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Schindler M, Osterwalder M, Harabula I, Wittler L, Tzika AC, Dechmann DKN, Vingron M, Visel A, Haas SA, Real FM. Induction of kidney-related gene programs through co-option of SALL1 in mole ovotestes. Development 2023; 150:dev201562. [PMID: 37519269 PMCID: PMC10499028 DOI: 10.1242/dev.201562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/21/2023] [Indexed: 08/01/2023]
Abstract
Changes in gene expression represent an important source of phenotypic innovation. Yet how such changes emerge and impact the evolution of traits remains elusive. Here, we explore the molecular mechanisms associated with the development of masculinizing ovotestes in female moles. By performing integrative analyses of epigenetic and transcriptional data in mole and mouse, we identified the co-option of SALL1 expression in mole ovotestes formation. Chromosome conformation capture analyses highlight a striking conservation of the 3D organization at the SALL1 locus, but an evolutionary divergence of enhancer activity. Interspecies reporter assays support the capability of mole-specific enhancers to activate transcription in urogenital tissues. Through overexpression experiments in transgenic mice, we further demonstrate the capability of SALL1 to induce kidney-related gene programs, which are a signature of mole ovotestes. Our results highlight the co-option of gene expression, through changes in enhancer activity, as a plausible mechanism for the evolution of traits.
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Affiliation(s)
- Magdalena Schindler
- Gene Regulation & Evolution, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
- Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany
| | - Marco Osterwalder
- Department for BioMedical Research (DBMR), University of Bern, Bern 3008, Switzerland
- Department of Cardiology, Bern University Hospital, Bern 3010, Switzerland
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Izabela Harabula
- Epigenetic Regulation and Chromatin Architecture, Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin 10115, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Athanasia C. Tzika
- Department of Genetics & Evolution, University of Geneva, Geneva 1205, Switzerland
| | - Dina K. N. Dechmann
- Department of Migration, Max Planck Institute for Animal Behavior, Radolfzell 78315, Germany
- Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Stefan A. Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Francisca M. Real
- Gene Regulation & Evolution, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
- Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany
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2
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Ringel AR, Szabo Q, Chiariello AM, Chudzik K, Schöpflin R, Rothe P, Mattei AL, Zehnder T, Harnett D, Laupert V, Bianco S, Hetzel S, Glaser J, Phan MHQ, Schindler M, Ibrahim DM, Paliou C, Esposito A, Prada-Medina CA, Haas SA, Giere P, Vingron M, Wittler L, Meissner A, Nicodemi M, Cavalli G, Bantignies F, Mundlos S, Robson MI. Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes. Cell 2022; 185:3689-3704.e21. [PMID: 36179666 PMCID: PMC9567273 DOI: 10.1016/j.cell.2022.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 10/13/2021] [Revised: 06/03/2022] [Accepted: 08/30/2022] [Indexed: 01/26/2023]
Abstract
Regulatory landscapes drive complex developmental gene expression, but it remains unclear how their integrity is maintained when incorporating novel genes and functions during evolution. Here, we investigated how a placental mammal-specific gene, Zfp42, emerged in an ancient vertebrate topologically associated domain (TAD) without adopting or disrupting the conserved expression of its gene, Fat1. In ESCs, physical TAD partitioning separates Zfp42 and Fat1 with distinct local enhancers that drive their independent expression. This separation is driven by chromatin activity and not CTCF/cohesin. In contrast, in embryonic limbs, inactive Zfp42 shares Fat1's intact TAD without responding to active Fat1 enhancers. However, neither Fat1 enhancer-incompatibility nor nuclear envelope-attachment account for Zfp42's unresponsiveness. Rather, Zfp42's promoter is rendered inert to enhancers by context-dependent DNA methylation. Thus, diverse mechanisms enabled the integration of independent Zfp42 regulation in the Fat1 locus. Critically, such regulatory complexity appears common in evolution as, genome wide, most TADs contain multiple independently expressed genes.
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Affiliation(s)
- Alessa R Ringel
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Quentin Szabo
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Konrad Chudzik
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Patricia Rothe
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandra L Mattei
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Tobias Zehnder
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Dermot Harnett
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Verena Laupert
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Sara Hetzel
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Juliane Glaser
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mai H Q Phan
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Magdalena Schindler
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Daniel M Ibrahim
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Christina Paliou
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Cesar A Prada-Medina
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Stefan A Haas
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Peter Giere
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, Naples, Italy; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Giacomo Cavalli
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Frédéric Bantignies
- Institute of Human Genetics, University of Montpellier, CNRS, Montpellier, France
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Charité-Universitätsmedizin Berlin, BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany.
| | - Michael I Robson
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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3
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M Real F, Haas SA, Franchini P, Xiong P, Simakov O, Kuhl H, Schöpflin R, Heller D, Moeinzadeh MH, Heinrich V, Krannich T, Bressin A, Hartmann MF, Wudy SA, Dechmann DKN, Hurtado A, Barrionuevo FJ, Schindler M, Harabula I, Osterwalder M, Hiller M, Wittler L, Visel A, Timmermann B, Meyer A, Vingron M, Jiménez R, Mundlos S, Lupiáñez DG. The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. Science 2020; 370:208-214. [PMID: 33033216 DOI: 10.1126/science.aaz2582] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 04/19/2020] [Accepted: 08/17/2020] [Indexed: 01/01/2023]
Abstract
Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. These include a tandem triplication involving CYP17A1, a gene controlling androgen synthesis, and an intrachromosomal inversion involving the pro-testicular growth factor gene FGF9, which is heterochronically expressed in mole ovotestes. Transgenic mice with a knock-in mole CYP17A1 enhancer or overexpressing FGF9 showed phenotypes recapitulating mole sexual features. Our results highlight how integrative genomic approaches can reveal the phenotypic impact of noncoding sequence changes.
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Affiliation(s)
- Francisca M Real
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Paolo Franchini
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Peiwen Xiong
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, 1090 Vienna, Austria
| | - Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Robert Schöpflin
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - David Heller
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M-Hossein Moeinzadeh
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Verena Heinrich
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thomas Krannich
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annkatrin Bressin
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michaela F Hartmann
- Steroid Research & Mass Spectrometry Unit, Laboratory for Translational Hormone Analytics in Paediatric Endocrinology, Division of Paediatric Endocrinology & Diabetology, Center of Child and Adolescent Medicine, Justus Liebig University, Giessen, Germany
| | - Stefan A Wudy
- Steroid Research & Mass Spectrometry Unit, Laboratory for Translational Hormone Analytics in Paediatric Endocrinology, Division of Paediatric Endocrinology & Diabetology, Center of Child and Adolescent Medicine, Justus Liebig University, Giessen, Germany
| | - Dina K N Dechmann
- Department of Migration and Immuno-Ecology, Max Planck Institute for Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alicia Hurtado
- Departamento de Genética, Universidad de Granada, Granada, Spain.,Instituto de Biotecnología, Centro de Investigación Biomédica, Universidad de Granada, Armilla, Granada, Spain
| | - Francisco J Barrionuevo
- Departamento de Genética, Universidad de Granada, Granada, Spain.,Instituto de Biotecnología, Centro de Investigación Biomédica, Universidad de Granada, Armilla, Granada, Spain
| | - Magdalena Schindler
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Izabela Harabula
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,U.S. Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA.,School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Bernd Timmermann
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rafael Jiménez
- Departamento de Genética, Universidad de Granada, Granada, Spain.,Instituto de Biotecnología, Centro de Investigación Biomédica, Universidad de Granada, Armilla, Granada, Spain
| | - Stefan Mundlos
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Darío G Lupiáñez
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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4
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Löser B, Lattau T, Sies V, Recio Ariza O, Reuter DA, Schlömerkemper N, Petzoldt M, Haas SA. International survey of neurosurgical anesthesia (iSonata) : An international survey of current practices in neurosurgical anesthesia. Anaesthesist 2020; 69:183-191. [PMID: 32006080 DOI: 10.1007/s00101-019-00727-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/18/2019] [Revised: 11/10/2019] [Accepted: 12/03/2019] [Indexed: 01/23/2023]
Abstract
BACKGROUND No standardized recommendations have been currently defined for anesthesia management of patients undergoing elective intracranial surgery. It can therefore be assumed that international clinical institutions have diverging approaches or standard operating procedures (SOP) which determine the type of general anesthesia, hemodynamic management, neuromuscular blockade, implementation of hypothermia and postoperative patient care. OBJECTIVE This international survey aimed to assess perioperative patient management during elective intracranial procedures. This survey was performed from February to October 2018 and 311 neurosurgical, maximum care centers across 19 European countries were contacted. The aim was to evaluate the anesthesia management to provide relevant data of neuroanesthesia practices across European centers. The survey differentiated between vascular and non-vascular as well as supratentorial and infratentorial procedures. RESULTS A total of 109 (35.0%) completed questionnaires from 15 European countries were analyzed. The results illustrated that total intravenous anesthesia was most commonly implemented during elective intracranial procedures (83.8%). All centers performed endotracheal intubation prior to major intracranial surgery (100%). Central venous lines were placed in 63.3% of cases. Moderate intraoperative hypothermia was carried out in 12.8% of the procedures, especially during vascular supratentorial and infratentorial surgery. A neuromuscular blockade during surgery was implemented in 74.1% of patients. Assessment of the neuromuscular junction was performed in 59.2% of cases, 76.7% of patients were immediately extubated in the operating room. 84.7% of these patients were directly transferred to a monitoring ward or an intensive care unit (ICU) and 55.1% of ventilated patients were transferred directly to an ICU. CONCLUSION The data demonstrate that many aspects of anesthesia management during elective intracranial surgery vary between European institutions. The data also suggest that a broad consensus exists regarding the implementation of total intravenous anesthesia, airway management (endotracheal intubation), the implementation of urinary catheters, large bore peripheral venous lines and the broad availability of cross-matched red blood cell concentrates. Nevertheless, anesthesia management (e.g. central venous catheterization, moderate hypothermia, neuromuscular monitoring) is still handled differently across many European institutions. A lack of standardized guidelines defining anesthetic management in patients undergoing intracranial procedures could explain this variability. Further studies could help establish optimal anesthesia management for these patients. This in turn could help in the development of national and international guidelines and SOPs which could define optimal management strategies for intracranial procedures.
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Affiliation(s)
- B Löser
- Department of Anesthesiology, Center of Anesthesiology and Intensive Care Medicine, University Medicine Rostock, Schillingallee 35, 18057, Rostock, Germany.
| | - T Lattau
- Department of Anesthesiology, Center of Anesthesiology and Intensive Care Medicine, University Medicine Rostock, Schillingallee 35, 18057, Rostock, Germany
| | - V Sies
- Department of Anesthesiology, Center of Anesthesiology and Intensive Care Medicine, University Medicine Rostock, Schillingallee 35, 18057, Rostock, Germany
| | - O Recio Ariza
- Department of Anesthesiology, Center of Anesthesiology and Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251, Hamburg, Germany
| | - D A Reuter
- Department of Anesthesiology, Center of Anesthesiology and Intensive Care Medicine, University Medicine Rostock, Schillingallee 35, 18057, Rostock, Germany
| | - N Schlömerkemper
- Department of Anesthesiology and Pain Medicine, UC Davis Medical Center, 2315 Stockton Blvd, 95817, Sacramento, CA, USA
| | - M Petzoldt
- Department of Anesthesiology, Center of Anesthesiology and Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251, Hamburg, Germany
| | - S A Haas
- Department of Anesthesiology, Center of Anesthesiology and Intensive Care Medicine, University Medicine Rostock, Schillingallee 35, 18057, Rostock, Germany
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5
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Frints SGM, Ozanturk A, Rodríguez Criado G, Grasshoff U, de Hoon B, Field M, Manouvrier-Hanu S, E Hickey S, Kammoun M, Gripp KW, Bauer C, Schroeder C, Toutain A, Mihalic Mosher T, Kelly BJ, White P, Dufke A, Rentmeester E, Moon S, Koboldt DC, van Roozendaal KEP, Hu H, Haas SA, Ropers HH, Murray L, Haan E, Shaw M, Carroll R, Friend K, Liebelt J, Hobson L, De Rademaeker M, Geraedts J, Fryns JP, Vermeesch J, Raynaud M, Riess O, Gribnau J, Katsanis N, Devriendt K, Bauer P, Gecz J, Golzio C, Gontan C, Kalscheuer VM. Pathogenic variants in E3 ubiquitin ligase RLIM/RNF12 lead to a syndromic X-linked intellectual disability and behavior disorder. Mol Psychiatry 2019; 24:1748-1768. [PMID: 29728705 DOI: 10.1038/s41380-018-0065-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/28/2018] [Indexed: 12/25/2022]
Abstract
RLIM, also known as RNF12, is an X-linked E3 ubiquitin ligase acting as a negative regulator of LIM-domain containing transcription factors and participates in X-chromosome inactivation (XCI) in mice. We report the genetic and clinical findings of 84 individuals from nine unrelated families, eight of whom who have pathogenic variants in RLIM (RING finger LIM domain-interacting protein). A total of 40 affected males have X-linked intellectual disability (XLID) and variable behavioral anomalies with or without congenital malformations. In contrast, 44 heterozygous female carriers have normal cognition and behavior, but eight showed mild physical features. All RLIM variants identified are missense changes co-segregating with the phenotype and predicted to affect protein function. Eight of the nine altered amino acids are conserved and lie either within a domain essential for binding interacting proteins or in the C-terminal RING finger catalytic domain. In vitro experiments revealed that these amino acid changes in the RLIM RING finger impaired RLIM ubiquitin ligase activity. In vivo experiments in rlim mutant zebrafish showed that wild type RLIM rescued the zebrafish rlim phenotype, whereas the patient-specific missense RLIM variants failed to rescue the phenotype and thus represent likely severe loss-of-function mutations. In summary, we identified a spectrum of RLIM missense variants causing syndromic XLID and affecting the ubiquitin ligase activity of RLIM, suggesting that enzymatic activity of RLIM is required for normal development, cognition and behavior.
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Affiliation(s)
- Suzanna G M Frints
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands. .,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands.
| | - Aysegul Ozanturk
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | | | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Bas de Hoon
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands.,Department of Gynaecology and Obstetrics, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Michael Field
- GOLD (Genetics of Learning and Disability) Service, Hunter Genetics, Waratah, NSW, 2298, Australia
| | - Sylvie Manouvrier-Hanu
- Clinique de Génétique médicale Guy Fontaine, Centre de référence maladies rares Anomalies du développement Hôpital Jeanne de Flandre, Lille, 59000, France.,EA 7364 RADEME Maladies Rares du Développement et du Métabolisme, Faculté de Médecine, Université de Lille, Lille, 59000, France
| | - Scott E Hickey
- Division of Molecular & Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA
| | - Molka Kammoun
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Karen W Gripp
- Alfred I. duPont Hospital for Children Nemours, Wilmington, DE, 19803, USA
| | - Claudia Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Annick Toutain
- Service de Génétique, Hôpital Bretonneau, CHU de Tours, Tours, 37044, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, 37032, France
| | - Theresa Mihalic Mosher
- Division of Molecular & Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Benjamin J Kelly
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Peter White
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Eveline Rentmeester
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Sungjin Moon
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | - Daniel C Koboldt
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Kees E P van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Hao Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Lucinda Murray
- GOLD (Genetics of Learning and Disability) Service, Hunter Genetics, Waratah, NSW, 2298, Australia
| | - Eric Haan
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, 5006, Australia
| | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Renee Carroll
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, 5006, Australia
| | - Jan Liebelt
- South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, 5006, Australia
| | - Lynne Hobson
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, 5006, Australia
| | - Marjan De Rademaeker
- Centre for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, 1090, Brussels, Belgium
| | - Joep Geraedts
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Jean-Pierre Fryns
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Joris Vermeesch
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Martine Raynaud
- Service de Génétique, Hôpital Bretonneau, CHU de Tours, Tours, 37044, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, 37032, France
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Nicholas Katsanis
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Christelle Golzio
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics; Centre National de la Recherche Scientifique, UMR7104; Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, 67400, Illkirch, France
| | - Cristina Gontan
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany.
