Alternative splicing of BUD13 determines the severity of a developmental disorder with lipodystrophy and progeroid features

Uwe Kornak; Namrata Saha; Boris Keren; Alexander Neumann; Ana Lisa Taylor Tavares; Juliette Piard; Johannes Kopp; João Guilherme Rodrigues Alves; Miguel Rodríguez de Los Santos; Naji El Choubassi; Nadja Ehmke; Marten Jäger; Malte Spielmann; Jean Tori Pantel; Elodie Lejeune; Beatrix Fauler; Thorsten Mielke; Jochen Hecht; David Meierhofer; Tim M Strom; Vincent Laugel; Alexis Brice; Stefan Mundlos; Aida Bertoli-Avella; Peter Bauer; Florian Heyd; Odile Boute; Juliette Dupont; Christel Depienne; Lionel Van Maldergem; Björn Fischer-Zirnsak

doi:10.1016/j.gim.2022.05.004

Alternative splicing of BUD13 determines the severity of a developmental disorder with lipodystrophy and progeroid features

Genet Med. 2022 Sep;24(9):1927-1940. doi: 10.1016/j.gim.2022.05.004. Epub 2022 Jun 7.

Authors

Uwe Kornak¹, Namrata Saha², Boris Keren³, Alexander Neumann⁴, Ana Lisa Taylor Tavares⁵, Juliette Piard⁶, Johannes Kopp⁷, João Guilherme Rodrigues Alves⁸, Miguel Rodríguez de Los Santos⁹, Naji El Choubassi¹⁰, Nadja Ehmke¹¹, Marten Jäger¹², Malte Spielmann¹³, Jean Tori Pantel¹¹, Elodie Lejeune³, Beatrix Fauler¹⁴, Thorsten Mielke¹⁴, Jochen Hecht¹⁵, David Meierhofer¹⁶, Tim M Strom¹⁷, Vincent Laugel¹⁸, Alexis Brice¹⁹, Stefan Mundlos¹⁰, Aida Bertoli-Avella²⁰, Peter Bauer²¹, Florian Heyd²², Odile Boute²³, Juliette Dupont²⁴, Christel Depienne²⁵, Lionel Van Maldergem²⁶, Björn Fischer-Zirnsak²⁷

Affiliations

¹ Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany. Electronic address: uwe.kornak@med.uni-goettingen.de.
² Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies, Charité-Universtitätsmedizin Berlin, Germany; Max Planck International Research Network on Aging, Max Planck Society, Rostock, Germany.
³ Department of Genetics, DMU BioGem, Assistance Publique - Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France.
⁴ Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany; Omiqa Bioinformatics, Berlin, Germany.
⁵ East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom; Genomics England, London, United Kingdom.
⁶ Centre de Génétique Humaine, Université de Franche-Comté, Besançon, France. Electronic address: jpiard@chu-besancon.fr.
⁷ Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany.
⁸ Serviço de Genética, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospital Universitário Lisboa Norte, Lisboa, Portugal.
⁹ Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Berlin-Brandenburg School for Regenerative Therapies, Charité-Universtitätsmedizin Berlin, Germany.
¹⁰ Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.
¹¹ Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
¹² Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; BIH Genomics Core Unit, Berlin Institute of Health (BIH), Berlin, Germany.
¹³ Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute of Human Genetics, University of Lübeck, Lübeck, Germany.
¹⁴ Microscopy and Cryo-electron Microscopy Group, Max Planck Institute for Molecular Genetics, Berlin, Germany.
¹⁵ Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
¹⁶ Mass-Spectrometry Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany.
¹⁷ Institute of Human Genetics, Klinikum rechts der Isar, Technical University Munich, Munich, Germany.
¹⁸ Service de Pédiatrie 1, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France; Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, Faculté de Médecine de Strasbourg, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
¹⁹ Department of Genetics, DMU BioGem, Assistance Publique - Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France; Institut du Cerveau - Paris Brain Institute - ICM, Inserm, Centre National de la Recherche Scientifique, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France.
²⁰ CENTOGENE GmbH, Rostock, Germany.
²¹ CENTOGENE GmbH, Rostock, Germany; Department of Medicine Clinic III, Hematology, Oncology and Palliative Medicine, Rostock University Medical Center, Rostock, Germany.
²² Laboratory of RNA Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
²³ Génétique Clinique, Centre Hospitalier Universitaire de Lille, Hôpital Jeanne de Flandre, Lille, France. Electronic address: odile.boute@chru-lille.fr.
²⁴ Serviço de Genética, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospital Universitário Lisboa Norte, Lisboa, Portugal. Electronic address: juliette.dupont@chln.min-saude.pt.
²⁵ Institut du Cerveau - Paris Brain Institute - ICM, Inserm, Centre National de la Recherche Scientifique, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France; Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
²⁶ Centre de Génétique Humaine, Université de Franche-Comté, Besançon, France; Center of Clinical investigation 1431, National Institute of Health and Medical Research (INSERM), CHU, Besancon, France.
²⁷ Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. Electronic address: bjoern.fischer@charite.de.

PMID: 35670808
DOI: 10.1016/j.gim.2022.05.004

Abstract

Purpose: In this study we aimed to identify the molecular genetic cause of a progressive multisystem disease with prominent lipodystrophy.

Methods: In total, 5 affected individuals were investigated using exome sequencing. Dermal fibroblasts were characterized using RNA sequencing, proteomics, immunoblotting, immunostaining, and electron microscopy. Subcellular localization and rescue studies were performed.

Results: We identified a lipodystrophy phenotype with a typical facial appearance, corneal clouding, achalasia, progressive hearing loss, and variable severity. Although 3 individuals showed stunted growth, intellectual disability, and died within the first decade of life (A1, A2, and A3), 2 are adults with normal intellectual development (A4 and A5). All individuals harbored an identical homozygous nonsense variant affecting the retention and splicing complex component BUD13. The nucleotide substitution caused alternative splicing of BUD13 leading to a stable truncated protein whose expression positively correlated with disease expression and life expectancy. In dermal fibroblasts, we found elevated intron retention, a global reduction of spliceosomal proteins, and nuclei with multiple invaginations, which were more pronounced in A1, A2, and A3. Overexpression of both BUD13 isoforms normalized the nuclear morphology.

Conclusion: Our results define a hitherto unknown syndrome and show that the alternative splice product converts a loss-of-function into a hypomorphic allele, thereby probably determining the severity of the disease and the survival of affected individuals.

Keywords: Alternative splicing; BUD13; Lipodystrophy; Progeroid disorder; RES complex.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alternative Splicing*
Child
Developmental Disabilities / genetics
Humans
Introns
Lipodystrophy* / genetics
RNA Splicing
RNA-Binding Proteins / genetics*

Substances

BUD13 homolog protein, human
RNA-Binding Proteins