidence of MR, 2-3% in most populations, and the high burden for families and society makes this condition one of the major unsolved problems in modern medicine. Gene defects account for about half of all patients and more than 300 genes are known that, when mutated, lead to cognitive dysfunction. A strikingly high number of these MR genes encode regulators of chromatin structure and of chromatin-mediated transcription regulation. Prominent examples of these include the methyl CpG-binding protein MECP2, the H3K4 demethylase JARID1c and the H3K9 histone methyltransferase EHMT1. Moreover, several of these epigenetic MR proteins have been found to directly interact with one another or act in complexes that regulate the local chromatin structure at target genes that are key to normal neuronal activities. Thus, it appears that the function of individual MR genes converges to similar biological processes. More detailed knowledge about the altered DNA methylation and histone marks that are introduced by epigenetic gene mutations as well as more insight into neuronal genes whose expression is disrupted by this will provide a rationale for therapeutic strategies.
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