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6
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Chiou TT, Long P, Schumann-Gillett A, Kanamarlapudi V, Haas SA, Harvey K, O'Mara ML, De Blas AL, Kalscheuer VM, Harvey RJ. Mutation p.R356Q in the Collybistin Phosphoinositide Binding Site Is Associated With Mild Intellectual Disability. Front Mol Neurosci 2019; 12:60. [PMID: 30914922 PMCID: PMC6422930 DOI: 10.3389/fnmol.2019.00060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 10/02/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
The recruitment of inhibitory GABAA receptors to neuronal synapses requires a complex interplay between receptors, neuroligins, the scaffolding protein gephyrin and the GDP-GTP exchange factor collybistin (CB). Collybistin is regulated by protein-protein interactions at the N-terminal SH3 domain, which can bind neuroligins 2/4 and the GABAAR α2 subunit. Collybistin also harbors a RhoGEF domain which mediates interactions with gephyrin and catalyzes GDP-GTP exchange on Cdc42. Lastly, collybistin has a pleckstrin homology (PH) domain, which binds phosphoinositides, such as phosphatidylinositol 3-phosphate (PI3P/PtdIns3P) and phosphatidylinositol 4-monophosphate (PI4P/PtdIns4P). PI3P located in early/sorting endosomes has recently been shown to regulate the postsynaptic clustering of gephyrin and GABAA receptors and consequently the strength of inhibitory synapses in cultured hippocampal neurons. This process is disrupted by mutations in the collybistin gene (ARHGEF9), which cause X-linked intellectual disability (XLID) by a variety of mechanisms converging on disrupted gephyrin and GABAA receptor clustering at central synapses. Here we report a novel missense mutation (chrX:62875607C>T, p.R356Q) in ARHGEF9 that affects one of the two paired arginine residues in the PH domain that were predicted to be vital for binding phosphoinositides. Functional assays revealed that recombinant collybistin CB3SH3- R356Q was deficient in PI3P binding and was not able to translocate EGFP-gephyrin to submembrane microaggregates in an in vitro clustering assay. Expression of the PI3P-binding mutants CB3SH3- R356Q and CB3SH3- R356N/R357N in cultured hippocampal neurones revealed that the mutant proteins did not accumulate at inhibitory synapses, but instead resulted in a clear decrease in the overall number of synaptic gephyrin clusters compared to controls. Molecular dynamics simulations suggest that the p.R356Q substitution influences PI3P binding by altering the range of structural conformations adopted by collybistin. Taken together, these results suggest that the p.R356Q mutation in ARHGEF9 is the underlying cause of XLID in the probands, disrupting gephyrin clustering at inhibitory GABAergic synapses via loss of collybistin PH domain phosphoinositide binding.
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Affiliation(s)
- Tzu-Ting Chiou
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
| | - Philip Long
- Department of Pharmacology, UCL School of Pharmacy, London, United Kingdom
| | | | | | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Kirsten Harvey
- Department of Pharmacology, UCL School of Pharmacy, London, United Kingdom
| | - Megan L O'Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT, Australia
| | - Angel L De Blas
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
| | - Vera M Kalscheuer
- Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Robert J Harvey
- School of Health and Sport Sciences, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Sunshine Coast Health Institute, Birtinya, QLD, Australia
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7
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Niturad CE, Lev D, Kalscheuer VM, Charzewska A, Schubert J, Lerman-Sagie T, Kroes HY, Oegema R, Traverso M, Specchio N, Lassota M, Chelly J, Bennett-Back O, Carmi N, Koffler-Brill T, Iacomino M, Trivisano M, Capovilla G, Striano P, Nawara M, Rzonca S, Fischer U, Bienek M, Jensen C, Hu H, Thiele H, Altmüller J, Krause R, May P, Becker F, Balling R, Biskup S, Haas SA, Nürnberg P, van Gassen KLI, Lerche H, Zara F, Maljevic S, Leshinsky-Silver E. Rare GABRA3 variants are associated with epileptic seizures, encephalopathy and dysmorphic features. Brain 2017; 140:2879-2894. [PMID: 29053855 DOI: 10.1093/brain/awx236] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/26/2017] [Indexed: 11/15/2022]
Abstract
Genetic epilepsies are caused by mutations in a range of different genes, many of them encoding ion channels, receptors or transporters. While the number of detected variants and genes increased dramatically in the recent years, pleiotropic effects have also been recognized, revealing that clinical syndromes with various degrees of severity arise from a single gene, a single mutation, or from different mutations showing similar functional defects. Accordingly, several genes coding for GABAA receptor subunits have been linked to a spectrum of benign to severe epileptic disorders and it was shown that a loss of function presents the major correlated pathomechanism. Here, we identified six variants in GABRA3 encoding the α3-subunit of the GABAA receptor. This gene is located on chromosome Xq28 and has not been previously associated with human disease. Five missense variants and one microduplication were detected in four families and two sporadic cases presenting with a range of epileptic seizure types, a varying degree of intellectual disability and developmental delay, sometimes with dysmorphic features or nystagmus. The variants co-segregated mostly but not completely with the phenotype in the families, indicating in some cases incomplete penetrance, involvement of other genes, or presence of phenocopies. Overall, males were more severely affected and there were three asymptomatic female mutation carriers compared to only one male without a clinical phenotype. X-chromosome inactivation studies could not explain the phenotypic variability in females. Three detected missense variants are localized in the extracellular GABA-binding NH2-terminus, one in the M2-M3 linker and one in the M4 transmembrane segment of the α3-subunit. Functional studies in Xenopus laevis oocytes revealed a variable but significant reduction of GABA-evoked anion currents for all mutants compared to wild-type receptors. The degree of current reduction correlated partially with the phenotype. The microduplication disrupted GABRA3 expression in fibroblasts of the affected patient. In summary, our results reveal that rare loss-of-function variants in GABRA3 increase the risk for a varying combination of epilepsy, intellectual disability/developmental delay and dysmorphic features, presenting in some pedigrees with an X-linked inheritance pattern.
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Affiliation(s)
- Cristina Elena Niturad
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Dorit Lev
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel.,Metabolic-Neurogenetic Clinic, Wolfson Medical Center, Holon, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Vera M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Agnieszka Charzewska
- Institute of Mother and Child, Department of Medical Genetics, Kasprzaka 17A, 01-211 Warsaw, Poland
| | - Julian Schubert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg
| | - Tally Lerman-Sagie
- Metabolic-Neurogenetic Clinic, Wolfson Medical Center, Holon, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Pediatric Neurology Unit, Wolfson Medical Center, Holon, Israel
| | - Hester Y Kroes
- Department of Genetics, University Medical Center Utrecht, 3508 AB, The Netherlands
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, 3508 AB, The Netherlands
| | - Monica Traverso
- Laboratory of Neurogenetics and Neuroscience, Institute G. Gaslini, Genova, Italy
| | - Nicola Specchio
- Neurology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Lassota
- Genetic Clinic, Hetmanska 21, 35-045 Rzeszów, Poland
| | | | | | - Nirit Carmi
- Metabolic-Neurogenetic Clinic, Wolfson Medical Center, Holon, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Genetics, University Medical Center Utrecht, 3508 AB, The Netherlands
| | - Tal Koffler-Brill
- Molecular Genetics Laboratory, Wolfson Medical Center, Holon, Israel
| | - Michele Iacomino
- Laboratory of Neurogenetics and Neuroscience, Institute G. Gaslini, Genova, Italy
| | - Marina Trivisano
- Neurology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giuseppe Capovilla
- Epilepsy Center, Department of Child Neuropsychiatry, C. Poma Hospital, Mantova, Italy
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophtalmology, Genetics, Maternal and Child Health, Institute G. Gaslini, Genoa, Italy
| | - Magdalena Nawara
- Institute of Mother and Child, Department of Medical Genetics, Kasprzaka 17A, 01-211 Warsaw, Poland
| | - Sylwia Rzonca
- Institute of Mother and Child, Department of Medical Genetics, Kasprzaka 17A, 01-211 Warsaw, Poland
| | - Ute Fischer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Melanie Bienek
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Corinna Jensen
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hao Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Holger Thiele
- Cologne Center for Genomics, Universität zu Köln, Köln, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, Universität zu Köln, Köln, Germany.,Institute of Human Genetics Universitätsklinik, Köln, Germany
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg
| | - Felicitas Becker
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | | | - Rudi Balling
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg
| | | | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, Universität zu Köln, Köln, Germany
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, 3508 AB, The Netherlands
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, Institute G. Gaslini, Genova, Italy
| | - Snezana Maljevic
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Esther Leshinsky-Silver
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel.,Metabolic-Neurogenetic Clinic, Wolfson Medical Center, Holon, Israel.,Molecular Genetics Laboratory, Wolfson Medical Center, Holon, Israel
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8
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Skopkova M, Hennig F, Shin BS, Turner CE, Stanikova D, Brennerova K, Stanik J, Fischer U, Henden L, Müller U, Steinberger D, Leshinsky-Silver E, Bottani A, Kurdiova T, Ukropec J, Nyitrayova O, Kolnikova M, Klimes I, Borck G, Bahlo M, Haas SA, Kim JR, Lotspeich-Cole LE, Gasperikova D, Dever TE, Kalscheuer VM. EIF2S3 Mutations Associated with Severe X-Linked Intellectual Disability Syndrome MEHMO. Hum Mutat 2017; 38:409-425. [PMID: 28055140 DOI: 10.1002/humu.23170] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/19/2016] [Accepted: 01/02/2017] [Indexed: 12/15/2022]
Abstract
Impairment of translation initiation and its regulation within the integrated stress response (ISR) and related unfolded-protein response has been identified as a cause of several multisystemic syndromes. Here, we link MEHMO syndrome, whose genetic etiology was unknown, to this group of disorders. MEHMO is a rare X-linked syndrome characterized by profound intellectual disability, epilepsy, hypogonadism and hypogenitalism, microcephaly, and obesity. We have identified a C-terminal frameshift mutation (Ile465Serfs) in the EIF2S3 gene in three families with MEHMO syndrome and a novel maternally inherited missense EIF2S3 variant (c.324T>A; p.Ser108Arg) in another male patient with less severe clinical symptoms. The EIF2S3 gene encodes the γ subunit of eukaryotic translation initiation factor 2 (eIF2), crucial for initiation of protein synthesis and regulation of the ISR. Studies in patient fibroblasts confirm increased ISR activation due to the Ile465Serfs mutation and functional assays in yeast demonstrate that the Ile465Serfs mutation impairs eIF2γ function to a greater extent than tested missense mutations, consistent with the more severe clinical phenotype of the Ile465Serfs male mutation carriers. Thus, we propose that more severe EIF2S3 mutations cause the full MEHMO phenotype, while less deleterious mutations cause a milder form of the syndrome with only a subset of the symptoms.
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Affiliation(s)
- Martina Skopkova
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Friederike Hennig
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Byung-Sik Shin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Clesson E Turner
- Department of Genetics, Walter Reed National Military Medical Center, Bethesda, Maryland, USA
| | - Daniela Stanikova
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.,First Department of Pediatrics, Medical Faculty of Comenius University, Bratislava, Slovakia
| | - Katarina Brennerova
- First Department of Pediatrics, Medical Faculty of Comenius University, Bratislava, Slovakia
| | - Juraj Stanik
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.,First Department of Pediatrics, Medical Faculty of Comenius University, Bratislava, Slovakia.,Center for Pediatric Research Leipzig, Hospital for Children & Adolescents, University of Leipzig, Germany
| | - Ute Fischer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lyndal Henden
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Ulrich Müller
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Daniela Steinberger
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany.,bio.logis Center for Human Genetics, Frankfurt a. M., Germany
| | - Esther Leshinsky-Silver
- Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel.,Metabolic-Neurogenetic Clinic, Wolfson Medical Center, Holon, Israel.,Molecular Genetics Laboratory, Wolfson Medical Center, Holon, Israel
| | - Armand Bottani
- Service of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Timea Kurdiova
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jozef Ukropec
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Miriam Kolnikova
- Department of Pediatric Neurology, Medical Faculty of Comenius University, Bratislava, Slovakia
| | - Iwar Klimes
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Guntram Borck
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Joo-Ran Kim
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Leda E Lotspeich-Cole
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Daniela Gasperikova
- DIABGENE & Laboratory of Diabetes and Metabolic Disorders, Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
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9
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Greiwe G, Tariparast PA, Behem C, Petzoldt M, Herich L, Trepte CJ, Reuter DA, Haas SA. Is applanation tonometry a reliable method for monitoring blood pressure in morbidly obese patients undergoing bariatric surgery? Br J Anaesth 2016; 116:790-6. [PMID: 27095239 DOI: 10.1093/bja/aew100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2016] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The aim of this study was to evaluate the validity of non-invasive continuous BP measurement by applanation tonometry in morbidly obese patients undergoing bariatric surgery. METHODS Arterial blood pressure (AP) was recorded intraoperatively both by applanation tonometry (AT) (T-Line 200pro, Tensys Medical(®), USA) and an arterial line (AL) after radial cannulation in obese patients undergoing bariatric surgery. Discrepancies between the two methods were assessed as bias, limits of agreement and percentage error. Mean, systolic, and diastolic arterial pressures were assessed (MAP, SAP, DAP respectively). Trending ability was assessed by concordance based on four-quadrant plotting. RESULTS Mean (sd) BMI of the 28 patients was 49.4 (9.7 kg m(-2)). A total of 201 907 time points were available for analysis. Bias for MAPAT compared with MAPAL was +3.97 mm Hg (SAPAT +3.45 mm Hg; DAPAT +3.66 mm Hg) with limits of agreement for MAPAT of -14.47 and +22.41 mm Hg (SAPAT -22.0 and +28.9 mm Hg; DAPAT -15.7 and +23.1 mm Hg). Percentage error for MAPAT was 23.5% (23.4% for SAPAT; 30.5% for DAPAT). Trending ability for MAP, SAP, and DAP revealed a concordance of 0.74, 0.72, and 0.71, respectively. CONCLUSIONS Continuous BP assessment by applanation tonometry is feasible in morbidly obese patients undergoing bariatric surgery. However, despite a low mean difference, 95% limits of agreement and trending ability indicate that the technology needs to be improved further, before being recommended for routine use in this group of patients.
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Affiliation(s)
| | - P A Tariparast
- Department of Intensive Care Medicine, University Medical Centre Hamburg-Eppendorf, Centre of Anaesthesiology and Intensive Care Medicine, Martinistrasse 52, 20246 Hamburg, Germany
| | - C Behem
- Department of Anaesthesiology
| | | | - L Herich
- University of Cologne, Institute of Medical Statistics, Informatics and Epidemiology, Kerpener Str.62, 50937 Köln, Germany
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10
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Kalscheuer VM, James VM, Himelright ML, Long P, Oegema R, Jensen C, Bienek M, Hu H, Haas SA, Topf M, Hoogeboom AJM, Harvey K, Walikonis R, Harvey RJ. Novel Missense Mutation A789V in IQSEC2 Underlies X-Linked Intellectual Disability in the MRX78 Family. Front Mol Neurosci 2016; 8:85. [PMID: 26793055 PMCID: PMC4707274 DOI: 10.3389/fnmol.2015.00085] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 10/23/2015] [Accepted: 12/14/2015] [Indexed: 12/04/2022] Open
Abstract
Disease gene discovery in neurodevelopmental disorders, including X-linked intellectual disability (XLID) has recently been accelerated by next-generation DNA sequencing approaches. To date, more than 100 human X chromosome genes involved in neuronal signaling pathways and networks implicated in cognitive function have been identified. Despite these advances, the mutations underlying disease in a large number of XLID families remained unresolved. We report the resolution of MRX78, a large family with six affected males and seven affected females, showing X-linked inheritance. Although a previous linkage study had mapped the locus to the short arm of chromosome X (Xp11.4-p11.23), this region contained too many candidate genes to be analyzed using conventional approaches. However, our X-chromosome exome resequencing, bioinformatics analysis and inheritance testing revealed a missense mutation (c.C2366T, p.A789V) in IQSEC2, encoding a neuronal GDP-GTP exchange factor for Arf family GTPases (ArfGEF) previously implicated in XLID. Molecular modeling of IQSEC2 revealed that the A789V substitution results in the insertion of a larger side-chain into a hydrophobic pocket in the catalytic Sec7 domain of IQSEC2. The A789V change is predicted to result in numerous clashes with adjacent amino acids and disruption of local folding of the Sec7 domain. Consistent with this finding, functional assays revealed that recombinant IQSEC2A789V was not able to catalyze GDP-GTP exchange on Arf6 as efficiently as wild-type IQSEC2. Taken together, these results strongly suggest that the A789V mutation in IQSEC2 is the underlying cause of XLID in the MRX78 family.
