1
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Pérez Baca MDR, Jacobs EZ, Vantomme L, Leblanc P, Bogaert E, Dheedene A, De Cock L, Haghshenas S, Foroutan A, Levy MA, Kerkhof J, McConkey H, Chen CA, Batzir NA, Wang X, Palomares M, Carels M, Dermaut B, Sadikovic B, Menten B, Yuan B, Vergult S, Callewaert B. Haploinsufficiency of ZFHX3, encoding a key player in neuronal development, causes syndromic intellectual disability. Am J Hum Genet 2024; 111:509-528. [PMID: 38412861 PMCID: PMC10940049 DOI: 10.1016/j.ajhg.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/29/2024] Open
Abstract
Neurodevelopmental disorders (NDDs) result from impaired development and functioning of the brain. Here, we identify loss-of-function (LoF) variation in ZFHX3 as a cause for syndromic intellectual disability (ID). ZFHX3 is a zinc-finger homeodomain transcription factor involved in various biological processes, including cell differentiation and tumorigenesis. We describe 42 individuals with protein-truncating variants (PTVs) or (partial) deletions of ZFHX3, exhibiting variable intellectual disability and autism spectrum disorder, recurrent facial features, relative short stature, brachydactyly, and, rarely, cleft palate. ZFHX3 LoF associates with a specific methylation profile in whole blood extracted DNA. Nuclear abundance of ZFHX3 increases during human brain development and neuronal differentiation. ZFHX3 was found to interact with the chromatin remodeling BRG1/Brm-associated factor complex and the cleavage and polyadenylation complex, suggesting a function in chromatin remodeling and mRNA processing. Furthermore, ChIP-seq for ZFHX3 revealed that it predominantly binds promoters of genes involved in nervous system development. We conclude that loss-of-function variants in ZFHX3 are a cause of syndromic ID associating with a specific DNA methylation profile.
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Affiliation(s)
- María Del Rocío Pérez Baca
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Eva Z Jacobs
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Lies Vantomme
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Pontus Leblanc
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Elke Bogaert
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Laurenz De Cock
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada; Children's Health Research Institute, Lawson Research Institute, London, ON N6C 2R5, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Chun-An Chen
- Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA
| | - Nurit Assia Batzir
- Schneider Children's Medical Center of Israel, Petach Tikvah 4920235, Israel
| | - Xia Wang
- Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA
| | - María Palomares
- INGEMM, Instituto de Genética Médica y Molecular, IdiPAZ, Hospital Universitario la Paz, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Marieke Carels
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; VIB UGent Center for Inflammation Research, Department for Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Bart Dermaut
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Björn Menten
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Bo Yuan
- Seattle Children's Hospital, Seattle and Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98105, USA
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium.
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2
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Wilderman A, D'haene E, Baetens M, Yankee TN, Winchester EW, Glidden N, Roets E, Van Dorpe J, Janssens S, Miller DE, Galey M, Brown KM, Stottmann RW, Vergult S, Weaver KN, Brugmann SA, Cox TC, Cotney J. A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development. Nat Commun 2024; 15:136. [PMID: 38167838 PMCID: PMC10762089 DOI: 10.1038/s41467-023-44506-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Craniofacial abnormalities account for approximately one third of birth defects. The regulatory programs that build the face require precisely controlled spatiotemporal gene expression, achieved through tissue-specific enhancers. Clusters of coactivated enhancers and their target genes, known as superenhancers, are important in determining cell identity but have been largely unexplored in development. In this study we identified superenhancer regions unique to human embryonic craniofacial tissue. To demonstrate the importance of such regions in craniofacial development and disease, we focused on an ~600 kb noncoding region located between NPVF and NFE2L3. We identified long range interactions with this region in both human and mouse embryonic craniofacial tissue with the anterior portion of the HOXA gene cluster. Mice lacking this superenhancer exhibit perinatal lethality, and present with highly penetrant skull defects and orofacial clefts phenocopying Hoxa2-/- mice. Moreover, we identified two cases of de novo copy number changes of the superenhancer in humans both with severe craniofacial abnormalities. This evidence suggests we have identified a critical noncoding locus control region that specifically regulates anterior HOXA genes and copy number changes are pathogenic in human patients.
