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Mudau MM, Seymour H, Nevondwe P, Kerr R, Spencer C, Feben C, Lombard Z, Honey E, Krause A, Carstens N. A feasible molecular diagnostic strategy for rare genetic disorders within resource-constrained environments. J Community Genet 2024; 15:39-48. [PMID: 37815686 PMCID: PMC10858011 DOI: 10.1007/s12687-023-00674-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
Timely and accurate diagnosis of rare genetic disorders is critical, as it enables improved patient management and prognosis. In a resource-constrained environment such as the South African State healthcare system, the challenge is to design appropriate and cost-effective assays that will enable accurate genetic diagnostic services in patients of African ancestry across a broad disease spectrum. Next-generation sequencing (NGS) has transformed testing approaches for many Mendelian disorders, but this technology is still relatively new in our setting and requires cost-effective ways to implement. As a proof of concept, we describe a feasible diagnostic strategy for genetic disorders frequently seen in our genetics clinics (RASopathies, Cornelia de Lange syndrome, Treacher Collins syndrome, and CHARGE syndrome). The custom-designed targeted NGS gene panel enabled concurrent variant screening for these disorders. Samples were batched during sequencing and analyzed selectively based on the clinical phenotype. The strategy employed in the current study was cost-effective, with sequencing and analysis done at USD849.68 per sample and achieving an overall detection rate of 54.5%. The strategy employed is cost-effective as it allows batching of samples from patients with different diseases in a single run, an approach that can be utilized with rare and less frequently ordered molecular diagnostic tests. The subsequent selective analysis pipeline allowed for timeous reporting back of patients results. This is feasible with a reasonable yield and can be employed for the molecular diagnosis of a wide range of rare monogenic disorders in a resource-constrained environment.
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Affiliation(s)
- Maria Mabyalwa Mudau
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Heather Seymour
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patracia Nevondwe
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Robyn Kerr
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Careni Spencer
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Engela Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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2
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Seymour H, Feben C, Nevondwe P, Kerr R, Spencer C, Mudau M, Honey E, Lombard Z, Krause A, Carstens N. Mutation profiling in South African patients with Cornelia de Lange syndrome phenotype. Mol Genet Genomic Med 2024; 12:e2342. [PMID: 38284454 PMCID: PMC10785556 DOI: 10.1002/mgg3.2342] [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: 09/07/2023] [Revised: 11/08/2023] [Accepted: 12/05/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Cornelia de Lange Syndrome (CdLS) presents with a variable multi-systemic phenotype and pathogenic variants have been identified in five main genes. This condition has been understudied in African populations with little phenotypic and molecular information available. METHODS AND RESULTS We present a cohort of 14 patients with clinical features suggestive of CdLS. Clinical phenotyping was carried out and cases were classified according to the international consensus criteria. According to this criteria, nine patients had classical CdLS, one had non-classical CdLS and four presented with a phenotype that suggested molecular testing for CdLS. Each patient underwent mutation profiling using a targeted next generation sequencing panel of 18 genes comprising known and suspected CdLS causal genes. Of the 14 patients tested, pathogenic and likely pathogenic variants were identified in nine: eight variants in the NIPBL gene and one in the STAG1 gene. CONCLUSIONS We present the first molecular data for a cohort of South African patients with CdLS. Eight of the nine variants identified were in the NIPBL gene, the most commonly involved gene in cases of CdLS. This is also the first report of a patient of African ancestry presenting with STAG1-related CdLS.
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Affiliation(s)
- Heather Seymour
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Patracia Nevondwe
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Robyn Kerr
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Careni Spencer
- Division of Human Genetics, Department of MedicineUniversity of Cape Town and Groote Schuur HospitalCape TownSouth Africa
| | - Maria Mudau
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Engela Honey
- Department of Biochemistry, Genetics, Microbiology, Faculty of Natural and Agricultural ScienceUniversity of PretoriaPretoriaSouth Africa
| | - Zane Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Genomics Platform, South African Medical Research CouncilCape TownSouth Africa
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Ura H, Togi S, Iwata Y, Ozaki M, Niida Y. Establishment of a human induced pluripotent stem cell line, KMUGMCi002-A, from a patient bearing a heterozygous c.6362_6364del mutation in the NIPBL gene leading Cornelia de Lange syndrome (CdLS). Stem Cell Res 2022; 63:102860. [PMID: 35834947 DOI: 10.1016/j.scr.2022.102860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/27/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a multiple congenital anomalies syndrome caused by mutations in the cohesion complex. The mutations in NIPBL, one of cohesion regulatory proteins, are the most frequent cause of CdLS. The peripheral blood mononuclear cells (PBMCs) from a patient carrying a heterozygous 3 bp deletion in Exon 37 of the NIPBL gene were reprogrammed using the CytoTune-iPS2.0 Sendai Reprogramming Kit. The deleted mutation in NIPBL will cause the abnormal truncated protein, which is known to associated with CdLS. The established human induced pluripotent cell (hiPSC) line will enable proper in vitro disease modelling of CdLS. Resource Table.
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Affiliation(s)
- Hiroki Ura
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa 920-0923, Japan; Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa 920-0923, Japan.
| | - Sumihito Togi
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa 920-0923, Japan; Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa 920-0923, Japan
| | - Yumiko Iwata
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa 920-0923, Japan
| | - Mamoru Ozaki
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa 920-0923, Japan
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa 920-0923, Japan; Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa 920-0923, Japan
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4
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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Tan J, Chow YP, Zainul Abidin N, Chang KM, Selvaratnam V, Tumian NR, Poh YM, Veerakumarasivam A, Laffan MA, Wong CL. Analysis of genetic variants in myeloproliferative neoplasms using a 22-gene next-generation sequencing panel. BMC Med Genomics 2022; 15:10. [PMID: 35033063 PMCID: PMC8760696 DOI: 10.1186/s12920-021-01145-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/06/2021] [Indexed: 12/18/2022] Open
Abstract
Background The Philadelphia (Ph)-negative myeloproliferative neoplasms (MPNs), namely essential thrombocythaemia (ET), polycythaemia vera (PV) and primary myelofibrosis (PMF), are a group of chronic clonal haematopoietic disorders that have the propensity to advance into bone marrow failure or acute myeloid leukaemia; often resulting in fatality. Although driver mutations have been identified in these MPNs, subtype-specific markers of the disease have yet to be discovered. Next-generation sequencing (NGS) technology can potentially improve the clinical management of MPNs by allowing for the simultaneous screening of many disease-associated genes. Methods The performance of a custom, in-house designed 22-gene NGS panel was technically validated using reference standards across two independent replicate runs. The panel was subsequently used to screen a total of 10 clinical MPN samples (ET n = 3, PV n = 3, PMF n = 4). The resulting NGS data was then analysed via a bioinformatics pipeline. Results The custom NGS panel had a detection limit of 1% variant allele frequency (VAF). A total of 20 unique variants with VAFs above 5% (4 of which were putatively novel variants with potential biological significance) and one pathogenic variant with a VAF of between 1 and 5% were identified across all of the clinical MPN samples. All single nucleotide variants with VAFs ≥ 15% were confirmed via Sanger sequencing. Conclusions The high fidelity of the NGS analysis and the identification of known and novel variants in this study cohort support its potential clinical utility in the management of MPNs. However, further optimisation is needed to avoid false negatives in regions with low sequencing coverage, especially for the detection of driver mutations in MPL. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01145-0.
