1
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Reijns MAM, Thompson L, Acosta JC, Black HA, Sanchez-Luque FJ, Diamond A, Parry DA, Daniels A, O'Shea M, Uggenti C, Sanchez MC, O'Callaghan A, McNab MLL, Adamowicz M, Friman ET, Hurd T, Jarman EJ, Chee FLM, Rainger JK, Walker M, Drake C, Longman D, Mordstein C, Warlow SJ, McKay S, Slater L, Ansari M, Tomlinson IPM, Moore D, Wilkinson N, Shepherd J, Templeton K, Johannessen I, Tait-Burkard C, Haas JG, Gilbert N, Adams IR, Jackson AP. A sensitive and affordable multiplex RT-qPCR assay for SARS-CoV-2 detection. PLoS Biol 2020; 18:e3001030. [PMID: 33320856 PMCID: PMC7771873 DOI: 10.1371/journal.pbio.3001030] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/29/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
With the ongoing COVID-19 (Coronavirus Disease 2019) pandemic, caused by the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), there is a need for sensitive, specific, and affordable diagnostic tests to identify infected individuals, not all of whom are symptomatic. The most sensitive test involves the detection of viral RNA using RT-qPCR (quantitative reverse transcription PCR), with many commercial kits now available for this purpose. However, these are expensive, and supply of such kits in sufficient numbers cannot always be guaranteed. We therefore developed a multiplex assay using well-established SARS-CoV-2 targets alongside a human cellular control (RPP30) and a viral spike-in control (Phocine Herpes Virus 1 [PhHV-1]), which monitor sample quality and nucleic acid extraction efficiency, respectively. Here, we establish that this test performs as well as widely used commercial assays, but at substantially reduced cost. Furthermore, we demonstrate >1,000-fold variability in material routinely collected by combined nose and throat swabbing and establish a statistically significant correlation between the detected level of human and SARS-CoV-2 nucleic acids. The inclusion of the human control probe in our assay therefore provides a quantitative measure of sample quality that could help reduce false-negative rates. We demonstrate the feasibility of establishing a robust RT-qPCR assay at approximately 10% of the cost of equivalent commercial assays, which could benefit low-resource environments and make high-volume testing affordable.
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Affiliation(s)
- Martin A. M. Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Louise Thompson
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
| | - Juan Carlos Acosta
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Holly A. Black
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Francisco J. Sanchez-Luque
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
- Centre Pfizer-University of Granada-Andalusian Government for Genomics and Oncological Research (Genyo), Granada, Spain
| | - Austin Diamond
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
| | - David A. Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Alison Daniels
- Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh, Edinburgh, United Kingdom
| | - Marie O'Shea
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | - Carolina Uggenti
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Maria C. Sanchez
- Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh, Edinburgh, United Kingdom
| | - Alan O'Callaghan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Michelle L. L. McNab
- Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh, Edinburgh, United Kingdom
| | - Martyna Adamowicz
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Elias T. Friman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Toby Hurd
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Edward J. Jarman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Frederic Li Mow Chee
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jacqueline K. Rainger
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Marion Walker
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Camilla Drake
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Dasa Longman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Christine Mordstein
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sophie J. Warlow
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stewart McKay
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Louise Slater
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
| | - Morad Ansari
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
| | - Ian P. M. Tomlinson
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - David Moore
- The South East of Scotland Clinical Genetic Service, Western General Hospital, NHS Lothian, Edinburgh, United Kingdom
| | - Nadine Wilkinson
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Jill Shepherd
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Kate Templeton
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Ingolfur Johannessen
- Medical Microbiology and Virology Service, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Christine Tait-Burkard
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jürgen G. Haas
- Division of Infection Medicine, Edinburgh Medical School, The University of Edinburgh, Edinburgh, United Kingdom
| | - Nick Gilbert
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Ian R. Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew P. Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, United Kingdom
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2
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Mackenzie KJ, Carroll P, Martin CA, Murina O, Fluteau A, Simpson DJ, Olova N, Sutcliffe H, Rainger JK, Leitch A, Osborn RT, Wheeler AP, Nowotny M, Gilbert N, Chandra T, Reijns MAM, Jackson AP. cGAS surveillance of micronuclei links genome instability to innate immunity. Nature 2017; 548:461-465. [PMID: 28738408 PMCID: PMC5870830 DOI: 10.1038/nature23449] [Citation(s) in RCA: 1022] [Impact Index Per Article: 146.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 07/04/2017] [Indexed: 12/12/2022]
Abstract
DNA is strictly compartmentalized within the nucleus to prevent autoimmunity; despite this, cyclic GMP-AMP synthase (cGAS), a cytosolic sensor of double-stranded DNA, is activated in autoinflammatory disorders and by DNA damage. Precisely how cellular DNA gains access to the cytoplasm remains to be determined. Here, we report that cGAS localizes to micronuclei arising from genome instability in a mouse model of monogenic autoinflammation, after exogenous DNA damage and spontaneously in human cancer cells. Such micronuclei occur after mis-segregation of DNA during cell division and consist of chromatin surrounded by its own nuclear membrane. Breakdown of the micronuclear envelope, a process associated with chromothripsis, leads to rapid accumulation of cGAS, providing a mechanism by which self-DNA becomes exposed to the cytosol. cGAS is activated by chromatin, and consistent with a mitotic origin, micronuclei formation and the proinflammatory response following DNA damage are cell-cycle dependent. By combining live-cell laser microdissection with single cell transcriptomics, we establish that interferon-stimulated gene expression is induced in micronucleated cells. We therefore conclude that micronuclei represent an important source of immunostimulatory DNA. As micronuclei formed from lagging chromosomes also activate this pathway, recognition of micronuclei by cGAS may act as a cell-intrinsic immune surveillance mechanism that detects a range of neoplasia-inducing processes.