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Affiliation(s)
| | - Eva D'haene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Machteld Baetens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Emma Wentworth Winchester
- Graduate Program UConn Health, Farmington, CT, USA
- University of Connecticut School of Dental Medicine, Farmington, CT, USA
| | - Nicole Glidden
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Ellen Roets
- Department of Obstetrics, Women's Clinic, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute of Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Miranda Galey
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Washington, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Kari M Brown
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Rolf W Stottmann
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University School of Medicine, Columbus, OH, USA
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - K Nicole Weaver
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Timothy C Cox
- Department of Oral & Craniofacial Sciences, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pediatrics, University of Missouri Kansas City, Kansas City, MO, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
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3
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Del Rocío Pérez Baca M, Jacobs EZ, Vantomme L, Leblanc P, Bogaert E, Dheedene A, De Cock L, Haghshenas S, Foroutan A, Levy MA, Kerkhof J, McConkey H, Chen CA, Batzir NA, Wang X, Palomares M, Carels M, Demaut B, Sadikovic B, Menten B, Yuan B, Vergult S, Callewaert B. A novel neurodevelopmental syndrome caused by loss-of-function of the Zinc Finger Homeobox 3 (ZFHX3) gene. medRxiv 2023:2023.05.22.23289895. [PMID: 37292950 PMCID: PMC10246128 DOI: 10.1101/2023.05.22.23289895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Neurodevelopmental disorders (NDDs) result from impaired development and functioning of the brain. Here, we identify loss-of-function variation in ZFHX3 as a novel cause for syndromic intellectual disability (ID). ZFHX3, previously known as ATBF1, is a zinc-finger homeodomain transcription factor involved in multiple biological processes including cell differentiation and tumorigenesis. Through international collaboration, we collected clinical and morphometric data (Face2Gene) of 41 individuals with protein truncating variants (PTVs) or (partial) deletions of ZFHX3 . We used data mining, RNA and protein analysis to identify the subcellular localization and spatiotemporal expression of ZFHX3 in multiple in vitro models. We identified the DNA targets of ZFHX3 using ChIP seq. Immunoprecipitation followed by mass spectrometry indicated potential binding partners of endogenous ZFHX3 in neural stem cells that were subsequently confirmed by reversed co-immunoprecipitation and western blot. We evaluated a DNA methylation profile associated with ZFHX3 haploinsufficiency using DNA methylation analysis on whole blood extracted DNA of six individuals with ZFHX3 PTVs and four with a (partial) deletion of ZFHX3 . A reversed genetic approach characterized the ZFHX3 orthologue in Drosophila melanogaster . Loss-of-function variation of ZFHX3 consistently associates with (mild) ID and/or behavioural problems, postnatal growth retardation, feeding difficulties, and recognizable facial characteristics, including the rare occurrence of cleft palate. Nuclear abundance of ZFHX3 increases during human brain development and neuronal differentiation in neural stem cells and SH-SY5Y cells, ZFHX3 interacts with the chromatin remodelling BRG1/Brm-associated factor complex and the cleavage and polyadenylation complex. In line with a role for chromatin remodelling, ZFHX3 haploinsufficiency associates with a specific DNA methylation profile in leukocyte-derived DNA. The target genes of ZFHX3 are implicated in neuron and axon development. In Drosophila melanogaster , z fh2, considered to be the ZFHX3 orthologue, is expressed in the third instar larval brain. Ubiquitous and neuron-specific knockdown of zfh2 results in adult lethality underscoring a key role for zfh2 in development and neurodevelopment. Interestingly, ectopic expression of zfh2 as well as ZFHX3 in the developing wing disc results in a thoracic cleft phenotype. Collectively, our data shows that loss-of-function variants in ZFHX3 are a cause of syndromic ID, that associates with a specific DNA methylation profile. Furthermore, we show that ZFHX3 participates in chromatin remodelling and mRNA processing.
