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Mah-Som AY, Daw J, Huynh D, Wu M, Creekmore BC, Burns W, Skinner SA, Holla ØL, Smeland MF, Planes M, Uguen K, Redon S, Bierhals T, Scholz T, Denecke J, Mensah MA, Sczakiel HL, Tichy H, Verheyen S, Blatterer J, Schreiner E, Thies J, Lam C, Spaeth CG, Pena L, Ramsey K, Narayanan V, Seaver LH, Rodriguez D, Afenjar A, Burglen L, Lee EB, Chou TF, Weihl CC, Shinawi MS. An autosomal-dominant childhood-onset disorder associated with pathogenic variants in VCP. Am J Hum Genet 2023; 110:1959-1975. [PMID: 37883978 PMCID: PMC10645565 DOI: 10.1016/j.ajhg.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/10/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
Valosin-containing protein (VCP) is an AAA+ ATPase that plays critical roles in multiple ubiquitin-dependent cellular processes. Dominant pathogenic variants in VCP are associated with adult-onset multisystem proteinopathy (MSP), which manifests as myopathy, bone disease, dementia, and/or motor neuron disease. Through GeneMatcher, we identified 13 unrelated individuals who harbor heterozygous VCP variants (12 de novo and 1 inherited) associated with a childhood-onset disorder characterized by developmental delay, intellectual disability, hypotonia, and macrocephaly. Trio exome sequencing or a multigene panel identified nine missense variants, two in-frame deletions, one frameshift, and one splicing variant. We performed in vitro functional studies and in silico modeling to investigate the impact of these variants on protein function. In contrast to MSP variants, most missense variants had decreased ATPase activity, and one caused hyperactivation. Other variants were predicted to cause haploinsufficiency, suggesting a loss-of-function mechanism. This cohort expands the spectrum of VCP-related disease to include neurodevelopmental disease presenting in childhood.
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Affiliation(s)
- Annelise Y Mah-Som
- Genetics Training Program, Harvard Medical School and Brigham & Women's Hospital, Boston, MA 02115, USA; Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jil Daw
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Diana Huynh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mengcheng Wu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Benjamin C Creekmore
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | | | - Øystein L Holla
- Department of Medical Genetics, Telemark Hospital, 3710 Skien, Norway
| | - Marie F Smeland
- Department of Pediatric Rehabilitation, University Hospital of North Norway and the Arctic, University of Norway, 9019 Tromsø, Norway
| | - Marc Planes
- Service de Génétique Médicale et Biologie de la Reproduction, and Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, 29200 Brest, France
| | - Kevin Uguen
- Service de Génétique Médicale et Biologie de la Reproduction, and Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, 29200 Brest, France; University Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France
| | - Sylvia Redon
- Service de Génétique Médicale et Biologie de la Reproduction, and Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, 29200 Brest, France; University Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Tasja Scholz
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Martin A Mensah
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; BIH Biomedical Innovation Academy, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Henrike L Sczakiel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; BIH Biomedical Innovation Academy, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; RG Development and Disease, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Heidelis Tichy
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria
| | - Sarah Verheyen
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria
| | - Jasmin Blatterer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria
| | - Elisabeth Schreiner
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria
| | - Jenny Thies
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Christina Lam
- Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Christine G Spaeth
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Loren Pena
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Laurie H Seaver
- Corewell Health Helen Devos Children's Hospital, Department of Pediatrics and Human Development, Michigan State University College of Human Medicine, Grand Rapids, MI 49503, USA
| | - Diana Rodriguez
- Departement of Pediatric Neurology & Reference Centre for Congenital Malformations and Diseases of the Cerebellum, AP-HP.Sorbonne Université - Hôpital d'Enfants Armand-Trousseau, 75012 Paris, France
| | - Alexandra Afenjar
- Cerebellar Malformations and Congenital Diseases Reference Center and Neurogenetics Lab, Department of Genetics, Armand Trousseau Hospital, AP-HP Sorbonne Université, 75006 Paris, France
| | - Lydie Burglen
- Cerebellar Malformations and Congenital Diseases Reference Center and Neurogenetics Lab, Department of Genetics, Armand Trousseau Hospital, AP-HP Sorbonne Université, 75006 Paris, France
| | - Edward B Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Conrad C Weihl
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Marwan S Shinawi
- Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Gottschalk A, Sczakiel HL, Hülsemann W, Schwartzmann S, Abad-Perez AT, Grünhagen J, Ott CE, Spielmann M, Horn D, Mundlos S, Jamsheer A, Mensah MA. HOXD13-associated synpolydactyly: Extending and validating the genotypic and phenotypic spectrum with 38 new and 49 published families. Genet Med 2023; 25:100928. [PMID: 37427568 DOI: 10.1016/j.gim.2023.100928] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/02/2023] [Accepted: 07/02/2023] [Indexed: 07/11/2023] Open
Abstract
PURPOSE HOXD13 is an important regulator of limb development. Pathogenic variants in HOXD13 cause synpolydactyly type 1 (SPD1). How different types and positions of HOXD13 variants contribute to genotype-phenotype correlations, penetrance, and expressivity of SPD1 remains elusive. Here, we present a novel cohort and a literature review to elucidate HOXD13 phenotype-genotype correlations. METHODS Patients with limb anomalies suggestive of SPD1 were selected for analysis of HOXD13 by Sanger sequencing, repeat length analysis, and next-generation sequencing. Literature was reviewed for HOXD13 heterozygotes. Variants were annotated for phenotypic data. Severity was calculated, and cluster and decision-tree analyses were performed. RESULTS We identified 98 affected members of 38 families featuring 11 different (likely) causative variants and 4 variants of uncertain significance. The most frequent (25/38) were alanine repeat expansions. Phenotypes ranged from unaffected heterozygotes to severe osseous synpolydactyly, with intra- and inter-familial heterogeneity and asymmetry. A literature review provided 160 evaluable affected members of 49 families with SPD1. Computer-aided analysis only corroborated a positive correlation between alanine repeat length and phenotype severity. CONCLUSION Our findings support that HOXD13-protein condensation in addition to haploinsufficiency is the molecular pathomechanism of SPD1. Our data may, also, facilitate the interpretation of synpolydactyly radiographs by future automated tools.
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Affiliation(s)
- Annika Gottschalk
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Henrike L Sczakiel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany; Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, Berlin, Germany
| | - Wiebke Hülsemann
- Handsurgery Department, Children's Hospital Wilhelmstift, Hamburg, Germany
| | - Sarina Schwartzmann
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Angela T Abad-Perez
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Johannes Grünhagen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany; Labor Berlin Charité Vivantes GmbH, Department of Human Genetics, Berlin, Germany
| | - Claus-Eric Ott
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Human Molecular Genomics Group, Berlin, Germany; Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - Denise Horn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Stefan Mundlos
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany; Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland; Centers for Medical Genetics, GENESIS, Poznan, Poland
| | - Martin A Mensah
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany; Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Program, Berlin, Germany.
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3
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Sczakiel HL, Zhao M, Wollert-Wulf B, Danyel M, Ehmke N, Stoltenburg C, Damseh N, Al-Ashhab M, Balci TB, Osmond M, Andrade A, Schallner J, Porrmann J, McDonald K, Liao M, Oppermann H, Platzer K, Dierksen N, Mojarrad M, Eslahi A, Bakaeean B, Calame DG, Lupski JR, Firoozfar Z, Seyedhassani SM, Mohammadi SA, Anwaar N, Rahman F, Seelow D, Janz M, Horn D, Maroofian R, Boschann F. Broadening the phenotypic and molecular spectrum of FINCA syndrome: Biallelic NHLRC2 variants in 15 novel individuals. Eur J Hum Genet 2023; 31:905-917. [PMID: 37188825 PMCID: PMC10400545 DOI: 10.1038/s41431-023-01382-0] [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: 11/09/2022] [Revised: 04/17/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
FINCA syndrome [MIM: 618278] is an autosomal recessive multisystem disorder characterized by fibrosis, neurodegeneration and cerebral angiomatosis. To date, 13 patients from nine families with biallelic NHLRC2 variants have been published. In all of them, the recurrent missense variant p.(Asp148Tyr) was detected on at least one allele. Common manifestations included lung or muscle fibrosis, respiratory distress, developmental delay, neuromuscular symptoms and seizures often followed by early death due to rapid disease progression.Here, we present 15 individuals from 12 families with an overlapping phenotype associated with nine novel NHLRC2 variants identified by exome analysis. All patients described here presented with moderate to severe global developmental delay and variable disease progression. Seizures, truncal hypotonia and movement disorders were frequently observed. Notably, we also present the first eight cases in which the recurrent p.(Asp148Tyr) variant was not detected in either homozygous or compound heterozygous state.We cloned and expressed all novel and most previously published non-truncating variants in HEK293-cells. From the results of these functional studies, we propose a potential genotype-phenotype correlation, with a greater reduction in protein expression being associated with a more severe phenotype.Taken together, our findings broaden the known phenotypic and molecular spectrum and emphasize that NHLRC2-related disease should be considered in patients presenting with intellectual disability, movement disorders, neuroregression and epilepsy with or without pulmonary involvement.