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Affiliation(s)
- Karen J Mackenzie
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Paula Carroll
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Carol-Anne Martin
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Olga Murina
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Adeline Fluteau
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Daniel J Simpson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Nelly Olova
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Hannah Sutcliffe
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Jacqueline K Rainger
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Andrea Leitch
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ruby T Osborn
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ann P Wheeler
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Nick Gilbert
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Tamir Chandra
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Martin A M Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Andrew P Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
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3
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Shaw ND, Brand H, Kupchinsky ZA, Bengani H, Plummer L, Jones TI, Erdin S, Williamson KA, Rainger J, Stortchevoi A, Samocha K, Currall BB, Dunican DS, Collins RL, Willer JR, Lek A, Lek M, Nassan M, Pereira S, Kammin T, Lucente D, Silva A, Seabra CM, Chiang C, An Y, Ansari M, Rainger JK, Joss S, Smith JC, Lippincott MF, Singh SS, Patel N, Jing JW, Law JR, Ferraro N, Verloes A, Rauch A, Steindl K, Zweier M, Scheer I, Sato D, Okamoto N, Jacobsen C, Tryggestad J, Chernausek S, Schimmenti LA, Brasseur B, Cesaretti C, García-Ortiz JE, Buitrago TP, Silva OP, Hoffman JD, Mühlbauer W, Ruprecht KW, Loeys BL, Shino M, Kaindl AM, Cho CH, Morton CC, Meehan RR, van Heyningen V, Liao EC, Balasubramanian R, Hall JE, Seminara SB, Macarthur D, Moore SA, Yoshiura KI, Gusella JF, Marsh JA, Graham JM, Lin AE, Katsanis N, Jones PL, Crowley WF, Davis EE, FitzPatrick DR, Talkowski ME. Corrigendum: SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome. Nat Genet 2017; 49:969. [PMID: 28546579 DOI: 10.1038/ng0617-969c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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4
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Shaw ND, Brand H, Kupchinsky ZA, Bengani H, Plummer L, Jones TI, Erdin S, Williamson KA, Rainger J, Stortchevoi A, Samocha K, Currall BB, Dunican DS, Collins RL, Willer JR, Lek A, Lek M, Nassan M, Pereira S, Kammin T, Lucente D, Silva A, Seabra CM, Chiang C, An Y, Ansari M, Rainger JK, Joss S, Smith JC, Lippincott MF, Singh SS, Patel N, Jing JW, Law JR, Ferraro N, Verloes A, Rauch A, Steindl K, Zweier M, Scheer I, Sato D, Okamoto N, Jacobsen C, Tryggestad J, Chernausek S, Schimmenti LA, Brasseur B, Cesaretti C, García-Ortiz JE, Buitrago TP, Silva OP, Hoffman JD, Mühlbauer W, Ruprecht KW, Loeys BL, Shino M, Kaindl AM, Cho CH, Morton CC, Meehan RR, van Heyningen V, Liao EC, Balasubramanian R, Hall JE, Seminara SB, Macarthur D, Moore SA, Yoshiura KI, Gusella JF, Marsh JA, Graham JM, Lin AE, Katsanis N, Jones PL, Crowley WF, Davis EE, FitzPatrick DR, Talkowski ME. SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome. Nat Genet 2017; 49:238-248. [PMID: 28067909 DOI: 10.1038/ng.3743] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/16/2016] [Indexed: 12/14/2022]
Abstract
Arhinia, or absence of the nose, is a rare malformation of unknown etiology that is often accompanied by ocular and reproductive defects. Sequencing of 40 people with arhinia revealed that 84% of probands harbor a missense mutation localized to a constrained region of SMCHD1 encompassing the ATPase domain. SMCHD1 mutations cause facioscapulohumeral muscular dystrophy type 2 (FSHD2) via a trans-acting loss-of-function epigenetic mechanism. We discovered shared mutations and comparable DNA hypomethylation patterning between these distinct disorders. CRISPR/Cas9-mediated alteration of smchd1 in zebrafish yielded arhinia-relevant phenotypes. Transcriptome and protein analyses in arhinia probands and controls showed no differences in SMCHD1 mRNA or protein abundance but revealed regulatory changes in genes and pathways associated with craniofacial patterning. Mutations in SMCHD1 thus contribute to distinct phenotypic spectra, from craniofacial malformation and reproductive disorders to muscular dystrophy, which we speculate to be consistent with oligogenic mechanisms resulting in pleiotropic outcomes.