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Affiliation(s)
- Jaymi Tan
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia
| | - Yock Ping Chow
- Clinical Research Centre, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Norziha Zainul Abidin
- Molecular Diagnostics Laboratory, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Kian Meng Chang
- Haematology Unit, Department of Medicine, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | | | - Nor Rafeah Tumian
- Haematology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Yang Ming Poh
- School of Data Sciences, Perdana University, Serdang, Selangor, Malaysia
| | - Abhi Veerakumarasivam
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia
| | - Michael Arthur Laffan
- Centre for Haematology, Hammersmith Hospital, London, UK.,Faculty of Medicine, Imperial College London, London, UK
| | - Chieh Lee Wong
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Selangor, Malaysia. .,Clinical Research Centre, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia. .,Molecular Diagnostics Laboratory, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia. .,Haematology Unit, Department of Medicine, Sunway Medical Centre, Petaling Jaya, Selangor Darul Ehsan, Malaysia. .,Centre for Haematology, Hammersmith Hospital, London, UK. .,Faculty of Medicine, Imperial College London, London, UK.
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6
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Latorre-Pellicer A, Gil-Salvador M, Parenti I, Lucia-Campos C, Trujillano L, Marcos-Alcalde I, Arnedo M, Ascaso Á, Ayerza-Casas A, Antoñanzas-Pérez R, Gervasini C, Piccione M, Mariani M, Weber A, Kanber D, Kuechler A, Munteanu M, Khuller K, Bueno-Lozano G, Puisac B, Gómez-Puertas P, Selicorni A, Kaiser FJ, Ramos FJ, Pié J. Clinical relevance of postzygotic mosaicism in Cornelia de Lange syndrome and purifying selection of NIPBL variants in blood. Sci Rep 2021; 11:15459. [PMID: 34326454 PMCID: PMC8322329 DOI: 10.1038/s41598-021-94958-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/09/2022] Open
Abstract
Postzygotic mosaicism (PZM) in NIPBL is a strong source of causality for Cornelia de Lange syndrome (CdLS) that can have major clinical implications. Here, we further delineate the role of somatic mosaicism in CdLS by describing a series of 11 unreported patients with mosaic disease-causing variants in NIPBL and performing a retrospective cohort study from a Spanish CdLS diagnostic center. By reviewing the literature and combining our findings with previously published data, we demonstrate a negative selection against somatic deleterious NIPBL variants in blood. Furthermore, the analysis of all reported cases indicates an unusual high prevalence of mosaicism in CdLS, occurring in 13.1% of patients with a positive molecular diagnosis. It is worth noting that most of the affected individuals with mosaicism have a clinical phenotype at least as severe as those with constitutive pathogenic variants. However, the type of genetic change does not vary between germline and somatic events and, even in the presence of mosaicism, missense substitutions are located preferentially within the HEAT repeat domain of NIPBL. In conclusion, the high prevalence of mosaicism in CdLS as well as the disparity in tissue distribution provide a novel orientation for the clinical management and genetic counselling of families.
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Affiliation(s)
- Ana Latorre-Pellicer
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Marta Gil-Salvador
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Cristina Lucia-Campos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Laura Trujillano
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Iñigo Marcos-Alcalde
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), 28049, Madrid, Spain
- Biosciences Research Institute, School of Experimental Sciences, Universidad Francisco de Vitoria, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - María Arnedo
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ángela Ascaso
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Ariadna Ayerza-Casas
- Unit of Paediatric Cardiology, Service of Paediatrics, Hospital Universitario Miguel Servet, 50009, Zaragoza, Spain
| | - Rebeca Antoñanzas-Pérez
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Cristina Gervasini
- Genetica Medica, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Maria Piccione
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Milena Mariani
- Centro Fondazione Mariani per il Bambino Fragile, Department of Pediatrics, ASST-Lariana Sant'Anna Hospital, San Fermo della Battaglia (Como), Italy
| | - Axel Weber
- Institute of Human Genetics, Justus-Liebig-University, Giessen, Germany
| | - Deniz Kanber
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Martin Munteanu
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Katharina Khuller
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Gloria Bueno-Lozano
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain
| | - Paulino Gómez-Puertas
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), 28049, Madrid, Spain
| | - Angelo Selicorni
- Centro Fondazione Mariani per il Bambino Fragile, Department of Pediatrics, ASST-Lariana Sant'Anna Hospital, San Fermo della Battaglia (Como), Italy
| | - Frank J Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
- Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsmedizin Essen, Universitätsklinikum Essen, Essen, Germany
| | - Feliciano J Ramos
- Unit of Clinical Genetics, Service of Paediatrics, Hospital Clínico Universitario Lozano Blesa, Department of Paediatrics, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain.
| | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, Universidad de Zaragoza, CIBERER-GCV02 and IIS-Aragon, 50009, Zaragoza, Spain.
