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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: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [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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