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Affiliation(s)
- Natalie D Shaw
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Harrison Brand
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Zachary A Kupchinsky
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - Hemant Bengani
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Lacey Plummer
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Takako I Jones
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Serkan Erdin
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kathleen A Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Joe Rainger
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Alexei Stortchevoi
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kaitlin Samocha
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin B Currall
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Donncha S Dunican
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Ryan L Collins
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason R Willer
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - Angela Lek
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Malik Nassan
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, Minnesota, USA
| | - Shahrin Pereira
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Tammy Kammin
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Diane Lucente
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alexandra Silva
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Catarina M Seabra
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.,GABBA Program, University of Porto, Porto, Portugal
| | - Colby Chiang
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yu An
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Morad Ansari
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Jacqueline K Rainger
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Shelagh Joss
- West of Scotland Genetics Service, South Glasgow University Hospitals, Glasgow, UK
| | - Jill Clayton Smith
- Faculty of Medical and Human Sciences, Institute of Human Development, Manchester Centre for Genomic Medicine, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Margaret F Lippincott
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sylvia S Singh
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Nirav Patel
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jenny W Jing
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jennifer R Law
- Division of Pediatric Endocrinology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nalton Ferraro
- Department of Oral and Maxillofacial Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alain Verloes
- Department of Genetics, Robert Debré Hospital, Paris, France
| | - Anita Rauch
- Institute of Medical Genetics and Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics and Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Schlieren-Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics and Radiz-Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, Schlieren-Zurich, Switzerland
| | - Ianina Scheer
- Department of Diagnostic Imaging, Children's Hospital, Zurich, Switzerland
| | - Daisuke Sato
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Christina Jacobsen
- Division of Endocrinology and Genetics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jeanie Tryggestad
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Steven Chernausek
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Lisa A Schimmenti
- Departments of Otorhinolaryngology and Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Benjamin Brasseur
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, Miami, Florida, USA
| | - Claudia Cesaretti
- Medical Genetics Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Jose E García-Ortiz
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Mexico
| | | | | | - Jodi D Hoffman
- Divisions of Genetics and Maternal Fetal Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Wolfgang Mühlbauer
- Department of Plastic and Aesthetic Surgery, ATOS Klinik, Munich, Germany
| | - Klaus W Ruprecht
- Department of Ophthalmology, University Hospital of the Saarland, Homburg, Germany
| | - Bart L Loeys
- Center for Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Masato Shino
- Department of Otolaryngology and Head and Neck Surgery, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Angela M Kaindl
- Biology and Neurobiology, Charité-University Medicine Berlin and Berlin Institute of Health, Berlin, Germany
| | - Chie-Hee Cho
- Department of Diagnostic, Interventional and Pediatric Radiology, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Cynthia C Morton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Veronica van Heyningen
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Eric C Liao
- Center for Regenerative Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
| | - Ravikumar Balasubramanian
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Janet E Hall
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Stephanie B Seminara
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Daniel Macarthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steven A Moore
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - James F Gusella
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - John M Graham
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Angela E Lin
- Medical Genetics, MassGeneral Hospital for Children and Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - Peter L Jones
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - William F Crowley
- Harvard Reproductive Endocrine Sciences Center and NICHD Center of Excellence in Translational Research in Fertility and Infertility, Reproductive Endocrine Unit of the Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Michael E Talkowski
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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5