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Weiss FD, Calderon L, Wang YF, Georgieva R, Guo Y, Cvetesic N, Kaur M, Dharmalingam G, Krantz ID, Lenhard B, Fisher AG, Merkenschlager M. Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin. Nat Commun 2021; 12:2919. [PMID: 34006846 PMCID: PMC8131595 DOI: 10.1038/s41467-021-23141-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a human developmental disorder caused by mutations that compromise the function of cohesin, a major regulator of 3D genome organization. Cognitive impairment is a universal and as yet unexplained feature of CdLS. We characterize the transcriptional profile of cortical neurons from CdLS patients and find deregulation of hundreds of genes enriched for neuronal functions related to synaptic transmission, signalling processes, learning and behaviour. Inducible proteolytic cleavage of cohesin disrupts 3D genome organization and transcriptional control in post-mitotic cortical mouse neurons, demonstrating that cohesin is continuously required for neuronal gene expression. The genes affected by acute depletion of cohesin belong to similar gene ontology classes and show significant numerical overlap with genes deregulated in CdLS. Interestingly, reconstitution of cohesin function largely rescues altered gene expression, including the expression of genes deregulated in CdLS.
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Affiliation(s)
- Felix D Weiss
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Lesly Calderon
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Research Institute of Molecular Pathology, Vienna, Austria
| | - Yi-Fang Wang
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Radina Georgieva
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Computational Regulatory Genomics Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Ya Guo
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Nevena Cvetesic
- Computational Regulatory Genomics Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Maninder Kaur
- Division of Human Genetics, The Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Ian D Krantz
- Division of Human Genetics, The Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Boris Lenhard
- Computational Regulatory Genomics Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Amanda G Fisher
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, Epigenetics Section, MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
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8
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Dai C, Cheng D, Li W, Zeng S, Lu G, Zhang Q. Identification of paternal germline mosaicism by MicroSeq and targeted next-generation sequencing. Mol Genet Genomic Med 2020; 8:e1394. [PMID: 32643877 PMCID: PMC7507370 DOI: 10.1002/mgg3.1394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/26/2020] [Accepted: 06/08/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Prezygotic de novo mutations may be inherited from parents with germline mosaicism and are often overlooked when the resulting phenotype affects only one child. We aimed to identify paternal germline mosaicism in an index family and provide a strategy to determine germline mosaicism.' METHODS Whole-exome sequencing was performed on an Alport syndrome-affected child. Variants were validated using Sanger sequencing in the pedigree analysis. An apparent de novo mutation was tested by next-generation sequencing (NGS) following chromosome microdissection of the mutant region (MicroSeq) to clarify its homologous chromosome source. Mosaic mutation in sperm samples was detected using targeted next-generation sequencing (TNGS). Self-prepared mosaic DNA samples of the 3% and 0.1% mutant fractions were used to evaluate the TNGS detection sensitivity. RESULTS Two novel heterozygous variants, maternally inherited c.1322delT (p.Ile441Thrfs*17) and the de novo mutation c.2939T>A (p.Leu980Ter), in the COL4A3 gene were discovered in the propositus. MicroSeq identified c.2939T>A in the paternal chromosome, which was in trans with c.1322delT. The frequency of c.2937A was 2.65% in the father's sperm sample. We also showed that a 500X depth coverage may detect a mosaic mutation with an allele frequency as low as 2%-3% using TNGS. CONCLUSION MicroSeq is a valuable tool to identify the allele source of de novo mutations in a single patient. TNGS can be used to assess the mosaic ratios of known sites. We provided a systematic algorithm to detect germinal mosaicism in a single patient. This algorithm may have implications for genetic and reproductive counseling on germline mosaicism.
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Affiliation(s)
- Congling Dai
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Hunan, China
| | - Dehua Cheng
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Hunan, China.,Reproductive and Genetic Hospital ofCITIC-Xiangya, Hunan, China
| | - Weina Li
- Reproductive and Genetic Hospital ofCITIC-Xiangya, Hunan, China
| | - Sicong Zeng
- Reproductive and Genetic Hospital ofCITIC-Xiangya, Hunan, China.,School of medicine, Hunan Normal University, Hunan, China
| | - Guangxiu Lu
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Hunan, China.,Reproductive and Genetic Hospital ofCITIC-Xiangya, Hunan, China.,School of medicine, Hunan Normal University, Hunan, China.,Hunan Guangxiu Hospital, Hunan, China
| | - Qianjun Zhang
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Hunan, China.,Reproductive and Genetic Hospital ofCITIC-Xiangya, Hunan, China.,Hunan Guangxiu Hospital, Hunan, China
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9
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Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, van Staveren T, van IJcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome. Cell Rep 2020; 31:107647. [PMID: 32433956 DOI: 10.1016/j.celrep.2020.107647] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/30/2019] [Accepted: 04/24/2020] [Indexed: 12/26/2022] Open
Abstract
The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations in NIPBL account for most cases of the rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report a MAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus. Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable for normal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fatal outcome of an out-of-frame single nucleotide duplication in NIPBL, engineered in two different cell lines, alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interact with MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protective against out-of-frame mutations that is potentially relevant for other genetic conditions.
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Affiliation(s)
- Ilaria Parenti
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Farah Diab
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Sara Ruiz Gil
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | | | - Valentina Casa
- Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands
| | - Riccardo Berutti
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Rutger W W Brouwer
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Center for Biomics, the Netherlands
| | - Valerie Dupé
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Juliane Eckhold
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Feliciano Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Wilfred F J van IJcken
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Center for Biomics, the Netherlands
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, 50009 Zaragoza, Spain
| | - Erwan Watrin
- Centre National de la Recherche Scientifique, UMR6290, Rennes, France; Institut de Génétique et Développement de Rennes, Université de Rennes, Rennes, France
| | - Frank J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany; Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany; DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany.
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, the Netherlands.
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10
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Ohuchi H, Sato K, Habuta M, Fujita H, Bando T. Congenital eye anomalies: More mosaic than thought? Congenit Anom (Kyoto) 2019; 59:56-73. [PMID: 30039880 DOI: 10.1111/cga.12304] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/13/2022]
Abstract
The eye is a sensory organ that primarily captures light and provides the sense of sight, as well as delivering non-visual light information involving biological rhythms and neurophysiological activities to the brain. Since the early 1990s, rapid advances in molecular biology have enabled the identification of developmental genes, genes responsible for human congenital diseases, and relevant genes of mutant animals with various anomalies. In this review, we first look at the development of the eye, and we highlight seminal reports regarding archetypal gene defects underlying three developmental ocular disorders in humans: (1) holoprosencephaly (HPE), with cyclopia being exhibited in the most severe cases; (2) microphthalmia, anophthalmia, and coloboma (MAC) phenotypes; and (3) anterior segment dysgenesis (ASDG), known as Peters anomaly and its related disorders. The recently developed methods, such as next-generation sequencing and genome editing techniques, have aided the discovery of gene mutations in congenital eye diseases and gene functions in normal eye development. Finally, we discuss Pax6-genome edited mosaic eyes and propose that somatic mosaicism in developmental gene mutations should be considered a causal factor for variable phenotypes, sporadic cases, and de novo mutations in human developmental disorders.