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4
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Mohajeri K, Yadav R, D'haene E, Boone PM, Erdin S, Gao D, Moyses-Oliveira M, Bhavsar R, Currall BB, O'Keefe K, Burt ND, Lowther C, Lucente D, Salani M, Larson M, Redin C, Dudchenko O, Aiden EL, Menten B, Tai DJC, Gusella JF, Vergult S, Talkowski ME. Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models. Am J Hum Genet 2022; 109:2049-2067. [PMID: 36283406 PMCID: PMC9674968 DOI: 10.1016/j.ajhg.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 01/26/2023] Open
Abstract
Point mutations and structural variants that directly disrupt the coding sequence of MEF2C have been associated with a spectrum of neurodevelopmental disorders (NDDs). However, the impact of MEF2C haploinsufficiency on neurodevelopmental pathways and synaptic processes is not well understood, nor are the complex mechanisms that govern its regulation. To explore the functional changes associated with structural variants that alter MEF2C expression and/or regulation, we generated an allelic series of 204 isogenic human induced pluripotent stem cell (hiPSC)-derived neural stem cells and glutamatergic induced neurons. These neuronal models harbored CRISPR-engineered mutations that involved direct deletion of MEF2C or deletion of the boundary points for topologically associating domains (TADs) and chromatin loops encompassing MEF2C. Systematic profiling of mutation-specific alterations, contrasted to unedited controls that were exposed to the same guide RNAs for each edit, revealed that deletion of MEF2C caused differential expression of genes associated with neurodevelopmental pathways and synaptic function. We also discovered significant reduction in synaptic activity measured by multielectrode arrays (MEAs) in neuronal cells. By contrast, we observed robust buffering against MEF2C regulatory disruption following deletion of a distal 5q14.3 TAD and loop boundary, whereas homozygous loss of a proximal loop boundary resulted in down-regulation of MEF2C expression and reduced electrophysiological activity on MEA that was comparable to direct gene disruption. Collectively, these studies highlight the considerable functional impact of MEF2C deletion in neuronal cells and systematically characterize the complex interactions that challenge a priori predictions of regulatory consequences from structural variants that disrupt three-dimensional genome organization.
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Affiliation(s)
- Kiana Mohajeri
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Rachita Yadav
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eva D'haene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Philip M Boone
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Serkan Erdin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dadi Gao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mariana Moyses-Oliveira
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Riya Bhavsar
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas D Burt
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Monica Salani
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mathew Larson
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Claire Redin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA; UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong, China
| | - Björn Menten
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Derek J C Tai
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - James F Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.
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5
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Hirsch N, Dahan I, D'haene E, Avni M, Vergult S, Vidal-García M, Magini P, Graziano C, Bonora E, Nardone AM, Brancati F, Fernández-Jaén A, Rory OJ, Hallgrimsson B, Birnbaum RY. HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations. Genome Res 2022; 32:1242-1253. [PMID: 35710300 PMCID: PMC9341515 DOI: 10.1101/gr.276196.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
Abstract
Structural variants (SVs) can affect protein-coding sequences as well as gene regulatory elements. However, SVs disrupting protein-coding sequences that also function as cis-regulatory elements remain largely uncharacterized. Here, we show that craniosynostosis patients with SVs containing the Histone deacetylase 9 (HDAC9) protein-coding sequence are associated with disruption of TWIST1 regulatory elements that reside within HDAC9 sequence. Based on SVs within the HDAC9-TWIST1 locus, we defined the 3'-HDAC9 sequence as a critical TWIST1 regulatory region, encompassing craniofacial TWIST1 enhancers and CTCF sites. Deletions of either Twist1 enhancers (eTw5-7Δ/Δ) or Ctcf site (CtcfΔ/Δ) within the Hdac9 protein-coding sequence led to decreased Twist1 expression and altered anterior\posterior limb expression patterns of Shh pathway genes. This decreased Twist1 expression results in a smaller sized and asymmetric skull and polydactyly that resembles Twist1+/- mouse phenotype. Chromatin conformation analysis revealed that the Twist1 promoter interacts with Hdac9 sequences that encompass Twist1 enhancers and a Ctcf site and that interactions depended on the presence of both regulatory regions. Finally, a large inversion of the entire Hdac9 sequence (Hdac9INV/+) in mice that does not disrupt HDAC9 expression but repositions Twist1 regulatory elements showed decreased Twist1 expression and led to a craniosynostosis-like phenotype and polydactyly. Thus, our study elucidated essential components of TWIST1 transcriptional machinery that reside within the HDAC9 sequence It suggests that SVs, encompassing protein-coding sequence could lead to a phenotype that is not attributed to its protein function but rather to a disruption of the transcriptional regulation of a nearby gene.