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McEntagart M, Williamson KA, Rainger JK, Wheeler A, Seawright A, De Baere E, Verdin H, Bergendahl LT, Quigley A, Rainger J, Dixit A, Sarkar A, López Laso E, Sanchez-Carpintero R, Barrio J, Bitoun P, Prescott T, Riise R, McKee S, Cook J, McKie L, Ceulemans B, Meire F, Temple IK, Prieur F, Williams J, Clouston P, Németh AH, Banka S, Bengani H, Handley M, Freyer E, Ross A, van Heyningen V, Marsh JA, Elmslie F, FitzPatrick DR. A Restricted Repertoire of De Novo Mutations in ITPR1 Cause Gillespie Syndrome with Evidence for Dominant-Negative Effect. Am J Hum Genet 2016; 98:981-992. [PMID: 27108798 PMCID: PMC4863663 DOI: 10.1016/j.ajhg.2016.03.018] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/16/2016] [Indexed: 12/19/2022] Open
Abstract
Gillespie syndrome (GS) is characterized by bilateral iris hypoplasia, congenital hypotonia, non-progressive ataxia, and progressive cerebellar atrophy. Trio-based exome sequencing identified de novo mutations in ITPR1 in three unrelated individuals with GS recruited to the Deciphering Developmental Disorders study. Whole-exome or targeted sequence analysis identified plausible disease-causing ITPR1 mutations in 10/10 additional GS-affected individuals. These ultra-rare protein-altering variants affected only three residues in ITPR1: Glu2094 missense (one de novo, one co-segregating), Gly2539 missense (five de novo, one inheritance uncertain), and Lys2596 in-frame deletion (four de novo). No clinical or radiological differences were evident between individuals with different mutations. ITPR1 encodes an inositol 1,4,5-triphosphate-responsive calcium channel. The homo-tetrameric structure has been solved by cryoelectron microscopy. Using estimations of the degree of structural change induced by known recessive- and dominant-negative mutations in other disease-associated multimeric channels, we developed a generalizable computational approach to indicate the likely mutational mechanism. This analysis supports a dominant-negative mechanism for GS variants in ITPR1. In GS-derived lymphoblastoid cell lines (LCLs), the proportion of ITPR1-positive cells using immunofluorescence was significantly higher in mutant than control LCLs, consistent with an abnormality of nuclear calcium signaling feedback control. Super-resolution imaging supports the existence of an ITPR1-lined nucleoplasmic reticulum. Mice with Itpr1 heterozygous null mutations showed no major iris defects. Purkinje cells of the cerebellum appear to be the most sensitive to impaired ITPR1 function in humans. Iris hypoplasia is likely to result from either complete loss of ITPR1 activity or structure-specific disruption of multimeric interactions.
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Affiliation(s)
- Meriel McEntagart
- Medical Genetics, St George's University Hospitals NHS Foundation Trust, Cranmer Terrace, London SW17 0RE, UK
| | - Kathleen A Williamson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Jacqueline K Rainger
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Ann Wheeler
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Anne Seawright
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Medical Research Building (MRB), 1st Floor, Room 110.029, De Pintelaan 185, 9000 Ghent, Belgium
| | - Hannah Verdin
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Medical Research Building (MRB), 1st Floor, Room 110.029, De Pintelaan 185, 9000 Ghent, Belgium
| | - L Therese Bergendahl
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Alan Quigley
- Department of Radiology, Royal Hospital for Sick Children, Edinburgh EH9 1LF, UK
| | - Joe Rainger
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK; Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Abhijit Dixit
- Clinical Genetics, Nottingham City Hospital, Hucknall Road, Nottingham NG5 1PB, UK
| | - Ajoy Sarkar
- Clinical Genetics, Nottingham City Hospital, Hucknall Road, Nottingham NG5 1PB, UK
| | - Eduardo López Laso
- Pediatric Neurology Unit, Department of Pediatrics, Reina Sofia University Hospital, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Rocio Sanchez-Carpintero
- Paediatric Neurology Unit, Department of Paediatrics, Clinica Universidad de Navarra, 31008 Pamplona, Spain
| | - Jesus Barrio
- Department of Ophthalmology, Clinica Universidad de Navarra, 31008 Pamplona, Spain
| | - Pierre Bitoun
- Service de pédiatrie, CHU Paris Seine-Saint-Denis - Hôpital Jean Verdier Avenue du 14 juillet, 93140 Bondy, France
| | - Trine Prescott
- Department of Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Ruth Riise
- Department of Ophthalmology, Innland Hospital, 2418 Elverum, Norway
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast BT9 7AB, UK
| | - Jackie Cook
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Western Bank, Sheffield S10 2TH, UK
| | - Lisa McKie
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Berten Ceulemans
- Department of Neurology-Pediatric Neurology, University and University Hospital Antwerp, Antwerp 2650, Belgium
| | - Françoise Meire
- Department of Ophthalmology, Queen Fabiola Children's University Hospital, 1020 Brussels, Belgium
| | - I Karen Temple
- Human Development and Health Academic Unit, University Hospital Southampton, Tremona Road, University of Southampton, Southampton SO16 6YD, UK
| | - Fabienne Prieur
- Service Génétique, Plateau de biologie, CHU Saint Etienne, 42055 Saint Etienne cedex 2, France
| | - Jonathan Williams
- Oxford University Hospitals NHS Trust, Oxford Medical Genetics Laboratories, The Churchill Hospital, Old Road, Headington, Oxford OX3 7LE, UK
| | - Penny Clouston
- Oxford University Hospitals NHS Trust, Oxford Medical Genetics Laboratories, The Churchill Hospital, Old Road, Headington, Oxford OX3 7LE, UK
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 7LJ, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, University of Manchester, St. Mary's Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Hemant Bengani
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Mark Handley
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Elisabeth Freyer
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Allyson Ross
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Veronica van Heyningen
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Frances Elmslie
- Medical Genetics, St George's University Hospitals NHS Foundation Trust, Cranmer Terrace, London SW17 0RE, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK.