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Affiliation(s)
- Vera M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular GeneticsBerlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular GeneticsBerlin, Germany
| | | | - Miranda L Himelright
- Department of Physiology and Neurobiology, University of Connecticut Storrs, CT, USA
| | - Philip Long
- Department of Pharmacology, UCL School of Pharmacy London, UK
| | - Renske Oegema
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam Rotterdam, Netherlands
| | - Corinna Jensen
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Melanie Bienek
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Hao Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics Berlin, Germany
| | - Maya Topf
- Department of Biological Sciences, Institute for Structural and Molecular Biology, Birkbeck College London, UK
| | - A Jeannette M Hoogeboom
- Department of Clinical Genetics, Erasmus MC University Medical Center Rotterdam Rotterdam, Netherlands
| | - Kirsten Harvey
- Department of Pharmacology, UCL School of Pharmacy London, UK
| | - Randall Walikonis
- Department of Physiology and Neurobiology, University of Connecticut Storrs, CT, USA
| | - Robert J Harvey
- Department of Pharmacology, UCL School of Pharmacy London, UK
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11
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Hu H, Haas SA, Chelly J, Van Esch H, Raynaud M, de Brouwer APM, Weinert S, Froyen G, Frints SGM, Laumonnier F, Zemojtel T, Love MI, Richard H, Emde AK, Bienek M, Jensen C, Hambrock M, Fischer U, Langnick C, Feldkamp M, Wissink-Lindhout W, Lebrun N, Castelnau L, Rucci J, Montjean R, Dorseuil O, Billuart P, Stuhlmann T, Shaw M, Corbett MA, Gardner A, Willis-Owen S, Tan C, Friend KL, Belet S, van Roozendaal KEP, Jimenez-Pocquet M, Moizard MP, Ronce N, Sun R, O'Keeffe S, Chenna R, van Bömmel A, Göke J, Hackett A, Field M, Christie L, Boyle J, Haan E, Nelson J, Turner G, Baynam G, Gillessen-Kaesbach G, Müller U, Steinberger D, Budny B, Badura-Stronka M, Latos-Bieleńska A, Ousager LB, Wieacker P, Rodríguez Criado G, Bondeson ML, Annerén G, Dufke A, Cohen M, Van Maldergem L, Vincent-Delorme C, Echenne B, Simon-Bouy B, Kleefstra T, Willemsen M, Fryns JP, Devriendt K, Ullmann R, Vingron M, Wrogemann K, Wienker TF, Tzschach A, van Bokhoven H, Gecz J, Jentsch TJ, Chen W, Ropers HH, Kalscheuer VM. X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes. Mol Psychiatry 2016; 21:133-48. [PMID: 25644381 PMCID: PMC5414091 DOI: 10.1038/mp.2014.193] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/17/2014] [Accepted: 12/08/2014] [Indexed: 12/27/2022]
Abstract
X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4(-/-) mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.
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Affiliation(s)
- H Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - S A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - J Chelly
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - H Van Esch
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - M Raynaud
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France,Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - A P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - S Weinert
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany,Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - G Froyen
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium,Human Genome Laboratory, Department of Human Genetics, K.U. Leuven, Leuven, Belgium
| | - S G M Frints
- Department of Clinical Genetics, Maastricht University Medical Center, azM, Maastricht, The Netherlands,School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - F Laumonnier
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France
| | - T Zemojtel
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M I Love
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - H Richard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A-K Emde
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M Bienek
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - C Jensen
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M Hambrock
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - U Fischer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - C Langnick
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - M Feldkamp
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - W Wissink-Lindhout
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - N Lebrun
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - L Castelnau
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - J Rucci
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - R Montjean
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - O Dorseuil
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - P Billuart
- University Paris Descartes, Paris, France,Centre National de la Recherche Scientifique Unité Mixte de Recherche 8104, Institut National de la Santé et de la Recherche Médicale Unité 1016, Institut Cochin, Paris, France
| | - T Stuhlmann
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany,Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - M Shaw
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - M A Corbett
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - A Gardner
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - S Willis-Owen
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,National Heart and Lung Institute, Imperial College London, London, UK
| | - C Tan
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia
| | - K L Friend
- SA Pathology, Women's and Children's Hospital, Adelaide, SA, Australia
| | - S Belet
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium,Human Genome Laboratory, Department of Human Genetics, K.U. Leuven, Leuven, Belgium
| | - K E P van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Center, azM, Maastricht, The Netherlands,School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - M Jimenez-Pocquet
- Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - M-P Moizard
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France,Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - N Ronce
- Inserm U930 ‘Imaging and Brain', Tours, France,University François-Rabelais, Tours, France,Centre Hospitalier Régional Universitaire, Service de Génétique, Tours, France
| | - R Sun
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - S O'Keeffe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - R Chenna
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A van Bömmel
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - J Göke
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A Hackett
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - M Field
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - L Christie
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - J Boyle
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - E Haan
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,SA Pathology, Women's and Children's Hospital, Adelaide, SA, Australia
| | - J Nelson
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia
| | - G Turner
- Genetics of Learning and Disability Service, Hunter Genetics, Waratah, NSW, Australia
| | - G Baynam
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia,School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia,Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia,Telethon Kids Institute, Perth, WA, Australia
| | | | - U Müller
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany,bio.logis Center for Human Genetics, Frankfurt a. M., Germany
| | - D Steinberger
- Institut für Humangenetik, Justus-Liebig-Universität Giessen, Giessen, Germany,bio.logis Center for Human Genetics, Frankfurt a. M., Germany
| | - B Budny
- Chair and Department of Endocrinology, Metabolism and Internal Diseases, Ponzan University of Medical Sciences, Poznan, Poland
| | - M Badura-Stronka
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - A Latos-Bieleńska
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - L B Ousager
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - P Wieacker
- Institut für Humangenetik, Universitätsklinikum Münster, Muenster, Germany
| | | | - M-L Bondeson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - G Annerén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - A Dufke
- Institut für Medizinische Genetik und Angewandte Genomik, Tübingen, Germany
| | - M Cohen
- Kinderzentrum München, München, Germany
| | - L Van Maldergem
- Centre de Génétique Humaine, Université de Franche-Comté, Besançon, France
| | - C Vincent-Delorme
- Service de Génétique, Hôpital Jeanne de Flandre CHRU de Lilles, Lille, France
| | - B Echenne
- Service de Neuro-Pédiatrie, CHU Montpellier, Montpellier, France
| | - B Simon-Bouy
- Laboratoire SESEP, Centre hospitalier de Versailles, Le Chesnay, France
| | - T Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - M Willemsen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - J-P Fryns
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - K Devriendt
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - R Ullmann
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - K Wrogemann
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - T F Wienker
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - A Tzschach
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - H van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - J Gecz
- School of Paediatrics and Reproductive Health, The University of Adelaide, Adelaide, SA, Australia,Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - T J Jentsch
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany,Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - W Chen
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany,Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - H-H Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - V M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany,Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany. E-mail:
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12
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Kumar R, Corbett MA, Van Bon BWM, Gardner A, Woenig JA, Jolly LA, Douglas E, Friend K, Tan C, Van Esch H, Holvoet M, Raynaud M, Field M, Leffler M, Budny B, Wisniewska M, Badura-Stronka M, Latos-Bieleńska A, Batanian J, Rosenfeld JA, Basel-Vanagaite L, Jensen C, Bienek M, Froyen G, Ullmann R, Hu H, Love MI, Haas SA, Stankiewicz P, Cheung SW, Baxendale A, Nicholl J, Thompson EM, Haan E, Kalscheuer VM, Gecz J. Increased STAG2 dosage defines a novel cohesinopathy with intellectual disability and behavioral problems. Hum Mol Genet 2015; 24:7171-81. [PMID: 26443594 DOI: 10.1093/hmg/ddv414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
Next generation genomic technologies have made a significant contribution to the understanding of the genetic architecture of human neurodevelopmental disorders. Copy number variants (CNVs) play an important role in the genetics of intellectual disability (ID). For many CNVs, and copy number gains in particular, the responsible dosage-sensitive gene(s) have been hard to identify. We have collected 18 different interstitial microduplications and 1 microtriplication of Xq25. There were 15 affected individuals from 6 different families and 13 singleton cases, 28 affected males in total. The critical overlapping region involved the STAG2 gene, which codes for a subunit of the cohesin complex that regulates cohesion of sister chromatids and gene transcription. We demonstrate that STAG2 is the dosage-sensitive gene within these CNVs, as gains of STAG2 mRNA and protein dysregulate disease-relevant neuronal gene networks in cells derived from affected individuals. We also show that STAG2 gains result in increased expression of OPHN1, a known X-chromosome ID gene. Overall, we define a novel cohesinopathy due to copy number gain of Xq25 and STAG2 in particular.
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Affiliation(s)
- Raman Kumar
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Mark A Corbett
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | | | - Alison Gardner
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Joshua A Woenig
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Lachlan A Jolly
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Chuan Tan
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Maureen Holvoet
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Martine Raynaud
- Centre Hospitalier Régional Universitaire, Service de Génétique, 37000 Tours, France
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Melanie Leffler
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Bartłomiej Budny
- Department of Endocrinology, Metabolism and Internal Diseases and
| | - Marzena Wisniewska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan 60-355, Poland
| | | | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan 60-355, Poland
| | | | - Jill A Rosenfeld
- Signature Genomic Laboratories, Spokane, WA 99207, USA, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lina Basel-Vanagaite
- Raphael Recanati Genetic Institute and Felsenstein Medical Research Center, Rabin Medical Center, Beilinson Campus, Petah Tikva 49100, Israel
| | | | | | - Guy Froyen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium and
| | - Reinhard Ullmann
- Department of Human Molecular Genetics and, Bundeswehr Institute of Radiobiology, 80937 Munich, Germany
| | - Hao Hu
- Department of Human Molecular Genetics and
| | - Michael I Love
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne Baxendale
- South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | - Jillian Nicholl
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Elizabeth M Thompson
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia, South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | - Eric Haan
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia, South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | | | - Jozef Gecz
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia,
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13
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Zanni G, Kalscheuer VM, Friedrich A, Barresi S, Alfieri P, Di Capua M, Haas SA, Piccini G, Karl T, Klauck SM, Bellacchio E, Emma F, Cappa M, Bertini E, Breitenbach-Koller L. A Novel Mutation in RPL10 (Ribosomal Protein L10) Causes X-Linked Intellectual Disability, Cerebellar Hypoplasia, and Spondylo-Epiphyseal Dysplasia. Hum Mutat 2015; 36:1155-8. [PMID: 26290468 DOI: 10.1002/humu.22860] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 05/04/2015] [Accepted: 08/12/2015] [Indexed: 11/12/2022]
Abstract
RPL10 encodes ribosomal protein L10 (uL16), a highly conserved multifunctional component of the large ribosomal subunit, involved in ribosome biogenesis and function. Using X-exome resequencing, we identified a novel missense mutation (c.191C>T; p.(A64V)) in the N-terminal domain of the protein, in a family with two affected cousins presenting with X-linked intellectual disability, cerebellar hypoplasia, and spondylo-epiphyseal dysplasia (SED). We assessed the impact of the mutation on the translational capacity of the cell using yeast as model system. The mutation generates a functional ribosomal protein, able to complement the translational defects of a conditional lethal mutation of yeast rpl10. However, unlike previously reported mutations, this novel RPL10 missense mutation results in an increase in the actively translating ribosome population. Our results expand the mutational and clinical spectrum of RPL10 identifying a new genetic cause of SED and highlight the emerging role of ribosomal proteins in the pathogenesis of neurodevelopmental disorders.
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Affiliation(s)
- Ginevra Zanni
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital, IRRCS, Rome, Italy
| | - Vera M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Andreas Friedrich
- Department of Cell Biology, University of Salzburg, Salzburg, Austria
| | - Sabina Barresi
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital, IRRCS, Rome, Italy
| | - Paolo Alfieri
- Unit of Child Neuropsychiatry, Department of Neurosciences, Bambino Gesù Children's Hospital, IRRCS, Rome, Italy
| | - Matteo Di Capua
- Unit of Neurology, Department of Neurosciences, Bambino Gesù Children's Hospital, IRRCS, Rome, Italy
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Giorgia Piccini
- Unit of Child Neuropsychiatry, Department of Neurosciences, Bambino Gesù Children's Hospital, IRRCS, Rome, Italy
| | - Thomas Karl
- Department of Cell Biology, University of Salzburg, Salzburg, Austria
| | - Sabine M Klauck
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Francesco Emma
- Unit of Nephrology, Department of Pediatrics, Bambino Gesù Children's Hospital, IRRCS, Rome, Italy
| | - Marco Cappa
- Unit of Clinical Endocrinology, Department of Pediatrics, Bambino Gesù Children's Hospital, IRRCS, Rome, Italy
| | - Enrico Bertini
- Unit of Molecular Medicine for Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children's Hospital, IRRCS, Rome, Italy
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14
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Hackmann K, Rump A, Haas SA, Lemke JR, Fryns JP, Tzschach A, Wieczorek D, Albrecht B, Kuechler A, Ripperger T, Kobelt A, Oexle K, Tinschert S, Schrock E, Kalscheuer VM, Di Donato N. Tentative clinical diagnosis of Lujan-Fryns syndrome-A conglomeration of different genetic entities? Am J Med Genet A 2015; 170A:94-102. [DOI: 10.1002/ajmg.a.37378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 08/24/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Karl Hackmann
- Institut fuer Klinische Genetik; Medizinische Fakultaet Carl Gustav Carus; Technische Universitaet Dresden; Dresden Germany
| | - Andreas Rump
- Institut fuer Klinische Genetik; Medizinische Fakultaet Carl Gustav Carus; Technische Universitaet Dresden; Dresden Germany
| | - Stefan A. Haas
- Department of Computational Molecular Biology; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Johannes R. Lemke
- Division of Human Genetics; University Children's Hospital Inselspital; Bern Switzerland
| | - Jean-Pierre Fryns
- Centre for Human Genetics; KU Leuven/University Hospital Leuven; Leuven Belgium
| | - Andreas Tzschach
- Institut fuer Medizinische Genetik und Angewandte Genomik; Universitaetsklinikum; Tuebingen Germany
| | - Dagmar Wieczorek
- Institut für Humangenetik; Universitätsklinikum Essen; Universitaet Duisburg-Essen; Essen Germany
| | - Beate Albrecht
- Institut für Humangenetik; Universitätsklinikum Essen; Universitaet Duisburg-Essen; Essen Germany
| | - Alma Kuechler
- Institut für Humangenetik; Universitätsklinikum Essen; Universitaet Duisburg-Essen; Essen Germany
| | - Tim Ripperger
- Institute of Cell and Molecular Pathology; Hannover Medical School; Hannover Germany
| | - Albrecht Kobelt
- Zentrum fuer Diagnostik GmbH MVZ; Praxis fuer Humangenetik; Klinikum Chemnitz; Chemnitz Germany
| | - Konrad Oexle
- Institut fuer Klinische Genetik; Medizinische Fakultaet Carl Gustav Carus; Technische Universitaet Dresden; Dresden Germany
| | - Sigrid Tinschert
- Institut fuer Klinische Genetik; Medizinische Fakultaet Carl Gustav Carus; Technische Universitaet Dresden; Dresden Germany
| | - Evelin Schrock
- Institut fuer Klinische Genetik; Medizinische Fakultaet Carl Gustav Carus; Technische Universitaet Dresden; Dresden Germany
| | - Vera M. Kalscheuer
- Department of Human Molecular Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Nataliya Di Donato
- Institut fuer Klinische Genetik; Medizinische Fakultaet Carl Gustav Carus; Technische Universitaet Dresden; Dresden Germany
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15
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Vulto-van Silfhout AT, Nakagawa T, Bahi-Buisson N, Haas SA, Hu H, Bienek M, Vissers LELM, Gilissen C, Tzschach A, Busche A, Müsebeck J, Rump P, Mathijssen IB, Avela K, Somer M, Doagu F, Philips AK, Rauch A, Baumer A, Voesenek K, Poirier K, Vigneron J, Amram D, Odent S, Nawara M, Obersztyn E, Lenart J, Charzewska A, Lebrun N, Fischer U, Nillesen WM, Yntema HG, Järvelä I, Ropers HH, de Vries BBA, Brunner HG, van Bokhoven H, Raymond FL, Willemsen MAAP, Chelly J, Xiong Y, Barkovich AJ, Kalscheuer VM, Kleefstra T, de Brouwer APM. Variants in CUL4B are associated with cerebral malformations. Hum Mutat 2015; 36:106-17. [PMID: 25385192 DOI: 10.1002/humu.22718] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 08/21/2014] [Accepted: 10/17/2014] [Indexed: 11/08/2022]
Abstract
Variants in cullin 4B (CUL4B) are a known cause of syndromic X-linked intellectual disability. Here, we describe an additional 25 patients from 11 families with variants in CUL4B. We identified nine different novel variants in these families and confirmed the pathogenicity of all nontruncating variants. Neuroimaging data, available for 15 patients, showed the presence of cerebral malformations in ten patients. The cerebral anomalies comprised malformations of cortical development (MCD), ventriculomegaly, and diminished white matter volume. The phenotypic heterogeneity of the cerebral malformations might result from the involvement of CUL-4B in various cellular pathways essential for normal brain development. Accordingly, we show that CUL-4B interacts with WDR62, a protein in which variants were previously identified in patients with microcephaly and a wide range of MCD. This interaction might contribute to the development of cerebral malformations in patients with variants in CUL4B.