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Affiliation(s)
- Hideyo Ohuchi
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Keita Sato
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Munenori Habuta
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hirofumi Fujita
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Tetsuya Bando
- Department of Cytology and Histology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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11
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Dubourg C, Kim A, Watrin E, de Tayrac M, Odent S, David V, Dupé V. Recent advances in understanding inheritance of holoprosencephaly. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2018; 178:258-269. [PMID: 29785796 DOI: 10.1002/ajmg.c.31619] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/16/2022]
Abstract
Holoprosencephaly (HPE) is a complex genetic disorder of the developing forebrain characterized by high phenotypic and genetic heterogeneity. HPE was initially defined as an autosomal dominant disease, but recent research has shown that its mode of transmission is more complex. The past decade has witnessed rapid development of novel genetic technologies and significant progresses in clinical studies of HPE. In this review, we recapitulate genetic epidemiological studies of the largest European HPE cohort and summarize the novel genetic discoveries of HPE based on recently developed diagnostic methods. Our main purpose is to present different inheritance patterns that exist for HPE with a particular emphasis on oligogenic inheritance and its implications in genetic counseling.
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Affiliation(s)
- Christèle Dubourg
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Artem Kim
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France
| | - Erwan Watrin
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France
| | - Marie de Tayrac
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Sylvie Odent
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France.,Service de Génétique Clinique, CHU, Rennes, France
| | - Véronique David
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Valérie Dupé
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F - 35000, Rennes, France
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12
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Hauser NS, Solomon BD, Vilboux T, Khromykh A, Baveja R, Bodian DL. Experience with genomic sequencing in pediatric patients with congenital cardiac defects in a large community hospital. Mol Genet Genomic Med 2018; 6:200-212. [PMID: 29368431 PMCID: PMC5902396 DOI: 10.1002/mgg3.357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Congenital cardiac defects, whether isolated or as part of a larger syndrome, are the most common type of human birth defect occurring on average in about 1% of live births depending on the malformation. As there is an expanding understanding of the underlying molecular mechanisms by which a cardiac defect may occur, there is a need to assess the current rates of diagnosis of cardiac defects by molecular sequencing in a clinical setting. METHODS AND RESULTS In this report, we evaluated 34 neonatal and pediatric patients born with a cardiac defect and their parents using exomized preexisting whole genome sequencing (WGS) data to model clinically available exon-based tests. Overall, we identified candidate variants in previously reported cardiac-related genes in 35% (12/34) of the probands. These include clearly pathogenic variants in two of 34 patients (6%) and variants of uncertain significance in relevant genes in 10 patients (26%), of these latter 10, 2 segregated with clinically apparent findings in the family trios. CONCLUSIONS These findings suggest that with current knowledge of the proteins underlying CHD, genomic sequencing can identify the underlying genetic etiology in certain patients; however, this technology currently does not have a high enough yield to be of routine clinical use in the screening of pediatric congenital cardiac defects.
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Affiliation(s)
- Natalie S. Hauser
- Inova Translational Medicine InstituteFalls ChurchVAUSA
- Inova Children's HospitalInova Health SystemFalls ChurchVAUSA
| | - Benjamin D. Solomon
- Inova Translational Medicine InstituteFalls ChurchVAUSA
- Present address:
GeneDxGaithersburgMDUSA
| | | | | | - Rajiv Baveja
- Inova Children's HospitalInova Health SystemFalls ChurchVAUSA
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13
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Zuin J, Casa V, Pozojevic J, Kolovos P, van den Hout MCGN, van Ijcken WFJ, Parenti I, Braunholz D, Baron Y, Watrin E, Kaiser FJ, Wendt KS. Regulation of the cohesin-loading factor NIPBL: Role of the lncRNA NIPBL-AS1 and identification of a distal enhancer element. PLoS Genet 2017; 13:e1007137. [PMID: 29261648 PMCID: PMC5754091 DOI: 10.1371/journal.pgen.1007137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 01/04/2018] [Accepted: 11/28/2017] [Indexed: 12/13/2022] Open
Abstract
Cohesin is crucial for genome stability, cell division, transcription and chromatin organization. Its functions critically depend on NIPBL, the cohesin-loader protein that is found to be mutated in >60% of the cases of Cornelia de Lange syndrome (CdLS). Other mutations are described in the cohesin subunits SMC1A, RAD21, SMC3 and the HDAC8 protein. In 25-30% of CdLS cases no mutation in the known CdLS genes is detected. Until now, functional elements in the noncoding genome were not characterized in the molecular etiology of CdLS and therefore are excluded from mutation screening, although the impact of such mutations has now been recognized for a wide range of diseases. We have identified different elements of the noncoding genome involved in regulation of the NIPBL gene. NIPBL-AS1 is a long non-coding RNA transcribed upstream and antisense to NIPBL. By knockdown and transcription blocking experiments, we could show that not the NIPBL-AS1 gene product, but its actual transcription is important to regulate NIPBL expression levels. This reveals a possibility to boost the transcriptional activity of the NIPBL gene by interfering with the NIPBL-AS1 lncRNA. Further, we have identified a novel distal enhancer regulating both NIPBL and NIPBL-AS1. Deletion of the enhancer using CRISPR genome editing in HEK293T cells reduces expression of NIPBL, NIPBL-AS1 as well as genes found to be dysregulated in CdLS.