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Metsu S, Rainger JK, Debacker K, Bernhard B, Rooms L, Grafodatskaya D, Weksberg R, Fombonne E, Taylor MS, Scherer SW, Kooy RF, FitzPatrick DR. A CGG-repeat expansion mutation in ZNF713 causes FRA7A: association with autistic spectrum disorder in two families. Hum Mutat 2015; 35:1295-300. [PMID: 25196122 DOI: 10.1002/humu.22683] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/15/2014] [Indexed: 11/09/2022]
Abstract
We report de novo occurrence of the 7p11.2 folate-sensitive fragile site FRA7A in a male with an autistic spectrum disorder (ASD) due to a CGG-repeat expansion mutation (∼450 repeats) in a 5' intron of ZNF713. This expanded allele showed hypermethylation of the adjacent CpG island with reduced ZNF713 expression observed in a proband-derived lymphoblastoid cell line (LCL). His unaffected mother carried an unmethylated premutation (85 repeats). This CGG-repeat showed length polymorphism in control samples (five to 22 repeats). In a second unrelated family, three siblings with ASD and their unaffected father were found to carry FRA7A premutations, which were partially or mosaically methylated. In one of the affected siblings, mitotic instability of the premutation was observed. ZNF713 expression in LCLs in this family was increased in three of these four premutation carriers. A firm link cannot yet be established between ASD and the repeat expansion mutation but plausible pathogenic mechanisms are discussed.
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Affiliation(s)
- Sofie Metsu
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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Ansari M, Rainger JK, Murray JE, Hanson I, Firth HV, Mehendale F, Amiel J, Gordon CT, Percesepe A, Mazzanti L, Fryer A, Ferrari P, Devriendt K, Temple IK, FitzPatrick DR. A syndromic form of Pierre Robin sequence is caused by 5q23 deletions encompassing FBN2 and PHAX. Eur J Med Genet 2014; 57:587-95. [PMID: 25195018 DOI: 10.1016/j.ejmg.2014.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/22/2014] [Indexed: 12/19/2022]
Abstract
Pierre Robin sequence (PRS) is an aetiologically distinct subgroup of cleft palate. We aimed to define the critical genomic interval from five different 5q22-5q31 deletions associated with PRS or PRS-associated features and assess each gene within the region as a candidate for the PRS component of the phenotype. Clinical array-based comparative genome hybridisation (aCGH) data were used to define a 2.08 Mb minimum region of overlap among four de novo deletions and one mother-son inherited deletion associated with at least one component of PRS. Commonly associated anomalies were talipes equinovarus (TEV), finger contractures and crumpled ear helices. Expression analysis of the orthologous genes within the PRS critical region in embryonic mice showed that the strongest candidate genes were FBN2 and PHAX. Targeted aCGH of the critical region and sequencing of these genes in a cohort of 25 PRS patients revealed no plausible disease-causing mutations. In conclusion, deletion of ∼2 Mb on 5q23 region causes a clinically recognisable subtype of PRS. Haploinsufficiency for FBN2 accounts for the digital and auricular features. A possible critical region for TEV is distinct and telomeric to the PRS region. The molecular basis of PRS in these cases remains undetermined but haploinsufficiency for PHAX is a plausible mechanism.
