Aberrant phase separation and nucleolar dysfunction in rare genetic diseases

February 06, 2023

Martin A Mensah # 1 2 3, Henri Niskanen # 4, Alexandre P Magalhaes 4, Shaon Basu 4, Martin Kircher 5 6, Henrike L Sczakiel 1 2 3, Alisa M V Reiter 1, Jonas Elsner 1, Peter Meinecke 7, Saskia Biskup 8, Brian H Y Chung 9, Gregor Dombrowsky 10 11, Christel Eckmann-Scholz 12, Marc Phillip Hitz 10 11, Alexander Hoischen 13 14, Paul-Martin Holterhus 15, Wiebke Hülsemann 16, Kimia Kahrizi 17, Vera M Kalscheuer 3, Anita Kan 18, Mandy Krumbiegel 19, Ingo Kurth 20, Jonas Leubner 21, Ann Carolin Longardt 22, Jörg D Moritz 23, Hossein Najmabadi 17, Karolina Skipalova 1, Lot Snijders Blok 14, Andreas Tzschach 24, Eberhard Wiedersberg 25, Martin Zenker 26, Carla Garcia-Cabau 27, René Buschow 28, Xavier Salvatella 27 29, Matthew L Kraushar 4, Stefan Mundlos 1 2 3 30, Almuth Caliebe 6, Malte Spielmann 31 32 33, Denise Horn 34, Denes Hnisz 35

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.

  1. Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
  2. BIH Biomedical Innovation Academy, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
  3. RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  4. Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  5. Exploratory Diagnostic Sciences, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
  6. Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany.
  7. Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
  8. Center for Genomics and Transcriptomics (CeGaT), Tübingen, Germany.
  9. Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
  10. Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany.
  11. Department of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany.
  12. Department of Obstetrics and Gynecology, University Hospital Schleswig-Holstein, Kiel, Germany.
  13. Department 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.
  14. Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
  15. Department of Pediatrics, Pediatric Endocrinology and Diabetes, University Hospital Schleswig-Holstein, Schleswig-Holstein, Germany.
  16. Handchirurgie, Katholisches Kinderkrankenhaus Wilhelmstift, Hamburg, Germany.
  17. Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
  18. Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong.
  19. Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
  20. Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, Aachen, Germany.
  21. Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
  22. Department of Pediatrics, University Hospital Center Schleswig-Holstein, Kiel, Germany.
  23. Department of Radiology and Neuroradiology, Pediatric Radiology, University Hospital Schleswig-Holstein, Kiel, Germany.
  24. Institute of Human Genetics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
  25. Zentrum für Kinder-und Jugendmedizin, Helios Kliniken Schwerin, Schwerin, Germany.
  26. Institute of Human Genetics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany.
  27. Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
  28. Microscopy Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany.
  29. ICREA, Passeig Lluís Companys 23, Barcelona, Spain.
  30. BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany.
  31. RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. Malte.Spielmann@uksh.de.
  32. Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany. Malte.Spielmann@uksh.de.
  33. DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany. Malte.Spielmann@uksh.de.
  34. Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany. Denise.Horn@charite.de.
  35. Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany. hnisz@molgen.mpg.de.
#Contributed equally.