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Affiliation(s)
| | | | | | | | | | | | - Pamela Magini
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero Universitaria di Bologna
| | - Claudio Graziano
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero Universitaria di Bologna
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6
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Coursimault J, Guerrot AM, Morrow MM, Schramm C, Zamora FM, Shanmugham A, Liu S, Zou F, Bilan F, Le Guyader G, Bruel AL, Denommé-Pichon AS, Faivre L, Tran Mau-Them F, Tessarech M, Colin E, El Chehadeh S, Gérard B, Schaefer E, Cogne B, Isidor B, Nizon M, Doummar D, Valence S, Héron D, Keren B, Mignot C, Coutton C, Devillard F, Alaix AS, Amiel J, Colleaux L, Munnich A, Poirier K, Rio M, Rondeau S, Barcia G, Callewaert B, Dheedene A, Kumps C, Vergult S, Menten B, Chung WK, Hernan R, Larson A, Nori K, Stewart S, Wheless J, Kresge C, Pletcher BA, Caumes R, Smol T, Sigaudy S, Coubes C, Helm M, Smith R, Morrison J, Wheeler PG, Kritzer A, Jouret G, Afenjar A, Deleuze JF, Olaso R, Boland A, Poitou C, Frebourg T, Houdayer C, Saugier-Veber P, Nicolas G, Lecoquierre F. MYT1L-associated neurodevelopmental disorder: description of 40 new cases and literature review of clinical and molecular aspects. Hum Genet 2021; 141:65-80. [PMID: 34748075 DOI: 10.1007/s00439-021-02383-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/30/2021] [Indexed: 12/20/2022]
Abstract
Pathogenic variants of the myelin transcription factor-1 like (MYT1L) gene include heterozygous missense, truncating variants and 2p25.3 microdeletions and cause a syndromic neurodevelopmental disorder (OMIM#616,521). Despite enrichment in de novo mutations in several developmental disorders and autism studies, the data on clinical characteristics and genotype-phenotype correlations are scarce, with only 22 patients with single nucleotide pathogenic variants reported. We aimed to further characterize this disorder at both the clinical and molecular levels by gathering a large series of patients with MYT1L-associated neurodevelopmental disorder. We collected genetic information on 40 unreported patients with likely pathogenic/pathogenic MYT1L variants and performed a comprehensive review of published data (total = 62 patients). We confirm that the main phenotypic features of the MYT1L-related disorder are developmental delay with language delay (95%), intellectual disability (ID, 70%), overweight or obesity (58%), behavioral disorders (98%) and epilepsy (23%). We highlight novel clinical characteristics, such as learning disabilities without ID (30%) and feeding difficulties during infancy (18%). We further describe the varied dysmorphic features (67%) and present the changes in weight over time of 27 patients. We show that patients harboring highly clustered missense variants in the 2-3-ZNF domains are not clinically distinguishable from patients with truncating variants. We provide an updated overview of clinical and genetic data of the MYT1L-associated neurodevelopmental disorder, hence improving diagnosis and clinical management of these patients.