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Affiliation(s)
- Morad Ansari
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jacqueline K Rainger
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jennie E Murray
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; Southeast Scotland Clinical Genetics Services, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Isabel Hanson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Helen V Firth
- DECIPHER, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Felicity Mehendale
- Cleft Lip and Palate Service, Royal Hospital for Sick Children, Edinburgh EH9 1LF, UK
| | - Jeanne Amiel
- INSERM U-1163 Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Christopher T Gordon
- INSERM U-1163 Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Antonio Percesepe
- Departments of Medical Genetics and Pediatrics, University Hospital of Modena, Italy
| | | | - Alan Fryer
- Department of Clinical Genetics, Alder Hey Children's Hospital, Liverpool L12 2AP, UK
| | - Paola Ferrari
- Departments of Medical Genetics and Pediatrics, University Hospital of Modena, Italy
| | | | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton and Wessex Clinical Genetics Service, University Hospital NHS Trust, Princess Anne Hospital, Coxford Road, Southampton SO16 5YA, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; Southeast Scotland Clinical Genetics Services, Western General Hospital, Edinburgh EH4 2XU, UK.
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8
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Rainger J, Pehlivan D, Johansson S, Bengani H, Sanchez-Pulido L, Williamson KA, Ture M, Barker H, Rosendahl K, Spranger J, Horn D, Meynert A, Floyd JAB, Prescott T, Anderson CA, Rainger JK, Karaca E, Gonzaga-Jauregui C, Jhangiani S, Muzny DM, Seawright A, Soares DC, Kharbanda M, Murday V, Finch A, Gibbs RA, van Heyningen V, Taylor MS, Yakut T, Knappskog PM, Hurles ME, Ponting CP, Lupski JR, Houge G, FitzPatrick DR. Monoallelic and biallelic mutations in MAB21L2 cause a spectrum of major eye malformations. Am J Hum Genet 2014; 94:915-23. [PMID: 24906020 DOI: 10.1016/j.ajhg.2014.05.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/13/2014] [Indexed: 11/28/2022] Open
Abstract
We identified four different missense mutations in the single-exon gene MAB21L2 in eight individuals with bilateral eye malformations from five unrelated families via three independent exome sequencing projects. Three mutational events altered the same amino acid (Arg51), and two were identical de novo mutations (c.151C>T [p.Arg51Cys]) in unrelated children with bilateral anophthalmia, intellectual disability, and rhizomelic skeletal dysplasia. c.152G>A (p.Arg51His) segregated with autosomal-dominant bilateral colobomatous microphthalmia in a large multiplex family. The fourth heterozygous mutation (c.145G>A [p.Glu49Lys]) affected an amino acid within two residues of Arg51 in an adult male with bilateral colobomata. In a fifth family, a homozygous mutation (c.740G>A [p.Arg247Gln]) altering a different region of the protein was identified in two male siblings with bilateral retinal colobomata. In mouse embryos, Mab21l2 showed strong expression in the developing eye, pharyngeal arches, and limb bud. As predicted by structural homology, wild-type MAB21L2 bound single-stranded RNA, whereas this activity was lost in all altered forms of the protein. MAB21L2 had no detectable nucleotidyltransferase activity in vitro, and its function remains unknown. Induced expression of wild-type MAB21L2 in human embryonic kidney 293 cells increased phospho-ERK (pERK1/2) signaling. Compared to the wild-type and p.Arg247Gln proteins, the proteins with the Glu49 and Arg51 variants had increased stability. Abnormal persistence of pERK1/2 signaling in MAB21L2-expressing cells during development is a plausible pathogenic mechanism for the heterozygous mutations. The phenotype associated with the homozygous mutation might be a consequence of complete loss of MAB21L2 RNA binding, although the cellular function of this interaction remains unknown.
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Affiliation(s)
- Joe Rainger
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA
| | - Stefan Johansson
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Jonas Liesvei 65, 5021 Bergen, Norway; Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Hemant Bengani
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Luis Sanchez-Pulido
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | - Kathleen A Williamson
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Mehmet Ture
- Department of Medical Genetics, University of Uludag, 16120 Bursa, Turkey
| | - Heather Barker
- Edinburgh Cancer Research Centre, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Karen Rosendahl
- Paediatric Radiology Department, Haukeland University Hospital, 5021 Bergen, Norway
| | | | - Denise Horn
- Institut für Medizinische Genetik, Charité Campus Virchow-Klinikum, 13353 Berlin, Germany
| | - Alison Meynert
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - James A B Floyd
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Trine Prescott
- Medical Genetics, Oslo University Hospital, 0424 Oslo, Norway
| | - Carl A Anderson
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jacqueline K Rainger
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA
| | - Claudia Gonzaga-Jauregui
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Anne Seawright
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Dinesh C Soares
- Centre for Genomics and Experimental Medicine, Medical Research Council Institute Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Mira Kharbanda
- Clinical Genetics, Southern General Hospital, Glasgow G51 4TF, UK
| | - Victoria Murday
- Clinical Genetics, Southern General Hospital, Glasgow G51 4TF, UK
| | - Andrew Finch
- Edinburgh Cancer Research Centre, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Veronica van Heyningen
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Martin S Taylor
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK
| | - Tahsin Yakut
- Department of Medical Genetics, University of Uludag, 16120 Bursa, Turkey
| | - Per M Knappskog
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Jonas Liesvei 65, 5021 Bergen, Norway; Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Chris P Ponting
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 604B, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, MS BCM225, Houston, TX 77030, USA
| | - Gunnar Houge
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Jonas Liesvei 65, 5021 Bergen, Norway
| | - David R FitzPatrick
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, Edinburgh EH4 2XU, UK.