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Affiliation(s)
- Anneke T Vulto-van Silfhout
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
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16
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Kumar R, Corbett MA, van Bon BWM, Woenig JA, Weir L, Douglas E, Friend KL, Gardner A, Shaw M, Jolly LA, Tan C, Hunter MF, Hackett A, Field M, Palmer EE, Leffler M, Rogers C, Boyle J, Bienek M, Jensen C, Van Buggenhout G, Van Esch H, Hoffmann K, Raynaud M, Zhao H, Reed R, Hu H, Haas SA, Haan E, Kalscheuer VM, Gecz J. THOC2 Mutations Implicate mRNA-Export Pathway in X-Linked Intellectual Disability. Am J Hum Genet 2015; 97:302-10. [PMID: 26166480 DOI: 10.1016/j.ajhg.2015.05.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [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: 02/20/2015] [Accepted: 05/27/2015] [Indexed: 11/30/2022] Open
Abstract
Export of mRNA from the cell nucleus to the cytoplasm is essential for protein synthesis, a process vital to all living eukaryotic cells. mRNA export is highly conserved and ubiquitous. Mutations affecting mRNA and mRNA processing or export factors, which cause aberrant retention of mRNAs in the nucleus, are thus emerging as contributors to an important class of human genetic disorders. Here, we report that variants in THOC2, which encodes a subunit of the highly conserved TREX mRNA-export complex, cause syndromic intellectual disability (ID). Affected individuals presented with variable degrees of ID and commonly observed features included speech delay, elevated BMI, short stature, seizure disorders, gait disturbance, and tremors. X chromosome exome sequencing revealed four missense variants in THOC2 in four families, including family MRX12, first ascertained in 1971. We show that two variants lead to decreased stability of THOC2 and its TREX-complex partners in cells derived from the affected individuals. Protein structural modeling showed that the altered amino acids are located in the RNA-binding domains of two complex THOC2 structures, potentially representing two different intermediate RNA-binding states of THOC2 during RNA transport. Our results show that disturbance of the canonical molecular pathway of mRNA export is compatible with life but results in altered neuronal development with other comorbidities.
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MESH Headings
- Active Transport, Cell Nucleus/genetics
- Amino Acid Sequence
- Base Sequence
- Chromosomes, Human, X/genetics
- Humans
- Mental Retardation, X-Linked/genetics
- Mental Retardation, X-Linked/pathology
- Models, Molecular
- Molecular Sequence Data
- Mutation, Missense/genetics
- Pedigree
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- Sequence Analysis, DNA
- Syndrome
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Affiliation(s)
- Raman Kumar
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Mark A Corbett
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Bregje W M van Bon
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Joshua A Woenig
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Lloyd Weir
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Kathryn L Friend
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Alison Gardner
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Marie Shaw
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Lachlan A Jolly
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Chuan Tan
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Medical Centre, Clayton, VIC 3168, Australia; Department of Paediatrics, Monash University, Clayton, VIC 3168, Australia
| | - Anna Hackett
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Elizabeth E Palmer
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Melanie Leffler
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Carolyn Rogers
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Jackie Boyle
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Melanie Bienek
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Corinna Jensen
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | | | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Leuven 3000, Belgium
| | - Katrin Hoffmann
- Institute of Human Genetics, Martin Luther University Halle-Wittenberg, Magdeburger Strasse 2, 06112 Halle (Saale), Germany
| | - Martine Raynaud
- INSERM U930, Imaging and Brain, François-Rabelais University, 37000 Tours, France; INSERM U930, Service de Génétique, Centre Hospitalier Régional Universitaire, 37000 Tours, France
| | - Huiying Zhao
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Robin Reed
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Hao Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Eric Haan
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | - Vera M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Jozef Gecz
- School of Paediatrics and Reproductive Health, Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; School of Molecular and Biomedical Sciences, University of Adelaide, Adelaide, SA 5005, Australia.
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17
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George J, Lim JS, Jang SJ, Cun Y, Ozretić L, Kong G, Leenders F, Lu X, Fernández-Cuesta L, Bosco G, Müller C, Dahmen I, Jahchan NS, Park KS, Yang D, Karnezis AN, Vaka D, Torres A, Wang MS, Korbel JO, Menon R, Chun SM, Kim D, Wilkerson M, Hayes N, Engelmann D, Pützer B, Bos M, Michels S, Vlasic I, Seidel D, Pinther B, Schaub P, Becker C, Altmüller J, Yokota J, Kohno T, Iwakawa R, Tsuta K, Noguchi M, Muley T, Hoffmann H, Schnabel PA, Petersen I, Chen Y, Soltermann A, Tischler V, Choi CM, Kim YH, Massion PP, Zou Y, Jovanovic D, Kontic M, Wright GM, Russell PA, Solomon B, Koch I, Lindner M, Muscarella LA, la Torre A, Field JK, Jakopovic M, Knezevic J, Castaños-Vélez E, Roz L, Pastorino U, Brustugun OT, Lund-Iversen M, Thunnissen E, Köhler J, Schuler M, Botling J, Sandelin M, Sanchez-Cespedes M, Salvesen HB, Achter V, Lang U, Bogus M, Schneider PM, Zander T, Ansén S, Hallek M, Wolf J, Vingron M, Yatabe Y, Travis WD, Nürnberg P, Reinhardt C, Perner S, Heukamp L, Büttner R, Haas SA, Brambilla E, Peifer M, Sage J, Thomas RK. Comprehensive genomic profiles of small cell lung cancer. Nature 2015; 524:47-53. [PMID: 26168399 DOI: 10.1038/nature14664] [Citation(s) in RCA: 1406] [Impact Index Per Article: 156.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 06/15/2015] [Indexed: 02/06/2023]
Abstract
We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Δex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
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Affiliation(s)
- Julie George
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Jing Shan Lim
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California 94305, USA
| | - Se Jin Jang
- Department of Pathology and Center for Cancer Genome Discovery, University of Ulsan College of Medicine, Asan Medical Center 88, Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Korea
| | - Yupeng Cun
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Luka Ozretić
- Department of Pathology, University Hospital Cologne, 50937 Cologne, Germany
| | - Gu Kong
- Department of Pathology, College of Medicine, Hanyang University. 222 Wangsimniro, Seongdong-gu, Seoul 133-791, Korea
| | - Frauke Leenders
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Xin Lu
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Lynnette Fernández-Cuesta
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Graziella Bosco
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Christian Müller
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Ilona Dahmen
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Nadine S Jahchan
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California 94305, USA
| | - Kwon-Sik Park
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California 94305, USA
| | - Dian Yang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California 94305, USA
| | - Anthony N Karnezis
- Vancouver General Hospital, Terry Fox laboratory, Vancouver, British Columbia V5Z 1L3, Canada
| | - Dedeepya Vaka
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California 94305, USA
| | - Angela Torres
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California 94305, USA
| | - Maia Segura Wang
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Roopika Menon
- Institute of Pathology, Center of Integrated Oncology Cologne-Bonn, University Hospital of Bonn, 53127 Bonn, Germany
| | - Sung-Min Chun
- Department of Pathology and Center for Cancer Genome Discovery, University of Ulsan College of Medicine, Asan Medical Center 88, Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Korea
| | - Deokhoon Kim
- Center for Cancer Genome Discovery, University of Ulsan College of Medicine, Asan Medical Center 88, Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Korea
| | - Matt Wilkerson
- Department of Genetics, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, North Carolina 27599-7295, USA
| | - Neil Hayes
- UNC Lineberger Comprehensive Cancer Center School of Medicine, University of North Carolina at Chapel Hill, North Carolina 27599-7295, USA
| | - David Engelmann
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany
| | - Brigitte Pützer
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany
| | - Marc Bos
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Sebastian Michels
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, 50937 Cologne, Germany
| | - Ignacija Vlasic
- Department of Internal Medicine, University Hospital of Cologne, 50931 Cologne, Germany
| | - Danila Seidel
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Berit Pinther
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Philipp Schaub
- Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Christian Becker
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- 1] Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany. [2] Institute of Human Genetics, University Hospital Cologne, 50931 Cologne, Germany
| | - Jun Yokota
- 1] Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo 1040045, Japan. [2] Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Barcelona 08916, Spain
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo 1040045, Japan
| | - Reika Iwakawa
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo 1040045, Japan
| | - Koji Tsuta
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital Chuo-ku, Tokyo 1040045, Japan
| | - Masayuki Noguchi
- Department of Pathology, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8575, Japan
| | - Thomas Muley
- 1] Thoraxklinik at University Hospital Heidelberg, Amalienstrasse 5, 69126 Heidelberg, Germany. [2] Translational Lung Research Center Heidelberg (TLRC-H), Member of German Center for Lung Research (DZL), Amalienstrasse 5, 69126 Heidelberg, Germany
| | - Hans Hoffmann
- Thoraxklinik at University Hospital Heidelberg, Amalienstrasse 5, 69126 Heidelberg, Germany
| | - Philipp A Schnabel
- 1] Translational Lung Research Center Heidelberg (TLRC-H), Member of German Center for Lung Research (DZL), Amalienstrasse 5, 69126 Heidelberg, Germany. [2] Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 220, 69120 Heidelberg, Germany
| | - Iver Petersen
- Institute of Pathology, Jena University Hospital, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Yuan Chen
- Institute of Pathology, Jena University Hospital, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Alex Soltermann
- Institute of Surgical Pathology, University Hospital Zürich, 8091 Zürich, Switzerland
| | - Verena Tischler
- Institute of Surgical Pathology, University Hospital Zürich, 8091 Zürich, Switzerland
| | - Chang-min Choi
- Department of Oncology, University of Ulsan College of Medicine, Asan Medical Center, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Korea
| | - Yong-Hee Kim
- Department of Thoracic and Cardiovascular Surgery, University of Ulsan College of Medicine, Asan Medical Center, 88, Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Korea
| | - Pierre P Massion
- Thoracic Program, Vanderbilt-Ingram Cancer Center PRB 640, 2220 Pierce Avenue, Nashville, Tennessee 37232, USA
| | - Yong Zou
- Thoracic Program, Vanderbilt-Ingram Cancer Center PRB 640, 2220 Pierce Avenue, Nashville, Tennessee 37232, USA
| | - Dragana Jovanovic
- University Hospital of Pulmonology, Clinical Center of Serbia, Medical School, University of Belgrade, 11000 Belgrade, Serbia
| | - Milica Kontic
- University Hospital of Pulmonology, Clinical Center of Serbia, Medical School, University of Belgrade, 11000 Belgrade, Serbia
| | - Gavin M Wright
- Department of Surgery, St. Vincent's Hospital, Peter MacCallum Cancer Centre, 3065 Melbourne, Victoria, Australia
| | - Prudence A Russell
- Department of Pathology, St. Vincent's Hospital, Peter MacCallum Cancer Centre, 3065 Melbourne, Victoria, Australia
| | - Benjamin Solomon
- Department of Haematology and Medical Oncology, Peter MacCallum Cancer Centre, 3065 Melbourne, Victoria, Australia
| | - Ina Koch
- Asklepios Biobank für Lungenerkrankungen, Comprehensive Pneumology Center Munich, Member of the German Center for Lung Research (DZL), Asklepios Fachkliniken München-Gauting 82131, Germany
| | - Michael Lindner
- Asklepios Biobank für Lungenerkrankungen, Comprehensive Pneumology Center Munich, Member of the German Center for Lung Research (DZL), Asklepios Fachkliniken München-Gauting 82131, Germany
| | - Lucia A Muscarella
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini, 71013 San Giovanni, Rotondo, Italy
| | - Annamaria la Torre
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini, 71013 San Giovanni, Rotondo, Italy
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, The University of Liverpool Cancer Research Centre, 200 London Road, L69 3GA Liverpool, UK
| | - Marko Jakopovic
- University of Zagreb, School of Medicine, Department for Respiratory Diseases Jordanovac, University Hospital Center Zagreb, 10000 Zagreb, Croatia
| | - Jelena Knezevic
- Laboratory for Translational Medicine, Rudjer Boskovic Institute, 10000 Zagreb, Croatia
| | | | - Luca Roz
- Tumor Genomics Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS - Istituto Nazionale Tumori, Via Venezian 1, 20133 Milan, Italy
| | - Ugo Pastorino
- Thoracic Surgery Unit, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milan, Italy
| | - Odd-Terje Brustugun
- 1] Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, N-0424 Oslo, Norway. [2] Department of Oncology, Norwegian Radium Hospital, Oslo University Hospital, N-0310 Oslo, Norway
| | - Marius Lund-Iversen
- Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, N-0310 Oslo, Norway
| | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, 1007 MB Amsterdam, The Netherlands
| | - Jens Köhler
- 1] West German Cancer Center, Department of Medical Oncology, University Hospital Essen, 45147 Essen, Germany. [2] German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Martin Schuler
- 1] West German Cancer Center, Department of Medical Oncology, University Hospital Essen, 45147 Essen, Germany. [2] German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Johan Botling
- Departments of Immunology, Genetics and Pathology, and Medical Sciences, Respiratory, Allergy and Sleep Research, Uppsala University, 75185 Uppsala, Sweden
| | - Martin Sandelin
- Departments of Immunology, Genetics and Pathology, and Medical Sciences, Respiratory, Allergy and Sleep Research, Uppsala University, 75185 Uppsala, Sweden
| | - Montserrat Sanchez-Cespedes
- Genes and Cancer Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Barcelona, Spain
| | - Helga B Salvesen
- 1] Department of Clinical Science, Center for Cancer Biomarkers, University of Bergen, N-5058 Bergen, Norway. [2] Department of Gynecology and Obstetrics, Haukeland University Hospital, N-5058 Bergen, Norway
| | - Viktor Achter
- Computing Center, University of Cologne, 50931 Cologne, Germany
| | - Ulrich Lang
- 1] Computing Center, University of Cologne, 50931 Cologne, Germany. [2] Department of Informatics, University of Cologne, 50931 Cologne, Germany
| | - Magdalena Bogus
- Institute of Legal Medicine, University of Cologne, 50823 Cologne, Germany
| | - Peter M Schneider
- Institute of Legal Medicine, University of Cologne, 50823 Cologne, Germany
| | - Thomas Zander
- Gastrointestinal Cancer Group Cologne, Center of Integrated Oncology Cologne-Bonn, Department I for Internal Medicine, University Hospital of Cologne, 50937 Cologne, Germany
| | - Sascha Ansén
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, 50937 Cologne, Germany
| | - Michael Hallek
- 1] Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, 50937 Cologne, Germany. [2] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Jürgen Wolf
- Department I of Internal Medicine, Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, 50937 Cologne, Germany
| | - Martin Vingron
- Computational Molecular Biology Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, 464-8681 Nagoya, Japan
| | - William D Travis
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York 10065, USA
| | - Peter Nürnberg
- 1] Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany. [2] Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany. [3] Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Christian Reinhardt
- Department of Internal Medicine, University Hospital of Cologne, 50931 Cologne, Germany
| | - Sven Perner
- Center for Cancer Genome Discovery, University of Ulsan College of Medicine, Asan Medical Center 88, Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Korea
| | - Lukas Heukamp
- Department of Pathology, University Hospital Cologne, 50937 Cologne, Germany
| | - Reinhard Büttner
- Department of Pathology, University Hospital Cologne, 50937 Cologne, Germany
| | - Stefan A Haas
- Computational Molecular Biology Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Elisabeth Brambilla
- Department of Pathology, CHU Grenoble INSERM U823, University Joseph Fourier, Institute Albert Bonniot 38043, CS10217 Grenoble, France
| | - Martin Peifer
- 1] Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany. [2] Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Julien Sage
- Departments of Pediatrics and Genetics, Stanford University, Stanford, California 94305, USA
| | - Roman K Thomas
- 1] Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany. [2] Department of Pathology, University Hospital Cologne, 50937 Cologne, Germany
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18
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Abstract
Goal-directed hemodynamic therapy is becoming increasingly more interesting for anesthesiologists and intensive care physicians. Meta-analyses of studies evaluating perioperative therapy algorithms demonstrated a reduction of postoperative morbidity compared to the previous clinical practices. In this review article the basic concepts of goal-directed hemodynamic therapy and the principles of previously employed therapy algorithms are described and discussed. Furthermore, the questions of how these therapy strategies can be transferred into daily clinical practice and whether these therapeutic approaches might even bear risks for patients are elucidated.