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Affiliation(s)
- Juliette Coursimault
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | | | - Catherine Schramm
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | | | | | | | | | - Frédéric Bilan
- Service de Génétique, Centre Hospitalier Universitaire de Poitiers, BP577, 86021, Poitiers, France
| | - Gwenaël Le Guyader
- Service de Génétique, Centre Hospitalier Universitaire de Poitiers, BP577, 86021, Poitiers, France
| | - Ange-Line Bruel
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Inter-Région est, FHU TRANSLAD, CHU Dijon-Bourgogne, Dijon, France
| | - Frédéric Tran Mau-Them
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | | | - Estelle Colin
- Service de Génétique Médicale, CHU d'Angers, Angers, France.,Univ Angers, [CHU Angers], INSERM, CNRS, MITOVASC, ICAT, 49000, Angers, SFR, France
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Bénédicte Gérard
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Elise Schaefer
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | | | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Diane Doummar
- Hôpital Trousseau, APHP.Sorbonne Université, Service de Neuropédiatrie, Paris, France
| | - Stéphanie Valence
- Hôpital Trousseau, APHP.Sorbonne Université, Service de Neuropédiatrie, Paris, France
| | - Delphine Héron
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP.Sorbonne Université, Paris, France
| | - Boris Keren
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP.Sorbonne Université, Paris, France
| | - Cyril Mignot
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière-Hôpital Trousseau Centre de Référence Déficiences Intellectuelles de Causes Rares, APHP.Sorbonne Université, Paris, France
| | - Charles Coutton
- Genetic Epigenetic and Therapies of Infertility, Institute for Advanced Biosciences, UMR 5309, CNRS, Université Grenoble Alpes, Inserm U1209, Grenoble, France
| | | | - Anne-Sophie Alaix
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Jeanne Amiel
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Laurence Colleaux
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Arnold Munnich
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Karine Poirier
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Marlène Rio
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Sophie Rondeau
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Giulia Barcia
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Bert Callewaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Candy Kumps
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Wendy K Chung
- Columbia University Irving Medical Center, New York, NY, USA
| | - Rebecca Hernan
- Columbia University Irving Medical Center, New York, NY, USA
| | - Austin Larson
- School of Medicine and Children's Hospital, University of Colorado, Aurora, CO, USA
| | - Kelly Nori
- School of Medicine and Children's Hospital, University of Colorado, Aurora, CO, USA
| | - Sarah Stewart
- School of Medicine and Children's Hospital, University of Colorado, Aurora, CO, USA
| | - James Wheless
- Division of Pediatric Neurology, University of Tennessee, Health Science Center, Memphis, USA
| | - Christina Kresge
- Division of Clinical Genetics, Rutgers New Jersey Medical School, Newark, USA
| | - Beth A Pletcher
- Division of Clinical Genetics, Rutgers New Jersey Medical School, Newark, USA
| | - Roseline Caumes
- Université de Lille, CHU de Lille, Clinique de Génétique « Guy Fontaine », EA7364 RADEMEF-59000, Lille, France
| | - Thomas Smol
- Université de Lille, CHU de Lille, Institut de Génétique Médicale, EA7364 RADEMEF-59000, Lille, France
| | - Sabine Sigaudy
- Département de Génétique Médicale, Hôpital Timone Enfant, Marseille, France
| | - Christine Coubes
- Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, CHU Montpellier, Montpellier, France
| | - Margaret Helm
- Department of Pediatrics, Division of Genetics. Portland, Maine Medical Center, Maine, USA
| | - Rosemarie Smith
- Department of Pediatrics, Division of Genetics. Portland, Maine Medical Center, Maine, USA
| | | | | | - Amy Kritzer
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Guillaume Jouret
- National Center of Genetics (NCG), Laboratoire National de Santé (LNS), L-3555, Dudelange, Luxembourg
| | - Alexandra Afenjar
- Centre de Référence Malformations et Maladies Congénitales du Cervelet et Déficiences Intellectuelles de Causes Rares, Département de Génétique et Embryologie Médicale, APHP. Sorbonne Université, Hôpital Trousseau, 75012, Paris, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, 91057, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, 91057, Evry, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, 91057, Evry, France
| | - Christine Poitou
- Service de Nutrition, Hôpital de la Pitié Salpêtrière - AP-HP, Paris, France
| | - Thierry Frebourg
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Claude Houdayer
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Inserm U1245, FHU G4 Génomique, F-76000, Rouen, France.