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Rainger JK, Bhatia S, Bengani H, Gautier P, Rainger J, Pearson M, Ansari M, Crow J, Mehendale F, Palinkasova B, Dixon MJ, Thompson PJ, Matarin M, Sisodiya SM, Kleinjan DA, Fitzpatrick DR. Disruption of SATB2 or its long-range cis-regulation by SOX9 causes a syndromic form of Pierre Robin sequence. Hum Mol Genet 2013; 23:2569-79. [PMID: 24363063 PMCID: PMC3990159 DOI: 10.1093/hmg/ddt647] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Heterozygous loss-of-function (LOF) mutations in the gene encoding the DNA-binding protein, SATB2, result in micrognathia and cleft palate in both humans and mice. In three unrelated individuals, we show that translocation breakpoints (BPs) up to 896 kb 3′ of SATB2 polyadenylation site cause a phenotype which is indistinguishable from that caused by SATB2 LOF mutations. This syndrome comprises long nose, small mouth, micrognathia, cleft palate, arachnodactyly and intellectual disability. These BPs map to a gene desert between PLCL1 and SATB2. We identified three putative cis-regulatory elements (CRE1–3) using a comparative genomic approach each of which would be placed in trans relative to SATB2 by all three BPs. CRE1–3 each bind p300 and mono-methylated H3K4 consistent with enhancer function. In silico analysis suggested that CRE1–3 contain one or more conserved SOX9-binding sites, and this binding was confirmed using chromatin immunoprecipitation on cells derived from mouse embryonic pharyngeal arch. Interphase bacterial artificial chromosome fluorescence in situ hybridization measurements in embryonic craniofacial tissues showed that the orthologous region in mice exhibits Satb2 expression-dependent chromatin decondensation consistent with Satb2 being a target gene of CRE1–3. To assess their in vivo function, we made multiple stable reporter transgenic lines for each enhancer in zebrafish. CRE2 was shown to drive SATB2-like expression in the embryonic craniofacial region. This expression could be eliminated by mutating the SOX9-binding site of CRE2. These observations suggest that SATB2 and SOX9 may be acting together via complex cis-regulation to coordinate the growth of the developing jaw.
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Affiliation(s)
- Jacqueline K Rainger
- MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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10
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Rainger J, Keighren M, Keene DR, Charbonneau NL, Rainger JK, Fisher M, Mella S, Huang JTJ, Rose L, van't Hof R, Sakai LY, Jackson IJ, FitzPatrick DR. A trans-acting protein effect causes severe eye malformation in the Mp mouse. PLoS Genet 2013; 9:e1003998. [PMID: 24348270 PMCID: PMC3861116 DOI: 10.1371/journal.pgen.1003998] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 10/18/2013] [Indexed: 12/18/2022] Open
Abstract
Mp is an irradiation-induced mouse mutation associated with microphthalmia, micropinna and hind limb syndactyly. We show that Mp is caused by a 660 kb balanced inversion on chromosome 18 producing reciprocal 3-prime gene fusion events involving Fbn2 and Isoc1. The Isoc1-Fbn2 fusion gene (Isoc1Mp) mRNA has a frameshift and early stop codon resulting in nonsense mediated decay. Homozygous deletions of Isoc1 do not support a significant developmental role for this gene. The Fbn2-Isoc1 fusion gene (Fbn2Mp) predicted protein consists of the N-terminal Fibrillin-2 (amino acids 1–2646, exons 1–62) lacking the C-terminal furin-cleavage site with a short out-of-frame extension encoded by the final exon of Isoc1. The Mp limb phenotype is consistent with that reported in Fbn2 null embryos. However, severe eye malformations, a defining feature of Mp, are not seen in Fbn2 null animals. Fibrillin-2Mp forms large fibrillar structures within the rough endoplasmic reticulum (rER) associated with an unfolded protein response and quantitative mass spectrometry shows a generalised defect in protein secretion in conditioned media from mutant cells. In the embryonic eye Fbn2 is expressed within the peripheral ciliary margin (CM). Mp embryos show reduced canonical Wnt-signalling in the CM – known to be essential for ciliary body development - and show subsequent aplasia of CM-derived structures. We propose that the Mp “worse-than-null” eye phenotype plausibly results from a failure in normal trafficking of proteins that are co-expressed with Fbn2 within the CM. The prediction of similar trans-acting protein effects will be an important challenge in the medical interpretation of human mutations from whole exome sequencing. With the current increase in large-scale sequencing efforts, correct interpretation of mutation consequences has never been more important. Here, we present evidence for a trans-acting protein effect in a novel mutation of Fbn2, associated with severe developmental eye defects not found in loss of function Fibrillin-2 alleles. The mutant protein is expressed in the developing eye but is unable to exit the cells, instead forming large protein aggregates within the endoplasmic reticulum. We observed ER-stress in mutant eyes, and detected a general reduction to secretion of co-expressed proteins in cell cultures. We propose that similar effects could be caused by mutations to other proteins that are trafficked through the ER, highlighting a disease mechanism that results in different clinical outcomes than observed, or predicted, from loss-off-function alleles.