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MESH Headings
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosome Segregation
- De Lange Syndrome/genetics
- Enhancer Elements, Genetic
- Gene Expression Regulation
- Genome, Human
- HEK293 Cells
- Humans
- Mutation
- Oligonucleotides, Antisense/genetics
- Oligonucleotides, Antisense/metabolism
- Phenotype
- Promoter Regions, Genetic
- Proteins/genetics
- Proteins/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Sequence Analysis, DNA
- Cohesins
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Affiliation(s)
- Jessica Zuin
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Valentina Casa
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Jelena Pozojevic
- Section for Functional Genetics at the Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Petros Kolovos
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Ilaria Parenti
- Section for Functional Genetics at the Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | | | - Yorann Baron
- Centre National de la Recherche Scientifique, UMR 6290, Rennes, France
- Institut de Génétique et Développement de Rennes, Faculté de Médecine, Rennes, France
| | - Erwan Watrin
- Centre National de la Recherche Scientifique, UMR 6290, Rennes, France
- Institut de Génétique et Développement de Rennes, Faculté de Médecine, Rennes, France
| | - Frank J. Kaiser
- Section for Functional Genetics at the Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Kerstin S. Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
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14
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Pozojevic J, Parenti I, Graul-Neumann L, Ruiz Gil S, Watrin E, Wendt KS, Werner R, Strom TM, Gillessen-Kaesbach G, Kaiser FJ. Novel mosaic variants in two patients with Cornelia de Lange syndrome. Eur J Med Genet 2017; 61:680-684. [PMID: 29155047 DOI: 10.1016/j.ejmg.2017.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/11/2017] [Accepted: 11/12/2017] [Indexed: 02/05/2023]
Abstract
Cornelia de Lange syndrome (CdLS) is a dominantly inherited developmental disorder caused by mutations in genes that encode for either structural (SMC1A, SMC3, RAD21) or regulatory (NIPBL, HDAC8) subunits of the cohesin complex. NIPBL represents the major gene of the syndrome and heterozygous mutations can be identified in more than 65% of patients. Interestingly, large portions of these variants were described as somatic mosaicism and often escape standard molecular diagnostics using lymphocyte DNA. Here we discuss the role of somatic mosaicism in CdLS and describe two additional patients with NIPBL mosaicism detected by targeted gene panel or exome sequencing. In order to verify the next generation sequencing data, Sanger sequencing or pyrosequencing on DNA extracted from different tissues were applied. None of the pathogenic variants was originally detected by Sanger sequencing on blood DNA. Patient 1 displays an unusual combination of clinical features: he is cognitively only mildly affected, but shows severe limb reduction defects. Patient 2 presents with a moderate phenotype. Interestingly, Sanger sequencing analysis on fibroblast DNA of this patient did not detect the disease-causing variant previously observed on the same DNA sample by exome sequencing. Subsequent analyses could confirm the variants by Sanger sequencing on buccal mucosa DNA. Notably, this is the first report of a higher mutational load in buccal mucosa than in fibroblast cells of a CdLS patient. Detection of low-level mosaicism is of utmost importance for an accurate molecular diagnosis and a proper genetic counseling of patients with a clinical diagnosis of CdLS. Next-generation sequencing technologies greatly facilitate the detection of low-level mosaicism, which might otherwise remain undetected by conventional sequencing approaches.
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Affiliation(s)
- Jelena Pozojevic
- Section for Functional Genetics, Institute of Human Genetics, Lübeck, Germany
| | - Ilaria Parenti
- Section for Functional Genetics, Institute of Human Genetics, Lübeck, Germany
| | - Luitgard Graul-Neumann
- Ambulantes Gesundheitszentrum Humangenetik, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Sara Ruiz Gil
- Section for Functional Genetics, Institute of Human Genetics, Lübeck, Germany
| | - Erwan Watrin
- Faculté de Médecine, Institut de Génétique et Développement de Rennes, Rennes, France
| | - Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Ralf Werner
- Division of Experimental Paediatric Endocrinology and Diabetes, Department of Paediatrics and Adolescent Medicine, University of Lübeck, Lübeck, Germany
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany
| | | | - Frank J Kaiser
- Section for Functional Genetics, Institute of Human Genetics, Lübeck, Germany.
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15
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Mutations in chromatin regulators functionally link Cornelia de Lange syndrome and clinically overlapping phenotypes. Hum Genet 2017; 136:307-320. [PMID: 28120103 DOI: 10.1007/s00439-017-1758-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/16/2017] [Indexed: 12/31/2022]
Abstract
The coordinated tissue-specific regulation of gene expression is essential for the proper development of all organisms. Mutations in multiple transcriptional regulators cause a group of neurodevelopmental disorders termed "transcriptomopathies" that share core phenotypical features including growth retardation, developmental delay, intellectual disability and facial dysmorphism. Cornelia de Lange syndrome (CdLS) belongs to this class of disorders and is caused by mutations in different subunits or regulators of the cohesin complex. Herein, we report on the clinical and molecular characterization of seven patients with features overlapping with CdLS who were found to carry mutations in chromatin regulators previously associated to other neurodevelopmental disorders that are frequently considered in the differential diagnosis of CdLS. The identified mutations affect the methyltransferase-encoding genes KMT2A and SETD5 and different subunits of the SWI/SNF chromatin-remodeling complex. Complementary to this, a patient with Coffin-Siris syndrome was found to carry a missense substitution in NIPBL. Our findings indicate that mutations in a variety of chromatin-associated factors result in overlapping clinical phenotypes, underscoring the genetic heterogeneity that should be considered when assessing the clinical and molecular diagnosis of neurodevelopmental syndromes. It is clear that emerging molecular mechanisms of chromatin dysregulation are central to understanding the pathogenesis of these clinically overlapping genetic disorders.
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16
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van den Berg DLC, Azzarelli R, Oishi K, Martynoga B, Urbán N, Dekkers DHW, Demmers JA, Guillemot F. Nipbl Interacts with Zfp609 and the Integrator Complex to Regulate Cortical Neuron Migration. Neuron 2017; 93:348-361. [PMID: 28041881 PMCID: PMC5263256 DOI: 10.1016/j.neuron.2016.11.047] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 10/10/2016] [Accepted: 11/17/2016] [Indexed: 12/18/2022]
Abstract
Mutations in NIPBL are the most frequent cause of Cornelia de Lange syndrome (CdLS), a developmental disorder encompassing several neurological defects, including intellectual disability and seizures. How NIPBL mutations affect brain development is not understood. Here we identify Nipbl as a functional interaction partner of the neural transcription factor Zfp609 in brain development. Depletion of Zfp609 or Nipbl from cortical neural progenitors in vivo is detrimental to neuronal migration. Zfp609 and Nipbl overlap at genomic binding sites independently of cohesin and regulate genes that control cortical neuron migration. We find that Zfp609 and Nipbl interact with the Integrator complex, which functions in RNA polymerase 2 pause release. Indeed, Zfp609 and Nipbl co-localize at gene promoters containing paused RNA polymerase 2, and Integrator similarly regulates neuronal migration. Our data provide a rationale and mechanistic insights for the role of Nipbl in the neurological defects associated with CdLS.
