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Bosch E, Güse E, Kirchner P, Winterpacht A, Walther M, Alders M, Kerkhof J, Ekici AB, Sticht H, Sadikovic B, Reis A, Vasileiou G. The missing link: ARID1B non-truncating variants causing Coffin-Siris syndrome due to protein aggregation. Hum Genet 2024; 143:965-978. [PMID: 39028335 PMCID: PMC11303441 DOI: 10.1007/s00439-024-02688-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/07/2024] [Indexed: 07/20/2024]
Abstract
ARID1B is the most frequently mutated gene in Coffin-Siris syndrome (CSS). To date, the vast majority of causative variants reported in ARID1B are truncating, leading to nonsense-mediated mRNA decay. In the absence of experimental data, only few ARID1B amino acid substitutions have been classified as pathogenic, mainly based on clinical data and their de novo occurrence, while most others are currently interpreted as variants of unknown significance. The present study substantiates the pathogenesis of ARID1B non-truncating/NMD-escaping variants located in the SMARCA4-interacting EHD2 and DNA-binding ARID domains. Overexpression assays in cell lines revealed that the majority of EHD2 variants lead to protein misfolding and formation of cytoplasmic aggresomes surrounded by vimentin cage-like structures and co-localizing with the microtubule organisation center. ARID domain variants exhibited not only aggresomes, but also nuclear aggregates, demonstrating robust pathological effects. Protein levels were not compromised, as shown by quantitative western blot analysis. In silico structural analysis predicted the exposure of amylogenic segments in both domains due to the nearby variants, likely causing this aggregation. Genome-wide transcriptome and methylation analysis in affected individuals revealed expression and methylome patterns consistent with those of the pathogenic haploinsufficiency ARID1B alterations in CSS cases. These results further support pathogenicity and indicate two approaches for disambiguation of such variants in everyday practice. The few affected individuals harbouring EHD2 non-truncating variants described to date exhibit mild CSS clinical traits. In summary, this study paves the way for the re-evaluation of previously unclear ARID1B non-truncating variants and opens a new era in CSS genetic diagnosis.
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Affiliation(s)
- Elisabeth Bosch
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Esther Güse
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Philipp Kirchner
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Andreas Winterpacht
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Mona Walther
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Marielle Alders
- Amsterdam University Medical Center, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam, The Netherlands
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Arif B Ekici
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
- Centre for Rare Diseases Erlangen (ZSEER), Universitätsklinikum Erlangen, Erlangen, Germany
| | - Georgia Vasileiou
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany.
- Centre for Rare Diseases Erlangen (ZSEER), Universitätsklinikum Erlangen, Erlangen, Germany.
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Schmetz A, Lüdecke HJ, Surowy H, Sivalingam S, Bruel AL, Caumes R, Charles P, Chatron N, Chrzanowska K, Codina-Solà M, Colson C, Cuscó I, Denommé-Pichon AS, Edery P, Faivre L, Green A, Heide S, Hsieh TC, Hustinx A, Kleinendorst L, Knopp C, Kraft F, Krawitz PM, Lasa-Aranzasti A, Lesca G, López-González V, Maraval J, Mignot C, Neuhann T, Netzer C, Oehl-Jaschkowitz B, Petit F, Philippe C, Posmyk R, Putoux A, Reis A, Sánchez-Soler MJ, Suh J, Tkemaladze T, Tran Mau Them F, Travessa A, Trujillano L, Valenzuela I, van Haelst MM, Vasileiou G, Vincent-Delorme C, Walther M, Verde P, Bramswig NC, Wieczorek D. Delineation of the adult phenotype of Coffin-Siris syndrome in 35 individuals. Hum Genet 2024; 143:71-84. [PMID: 38117302 DOI: 10.1007/s00439-023-02622-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
Coffin-Siris syndrome (CSS) is a rare multisystemic autosomal dominant disorder. Since 2012, alterations in genes of the SWI/SNF complex were identified as the molecular basis of CSS, studying largely pediatric cohorts. Therefore, there is a lack of information on the phenotype in adulthood, particularly on the clinical outcome in adulthood and associated risks. In an international collaborative effort, data from 35 individuals ≥ 18 years with a molecularly ascertained CSS diagnosis (variants in ARID1B, ARID2, SMARCA4, SMARCB1, SMARCC2, SMARCE1, SOX11, BICRA) using a comprehensive questionnaire was collected. Our results indicate that overweight and obesity are frequent in adults with CSS. Visual impairment, scoliosis, and behavioral anomalies are more prevalent than in published pediatric or mixed cohorts. Cognitive outcomes range from profound intellectual disability (ID) to low normal IQ, with most individuals having moderate ID. The present study describes the first exclusively adult cohort of CSS individuals. We were able to delineate some features of CSS that develop over time and have therefore been underrepresented in previously reported largely pediatric cohorts, and provide recommendations for follow-up.