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Affiliation(s)
- Henrike L Sczakiel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Ihnestr. 63-73, 14195, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Max Zhao
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Ihnestr. 63-73, 14195, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Brigitte Wollert-Wulf
- Biology of Malignant Lymphomas, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, 13125, Germany
- Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Berlin, 13125, Germany
| | - Magdalena Danyel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany
| | - Nadja Ehmke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Corinna Stoltenburg
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Sozialpädiatrisches Zentrum Neuropädiatrie, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Nadirah Damseh
- Department of Pediatrics and Genetics, Al Makassed Hospital and Al-Quds University, Jerusalem, Palestine
| | - Motee Al-Ashhab
- Department of Pediatrics and Genetics, Al Makassed Hospital and Al-Quds University, Jerusalem, Palestine
| | - Tugce B Balci
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, Western University, London, ON, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Andrea Andrade
- Division of Pediatric Neurology, London Health Sciences Centre, Western University, London, ON, Canada
| | - Jens Schallner
- Department of Sozialpaediatrisches Zentrum, Klinik fuer Kinder und Jugendmedizin, Universitaetsklinikum Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Joseph Porrmann
- Institute for Clinical Genetics, Universitätsklinikum, Technischen Universität Dresden, Dresden, Germany
| | - Kimberly McDonald
- Pediatric Neurology, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | | | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atieh Eslahi
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Behnaz Bakaeean
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Daniel G Calame
- Section of Pediatric Neurology and Developmental Neurosciences, Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | | | | - Najwa Anwaar
- Department of Developmental - Behavioral Pediatrics, University of Child Health Sciences and The Children's Hospital, Lahore, Pakistan
| | - Fatima Rahman
- Department of Developmental - Behavioral Pediatrics, University of Child Health Sciences and The Children's Hospital, Lahore, Pakistan
| | - Dominik Seelow
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
- Bioinformatics and Translational Genetics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Martin Janz
- Biology of Malignant Lymphomas, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Berlin, 13125, Germany
- Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, Berlin, 13125, Germany
| | - Denise Horn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Reza Maroofian
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London, WC1N 3BG, UK
| | - Felix Boschann
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Augustenburger Platz 1, 13353, Berlin, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Charitéplatz 1, 10117, Berlin, Germany.
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4
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Azabdaftari A, Sczakiel HL, Danyel M, Kohlmaier B, Mache CJ, Stalke A, Pfister ED, Thumfart J, Henning S, Knisely AS, Bufler P. Biallelic known and novel DCDC2 variants in cholestatic liver disease: phenotype-genotype observations in four children. Liver Int 2023; 43:1089-1095. [PMID: 36938759 DOI: 10.1111/liv.15563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/10/2022] [Revised: 02/20/2023] [Accepted: 03/08/2023] [Indexed: 03/21/2023]
Abstract
Neonatal sclerosing cholangitis (NSC) is associated with progressing biliary fibrosis often requiring liver transplantation in childhood. Several recent studies have identified variants in DCDC2, encoding doublecortin domain-containing protein 2 (DCDC2), expressed in primary cilia, that accompany syndromic disease and NSC. We report 4 patients with hepatobiliary disease associated with two novel homozygous or compound heterozygous variants in DCDC2. Three patients with protein-truncating variants in DCDC2, expressing no DCDC2, presented with the originally described severe hepatic phenotype in infancy. One patient with a novel homozygous DCDC2 missense variant shows a markedly milder phenotype only manifest in childhood and with retained DCDC2 expression. Concomitant nephronophthisis is present in 3 patients and learning disability in 2. This report widens the phenotypic spectrum of DCDC2-associated hepatobiliary disease. Testing for DCDC2 expression and DCDC2 variants should be included in the evaluation of cholangiopathy of unknown aetiology in childhood as well as in infancy.
