Aberrant phase separation and nucleolar dysfunction in rare genetic diseases

February 06, 2023

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


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.