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Affiliation(s)
- S A Haas
- Klinik und Poliklinik für Anästhesiologie, Zentrum für Anästhesiologie und Intensivmedizin, Martinistr. 52, 20246, Hamburg, Deutschland,
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19
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Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz JM, Laxova R, Santos-Simarro F, Gilbert-Dussardier B, Wittler L, Borschiwer M, Haas SA, Osterwalder M, Franke M, Timmermann B, Hecht J, Spielmann M, Visel A, Mundlos S. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 2015; 161:1012-1025. [PMID: 25959774 DOI: 10.1016/j.cell.2015.04.004] [Citation(s) in RCA: 1294] [Impact Index Per Article: 143.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/12/2015] [Accepted: 03/24/2015] [Indexed: 12/21/2022]
Abstract
Mammalian genomes are organized into megabase-scale topologically associated domains (TADs). We demonstrate that disruption of TADs can rewire long-range regulatory architecture and result in pathogenic phenotypes. We show that distinct human limb malformations are caused by deletions, inversions, or duplications altering the structure of the TAD-spanning WNT6/IHH/EPHA4/PAX3 locus. Using CRISPR/Cas genome editing, we generated mice with corresponding rearrangements. Both in mouse limb tissue and patient-derived fibroblasts, disease-relevant structural changes cause ectopic interactions between promoters and non-coding DNA, and a cluster of limb enhancers normally associated with Epha4 is misplaced relative to TAD boundaries and drives ectopic limb expression of another gene in the locus. This rewiring occurred only if the variant disrupted a CTCF-associated boundary domain. Our results demonstrate the functional importance of TADs for orchestrating gene expression via genome architecture and indicate criteria for predicting the pathogenicity of human structural variants, particularly in non-coding regions of the human genome.
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Affiliation(s)
- Darío G Lupiáñez
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Katerina Kraft
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Verena Heinrich
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Peter Krawitz
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Francesco Brancati
- Medical Genetics Unit, Policlinico Tor Vergata University Hospital, 00133 Rome, Italy
| | - Eva Klopocki
- Institute of Human Genetics Biozentrum, Julius Maximilian University of Würzburg, 97070 Würzburg, Germany
| | - Denise Horn
- Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Hülya Kayserili
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, 34093 Istanbul, Turkey
| | - John M Opitz
- Department of Pediatrics, School of Medicine, University of Utah, Salt Lake City, UT 84108, USA
| | - Renata Laxova
- Department of Pediatrics, School of Medicine, University of Utah, Salt Lake City, UT 84108, USA
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, 28046 Madrid, Spain; U753 Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28046 Madrid, Spain
| | | | - Lars Wittler
- Department Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Marina Borschiwer
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Marco Osterwalder
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Martin Franke
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195 Berlin, Germany
| | - Jochen Hecht
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Axel Visel
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany.
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20
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Palmer EE, Leffler M, Rogers C, Shaw M, Carroll R, Earl J, Cheung NW, Champion B, Hu H, Haas SA, Kalscheuer VM, Gecz J, Field M. New insights into Brunner syndrome and potential for targeted therapy. Clin Genet 2015; 89:120-7. [PMID: 25807999 DOI: 10.1111/cge.12589] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [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: 01/29/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 01/20/2023]
Abstract
We report two families with Brunner syndrome living in one state of Australia. The first family had a predicted protein-truncating variant of monoamine oxidase A (MAOA) (p.S251KfsX2). Affected males had mild intellectual disability (ID), obsessive behaviour, limited friendships and were introverted and placid during clinical interview. The family disclosed episodic explosive aggression after a diagnosis was made. The second family had a missense variant in MAOA (p.R45W). Affected males had borderline-mild ID, attention deficit disorder and limited friendships. One had a history of explosive aggression in childhood and episodic symptoms of flushing, headaches and diarrhoea. Their carrier mother had normal intelligence but similar episodic symptoms. Characteristic biochemical abnormalities included high serum serotonin and urinary metanephrines and low urinary 5-hydroxyindoleacetic acid (5-HIAA) and vanillylmandelic acid (VMA). Symptomatic individuals in the second family had particularly high serotonin levels, and treatment with a serotonin reuptake inhibitor and dietary modification resulted in reversal of biochemical abnormalities, reduction of 'serotonergic' symptoms and behavioural improvement. Brunner syndrome should be considered as a cause of mild ID with paroxysmal behavioural symptoms. It can be screened for with serum/urine metanephrine and serotonin measurement. Cautious treatment with a serotonin reuptake inhibitor, dietary modifications and avoidance of medications contraindicated in patients on monoamine oxidase inhibitors can improve symptoms.
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Affiliation(s)
- E E Palmer
- Department of Clinical Genetics, GOLD (Genetics of Learning Disability) service, Waratah, New South Wales, Australia.,University of New South Wales, Waratah, New South Wales, Australia
| | - M Leffler
- Department of Clinical Genetics, GOLD (Genetics of Learning Disability) service, Waratah, New South Wales, Australia
| | - C Rogers
- Department of Clinical Genetics, GOLD (Genetics of Learning Disability) service, Waratah, New South Wales, Australia
| | - M Shaw
- School of Paediatrics and Reproductive Health and Robinson Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - R Carroll
- School of Paediatrics and Reproductive Health and Robinson Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - J Earl
- Department of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia.,Department of Biochemistry, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - N W Cheung
- Department of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia.,Department of Endocrinology, Nepean Hospital, Sydney, New South Wales, Australia
| | - B Champion
- Department of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia.,Department of Endocrinology, Nepean Hospital, Sydney, New South Wales, Australia
| | - H Hu
- Department of Human Molecular Genetics
| | - S A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - J Gecz
- School of Paediatrics and Reproductive Health and Robinson Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - M Field
- Department of Clinical Genetics, GOLD (Genetics of Learning Disability) service, Waratah, New South Wales, Australia
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21
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Fernandez-Cuesta L, Sun R, Menon R, George J, Lorenz S, Meza-Zepeda LA, Peifer M, Plenker D, Heuckmann JM, Leenders F, Zander T, Dahmen I, Koker M, Schöttle J, Ullrich RT, Altmüller J, Becker C, Nürnberg P, Seidel H, Böhm D, Göke F, Ansén S, Russell PA, Wright GM, Wainer Z, Solomon B, Petersen I, Clement JH, Sänger J, Brustugun OT, Helland Å, Solberg S, Lund-Iversen M, Buettner R, Wolf J, Brambilla E, Vingron M, Perner S, Haas SA, Thomas RK. Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data. Genome Biol 2015; 16:7. [PMID: 25650807 PMCID: PMC4300615 DOI: 10.1186/s13059-014-0558-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 12/03/2014] [Indexed: 02/08/2023] Open
Abstract
Genomic translocation events frequently underlie cancer development through generation of gene fusions with oncogenic properties. Identification of such fusion transcripts by transcriptome sequencing might help to discover new potential therapeutic targets. We developed TRUP (Tumor-specimen suited RNA-seq Unified Pipeline) (https://github.com/ruping/TRUP), a computational approach that combines split-read and read-pair analysis with de novo assembly for the identification of chimeric transcripts in cancer specimens. We apply TRUP to RNA-seq data of different tumor types, and find it to be more sensitive than alternative tools in detecting chimeric transcripts, such as secondary rearrangements in EML4-ALK-positive lung tumors, or recurrent inactivating rearrangements affecting RASSF8.
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22
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Wilson GR, Sim JCH, McLean C, Giannandrea M, Galea CA, Riseley JR, Stephenson SEM, Fitzpatrick E, Haas SA, Pope K, Hogan KJ, Gregg RG, Bromhead CJ, Wargowski DS, Lawrence CH, James PA, Churchyard A, Gao Y, Phelan DG, Gillies G, Salce N, Stanford L, Marsh APL, Mignogna ML, Hayflick SJ, Leventer RJ, Delatycki MB, Mellick GD, Kalscheuer VM, D'Adamo P, Bahlo M, Amor DJ, Lockhart PJ. Mutations in RAB39B cause X-linked intellectual disability and early-onset Parkinson disease with α-synuclein pathology. Am J Hum Genet 2014; 95:729-35. [PMID: 25434005 DOI: 10.1016/j.ajhg.2014.10.015] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/30/2014] [Indexed: 11/18/2022] Open
Abstract
Advances in understanding the etiology of Parkinson disease have been driven by the identification of causative mutations in families. Genetic analysis of an Australian family with three males displaying clinical features of early-onset parkinsonism and intellectual disability identified a ∼45 kb deletion resulting in the complete loss of RAB39B. We subsequently identified a missense mutation (c.503C>A [p.Thr168Lys]) in RAB39B in an unrelated Wisconsin kindred affected by a similar clinical phenotype. In silico and in vitro studies demonstrated that the mutation destabilized the protein, consistent with loss of function. In vitro small-hairpin-RNA-mediated knockdown of Rab39b resulted in a reduction in the density of α-synuclein immunoreactive puncta in dendritic processes of cultured neurons. In addition, in multiple cell models, we demonstrated that knockdown of Rab39b was associated with reduced steady-state levels of α-synuclein. Post mortem studies demonstrated that loss of RAB39B resulted in pathologically confirmed Parkinson disease. There was extensive dopaminergic neuron loss in the substantia nigra and widespread classic Lewy body pathology. Additional pathological features included cortical Lewy bodies, brain iron accumulation, tau immunoreactivity, and axonal spheroids. Overall, we have shown that loss-of-function mutations in RAB39B cause intellectual disability and pathologically confirmed early-onset Parkinson disease. The loss of RAB39B results in dysregulation of α-synuclein homeostasis and a spectrum of neuropathological features that implicate RAB39B in the pathogenesis of Parkinson disease and potentially other neurodegenerative disorders.
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Affiliation(s)
- Gabrielle R Wilson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Joe C H Sim
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia
| | - Catriona McLean
- Anatomical Pathology, The Alfred, Melbourne, VIC 3181, Australia; Australian Brain Bank Network, National Neuroscience Facility, Melbourne, VIC 3053, Australia
| | - Maila Giannandrea
- Dulbecco Telethon Institute at Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy; Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology, and Rare Diseases, F. Hoffmann-La Roche, Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Charles A Galea
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia
| | - Jessica R Riseley
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia
| | - Sarah E M Stephenson
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Elizabeth Fitzpatrick
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany
| | - Kate Pope
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia
| | - Kirk J Hogan
- Department of Anesthesiology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53792, USA
| | - Ronald G Gregg
- Department of Biochemistry and Molecular Biology, Center for Genetics and Molecular Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Catherine J Bromhead
- Bioinformatics Division, Walter and Eliza Hall Institute, Melbourne, VIC 3052, Australia
| | - David S Wargowski
- Waisman Center, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Christopher H Lawrence
- Office of the State Forensic Pathologist, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Paul A James
- Genetic Medicine Department, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia
| | - Andrew Churchyard
- Department of Neurology, Monash Children's Hospital, Melbourne, VIC 3168, Australia
| | - Yujing Gao
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia
| | - Dean G Phelan
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Greta Gillies
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia
| | - Nicholas Salce
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia
| | - Lynn Stanford
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239-3098, USA
| | - Ashley P L Marsh
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Maria L Mignogna
- Dulbecco Telethon Institute at Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy; Pharmaceutical Research and Early Development, Neuroscience, Ophthalmology, and Rare Diseases, F. Hoffmann-La Roche, Grenzacherstrasse 124, Basel 4070, Switzerland
| | - Susan J Hayflick
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239-3098, USA
| | - Richard J Leventer
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia; Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, VIC 3052, Australia; Department of Neurology, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia; Clinical Genetics, Austin Health, Melbourne, VIC 3084, Australia
| | - George D Mellick
- Eskitis Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Vera M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, Berlin 14195, Germany
| | - Patrizia D'Adamo
- Dulbecco Telethon Institute at Division of Neuroscience, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Melanie Bahlo
- Bioinformatics Division, Walter and Eliza Hall Institute, Melbourne, VIC 3052, Australia; Department of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - David J Amor
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Childrens Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia.