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Affiliation(s)
- Aline Azabdaftari
- Department of Paediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Henrike L Sczakiel
- Berlin Institute of Health (BIH), Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany.,Max Planck Institute for Molecular Genetics, RG Development & Disease, Ihnestr. 63-73, 14195, Berlin, Germany
| | - Magdalena Danyel
- Berlin Institute of Health (BIH), Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Benno Kohlmaier
- Department of General Paediatrics, Medical University of Graz, Auenbruggerplatz 34/2, 8036 Graz, Austria
| | - Christoph J Mache
- Department of General Paediatrics, Medical University of Graz, Auenbruggerplatz 34/2, 8036 Graz, Austria
| | - Amelie Stalke
- Division of Paediatric Gastroenterology and Hepatology, Department of Paediatric Liver, Kidney and Metabolic Diseases, Hannover Medical School, Hannover, Germany.,Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Eva-Doreen Pfister
- Division of Paediatric Gastroenterology and Hepatology, Department of Paediatric Liver, Kidney and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | - Julia Thumfart
- Department of Paediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Stephan Henning
- Department of Paediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - A S Knisely
- Diagnostik- und Forschungsinstitut für Pathologie, Medizinische Universität Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Philip Bufler
- Department of Paediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
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5
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Mensah MA, Niskanen H, Magalhaes AP, Basu S, Kircher M, Sczakiel HL, Reiter AMV, Elsner J, Meinecke P, Biskup S, Chung BHY, Dombrowsky G, Eckmann-Scholz C, Hitz MP, Hoischen A, Holterhus PM, Hülsemann W, Kahrizi K, Kalscheuer VM, Kan A, Krumbiegel M, Kurth I, Leubner J, Longardt AC, Moritz JD, Najmabadi H, Skipalova K, Snijders Blok L, Tzschach A, Wiedersberg E, Zenker M, Garcia-Cabau C, Buschow R, Salvatella X, Kraushar ML, Mundlos S, Caliebe A, Spielmann M, Horn D, Hnisz D. Aberrant phase separation and nucleolar dysfunction in rare genetic diseases. Nature 2023; 614:564-571. [PMID: 36755093 PMCID: PMC9931588 DOI: 10.1038/s41586-022-05682-1] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/22/2022] [Indexed: 02/10/2023]
Abstract
Thousands of genetic variants in protein-coding genes have been linked to disease. However, the functional impact of most variants is unknown as they occur within intrinsically disordered protein regions that have poorly defined functions1-3. Intrinsically disordered regions can mediate phase separation and the formation of biomolecular condensates, such as the nucleolus4,5. This suggests that mutations in disordered proteins may alter condensate properties and function6-8. Here we show that a subset of disease-associated variants in disordered regions alter phase separation, cause mispartitioning into the nucleolus and disrupt nucleolar function. We discover de novo frameshift variants in HMGB1 that cause brachyphalangy, polydactyly and tibial aplasia syndrome, a rare complex malformation syndrome. The frameshifts replace the intrinsically disordered acidic tail of HMGB1 with an arginine-rich basic tail. The mutant tail alters HMGB1 phase separation, enhances its partitioning into the nucleolus and causes nucleolar dysfunction. We built a catalogue of more than 200,000 variants in disordered carboxy-terminal tails and identified more than 600 frameshifts that create arginine-rich basic tails in transcription factors and other proteins. For 12 out of the 13 disease-associated variants tested, the mutation enhanced partitioning into the nucleolus, and several variants altered rRNA biogenesis. These data identify the cause of a rare complex syndrome and suggest that a large number of genetic variants may dysregulate nucleoli and other biomolecular condensates in humans.