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Affiliation(s)
- Ariane Schmetz
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany.
| | - Hermann-Josef Lüdecke
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Harald Surowy
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Sugirtahn Sivalingam
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Ange-Line Bruel
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, 21000, Dijon, France
| | | | - Perrine Charles
- Assistance Publique-Hôpitaux de Paris, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Bron, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261-INSERM U1315, Université de Lyon-Université Claude Bernard Lyon 1, Lyon, France
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Marta Codina-Solà
- Area of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Cindy Colson
- CHU Lille, Clinique de Génétique, 59000, Lille, France
| | - Ivon Cuscó
- Area of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Anne-Sophie Denommé-Pichon
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, 21000, Dijon, France
| | - Patrick Edery
- Service de Génétique, Hospices Civils de Lyon, Bron, France
- Centre de Recherche en Neurosciences de Lyon, Equipe GENDEV, INSERM U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurence Faivre
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Fédération Hospitalo-Universitaire TRANSLAD et Institut GIMI, Dijon Bourgogne University Hospital, 21000, Dijon, France
| | - Andrew Green
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, and University College Dublin School of Medicine and Medical Science, Dublin, Ireland
| | - Solveig Heide
- Assistance Publique-Hôpitaux de Paris, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Alexander Hustinx
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lotte Kleinendorst
- Department of Clinical Genetics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Cordula Knopp
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074, Aachen, Germany
| | - Florian Kraft
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074, Aachen, Germany
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Amaia Lasa-Aranzasti
- Area of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Gaetan Lesca
- Service de Génétique, Hospices Civils de Lyon, Bron, France
- Institute NeuroMyoGène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261-INSERM U1315, Université de Lyon-Université Claude Bernard Lyon 1, Lyon, France
| | - Vanesa López-González
- Sección Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), IMIB-Arrixaca, El Palmar, Murcia, Spain
| | - Julien Maraval
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Dijon Bourgogne University Hospital, 21000, Dijon, France
| | - Cyril Mignot
- Assistance Publique-Hôpitaux de Paris, Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | | | - Christian Netzer
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | | | | | - Christophe Philippe
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, 21000, Dijon, France
- Laboratory of Human Genetics, CHR Metz Thionville, Hôpital Mercy, Metz, France
| | - Renata Posmyk
- Department of Clinical Genetics, Medical University in Bialystok, Bialystok, Poland
| | - Audrey Putoux
- Service de Génétique, Hospices Civils de Lyon, Bron, France
- Centre de Recherche en Neurosciences de Lyon, Equipe GENDEV, INSERM U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
- Centre for Rare Diseases Erlangen (ZSEER), 91054, Erlangen, Germany
| | - María José Sánchez-Soler
- Sección Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca (HCUVA), IMIB-Arrixaca, El Palmar, Murcia, Spain
| | - Julia Suh
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074, Aachen, Germany
- Centre for Rare Diseases Aachen (ZSEA), 52076, Aachen, Germany
| | - Tinatin Tkemaladze
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Frédéric Tran Mau Them
- Inserm UMR1231 Team GAD, University of Burgundy and Franche-Comté, 21000, Dijon, France
- Functional Unit of Innovative Diagnosis for Rare Diseases, Dijon Bourgogne University Hospital, 21000, Dijon, France
| | - André Travessa
- Medical Genetics Department, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Laura Trujillano
- Area of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Irene Valenzuela
- Area of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035, Barcelona, Spain
| | - Mieke M van Haelst
- Department of Clinical Genetics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Georgia Vasileiou
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
- Centre for Rare Diseases Erlangen (ZSEER), 91054, Erlangen, Germany
| | | | - Mona Walther
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Pablo Verde
- Coordination Centre for Clinical Trials, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Nuria C Bramswig
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
- Center for Rare Diseases, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
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