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23
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Willemsen MH, Ba W, Wissink-Lindhout WM, de Brouwer APM, Haas SA, Bienek M, Hu H, Vissers LELM, van Bokhoven H, Kalscheuer V, Nadif Kasri N, Kleefstra T. Involvement of the kinesin family members KIF4A and KIF5C in intellectual disability and synaptic function. J Med Genet 2014; 51:487-94. [PMID: 24812067 DOI: 10.1136/jmedgenet-2013-102182] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Kinesin superfamily (KIF) genes encode motor proteins that have fundamental roles in brain functioning, development, survival and plasticity by regulating the transport of cargo along microtubules within axons, dendrites and synapses. Mouse knockout studies support these important functions in the nervous system. The role of KIF genes in intellectual disability (ID) has so far received limited attention, although previous studies have suggested that many ID genes impinge on synaptic function. METHODS By applying next-generation sequencing (NGS) in ID patients, we identified likely pathogenic mutations in KIF4A and KIF5C. To further confirm the pathogenicity of these mutations, we performed functional studies at the level of synaptic function in primary rat hippocampal neurons. RESULTS AND CONCLUSIONS Four males from a single family with a disruptive mutation in the X-linked KIF4A (c.1489-8_1490delins10; p.?- exon skipping) showed mild to moderate ID and epilepsy. A female patient with a de novo missense mutation in KIF5C (c.11465A>C; p.(Glu237Lys)) presented with severe ID, epilepsy, microcephaly and cortical malformation. Knock-down of Kif4a in rat primary hippocampal neurons altered the balance between excitatory and inhibitory synaptic transmission, whereas the mutation in Kif5c affected its protein function at excitatory synapses. Our results suggest that mutations in KIF4A and KIF5C cause ID by tipping the balance between excitatory and inhibitory synaptic excitability.
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Affiliation(s)
- Marjolein H Willemsen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Wei Ba
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | | | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Melanie Bienek
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hao Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Diseases, Radboud university medical center, Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Diseases, Radboud university medical center, Nijmegen, The Netherlands Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Vera Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Diseases, Radboud university medical center, Nijmegen, The Netherlands Department of Cognitive Neuroscience, Radboud university medical center, Nijmegen, The Netherlands Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands Nijmegen Centre for Molecular Life Sciences, Institute for Genetic and Metabolic Diseases, Radboud university medical center, Nijmegen, The Netherlands
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24
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Fernandez-Cuesta L, Peifer M, Lu X, Sun R, Ozretić L, Seidal D, Zander T, Leenders F, George J, Müller C, Dahmen I, Pinther B, Bosco G, Konrad K, Altmüller J, Nürnberg P, Achter V, Lang U, Schneider PM, Bogus M, Soltermann A, Brustugun OT, Helland Å, Solberg S, Lund-Iversen M, Ansén S, Stoelben E, Wright GM, Russell P, Wainer Z, Solomon B, Field JK, Hyde R, Davies MPA, Heukamp LC, Petersen I, Perner S, Lovly C, Cappuzzo F, Travis WD, Wolf J, Vingron M, Brambilla E, Haas SA, Buettner R, Thomas RK. Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids. Nat Commun 2014; 5:3518. [PMID: 24670920 PMCID: PMC4132974 DOI: 10.1038/ncomms4518] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [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: 08/13/2013] [Accepted: 02/26/2014] [Indexed: 02/07/2023] Open
Abstract
Pulmonary carcinoids are rare neuroendocrine tumours of the lung. The molecular alterations underlying the pathogenesis of these tumours have not been systematically studied so far. Here we perform gene copy number analysis (n=54), genome/exome (n=44) and transcriptome (n=69) sequencing of pulmonary carcinoids and observe frequent mutations in chromatin-remodelling genes. Covalent histone modifiers and subunits of the SWI/SNF complex are mutated in 40 and 22.2% of the cases, respectively, with MEN1, PSIP1 and ARID1A being recurrently affected. In contrast to small-cell lung cancer and large-cell neuroendocrine lung tumours, TP53 and RB1 mutations are rare events, suggesting that pulmonary carcinoids are not early progenitor lesions of the highly aggressive lung neuroendocrine tumours but arise through independent cellular mechanisms. These data also suggest that inactivation of chromatin-remodelling genes is sufficient to drive transformation in pulmonary carcinoids.
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Affiliation(s)
- Lynnette Fernandez-Cuesta
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Martin Peifer
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Xin Lu
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Ruping Sun
- Computational Molecular Biology Group, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Luka Ozretić
- Department of Pathology, University Hospital Medical Center, University of Cologne, 50937 Cologne, Germany
| | - Danila Seidal
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
- Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Cologne – Bonn, University of Cologne, 50924 Cologne, Germany
| | - Thomas Zander
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
- Department I of Internal Medicine, Center of Integrated Oncology Kö ln-Bonn, University of Cologne, 50924 Cologne, Germany
- Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne Bonn, 50924 Cologne, Germany
| | - Frauke Leenders
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
- Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Cologne – Bonn, University of Cologne, 50924 Cologne, Germany
| | - Julie George
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Christian Müller
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Ilona Dahmen
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Berit Pinther
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Graziella Bosco
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
| | - Kathryn Konrad
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931 Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931 Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Human Genetics, University of Cologne, Cologne 50931, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, 50931 Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Viktor Achter
- Computing Center, University of Cologne, 50931 Cologne, Germany
| | - Ulrich Lang
- Computing Center, University of Cologne, 50931 Cologne, Germany
- Department of Informatics, University of Cologne, 50931 Cologne, Germany
| | - Peter M Schneider
- Institute of Legal Medicine, University of Cologne, 50823 Cologne, Germany
| | - Magdalena Bogus
- Institute of Legal Medicine, University of Cologne, 50823 Cologne, Germany
| | - Alex Soltermann
- Institute for Surgical Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Odd Terje Brustugun
- Institute of clinical medicine, Faculty of Medicine, University of Oslo, N-0424 Oslo, Norway
- Department of oncology, Norwegian Radium Hospital, Oslo University Hospital, N-0310 Oslo, Norway
| | - Åslaug Helland
- Institute of clinical medicine, Faculty of Medicine, University of Oslo, N-0424 Oslo, Norway
- Department of oncology, Norwegian Radium Hospital, Oslo University Hospital, N-0310 Oslo, Norway
| | - Steinar Solberg
- Department of Thoracic Surgery, Rikshospitalet, Oslo University Hospital, N-0027 Oslo, Norway
| | - Marius Lund-Iversen
- Department of pathology, Norwegian Radium Hospital, Oslo University Hospital, N-0310 Oslo, Norway
| | - Sascha Ansén
- Department I of Internal Medicine, Center of Integrated Oncology Kö ln-Bonn, University of Cologne, 50924 Cologne, Germany
| | - Erich Stoelben
- Thoracic Surgery, Lungenklinik Merheim, Kliniken der Stadt Köln gGmbH, 51109 Cologne, Germany
| | - Gavin M. Wright
- University of Melbourne Department of Surgery, St Vincent’s Hospital, Melbourne, 3065 Victoria, Australia
| | - Prudence Russell
- Department of Pathology, St. Vincent’s Hospital, Melbourne, 3065 Victoria, Australia
| | - Zoe Wainer
- University of Melbourne Department of Surgery, St Vincent’s Hospital, Melbourne, 3065 Victoria, Australia
| | - Benjamin Solomon
- Department of Haematology and Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, 3002 Victoria, Australia
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool Cancer Research Centre, Liverpool, L3 9TA, UK
| | - Russell Hyde
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool Cancer Research Centre, Liverpool, L3 9TA, UK
| | - Michael PA. Davies
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool Cancer Research Centre, Liverpool, L3 9TA, UK
| | - Lukas C Heukamp
- Department of Pathology, University Hospital Medical Center, University of Cologne, 50937 Cologne, Germany
- Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne Bonn, 50924 Cologne, Germany
| | - Iver Petersen
- Institute of Pathology, Jena University Hospital, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Sven Perner
- Department of Prostate Cancer Research, Institute of Pathology, University Hospital of Bonn, 53127 Bonn, Germany
| | | | - Federico Cappuzzo
- Department of Medical Oncology, Istituto Toscano Tumouri, 57100 Livorno, Italy
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York 10065, USA
| | - Jürgen Wolf
- Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Cologne – Bonn, University of Cologne, 50924 Cologne, Germany
- Department I of Internal Medicine, Center of Integrated Oncology Kö ln-Bonn, University of Cologne, 50924 Cologne, Germany
- Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne Bonn, 50924 Cologne, Germany
| | - Martin Vingron
- Computational Molecular Biology Group, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Elisabeth Brambilla
- Department of Pathology, CHU Grenoble INSERM U823, Institute Albert Bonniot 38043 CS10217 Grenoble, France
| | - Stefan A. Haas
- Computational Molecular Biology Group, Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Reinhard Buettner
- Department of Pathology, University Hospital Medical Center, University of Cologne, 50937 Cologne, Germany
- Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Cologne – Bonn, University of Cologne, 50924 Cologne, Germany
- Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne Bonn, 50924 Cologne, Germany
| | - Roman K Thomas
- Department of Translational Genomics, Center of Integrated Oncology Cologne–Bonn, University of Cologne, 50924 Cologne, Germany
- Department of Pathology, University Hospital Medical Center, University of Cologne, 50937 Cologne, Germany
- Laboratory of Translational Cancer Genomics, Center of Integrated Oncology Cologne – Bonn, University of Cologne, 50924 Cologne, Germany
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25
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Fernandez-Cuesta L, Plenker D, Osada H, Sun R, Menon R, Leenders F, Ortiz-Cuaran S, Peifer M, Bos M, Daßler J, Malchers F, Schöttle J, Vogel W, Dahmen I, Koker M, Ullrich RT, Wright GM, Russell PA, Wainer Z, Solomon B, Brambilla E, Nagy-Mignotte H, Moro-Sibilot D, Brambilla CG, Lantuejoul S, Altmüller J, Becker C, Nürnberg P, Heuckmann JM, Stoelben E, Petersen I, Clement JH, Sänger J, Muscarella LA, la Torre A, Fazio VM, Lahortiga I, Perera T, Ogata S, Parade M, Brehmer D, Vingron M, Heukamp LC, Buettner R, Zander T, Wolf J, Perner S, Ansén S, Haas SA, Yatabe Y, Thomas RK. CD74-NRG1 fusions in lung adenocarcinoma. Cancer Discov 2014; 4:415-22. [PMID: 24469108 DOI: 10.1158/2159-8290.cd-13-0633] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
UNLABELLED We discovered a novel somatic gene fusion, CD74-NRG1, by transcriptome sequencing of 25 lung adenocarcinomas of never smokers. By screening 102 lung adenocarcinomas negative for known oncogenic alterations, we found four additional fusion-positive tumors, all of which were of the invasive mucinous subtype. Mechanistically, CD74-NRG1 leads to extracellular expression of the EGF-like domain of NRG1 III-β3, thereby providing the ligand for ERBB2-ERBB3 receptor complexes. Accordingly, ERBB2 and ERBB3 expression was high in the index case, and expression of phospho-ERBB3 was specifically found in tumors bearing the fusion (P < 0.0001). Ectopic expression of CD74-NRG1 in lung cancer cell lines expressing ERBB2 and ERBB3 activated ERBB3 and the PI3K-AKT pathway, and led to increased colony formation in soft agar. Thus, CD74-NRG1 gene fusions are activating genomic alterations in invasive mucinous adenocarcinomas and may offer a therapeutic opportunity for a lung tumor subtype with, so far, no effective treatment. SIGNIFICANCE CD74–NRG1 fusions may represent a therapeutic opportunity for invasive mucinous lung adenocarcinomas, a tumor with no effective treatment that frequently presents with multifocal unresectable disease.
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Affiliation(s)
- Lynnette Fernandez-Cuesta
- 1Department of Translational Genomics; 2Department I of Internal Medicine; 3Laboratory of Translational Cancer Genomics; 4Network Genomic Medicine, University Hospital Cologne, Center of Integrated Oncology Cologne-Bonn; 5Center for Molecular Medicine Cologne (CMMC); 6Cologne Center for Genomics (CCG); 7Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); 8Department of Pathology, University Hospital Medical Center, University of Cologne; 9Blackfield AG; 10Max Planck Institute for Neurological Research; 11Thoracic Surgery, Lungenklinik Merheim, Kliniken der Stadt Köln gGmbH; 12Institute of Human Genetics, Cologne; 13Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Berlin; 14Department of Prostate Cancer Research, Institute of Pathology; 15Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn; 16Institute of Pathology; 17Department of Internal Medicine II, Jena University Hospital, Friedrich-Schiller-University, Jena; 18Institute for Pathology Bad Berka, Bad Berka, Germany;19Division of Molecular Oncology, Aichi Cancer Center Research Institute; 20Department of Pathology and Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan; Departments of 21Surgery and22Pathology, St. Vincent's Hospital; 23Department of Haematology and Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia;24Department of Pathology, 25CHU Grenoble Institut National de la Santé et de la Recherche Medicale (INSERM) U823, Institute Albert Bonniot, Grenoble-Alpes University, Grenoble, France; 26Laboratory of Oncology IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo; 27Laboratory for Molecular Medicine and Biotechnology, University Campus Bio-Medico, Rome, Italy; 28Center for the Biology of Disease, VIB, Leuven; and 29Oncology Discovery, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
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26
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Lesca G, Moizard MP, Bussy G, Boggio D, Hu H, Haas SA, Ropers HH, Kalscheuer VM, Des Portes V, Labalme A, Sanlaville D, Edery P, Raynaud M, Lespinasse J. Clinical and neurocognitive characterization of a family with a novel MED12 gene frameshift mutation. Am J Med Genet A 2013; 161A:3063-71. [PMID: 24039113 DOI: 10.1002/ajmg.a.36162] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [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: 03/25/2013] [Accepted: 07/08/2013] [Indexed: 11/07/2022]
Abstract
FG syndrome, Lujan syndrome, and Ohdo syndrome, the Maat-Kievit-Brunner type, have been described as distinct syndromes with overlapping non-specific features and different missense mutations of the MED12 gene have been reported in all of them. We report a family including 10 males and 1 female affected with profound non-specific intellectual disability (ID) which was linked to a 30-cM region extending from Xp11.21 (ALAS2) to Xq22.3 (COL4A5). Parallel sequencing of all X-chromosome exons identified a frameshift mutation (c.5898dupC) of MED12. Mutated mRNA was not affected by non-sense mediated RNA decay and induced an additional abnormal isoform due to activation of cryptic splice-sites in exon 41. Dysmorphic features common to most affected males were long narrow face, high forehead, flat malar area, high nasal bridge, and short philtrum. Language was absent or very limited. Most patients had a friendly personality. Cognitive impairment, varying from borderline to profound ID was similarly observed in seven heterozygous females. There was no correlation between cognitive function and X-chromosome inactivation profiles in blood cells. The severe degree of ID in male patients, as well as variable cognitive impairment in heterozygous females suggests that the duplication observed in the present family may have a more severe effect on MED12 function than missense mutations. In a cognitively impaired male from this family, who also presented with tall stature and dysmorphism and did not have the MED12 mutation, a 600-kb duplication at 17p13.3 including the YWHAE gene, was found in a mosaic state.
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Affiliation(s)
- Gaetan Lesca
- Service de Génétique and Centre de Référence des Anomalies du Développement, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Lyon, France; INSERM U1028, CNRS, UMR5292, Lyon Neuroscience Research Center, TIGER Team, University Claude Bernard Lyon 1, Université de Lyon, Lyon, France
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27
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Trepte CJC, Eichhorn V, Haas SA, Stahl K, Schmid F, Nitzschke R, Goetz AE, Reuter DA. Comparison of an automated respiratory systolic variation test with dynamic preload indicators to predict fluid responsiveness after major surgery. Br J Anaesth 2013; 111:736-42. [PMID: 23811425 DOI: 10.1093/bja/aet204] [Citation(s) in RCA: 16] [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] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Predicting the response of cardiac output to volume administration remains an ongoing clinical challenge. The objective of our study was to compare the ability to predict volume responsiveness of various functional measures of cardiac preload. These included pulse pressure variation (PPV), stroke volume variation (SVV), and the recently launched automated respiratory systolic variation test (RSVT) in patients after major surgery. METHODS In this prospective study, 24 mechanically ventilated patients after major surgery were enrolled. Three consecutive volume loading steps consisting of 300 ml 6% hydroxyethylstarch 130/0.4 were performed and cardiac index (CI) was assessed by transpulmonary thermodilution. Volume responsiveness was considered as positive if CI increased by >10%. RESULTS In total 72 volume loading steps were analysed, of which 41 showed a positive volume response. Receiver operating characteristic (ROC) curve analysis revealed an area under the curve (AUC) of 0.70 for PPV, 0.72 for SVV and 0.77 for RSVT. Areas under the curves of all variables did not differ significantly from each other (P>0.05). Suggested cut-off values were 9.9% for SVV, 10.1% for PPV, and 19.7° for RSVT as calculated by the Youden Index. CONCLUSION In predicting fluid responsiveness the new automated RSVT appears to be as accurate as established dynamic indicators of preload PPV and SVV in patients after major surgery. The automated RSVT is clinically easy to use and may be useful in guiding fluid therapy in ventilated patients.