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Affiliation(s)
| | - Roberta Azzarelli
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Koji Oishi
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Ben Martynoga
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Noelia Urbán
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - Dick H W Dekkers
- Center for Proteomics, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - Jeroen A Demmers
- Center for Proteomics, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands
| | - François Guillemot
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK.
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17
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Chao WCH, Murayama Y, Muñoz S, Jones AW, Wade BO, Purkiss AG, Hu XW, Borg A, Snijders AP, Uhlmann F, Singleton MR. Structure of the cohesin loader Scc2. Nat Commun 2017; 8:13952. [PMID: 28059076 PMCID: PMC5227109 DOI: 10.1038/ncomms13952] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 11/16/2016] [Indexed: 01/07/2023] Open
Abstract
The functions of cohesin are central to genome integrity, chromosome organization and transcription regulation through its prevention of premature sister-chromatid separation and the formation of DNA loops. The loading of cohesin onto chromatin depends on the Scc2-Scc4 complex; however, little is known about how it stimulates the cohesion-loading activity. Here we determine the large 'hook' structure of Scc2 responsible for catalysing cohesin loading. We identify key Scc2 surfaces that are crucial for cohesin loading in vivo. With the aid of previously determined structures and homology modelling, we derive a pseudo-atomic structure of the full-length Scc2-Scc4 complex. Finally, using recombinantly purified Scc2-Scc4 and cohesin, we performed crosslinking mass spectrometry and interaction assays that suggest Scc2-Scc4 uses its modular structure to make multiple contacts with cohesin.
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Affiliation(s)
- William C. H. Chao
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yasuto Murayama
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Sofía Muñoz
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew W. Jones
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Benjamin O. Wade
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew G. Purkiss
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Xiao-Wen Hu
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Aaron Borg
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P. Snijders
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Martin R. Singleton
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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18
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Nizon M, Henry M, Michot C, Baumann C, Bazin A, Bessières B, Blesson S, Cordier-Alex MP, David A, Delahaye-Duriez A, Delezoïde AL, Dieux-Coeslier A, Doco-Fenzy M, Faivre L, Goldenberg A, Layet V, Loget P, Marlin S, Martinovic J, Odent S, Pasquier L, Plessis G, Prieur F, Putoux A, Rio M, Testard H, Bonnefont JP, Cormier-Daire V. A series of 38 novel germline and somatic mutations of NIPBL in Cornelia de Lange syndrome. Clin Genet 2016; 89:584-9. [PMID: 26701315 DOI: 10.1111/cge.12720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 01/15/2023]
Abstract
Cornelia de Lange syndrome is a multisystemic developmental disorder mainly related to de novo heterozygous NIPBL mutation. Recently, NIPBL somatic mosaicism has been highlighted through buccal cell DNA study in some patients with a negative molecular analysis on leukocyte DNA. Here, we present a series of 38 patients with a Cornelia de Lange syndrome related to a heterozygous NIPBL mutation identified by Sanger sequencing. The diagnosis was based on the following criteria: (i) intrauterine growth retardation and postnatal short stature, (ii) feeding difficulties and/or gastro-oesophageal reflux, (iii) microcephaly, (iv) intellectual disability, and (v) characteristic facial features. We identified 37 novel NIPBL mutations including 34 in leukocytes and 3 in buccal cells only. All mutations shown to have arisen de novo when parent blood samples were available. The present series confirms the difficulty in predicting the phenotype according to the NIPBL mutation. Until now, somatic mosaicism has been observed for 20 cases which do not seem to be consistently associated with a milder phenotype. Besides, several reports support a postzygotic event for those cases. Considering these elements, we recommend a first-line buccal cell DNA analysis in order to improve gene testing sensitivity in Cornelia de Lange syndrome and genetic counselling.
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Affiliation(s)
- M Nizon
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - M Henry
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - C Michot
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - C Baumann
- Département de Génétique, CHU Robert Debré, Paris, France
| | - A Bazin
- Département de Génétique, CH René Dubos, Pontoise, France
| | - B Bessières
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - S Blesson
- Service de Génétique, CHRU Tours, Hôpital Bretonneau, Tours, France
| | - M-P Cordier-Alex
- Service de Génétique Clinique, Hospices Civils de Lyon, Bron, France
| | - A David
- Service de Génétique Médicale, CHU, Nantes, France
| | - A Delahaye-Duriez
- Service de Génétique, CHU Paris Seine-Saint-Denis, Hôpital Jean Verdier, Bondy, France
| | - A-L Delezoïde
- Département de Génétique, CHU Robert Debré, Paris, France
| | - A Dieux-Coeslier
- Service de Génétique Clinique, CHRU de Lille, Hôpital Jeanne de Flandre, Lille, France
| | - M Doco-Fenzy
- Service de Génétique, CHU de Reims, Hôpital Maison Blanche, Reims, France
| | - L Faivre
- Centre de Génétique, CHU de Dijon, Dijon, France
| | | | - V Layet
- Service de Génétique Médicale, GH du Havre, Hôpital Jacques Monod, Le Havre, France
| | - P Loget
- Service d'anatomie et cytologie pathologiques, Hôpital Pontchaillou, Université de Rennes 1, CHU, Rennes, France
| | - S Marlin
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - J Martinovic
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - S Odent
- Service de Génétique Clinique, CHU Rennes, Hôpital Sud, Rennes, France
| | - L Pasquier
- Service de Génétique Clinique, CHU Rennes, Hôpital Sud, Rennes, France
| | - G Plessis
- Service de Génétique Médicale, CHU Clémenceau, Caen, France
| | - F Prieur
- Service de Génétique Clinique, CHU de Saint-Etienne, Hôpital Nord, Saint-Priest-en-Jarez, France
| | - A Putoux
- Service de Génétique Clinique, Hospices Civils de Lyon, Bron, France
| | - M Rio
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - H Testard
- Département de Pédiatrie, CHU Grenoble, Grenoble, France
| | - J-P Bonnefont
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
| | - V Cormier-Daire
- Département de Génétique, Université Paris Descartes-Sorbonne Paris Cité, INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France
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19
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Parenti I, Gervasini C, Pozojevic J, Wendt KS, Watrin E, Azzollini J, Braunholz D, Buiting K, Cereda A, Engels H, Garavelli L, Glazar R, Graffmann B, Larizza L, Lüdecke HJ, Mariani M, Masciadri M, Pié J, Ramos FJ, Russo S, Selicorni A, Stefanova M, Strom TM, Werner R, Wierzba J, Zampino G, Gillessen-Kaesbach G, Wieczorek D, Kaiser FJ. Expanding the clinical spectrum of the 'HDAC8-phenotype' - implications for molecular diagnostics, counseling and risk prediction. Clin Genet 2016; 89:564-73. [PMID: 26671848 DOI: 10.1111/cge.12717] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/30/2015] [Accepted: 12/12/2015] [Indexed: 01/25/2023]
Abstract
Cornelia de Lange syndrome (CdLS) is a clinically heterogeneous disorder characterized by typical facial dysmorphism, cognitive impairment and multiple congenital anomalies. Approximately 75% of patients carry a variant in one of the five cohesin-related genes NIPBL, SMC1A, SMC3, RAD21 and HDAC8. Herein we report on the clinical and molecular characterization of 11 patients carrying 10 distinct variants in HDAC8. Given the high number of variants identified so far, we advise sequencing of HDAC8 as an indispensable part of the routine molecular diagnostic for patients with CdLS or CdLS-overlapping features. The phenotype of our patients is very broad, whereas males tend to be more severely affected than females, who instead often present with less canonical CdLS features. The extensive clinical variability observed in the heterozygous females might be at least partially associated with a completely skewed X-inactivation, observed in seven out of eight female patients. Our cohort also includes two affected siblings whose unaffected mother was found to be mosaic for the causative mutation inherited to both affected children. This further supports the urgent need for an integration of highly sensitive sequencing technology to allow an appropriate molecular diagnostic, genetic counseling and risk prediction.