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Affiliation(s)
- Joe Rainger
- The MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Margaret Keighren
- The MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Douglas R. Keene
- Shriners Hospital for Children, Portland, Oregon, United States of America
| | - Noe L. Charbonneau
- Shriners Hospital for Children, Portland, Oregon, United States of America
| | - Jacqueline K. Rainger
- The MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Malcolm Fisher
- The MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Sebastien Mella
- The MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Jeffrey T-J. Huang
- Biomarker and Drug Analysis Core Facility, Medical Research Institute, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Lorraine Rose
- Molecular Medicine Centre, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Rob van't Hof
- Molecular Medicine Centre, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Lynne Y. Sakai
- Shriners Hospital for Children, Portland, Oregon, United States of America
| | - Ian J. Jackson
- The MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- * E-mail: (IJJ); (DRF)
| | - David R. FitzPatrick
- The MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- * E-mail: (IJJ); (DRF)
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Gerth-Kahlert C, Williamson K, Ansari M, Rainger JK, Hingst V, Zimmermann T, Tech S, Guthoff RF, van Heyningen V, Fitzpatrick DR. Clinical and mutation analysis of 51 probands with anophthalmia and/or severe microphthalmia from a single center. Mol Genet Genomic Med 2013; 1:15-31. [PMID: 24498598 PMCID: PMC3893155 DOI: 10.1002/mgg3.2] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 01/26/2013] [Accepted: 01/29/2013] [Indexed: 01/12/2023] Open
Abstract
Clinical evaluation and mutation analysis was performed in 51 consecutive probands with severe eye malformations - anophthalmia and/or severe microphthalmia - seen in a single specialist ophthalmology center. The mutation analysis consisted of bidirectional sequencing of the coding regions of SOX2, OTX2, PAX6 (paired domain), STRA6, BMP4, SMOC1, FOXE3, and RAX, and genome-wide array-based copy number assessment. Fifteen (29.4%) of the 51 probands had likely causative mutations affecting SOX2 (9/51), OTX2 (5/51), and STRA6 (1/51). Of the cases with bilateral anophthalmia, 9/12 (75%) were found to be mutation positive. Three of these mutations were large genomic deletions encompassing SOX2 (one case) or OTX2 (two cases). Familial inheritance of three intragenic, plausibly pathogenic, and heterozygous mutations was observed. An unaffected carrier parent of an affected child with an identified OTX2 mutation confirmed the previously reported nonpenetrance for this disorder. Two families with SOX2 mutations demonstrated a parent and child both with significant but highly variable eye malformations. Heterozygous loss-of-function mutations in SOX2 and OTX2 are the most common genetic pathology associated with severe eye malformations and bi-allelic loss-of-function in STRA6 is confirmed as an emerging cause of nonsyndromal eye malformations.
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Affiliation(s)
| | - Kathleen Williamson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital Edinburgh, EH4 2XU, United Kingdom
| | - Morad Ansari
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital Edinburgh, EH4 2XU, United Kingdom
| | - Jacqueline K Rainger
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital Edinburgh, EH4 2XU, United Kingdom
| | - Volker Hingst
- Department of Radiology, University of Rostock Germany
| | | | - Stefani Tech
- Department of Ophthalmology, University of Rostock Germany
| | | | - Veronica van Heyningen
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital Edinburgh, EH4 2XU, United Kingdom
| | - David R Fitzpatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine at the University of Edinburgh, Western General Hospital Edinburgh, EH4 2XU, United Kingdom
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