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Affiliation(s)
- C J C Trepte
- Department of Anesthesiology, Center of Anesthesiology and Intensive Care Medicine, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246 Hamburg, Germany
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28
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Van Maldergem L, Hou Q, Kalscheuer VM, Rio M, Doco-Fenzy M, Medeira A, de Brouwer APM, Cabrol C, Haas SA, Cacciagli P, Moutton S, Landais E, Motte J, Colleaux L, Bonnet C, Villard L, Dupont J, Man HY. Loss of function of KIAA2022 causes mild to severe intellectual disability with an autism spectrum disorder and impairs neurite outgrowth. Hum Mol Genet 2013; 22:3306-14. [PMID: 23615299 DOI: 10.1093/hmg/ddt187] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Existence of a discrete new X-linked intellectual disability (XLID) syndrome due to KIAA2022 deficiency was questioned by disruption of KIAA2022 by an X-chromosome pericentric inversion in a XLID family we reported in 2004. Three additional families with likely pathogenic KIAA2022 mutations were discovered within the frame of systematic parallel sequencing of familial cases of XLID or in the context of routine array-CGH evaluation of sporadic intellectual deficiency (ID) cases. The c.186delC and c.3597dupA KIAA2022 truncating mutations were identified by X-chromosome exome sequencing, while array CGH discovered a 70 kb microduplication encompassing KIAA2022 exon 1 in the third family. This duplication decreased KIAA2022 mRNA level in patients' lymphocytes by 60%. Detailed clinical examination of all patients, including the two initially reported, indicated moderate-to-severe ID with autistic features, strabismus in all patients, with no specific dysmorphic features other than a round face in infancy and no structural brain abnormalities on magnetic resonance imaging (MRI). Interestingly, the patient with decreased KIAA2022 expression had only mild ID with severe language delay and repetitive behaviors falling in the range of an autism spectrum disorder (ASD). Since little is known about KIAA2022 function, we conducted morphometric studies in cultured rat hippocampal neurons. We found that siRNA-mediated KIAA2022 knockdown resulted in marked impairment in neurite outgrowth including both the dendrites and the axons, suggesting a major role for KIAA2022 in neuron development and brain function.
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Affiliation(s)
- Lionel Van Maldergem
- Centre de Génétique Humaine, Université de Franche-Comté, 25000 Besançon, France.
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29
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Huang L, Jolly LA, Willis-Owen S, Gardner A, Kumar R, Douglas E, Shoubridge C, Wieczorek D, Tzschach A, Cohen M, Hackett A, Field M, Froyen G, Hu H, Haas SA, Ropers HH, Kalscheuer VM, Corbett MA, Gecz J. A noncoding, regulatory mutation implicates HCFC1 in nonsyndromic intellectual disability. Am J Hum Genet 2012; 91:694-702. [PMID: 23000143 DOI: 10.1016/j.ajhg.2012.08.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 06/26/2012] [Accepted: 08/13/2012] [Indexed: 11/28/2022] Open
Abstract
The discovery of mutations causing human disease has so far been biased toward protein-coding regions. Having excluded all annotated coding regions, we performed targeted massively parallel resequencing of the nonrepetitive genomic linkage interval at Xq28 of family MRX3. We identified in the binding site of transcription factor YY1 a regulatory mutation that leads to overexpression of the chromatin-associated transcriptional regulator HCFC1. When tested on embryonic murine neural stem cells and embryonic hippocampal neurons, HCFC1 overexpression led to a significant increase of the production of astrocytes and a considerable reduction in neurite growth. Two other nonsynonymous, potentially deleterious changes have been identified by X-exome sequencing in individuals with intellectual disability, implicating HCFC1 in normal brain function.
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Affiliation(s)
- Lingli Huang
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
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30
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Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA. Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics 2012; 28:1024-5. [DOI: 10.1093/bioinformatics/bts064] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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31
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Emde AK, Schulz MH, Weese D, Sun R, Vingron M, Kalscheuer VM, Haas SA, Reinert K. Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. ACTA ACUST UNITED AC 2012; 28:619-27. [PMID: 22238266 DOI: 10.1093/bioinformatics/bts019] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
MOTIVATION The reliable detection of genomic variation in resequencing data is still a major challenge, especially for variants larger than a few base pairs. Sequencing reads crossing boundaries of structural variation carry the potential for their identification, but are difficult to map. RESULTS Here we present a method for 'split' read mapping, where prefix and suffix match of a read may be interrupted by a longer gap in the read-to-reference alignment. We use this method to accurately detect medium-sized insertions and long deletions with precise breakpoints in genomic resequencing data. Compared with alternative split mapping methods, SplazerS significantly improves sensitivity for detecting large indel events, especially in variant-rich regions. Our method is robust in the presence of sequencing errors as well as alignment errors due to genomic mutations/divergence, and can be used on reads of variable lengths. Our analysis shows that SplazerS is a versatile tool applicable to unanchored or single-end as well as anchored paired-end reads. In addition, application of SplazerS to targeted resequencing data led to the interesting discovery of a complete, possibly functional gene retrocopy variant. AVAILABILITY SplazerS is available from http://www.seqan.de/projects/ splazers. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anne-Katrin Emde
- Department of Computer Science, Freie Universität Berlin, Takustrasse 9, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.
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32
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Schraders M, Haas SA, Weegerink NJD, Oostrik J, Hu H, Hoefsloot LH, Kannan S, Huygen PLM, Pennings RJE, Admiraal RJC, Kalscheuer VM, Kunst HPM, Kremer H. Next-generation sequencing identifies mutations of SMPX, which encodes the small muscle protein, X-linked, as a cause of progressive hearing impairment. Am J Hum Genet 2011; 88:628-34. [PMID: 21549342 DOI: 10.1016/j.ajhg.2011.04.012] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Revised: 04/07/2011] [Accepted: 04/18/2011] [Indexed: 01/12/2023] Open
Abstract
In a Dutch family with an X-linked postlingual progressive hearing impairment, a critical linkage interval was determined to span a region of 12.9 Mb flanked by the markers DXS7108 and DXS7110. This interval overlaps with the previously described DFNX4 locus and contains 75 annotated genes. Subsequent next-generation sequencing (NGS) detected one variant within the linkage interval, a nonsense mutation in SMPX. SMPX encodes the small muscle protein, X-linked (SMPX). Further screening was performed on 26 index patients from small families for which X-linked inheritance of nonsyndromic hearing impairment (NSHI) was not excluded. We detected a frameshift mutation in SMPX in one of the patients. Segregation analysis of both mutations in the families in whom they were found revealed that the mutations cosegregated with hearing impairment. Although we show that SMPX is expressed in many different organs, including the human inner ear, no obvious symptoms other than hearing impairment were observed in the patients. SMPX had previously been demonstrated to be specifically expressed in striated muscle and, therefore, seemed an unlikely candidate gene for hearing impairment. We hypothesize that SMPX functions in inner ear development and/or maintenance in the IGF-1 pathway, the integrin pathway through Rac1, or both.
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Affiliation(s)
- Margit Schraders
- Department of Otorhinolaryngology, Head and Neck Surgery, Nijmegen, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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33
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Warnatz HJ, Querfurth R, Guerasimova A, Cheng X, Haas SA, Hufton AL, Manke T, Vanhecke D, Nietfeld W, Vingron M, Janitz M, Lehrach H, Yaspo ML. Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Nucleic Acids Res 2010; 38:6112-23. [PMID: 20494980 PMCID: PMC2952857 DOI: 10.1093/nar/gkq402] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [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: 12/12/2022] Open
Abstract
Given the inherent limitations of in silico studies relying solely on DNA sequence analysis, the functional characterization of mammalian promoters and associated cis-regulatory elements requires experimental support, which demands cloning and analysis of putative promoter regions. Focusing on human chromosome 21, we cloned 182 gene promoters of 2500 bp in length and conducted reporter gene assays on transfected-cell arrays. We found 56 promoters that were active in HEK293 cells, while another 49 promoters could be activated by treatment of cells with Trichostatin A or depletion of serum. We observed high correlations between promoter activities and endogenous transcript levels, RNA polymerase II occupancy, CpG islands and core promoter elements. Truncation of a subset of 62 promoters to ∼500 bp revealed that truncation rarely resulted in loss of activity, but rather in loss of responses to external stimuli, suggesting the presence of cis-regulatory response elements within distal promoter regions. In these regions, we found a strong enrichment of transcription factor binding sites that could potentially activate gene expression in the presence of stimuli. This study illustrates the modular functional architecture of chromosome 21 promoters and helps to reveal the complex mechanisms governing transcriptional regulation.
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Affiliation(s)
- Hans-Jörg Warnatz
- Department for Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany.
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34
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Hu H, Wrogemann K, Kalscheuer V, Tzschach A, Richard H, Haas SA, Menzel C, Bienek M, Froyen G, Raynaud M, Van Bokhoven H, Chelly J, Ropers H, Chen W. Erratum to: Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing. Hugo J 2010; 3:83. [PMID: 20535404 PMCID: PMC2882641 DOI: 10.1007/s11568-010-9142-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
[This corrects the article DOI: 10.1007/s11568-010-9137-y.].
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35
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Hu H, Wrogemann K, Kalscheuer V, Tzschach A, Richard H, Haas SA, Menzel C, Bienek M, Froyen G, Raynaud M, Van Bokhoven H, Chelly J, Ropers H, Chen W. Mutation screening in 86 known X-linked mental retardation genes by droplet-based multiplex PCR and massive parallel sequencing. Hugo J 2010; 3:41-9. [PMID: 21836662 PMCID: PMC2882650 DOI: 10.1007/s11568-010-9137-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 02/24/2010] [Accepted: 03/12/2010] [Indexed: 12/25/2022]
Abstract
Massive parallel sequencing has revolutionized the search for pathogenic variants in the human genome, but for routine diagnosis, re-sequencing of the complete human genome in a large cohort of patients is still far too expensive. Recently, novel genome partitioning methods have been developed that allow to target re-sequencing to specific genomic compartments, but practical experience with these methods is still limited. In this study, we have combined a novel droplet-based multiplex PCR method and next generation sequencing to screen patients with X-linked mental retardation (XLMR) for mutations in 86 previously identified XLMR genes. In total, affected males from 24 large XLMR families were analyzed, including three in whom the mutations were already known. Amplicons corresponding to functionally relevant regions of these genes were sequenced on an Illumina/Solexa Genome Analyzer II platform. Highly specific and uniform enrichment was achieved: on average, 67.9% unambiguously mapped reads were derived from amplicons, and for 88.5% of the targeted bases, the sequencing depth was sufficient to reliably detect variations. Potentially disease-causing sequence variants were identified in 10 out of 24 patients, including the three mutations that were already known, and all of these could be confirmed by Sanger sequencing. The robust performance of this approach demonstrates the general utility of droplet-based multiplex PCR for parallel mutation screening in hundreds of genes, which is a prerequisite for the diagnosis of mental retardation and other disorders that may be due to defects of a wide variety of genes.
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Affiliation(s)
- Hao Hu
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Klaus Wrogemann
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB Canada
| | - Vera Kalscheuer
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | | | - Hugues Richard
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Stefan A. Haas
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Corinna Menzel
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Melanie Bienek
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Guy Froyen
- Human Genome Laboratory, Centre for Human Genetics, VIB, K.U.Leuven, Leuven, Belgium
| | - Martine Raynaud
- INSERM, U930; Centre Hospitalier Régional Universitaire de Tours, Service de Genetique, 37044 Tours, France
| | - Hans Van Bokhoven
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jamel Chelly
- Faculté de Médecine Cochin, INSERM 129-ICGM, Paris, France
| | - Hilger Ropers
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Wei Chen
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin Institute for Medical Systems Biology, Berlin, Germany
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Richard H, Schulz MH, Sultan M, Nürnberger A, Schrinner S, Balzereit D, Dagand E, Rasche A, Lehrach H, Vingron M, Haas SA, Yaspo ML. Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments. Nucleic Acids Res 2010; 38:e112. [PMID: 20150413 PMCID: PMC2879520 DOI: 10.1093/nar/gkq041] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [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: 12/22/2022] Open
Abstract
Alternative splicing, polyadenylation of pre-messenger RNA molecules and differential promoter usage can produce a variety of transcript isoforms whose respective expression levels are regulated in time and space, thus contributing specific biological functions. However, the repertoire of mammalian alternative transcripts and their regulation are still poorly understood. Second-generation sequencing is now opening unprecedented routes to address the analysis of entire transcriptomes. Here, we developed methods that allow the prediction and quantification of alternative isoforms derived solely from exon expression levels in RNA-Seq data. These are based on an explicit statistical model and enable the prediction of alternative isoforms within or between conditions using any known gene annotation, as well as the relative quantification of known transcript structures. Applying these methods to a human RNA-Seq dataset, we validated a significant fraction of the predictions by RT-PCR. Data further showed that these predictions correlated well with information originating from junction reads. A direct comparison with exon arrays indicated improved performances of RNA-Seq over microarrays in the prediction of skipped exons. Altogether, the set of methods presented here comprehensively addresses multiple aspects of alternative isoform analysis. The software is available as an open-source R-package called Solas at http://cmb.molgen.mpg.de/2ndGenerationSequencing/Solas/.
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Affiliation(s)
- Hugues Richard
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany.
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Roider HG, Lenhard B, Kanhere A, Haas SA, Vingron M. CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses. Nucleic Acids Res 2009; 37:6305-15. [PMID: 19736212 PMCID: PMC2770660 DOI: 10.1093/nar/gkp682] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [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: 12/26/2022] Open
Abstract
Motif overrepresentation analysis of proximal promoters is a common approach to characterize the regulatory properties of co-expressed sets of genes. Here we show that these approaches perform well on mammalian CpG-depleted promoter sets that regulate expression in terminally differentiated tissues such as liver and heart. In contrast, CpG-rich promoters show very little overrepresentation signal, even when associated with genes that display highly constrained spatiotemporal expression. For instance, while ∼50% of heart specific genes possess CpG-rich promoters we find that the frequently observed enrichment of MEF2-binding sites upstream of heart-specific genes is solely due to contributions from CpG-depleted promoters. Similar results are obtained for all sets of tissue-specific genes indicating that CpG-rich and CpG-depleted promoters differ fundamentally in their distribution of regulatory inputs around the transcription start site. In order not to dilute the respective transcription factor binding signals, the two promoter types should thus be treated as separate sets in any motif overrepresentation analysis.
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Affiliation(s)
- Helge G Roider
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin.
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38
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Abstract
MOTIVATION A major challenge in regulatory genomics is the identification of associations between functional categories of genes (e.g. tissues, metabolic pathways) and their regulating transcription factors (TFs). While, for a limited number of categories, the regulating TFs are already known, still for many functional categories the responsible factors remain to be elucidated. RESULTS We put forward a novel method (PASTAA) for detecting transcriptions factors associated with functional categories, which utilizes the prediction of binding affinities of a TF to promoters. This binding strength information is compared to the likelihood of membership of the corresponding genes in the functional category under study. Coherence between the two ranked datasets is seen as an indicator of association between a TF and the category. PASTAA is applied primarily to the determination of TFs driving tissue-specific expression. We show that PASTAA is capable of recovering many TFs acting tissue specifically and, in addition, provides novel associations so far not detected by alternative methods. The application of PASTAA to detect TFs involved in the regulation of tissue-specific gene expression revealed a remarkable number of experimentally supported associations. The validated success for various datasets implies that PASTAA can directly be applied for the detection of TFs associated with newly derived gene sets. AVAILABILITY The PASTAA source code as well as a corresponding web interface is freely available at http://trap.molgen.mpg.de.