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Affiliation(s)
- I Parenti
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany.,Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - C Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - J Pozojevic
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - K S Wendt
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - E Watrin
- Faculté de Médecine, Institut de Génétique et Développement de Rennes, UMR6290-CNRS, Rennes, France
| | - J Azzollini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - D Braunholz
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - K Buiting
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - A Cereda
- U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM, A.O. S.Gerardo, Monza, Italy
| | - H Engels
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - L Garavelli
- Clinical Genetics Unit, Department of Obstetrics and Pediatrics, IRCCS S. Maria Nuova Hospital, Reggio Emilia, Italy
| | - R Glazar
- The Center for Medical Genetics GENESIS Poznan, Poland
| | - B Graffmann
- Department of Pediatrics, University Hospital Linköping, Linköping, Sweden
| | - L Larizza
- Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - H J Lüdecke
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - M Mariani
- U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM, A.O. S.Gerardo, Monza, Italy
| | - M Masciadri
- Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - J Pié
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Pediatrics, Medical School, University of Zaragoza, CIBERER-GCV and ISS-Aragon, Zaragoza, Spain
| | - F J Ramos
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Pediatrics, Medical School, University of Zaragoza, CIBERER-GCV and ISS-Aragon, Zaragoza, Spain.,Unidad de Genetica Clınica, Servicio de Pediatrıa, Hospital Clınico Universitario "Lozano Blesa", CIBERER-GCV and ISS-Aragon, Zaragoza, Spain
| | - S Russo
- Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - A Selicorni
- U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM, A.O. S.Gerardo, Monza, Italy
| | - M Stefanova
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - T M Strom
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - R Werner
- Division of Experimental Paediatric Endocrinology and Diabetes, Department of Paediatrics and Adolescent Medicine, University of Lübeck, Lübeck, Germany
| | - J Wierzba
- Department and Clinic of Pediatrics, Hematooncology, Oncology and Endocrinology, Medical University of Gdańsk, Gdańsk, Poland.,Department of General Nursing, Medical University of Gdańsk, Gdańsk, Poland
| | - G Zampino
- Birth Defects Unit, Department of Pediatrics, Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - D Wieczorek
- Institut für Humangenetik, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - F J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
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20
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Unrevealed mosaicism in the next-generation sequencing era. Mol Genet Genomics 2015; 291:513-30. [PMID: 26481646 PMCID: PMC4819561 DOI: 10.1007/s00438-015-1130-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/07/2015] [Indexed: 12/19/2022]
Abstract
Mosaicism refers to the presence in an individual of normal and abnormal cells that are genotypically distinct and are derived from a single zygote. The incidence of mosaicism events in the human body is underestimated as the genotypes in the mosaic ratio, especially in the low-grade mosaicism, stay unrevealed. This review summarizes various research outcomes and diagnostic questions in relation to different types of mosaicism. The impact of both tested biological material and applied method on the mosaicism detection rate is especially highlighted. As next-generation sequencing technologies constitute a promising methodological solution in mosaicism detection in the coming years, revisions in current diagnostic protocols are necessary to increase the detection rate of the unrevealed mosaicism events. Since mosaicism identification is a complex process, numerous examples of multistep mosaicism investigations are presented and discussed.
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Gil-Rodríguez MC, Deardorff MA, Ansari M, Tan CA, Parenti I, Baquero-Montoya C, Ousager LB, Puisac B, Hernández-Marcos M, Teresa-Rodrigo ME, Marcos-Alcalde I, Wesselink JJ, Lusa-Bernal S, Bijlsma EK, Braunholz D, Bueno-Martinez I, Clark D, Cooper NS, Curry CJ, Fisher R, Fryer A, Ganesh J, Gervasini C, Gillessen-Kaesbach G, Guo Y, Hakonarson H, Hopkin RJ, Kaur M, Keating BJ, Kibaek M, Kinning E, Kleefstra T, Kline AD, Kuchinskaya E, Larizza L, Li YR, Liu X, Mariani M, Picker JD, Pié Á, Pozojevic J, Queralt E, Richer J, Roeder E, Sinha A, Scott RH, So J, Wusik KA, Wilson L, Zhang J, Gómez-Puertas P, Casale CH, Ström L, Selicorni A, Ramos FJ, Jackson LG, Krantz ID, Das S, Hennekam RCM, Kaiser FJ, FitzPatrick DR, Pié J. De novo heterozygous mutations in SMC3 cause a range of Cornelia de Lange syndrome-overlapping phenotypes. Hum Mutat 2015; 36:454-62. [PMID: 25655089 DOI: 10.1002/humu.22761] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/21/2015] [Accepted: 01/28/2015] [Indexed: 11/09/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is characterized by facial dysmorphism, growth failure, intellectual disability, limb malformations, and multiple organ involvement. Mutations in five genes, encoding subunits of the cohesin complex (SMC1A, SMC3, RAD21) and its regulators (NIPBL, HDAC8), account for at least 70% of patients with CdLS or CdLS-like phenotypes. To date, only the clinical features from a single CdLS patient with SMC3 mutation has been published. Here, we report the efforts of an international research and clinical collaboration to provide clinical comparison of 16 patients with CdLS-like features caused by mutations in SMC3. Modeling of the mutation effects on protein structure suggests a dominant-negative effect on the multimeric cohesin complex. When compared with typical CdLS, many SMC3-associated phenotypes are also characterized by postnatal microcephaly but with a less distinctive craniofacial appearance, a milder prenatal growth retardation that worsens in childhood, few congenital heart defects, and an absence of limb deficiencies. While most mutations are unique, two unrelated affected individuals shared the same mutation but presented with different phenotypes. This work confirms that de novo SMC3 mutations account for ∼ 1%-2% of CdLS-like phenotypes.