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Affiliation(s)
- Martin A. Mensah
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Henri Niskanen
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandre P. Magalhaes
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Shaon Basu
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Kircher
- grid.484013.a0000 0004 6879 971XExploratory Diagnostic Sciences, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.4562.50000 0001 0057 2672Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel Germany
| | - Henrike L. Sczakiel
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alisa M. V. Reiter
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jonas Elsner
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Meinecke
- grid.13648.380000 0001 2180 3484Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Saskia Biskup
- grid.498061.20000 0004 6008 5552Center for Genomics and Transcriptomics (CeGaT), Tübingen, Germany
| | - Brian H. Y. Chung
- grid.194645.b0000000121742757Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Gregor Dombrowsky
- grid.412468.d0000 0004 0646 2097Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany ,grid.5560.60000 0001 1009 3608Department of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany
| | - Christel Eckmann-Scholz
- grid.412468.d0000 0004 0646 2097Department of Obstetrics and Gynecology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Marc Phillip Hitz
- grid.412468.d0000 0004 0646 2097Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany ,grid.5560.60000 0001 1009 3608Department of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany
| | - Alexander Hoischen
- grid.10417.330000 0004 0444 9382Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul-Martin Holterhus
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, Pediatric Endocrinology and Diabetes, University Hospital Schleswig-Holstein, Schleswig-Holstein, Germany
| | - Wiebke Hülsemann
- grid.440182.b0000 0004 0580 3398Handchirurgie, Katholisches Kinderkrankenhaus Wilhelmstift, Hamburg, Germany
| | - Kimia Kahrizi
- grid.472458.80000 0004 0612 774XGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Vera M. Kalscheuer
- grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anita Kan
- grid.415550.00000 0004 1764 4144Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Mandy Krumbiegel
- grid.5330.50000 0001 2107 3311Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ingo Kurth
- grid.412301.50000 0000 8653 1507Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, Aachen, Germany
| | - Jonas Leubner
- grid.6363.00000 0001 2218 4662Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ann Carolin Longardt
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Center Schleswig‐Holstein, Kiel, Germany
| | - Jörg D. Moritz
- grid.412468.d0000 0004 0646 2097Department of Radiology and Neuroradiology, Pediatric Radiology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Hossein Najmabadi
- grid.472458.80000 0004 0612 774XGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Karolina Skipalova
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lot Snijders Blok
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andreas Tzschach
- grid.5963.9Institute of Human Genetics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eberhard Wiedersberg
- grid.491868.a0000 0000 9601 2399Zentrum für Kinder-und Jugendmedizin, Helios Kliniken Schwerin, Schwerin, Germany
| | - Martin Zenker
- grid.5807.a0000 0001 1018 4307Institute of Human Genetics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany
| | - Carla Garcia-Cabau
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - René Buschow
- grid.419538.20000 0000 9071 0620Microscopy Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Xavier Salvatella
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Passeig Lluís Companys 23, Barcelona, Spain
| | - Matthew L. Kraushar
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stefan Mundlos
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany ,grid.506128.8BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Almuth Caliebe
- grid.4562.50000 0001 0057 2672Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel Germany
| | - Malte Spielmann
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany.
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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6
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López C, Schleussner N, Bernhart SH, Kleinheinz K, Sungalee S, Sczakiel HL, Kretzmer H, Toprak UH, Glaser S, Wagener R, Ammerpohl O, Bens S, Giefing M, González Sánchez JC, Apic G, Hübschmann D, Janz M, Kreuz M, Mottok A, Müller JM, Seufert J, Hoffmann S, Korbel JO, Russell RB, Schüle R, Trümper L, Klapper W, Radlwimmer B, Lichter P, Küppers R, Schlesner M, Mathas S, Siebert R. Focal structural variants revealed by whole genome sequencing disrupt the histone demethylase KDM4C in B-cell lymphomas. Haematologica 2022; 108:543-554. [PMID: 35522148 PMCID: PMC9890021 DOI: 10.3324/haematol.2021.280005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Received: 09/13/2021] [Indexed: 02/03/2023] Open
Abstract
Histone methylation-modifiers, such as EZH2 and KMT2D, are recurrently altered in B-cell lymphomas. To comprehensively describe the landscape of alterations affecting genes encoding histone methylation-modifiers in lymphomagenesis we investigated whole genome and transcriptome data of 186 mature B-cell lymphomas sequenced in the ICGC MMML-Seq project. Besides confirming common alterations of KMT2D (47% of cases), EZH2 (17%), SETD1B (5%), PRDM9 (4%), KMT2C (4%), and SETD2 (4%), also identified by prior exome or RNA-sequencing studies, we here found recurrent alterations to KDM4C in chromosome 9p24, encoding a histone demethylase. Focal structural variation was the main mechanism of KDM4C alterations, and was independent from 9p24 amplification. We also identified KDM4C alterations in lymphoma cell lines including a focal homozygous deletion in a classical Hodgkin lymphoma cell line. By integrating RNA-sequencing and genome sequencing data we predict that KDM4C structural variants result in loss-offunction. By functional reconstitution studies in cell lines, we provide evidence that KDM4C can act as a tumor suppressor. Thus, we show that identification of structural variants in whole genome sequencing data adds to the comprehensive description of the mutational landscape of lymphomas and, moreover, establish KDM4C as a putative tumor suppressive gene recurrently altered in subsets of B-cell derived lymphomas.