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7
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Meerschaut I, Vergult S, Dheedene A, Menten B, De Groote K, De Wilde H, Muiño Mosquera L, Panzer J, Vandekerckhove K, Coucke PJ, De Wolf D, Callewaert B. A Reassessment of Copy Number Variations in Congenital Heart Defects: Picturing the Whole Genome. Genes (Basel) 2021; 12:genes12071048. [PMID: 34356064 PMCID: PMC8304049 DOI: 10.3390/genes12071048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022] Open
Abstract
Copy number variations (CNVs) can modulate phenotypes by affecting protein-coding sequences directly or through interference of gene expression. Recent studies in cancer and limb defects pinpointed the relevance of non-coding gene regulatory elements such as long non-coding RNAs (lncRNAs) and topologically associated domain (TAD)-related gene-enhancer interactions. The contribution of such non-coding elements is largely unexplored in congenital heart defects (CHD). We performed a retrospective analysis of CNVs reported in a cohort of 270 CHD patients. We reviewed the diagnostic yield of pathogenic CNVs, and performed a comprehensive reassessment of 138 CNVs of unknown significance (CNV-US), evaluating protein-coding genes, lncRNA genes, and potential interferences with TAD-related gene-enhancer interactions. Fifty-two of the 138 CNV-US may relate to CHD, revealing three candidate CHD regions, 19 candidate CHD genes, 80 lncRNA genes of interest, and six potentially CHD-related TAD interferences. Our study thus indicates a potential relevance of non-coding gene regulatory elements in CNV-related CHD pathogenesis. Shortcomings in our current knowledge on genomic variation call for continuous reporting of CNV-US in international databases, careful patient counseling, and additional functional studies to confirm these preliminary findings.
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Affiliation(s)
- Ilse Meerschaut
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Annelies Dheedene
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Katya De Groote
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Hans De Wilde
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Laura Muiño Mosquera
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Joseph Panzer
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Kristof Vandekerckhove
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Paul J. Coucke
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Daniël De Wolf
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
- Department of Pediatric Cardiology, Brussels University Hospital, 1090 Brussels, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Correspondence: ; Tel.: +32-9-332-3603
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8
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Kumps C, D'haenens E, Vergult S, Leus J, van Coster R, Jansen A, Devriendt K, Oostra A, Vanakker OM. Phenotypic spectrum of the RBM10-mediated intellectual disability and congenital malformation syndrome beyond classic TARP syndrome features. Clin Genet 2021; 99:449-456. [PMID: 33340101 DOI: 10.1111/cge.13901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/07/2020] [Accepted: 12/15/2020] [Indexed: 01/18/2023]
Abstract
Pathogenic variants in the RBM10 gene cause a rare X-linked disorder described as TARP (Talipes equinovarus, Atrial septal defect, Robin sequence, and Persistent left vena cava superior) syndrome. We report two novel patients with truncating RBM10 variants in view of the literature, presenting a total of 26 patients from 15 unrelated families. Our results illustrate the highly pleiotropic nature of RBM10 pathogenic variants, beyond the classic TARP syndrome features. Major clinical characteristics include severe developmental delay, failure to thrive, brain malformations, neurological symptoms, respiratory issues, and facial dysmorphism. Minor features are growth retardation, cardiac, gastrointestinal, limb, and skeletal abnormalities. Additional recurrent features include genital and renal abnormalities as well as hearing and visual impairment. Thus, RBM10 loss of function variants typically cause an intellectual disability and congenital malformation syndrome that requires assessment of multiple organ systems at diagnosis and for which provided clinical features might simplify diagnostic assessment. Furthermore, evidence for an RBM10-related genotype-phenotype correlation is emerging, which can be important for prognosis.