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Affiliation(s)
- María Concepción Gil-Rodríguez
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Pediatrics, Medical School, University of Zaragoza, CIBERER-GCV and ISS-Aragon, Zaragoza, Spain
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22
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Parenti I, Gervasini C, Pozojevic J, Graul-Neumann L, Azzollini J, Braunholz D, Watrin E, Wendt K, Cereda A, Cittaro D, Gillessen-Kaesbach G, Lazarevic D, Mariani M, Russo S, Werner R, Krawitz P, Larizza L, Selicorni A, Kaiser F. Broadening of cohesinopathies: exome sequencing identifies mutations in ANKRD11
in two patients with Cornelia de Lange-overlapping phenotype. Clin Genet 2015; 89:74-81. [DOI: 10.1111/cge.12564] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/28/2015] [Accepted: 01/29/2015] [Indexed: 02/06/2023]
Affiliation(s)
- I. Parenti
- Medical Genetics, Department of Health Sciences; Università degli Studi di Milano; Milan Italy
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck; Universität zu Lübeck; Lübeck Germany
| | - C. Gervasini
- Medical Genetics, Department of Health Sciences; Università degli Studi di Milano; Milan Italy
| | - J. Pozojevic
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck; Universität zu Lübeck; Lübeck Germany
| | - L. Graul-Neumann
- Ambulantes Gesundheitszentrum der Charité Campus Virchow, Humangenetik; Universitätsmedizin Berlin; Berlin Germany
| | - J. Azzollini
- Medical Genetics, Department of Health Sciences; Università degli Studi di Milano; Milan Italy
| | - D. Braunholz
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck; Universität zu Lübeck; Lübeck Germany
| | - E. Watrin
- Institut de Génétique et Développement de Rennes, Faculté de Médecine; UMR6290-CNRS; Rennes France
| | - K.S. Wendt
- Department of Cell Biology; Erasmus MC; Rotterdam Netherlands
| | - A. Cereda
- A.O. S.Gerardo; U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM; Monza Italy
| | - D. Cittaro
- Centre for Translational Genomics and Bioinformatics; San Raffaele Scientific Institute; Milan Italy
| | | | - D. Lazarevic
- Centre for Translational Genomics and Bioinformatics; San Raffaele Scientific Institute; Milan Italy
| | - M. Mariani
- A.O. S.Gerardo; U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM; Monza Italy
| | - S. Russo
- Laboratory of Medical Cytogenetics and Molecular Genetics; IRCCS Istituto Auxologico Italiano; Milan Italy
| | - R. Werner
- Department of Paediatrics and Adolescent Medicine, Division of Experimental Paediatric Endocrinology and Diabetes; University of Lübeck; Lübeck Germany
| | - P. Krawitz
- Ambulantes Gesundheitszentrum der Charité Campus Virchow, Humangenetik; Universitätsmedizin Berlin; Berlin Germany
- Max Planck Institute for Molecular Genetics; Berlin Germany
| | - L. Larizza
- Medical Genetics, Department of Health Sciences; Università degli Studi di Milano; Milan Italy
- Laboratory of Medical Cytogenetics and Molecular Genetics; IRCCS Istituto Auxologico Italiano; Milan Italy
| | - A. Selicorni
- A.O. S.Gerardo; U.O.S. Genetica Clinica Pediatrica, Clinica Pediatrica Fondazione MBBM; Monza Italy
| | - F.J. Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik Lübeck; Universität zu Lübeck; Lübeck Germany
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23
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Ramos FJ, Puisac B, Baquero-Montoya C, Gil-Rodríguez MC, Bueno I, Deardorff MA, Hennekam RC, Kaiser FJ, Krantz ID, Musio A, Selicorni A, FitzPatrick DR, Pié J. Clinical utility gene card for: Cornelia de Lange syndrome. Eur J Hum Genet 2014; 23:ejhg2014270. [PMID: 25537356 DOI: 10.1038/ejhg.2014.270] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 11/01/2014] [Accepted: 11/16/2014] [Indexed: 11/09/2022] Open
Affiliation(s)
- Feliciano J Ramos
- Clinical Genetics Unit, Service of Paediatrics, University Hospital 'Lozano Blesa' Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain.,Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Paediatrics Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Paediatrics Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain
| | | | - Ma Concepción Gil-Rodríguez
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Paediatrics Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain
| | - Inés Bueno
- Clinical Genetics Unit, Service of Paediatrics, University Hospital 'Lozano Blesa' Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain
| | - Matthew A Deardorff
- Department of Paediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Raoul C Hennekam
- Department of Paediatrics, Academic Medical Centre, Amsterdam, The Netherlands
| | - Frank J Kaiser
- Sektion für Funktionelle Genetik am Institut für Humangenetik, Universität zu Lübeck, Lübeck, Germany
| | - Ian D Krantz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Angelo Selicorni
- Pediatric Genetic Clinic Unit, MBBM Foundation University of Milano Bicocca, San Gerardo Hospital, Monza, Italy
| | | | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Departments of Pharmacology-Physiology and Paediatrics Medical School, University of Zaragoza, CIBERER-GCV and IIS-Aragón, Zaragoza, Spain
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