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Affiliation(s)
- Cristina López
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,*CL and NS contributed equally as co-first authors
| | - Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany,*CL and NS contributed equally as co-first authors
| | - Stephan H. Bernhart
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Kortine Kleinheinz
- Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany
| | | | - Henrike L. Sczakiel
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany
| | - Helene Kretzmer
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Umut H. Toprak
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany,Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Division of Neuroblastoma Genomics (B087), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Maciej Giefing
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Gordana Apic
- BioQuant and Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Heidelberg, Germany
| | - Daniel Hübschmann
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany,Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany
| | - Markus Kreuz
- Institute for Medical Informatics Statistics and Epidemiology, Leipzig, Germany
| | - Anja Mottok
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Judith M. Müller
- Klinik fur Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Julian Seufert
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steve Hoffmann
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany,Leibniz Institute on Ageing-Fritz Lipmann Institute (FLI), Computational Biology, Jena, Germany
| | - Jan O. Korbel
- EMBL Heidelberg, Genome Biology Unit, Heidelberg,, Germany
| | - Robert B. Russell
- BioQuant and Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Heidelberg, Germany
| | - Roland Schüle
- Klinik fur Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany,BIOSS Centre of Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August-University of Göttingen, Göttingen, Germany
| | - Wolfram Klapper
- Hematopathology Section, Christian-Albrechts-University, Kiel, Germany
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany, and German Cancer Consortium (DKTK)
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany,Biomedical Informatics, Data Mining and Data Analytics, Augsburg University, Augsburg, Germany
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany,SM and RS contributed equally as co-senior authors
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,SM and RS contributed equally as co-senior authors
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7
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Boschann F, Moreno DA, Mensah MA, Sczakiel HL, Skipalova K, Holtgrewe M, Mundlos S, Fischer-Zirnsak B. Xq27.1 palindrome mediated interchromosomal insertion likely causes familial congenital bilateral laryngeal abductor paralysis (Plott syndrome). J Hum Genet 2022; 67:405-410. [PMID: 35095096 PMCID: PMC9233990 DOI: 10.1038/s10038-022-01018-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 01/27/2023]
Abstract
Bilateral laryngeal abductor paralysis is a rare entity and the second most common cause of stridor in newborns. So far, no conclusive genetic or chromosomal aberration has been reported for X-linked isolated bilateral vocal cord paralysis, also referred to as Plott syndrome. Via whole genome sequencing (WGS), we identified a complex interchromosomal insertion in a large family with seven affected males. The 404 kb inserted fragment originates from chromosome 10q21.3, contains no genes and is inserted inversionally into the intergenic chromosomal region Xq27.1, 82 kb centromeric to the nearest gene SOX3. The patterns found at the breakpoint junctions resemble typical characteristics that arise in replication-based mechanisms with long-distance template switching. Non protein-coding insertions into the same genomic region have been described to result in different phenotypes, indicating that the phenotypic outcome likely depends on the introduction of regulatory elements. In conclusion, our data adds Plott syndrome as another entity, likely caused by the insertion of non-coding DNA into the intergenic chromosomal region Xq27.1. In this regard, we demonstrate the importance of WGS as a powerful diagnostic test in unsolved genetic diseases, as this genomic rearrangement has not been detected by current first-line diagnostic tests, i.e., exome sequencing and chromosomal microarray analysis.