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Affiliation(s)
- Helge G Roider
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin.
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39
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Hecht J, Kuhl H, Haas SA, Bauer S, Poustka AJ, Lienau J, Schell H, Stiege AC, Seitz V, Reinhardt R, Duda GN, Mundlos S, Robinson PN. Gene identification and analysis of transcripts differentially regulated in fracture healing by EST sequencing in the domestic sheep. BMC Genomics 2006; 7:172. [PMID: 16822315 PMCID: PMC1578570 DOI: 10.1186/1471-2164-7-172] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Accepted: 07/05/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The sheep is an important model animal for testing novel fracture treatments and other medical applications. Despite these medical uses and the well known economic and cultural importance of the sheep, relatively little research has been performed into sheep genetics, and DNA sequences are available for only a small number of sheep genes. RESULTS In this work we have sequenced over 47 thousand expressed sequence tags (ESTs) from libraries developed from healing bone in a sheep model of fracture healing. These ESTs were clustered with the previously available 10 thousand sheep ESTs to a total of 19087 contigs with an average length of 603 nucleotides. We used the newly identified sequences to develop RT-PCR assays for 78 sheep genes and measured differential expression during the course of fracture healing between days 7 and 42 postfracture. All genes showed significant shifts at one or more time points. 23 of the genes were differentially expressed between postfracture days 7 and 10, which could reflect an important role for these genes for the initiation of osteogenesis. CONCLUSION The sequences we have identified in this work are a valuable resource for future studies on musculoskeletal healing and regeneration using sheep and represent an important head-start for genomic sequencing projects for Ovis aries, with partial or complete sequences being made available for over 5,800 previously unsequenced sheep genes.
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Affiliation(s)
- Jochen Hecht
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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40
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Abstract
T-STAG (tissue-specific transcripts and genes) is a resource and web-interface, designated to analyze tissue/tumor-specific expression patterns in human and mouse transcriptomes. It integrates our refined prediction of specific expression patterns both in genes as well as in individual isoforms with man–mouse orthology data. In combination with the features for combining/contrasting the genes expressed in different tissues, T-STAG implicates important biological applications, such as the detection of differentially expressed genes in tumors, the retrieval of orthologs with significant expression in the same tissue etc. Additionally, our refined categorization of expressed sequence tags (ESTs) according to the normalization of cDNA libraries allows searching for putative low-abundant transcripts. The results are tightly linked to our visualization tools, GeneNest (expression patterns of genes) and SpliceNest (gene structure and alternative splicing). The user-friendly interface of T-STAG offers a platform for comprehensive analysis of tissue and/or tumor-specific expression patterns revealed by the EST data. T-STAG is freely accessible at .
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Affiliation(s)
- Shobhit Gupta
- Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany.
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Hui J, Hung LH, Heiner M, Schreiner S, Neumüller N, Reither G, Haas SA, Bindereif A. Intronic CA-repeat and CA-rich elements: a new class of regulators of mammalian alternative splicing. EMBO J 2005; 24:1988-98. [PMID: 15889141 PMCID: PMC1142610 DOI: 10.1038/sj.emboj.7600677] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2004] [Accepted: 04/14/2005] [Indexed: 01/17/2023] Open
Abstract
We have recently identified an intronic polymorphic CA-repeat region in the human endothelial nitric oxide synthase (eNOS) gene as an important determinant of the splicing efficiency, requiring specific binding of hnRNP L. Here, we analyzed the position requirements of this CA-repeat element, which revealed its potential role in alternative splicing. In addition, we defined the RNA binding specificity of hnRNP L by SELEX: not only regular CA repeats are recognized with high affinity but also certain CA-rich clusters. Therefore, we have systematically searched the human genome databases for CA-repeat and CA-rich elements associated with alternative 5' splice sites (5'ss), followed by minigene transfection assays. Surprisingly, in several specific human genes that we tested, intronic CA RNA elements could function either as splicing enhancers or silencers, depending on their proximity to the alternative 5'ss. HnRNP L was detected specifically bound to these diverse CA elements. These data demonstrated that intronic CA sequences constitute novel and widespread regulatory elements of alternative splicing.
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Affiliation(s)
- Jingyi Hui
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Lee-Hsueh Hung
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Monika Heiner
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Silke Schreiner
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Norma Neumüller
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Gregor Reither
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Albrecht Bindereif
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany
- Institut für Biochemie, Fachbereich Biologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 58, 35392 Gießen, Germany. Tel.: +49 641 9935 420; Fax: +49 641 9935 419; E-mail:
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Gupta S, Zink D, Korn B, Vingron M, Haas SA. Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing. BMC Genomics 2004; 5:72. [PMID: 15453915 PMCID: PMC521684 DOI: 10.1186/1471-2164-5-72] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2004] [Accepted: 09/28/2004] [Indexed: 12/15/2022] Open
Abstract
Background Alternative splicing contributes significantly to the complexity of the human transcriptome and proteome. Computational prediction of alternative splice isoforms are usually based on EST sequences that also allow to approximate the expression pattern of the related transcripts. However, the limited number of tissues represented in the EST data as well as the different cDNA construction protocols may influence the predictive capacity of ESTs to unravel tissue-specifically expressed transcripts. Methods We predict tissue and tumor specific splice isoforms based on the genomic mapping (SpliceNest) of the EST consensus sequences and library annotation provided in the GeneNest database. We further ascertain the potentially rare tissue specific transcripts as the ones represented only by ESTs derived from normalized libraries. A subset of the predicted tissue and tumor specific isoforms are then validated via RT-PCR experiments over a spectrum of 40 tissue types. Results Our strategy revealed 427 genes with at least one tissue specific transcript as well as 1120 genes showing tumor specific isoforms. While our experimental evaluation of computationally predicted tissue-specific isoforms revealed a high success rate in confirming the expression of these isoforms in the respective tissue, the strategy frequently failed to detect the expected restricted expression pattern. The analysis of putative lowly expressed transcripts using normalized cDNA libraries suggests that our ability to detect tissue-specific isoforms strongly depends on the expression level of the respective transcript as well as on the sensitivity of the experimental methods. Especially splice isoforms predicted to be disease-specific tend to represent transcripts that are expressed in a set of healthy tissues rather than novel isoforms. Conclusions We propose to combine the computational prediction of alternative splice isoforms with experimental validation for efficient delineation of an accurate set of tissue-specific transcripts.
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Affiliation(s)
- Shobhit Gupta
- Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73, D-14195 Berlin – Germany
| | - Dorothea Zink
- German Resource Center for Genome Research, INF 580, 69120 Heidelberg – Germany
| | - Bernhard Korn
- German Resource Center for Genome Research, INF 580, 69120 Heidelberg – Germany
| | - Martin Vingron
- Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73, D-14195 Berlin – Germany
| | - Stefan A Haas
- Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestr. 73, D-14195 Berlin – Germany
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43
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Abstract
MOTIVATION Alternative splicing is currently seen to explain the vast disparity between the number of predicted genes in the human genome and the highly diverse proteome. The mapping of expressed sequences tag (EST) consensus sequences derived from the GeneNest database onto the genome provides an efficient way of predicting exon-intron boundaries, gene structure and alternative splicing events. However, the alternative splicing events are obscured by a large number of putatively artificial exon boundaries arising due to genomic contamination or alignment errors. The current work describes a methodology to associate quality values to the predicted exon-intron boundaries. High quality exon-intron boundaries are used to predict constitutive and alternative splicing ranked by confidence values, aiming to facilitate large-scale analysis of alternative splicing and splicing in general. RESULTS Applying the current methodology, constitutive splicing is observed in 33,270 EST clusters, out of which 45% are alternatively spliced. The classification derived from the computed confidence values for 17 of these splice events frequently correlate (15/17) with RT-PCR experiments performed for 40 different tissue samples. As an application of the confidence measure, an evaluation of distribution of alternative splicing revealed that majority of variants correspond to the coding regions of the genes. However, still a significant fraction maps to non-coding regions, thereby indicating a functional relevance of alternative splicing in untranslated regions. AVAILABILITY The predicted alternative splice variants are visualized in the SpliceNest database at http://splicenest.molgen.mpg.de
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Affiliation(s)
- S Gupta
- Computational Molecular Biology Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany.
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44
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Xue Y, Haas SA, Brino L, Gusnanto A, Reimers M, Talibi D, Vingron M, Ekwall K, Wright APH. A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift. Yeast 2004; 21:25-39. [PMID: 14745780 DOI: 10.1002/yea.1053] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Completion of the fission yeast genome sequence has opened up possibilities for post-genomic approaches. We have constructed a DNA microarray for genome-wide gene expression analysis in fission yeast. The microarray contains DNA fragments, PCR-amplified from a genomic DNA template, that represent > 99% of the 5000 or so annotated fission yeast genes, as well as a number of control sequences. The GenomePRIDE software used attempts to design similarly sized DNA fragments corresponding to gene regions within single exons, near the 3'-end of genes that lack homology to other fission yeast genes. To validate the design and utility of the array, we studied expression changes after a 2 h temperature shift from 25 degrees C to 36 degrees C, conditions widely used when studying temperature-sensitive mutants. Obligingly, the vast majority of genes do not change more than two-fold, supporting the widely held view that temperature-shift experiments specifically reveal phenotypes associated with temperature-sensitive mutants. However, we did identify a small group of genes that showed a reproducible change in expression. Importantly, most of these corresponded to previously characterized heat-shock genes, whose expression has been reported to change after more extreme temperature shifts than those used here. We conclude that the DNA microarray represents a useful resource for fission yeast researchers as well as the broader yeast community, since it will facilitate comparison with the distantly related budding yeast, Saccharomyces cerevisiae. To maximize the utility of this resource, the array and its component parts are fully described in On-line Supplementary Information and are also available commercially.
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Affiliation(s)
- Yongtao Xue
- Natural Sciences Section, Södertörns University College, S-141 89 Huddinge, Sweden
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Boutros M, Kiger AA, Armknecht S, Kerr K, Hild M, Koch B, Haas SA, Paro R, Perrimon N. Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science 2004; 303:832-5. [PMID: 14764878 DOI: 10.1126/science.1091266] [Citation(s) in RCA: 578] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A crucial aim upon completion of whole genome sequences is the functional analysis of all predicted genes. We have applied a high-throughput RNA-interference (RNAi) screen of 19,470 double-stranded (ds) RNAs in cultured cells to characterize the function of nearly all (91%) predicted Drosophila genes in cell growth and viability. We found 438 dsRNAs that identified essential genes, among which 80% lacked mutant alleles. A quantitative assay of cell number was applied to identify genes of known and uncharacterized functions. In particular, we demonstrate a role for the homolog of a mammalian acute myeloid leukemia gene (AML1) in cell survival. Such a systematic screen for cell phenotypes, such as cell viability, can thus be effective in characterizing functionally related genes on a genome-wide scale.
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Affiliation(s)
- Michael Boutros
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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46
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Hild M, Beckmann B, Haas SA, Koch B, Solovyev V, Busold C, Fellenberg K, Boutros M, Vingron M, Sauer F, Hoheisel JD, Paro R. An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol 2003; 5:R3. [PMID: 14709175 PMCID: PMC395735 DOI: 10.1186/gb-2003-5-1-r3] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2003] [Revised: 10/13/2003] [Accepted: 11/19/2003] [Indexed: 11/19/2022] Open
Abstract
A novel Drosophila microarray constructed on the basis of an integrated in silico/wet biology approach provides evidence for the transcription of approximately 2,600 additional genes. Validation indicates a lower limit of 2,000 novel annotations, thus raising the number of genes that make a fly. Background While the genome sequences for a variety of organisms are now available, the precise number of the genes encoded is still a matter of debate. For the human genome several stringent annotation approaches have resulted in the same number of potential genes, but a careful comparison revealed only limited overlap. This indicates that only the combination of different computational prediction methods and experimental evaluation of such in silico data will provide more complete genome annotations. In order to get a more complete gene content of the Drosophila melanogaster genome, we based our new D. melanogaster whole-transcriptome microarray, the Heidelberg FlyArray, on the combination of the Berkeley Drosophila Genome Project (BDGP) annotation and a novel ab initio gene prediction of lower stringency using the Fgenesh software. Results Here we provide evidence for the transcription of approximately 2,600 additional genes predicted by Fgenesh. Validation of the developmental profiling data by RT-PCR and in situ hybridization indicates a lower limit of 2,000 novel annotations, thus substantially raising the number of genes that make a fly. Conclusions The successful design and application of this novel Drosophila microarray on the basis of our integrated in silico/wet biology approach confirms our expectation that in silico approaches alone will always tend to be incomplete. The identification of at least 2,000 novel genes highlights the importance of gathering experimental evidence to discover all genes within a genome. Moreover, as such an approach is independent of homology criteria, it will allow the discovery of novel genes unrelated to known protein families or those that have not been strictly conserved between species.
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Affiliation(s)
- M Hild
- Zentrum für Molekulare Biologie Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - B Beckmann
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - SA Haas
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - B Koch
- Zentrum für Molekulare Biologie Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - V Solovyev
- Softberry, Inc., 116 Radio Circle, Suite 400, Mount Kisko, NY 10549, USA
| | - C Busold
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - K Fellenberg
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - M Boutros
- Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - M Vingron
- Max Planck Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin, Germany
| | - F Sauer
- Zentrum für Molekulare Biologie Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
| | - JD Hoheisel
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - R Paro
- Zentrum für Molekulare Biologie Heidelberg (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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Haas SA, Hild M, Wright APH, Hain T, Talibi D, Vingron M. Genome-scale design of PCR primers and long oligomers for DNA microarrays. Nucleic Acids Res 2003; 31:5576-81. [PMID: 14500820 PMCID: PMC206452 DOI: 10.1093/nar/gkg752] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software for designing primers/oligomers for large-scale projects. The program is able to generate either long oligomers (40-70 bases), or PCR primers for the amplification of gene-specific DNA fragments of user-defined length. Additionally, primers can be designed in-frame in order to facilitate large-scale cloning into expression vectors. Furthermore, GenomePRIDE can be adapted to specific applications such as the generation of genomic amplicon arrays or the design of fragments specific for alternative splice isoforms. We tested the performance of GenomePRIDE on the entire genomes of Listeria monocytogenes (1584 gene-specific PCRs, 48 long oligomers) as well as of eukaryotes such as Schizosaccharomyces pombe (5006 gene-specific PCRs), and Drosophila melanogaster (21 306 gene-specific PCRs). With its computing speed of 1000 primer pairs per hour and a PCR amplification success of 99%, GenomePRIDE represents an extremely cost- and time-effective program.
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Affiliation(s)
- Stefan A Haas
- Department of Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany.
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Abstract
We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The SYSTERS protein sequence cluster set provides an automatically generated classification of all sequences of the SWISS-PROT, TrEMBL and PIR databases into disjoint protein family and superfamily clusters. GeneNest is a database and software package for producing and visualizing gene indices from ESTs and mRNAs. Currently, the database comprises gene indices of human, mouse, Arabidopsis thaliana and zebrafish. SpliceNest is a web-based graphical tool to explore gene structure, including alternative splicing, based on a mapping of the EST consensus sequences from GeneNest to the complete human genome. The integration of SYSTERS, GeneNest and SpliceNest into one framework now permits an overall exploration of the whole sequence space covering protein, mRNA and EST sequences, as well as genomic DNA. The databases are available for querying and browsing at http://cmb.molgen.mpg.de.
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Affiliation(s)
- Antje Krause
- Max-Planck-Institute for Molecular Genetics, Computational Molecular Biology, Ihnestrasse 73, 14195 Berlin, Germany.
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50
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Affiliation(s)
- S A Haas
- Deutsches Krebforschungs-zentrum, Department of Theoretical Bioinformatics, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
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