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8
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Schleussner N, Merkel O, Costanza M, Liang HC, Hummel F, Romagnani C, Durek P, Anagnostopoulos I, Hummel M, Jöhrens K, Niedobitek A, Griffin PR, Piva R, Sczakiel HL, Woessmann W, Damm-Welk C, Hinze C, Stoiber D, Gillissen B, Turner SD, Kaergel E, von Hoff L, Grau M, Lenz G, Dörken B, Scheidereit C, Kenner L, Janz M, Mathas S. The AP-1-BATF and -BATF3 module is essential for growth, survival and TH17/ILC3 skewing of anaplastic large cell lymphoma. Leukemia 2018; 32:1994-2007. [PMID: 29588546 PMCID: PMC6127090 DOI: 10.1038/s41375-018-0045-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [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] [Received: 03/08/2017] [Revised: 12/20/2017] [Accepted: 01/08/2018] [Indexed: 01/26/2023]
Abstract
Transcription factor AP-1 is constitutively activated and IRF4 drives growth and survival in ALK+ and ALK- anaplastic large cell lymphoma (ALCL). Here we demonstrate high-level BATF and BATF3 expression in ALCL. Both BATFs bind classical AP-1 motifs and interact with in ALCL deregulated AP-1 factors. Together with IRF4, they co-occupy AP-1-IRF composite elements, differentiating ALCL from non-ALCL. Gene-specific inactivation of BATFs, or global AP-1 inhibition results in ALCL growth retardation and/or cell death in vitro and in vivo. Furthermore, the AP-1-BATF module establishes TH17/group 3 innate lymphoid cells (ILC3)-associated gene expression in ALCL cells, including marker genes such as AHR, IL17F, IL22, IL26, IL23R and RORγt. Elevated IL-17A and IL-17F levels were detected in a subset of children and adolescents with ALK+ ALCL. Furthermore, a comprehensive analysis of primary lymphoma data confirms TH17-, and in particular ILC3-skewing in ALCL compared with PTCL. Finally, pharmacological inhibition of RORC as single treatment leads to cell death in ALCL cell lines and, in combination with the ALK inhibitor crizotinib, enforces death induction in ALK+ ALCL. Our data highlight the crucial role of AP-1/BATFs in ALCL and lead to the concept that some ALCL might originate from ILC3.
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Affiliation(s)
- Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Olaf Merkel
- Institute of Clinical Pathology, Medical University of Vienna, Vienna, Austria.,European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
| | - Mariantonia Costanza
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany.,European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
| | - Huan-Chang Liang
- Institute of Clinical Pathology, Medical University of Vienna, Vienna, Austria.,European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK
| | - Franziska Hummel
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Chiara Romagnani
- German Rheumatism Research Centre, German Rheumatism Research Centre (DRFZ), A Leibniz Institute, 10117, Berlin, Germany.,Medical Department I, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Pawel Durek
- German Rheumatism Research Centre, German Rheumatism Research Centre (DRFZ), A Leibniz Institute, 10117, Berlin, Germany
| | | | - Michael Hummel
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Korinna Jöhrens
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Antonia Niedobitek
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | | | - Roberto Piva
- Department of Molecular Biotechnology and Health Sciences, Center for Experimental Research and Medical Studies, University of Torino, Torino, Italy
| | - Henrike L Sczakiel
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Wilhelm Woessmann
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK.,NHL-BFM Study Centre and Department of Paediatric Haematology and Oncology, Justus-Liebig-University, Giessen, Germany
| | - Christine Damm-Welk
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK.,NHL-BFM Study Centre and Department of Paediatric Haematology and Oncology, Justus-Liebig-University, Giessen, Germany
| | - Christian Hinze
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Department of Nephrology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Dagmar Stoiber
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University Vienna, Vienna, Austria.,Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria
| | - Bernd Gillissen
- Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany
| | - Suzanne D Turner
- European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK.,Department of Pathology, University of Cambridge, Cambridge, CB21QP, UK
| | - Eva Kaergel
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Linda von Hoff
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany
| | - Michael Grau
- Department of Medicine A, Albert-Schweitzer-Campus 1, University Hospital Münster, 48149, Münster, Germany.,Cluster of Excellence EXC 1003, Cells in Motion, 48149, Münster, Germany
| | - Georg Lenz
- Department of Medicine A, Albert-Schweitzer-Campus 1, University Hospital Münster, 48149, Münster, Germany.,Cluster of Excellence EXC 1003, Cells in Motion, 48149, Münster, Germany
| | - Bernd Dörken
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | | | - Lukas Kenner
- Institute of Clinical Pathology, Medical University of Vienna, Vienna, Austria. .,European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK. .,Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria. .,University of Veterinary Medicine, Vienna, Austria. .,CBmed, Center for Biomarker Research in Medicine, 8010, Graz, Austria.
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany.,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany.,Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, 13125, Berlin, Germany
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine, 13125, Berlin, Germany. .,Hematology, Oncology, and Tumor Immunology, Charité-Universitätsmedizin Berlin, 12200, Berlin, Germany. .,European Research Initiative on ALK-Related Malignancies (ERIA), Cambridge, UK. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. .,Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, 13125, Berlin, Germany.
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