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Affiliation(s)
- Candy Kumps
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Erika D'haenens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Jasmine Leus
- Department of Pediatrics, AZ Maria Middelares Ghent, Ghent, Belgium
| | - Rudy van Coster
- Department of Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Anna Jansen
- Pediatric Neurology Unit, Department of Pediatrics, UZ Brussel, Jette, Belgium
| | - Koen Devriendt
- Center for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Anna Oostra
- Department of Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
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9
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Jacobs EZ, Brown K, Byler MC, D'haenens E, Dheedene A, Henderson LB, Humberson JB, van Jaarsveld RH, Kanani F, Lebel RR, Millan F, Oegema R, Oostra A, Parker MJ, Rhodes L, Saenz M, Seaver LH, Si Y, Vanlander A, Vergult S, Callewaert B. Expanding the molecular spectrum and the neurological phenotype related to CAMTA1 variants. Clin Genet 2020; 99:259-268. [PMID: 33131045 DOI: 10.1111/cge.13874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/18/2020] [Accepted: 10/28/2020] [Indexed: 12/13/2022]
Abstract
The CAMTA1-associated phenotype was initially defined in patients with intragenic deletions and duplications who showed nonprogressive congenital ataxia, with or without intellectual disability. Here, we describe 10 individuals with CAMTA1 variants: nine previously unreported (likely) pathogenic variants comprising one missense, four frameshift and four nonsense variants, and one missense variant of unknown significance. Six patients were diagnosed following whole exome sequencing and four individuals with exome-based targeted panel analysis. Most of them present with developmental delay, manifesting in speech and motor delay. Other frequent findings are hypotonia, cognitive impairment, cerebellar dysfunction, oculomotor abnormalities, and behavioral problems. Feeding problems occur more frequently than previously observed. In addition, we present a systematic review of 19 previously published individuals with causal variants, including copy number, truncating, and missense variants. We note a tendency of more severe cognitive impairment and recurrent dysmorphic features in individuals with a copy number variant. Pathogenic variants are predominantly observed in and near the N- and C- terminal functional domains. Clinical heterogeneity is observed, but 3'-terminal variants seem to associate with less pronounced cerebellar dysfunction.
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Affiliation(s)
- Eva Z Jacobs
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department for Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kathleen Brown
- University of Colorado, Section of Genetics, Department of Pediatrics, The Children's Hospital Colorado, Aurora, Colorado, USA
| | - Melissa C Byler
- Division of Development, Behavior and Genetics, SUNY Upstate Medical University, New York, New York, USA
| | - Erika D'haenens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department for Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department for Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Jennifer B Humberson
- Division of Genetics, Department of Pediatrics, University of Virginia Children's Hospital, Charlottesville, Virginia, USA
| | | | - Farah Kanani
- Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield, UK
| | - Robert Roger Lebel
- Division of Development, Behavior and Genetics, SUNY Upstate Medical University, New York, New York, USA
| | | | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ann Oostra
- Department for Biomolecular Medicine, Ghent University, Ghent, Belgium.,Department of Neuropediatrics, Ghent University Hospital, Ghent, Belgium
| | - Michael J Parker
- Sheffield Children's Hospital NHS Foundation Trust, Western Bank, Sheffield, UK
| | | | - Margarita Saenz
- University of Colorado, Section of Genetics, Department of Pediatrics, The Children's Hospital Colorado, Aurora, Colorado, USA
| | - Laurie H Seaver
- Medical Genetics and Genomics, Spectrum Health Helen Devos Children's Hospital, Grand Rapids, Michigan, USA.,Department of Pediatrics and Human Development, Michigan State University College of Human Medicine, Grand Rapids, Michigan, USA
| | - Yue Si
- GeneDx, Inc. Laboratory, Gaithersburg, Maryland, USA
| | - Arnaud Vanlander
- Department for Biomolecular Medicine, Ghent University, Ghent, Belgium.,Department of Neuropediatrics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department for Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department for Biomolecular Medicine, Ghent University, Ghent, Belgium
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10
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D'haene E, Bar-Yaacov R, Bariah I, Vantomme L, Van Loo S, Cobos FA, Verboom K, Eshel R, Alatawna R, Menten B, Birnbaum RY, Vergult S. A neuronal enhancer network upstream of MEF2C is compromised in patients with Rett-like characteristics. Hum Mol Genet 2020; 28:818-827. [PMID: 30445463 PMCID: PMC6381311 DOI: 10.1093/hmg/ddy393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 01/06/2023] Open
Abstract
Mutations in myocyte enhancer factor 2C (MEF2C), an important transcription factor in neurodevelopment, are associated with a Rett-like syndrome. Structural variants (SVs) upstream of MEF2C, which do not disrupt the gene itself, have also been found in patients with a similar phenotype, suggesting that disruption of MEF2C regulatory elements can also cause a Rett-like phenotype. To characterize those elements that regulate MEF2C during neural development and that are affected by these SVs, we used genomic tools coupled with both in vitro and in vivo functional assays. Through circularized chromosome conformation capture sequencing
(4C-seq) and the assay for transposase-accessible chromatin using sequencing
(ATAC-seq), we revealed a complex interaction network in which the MEF2C promoter physically contacts several distal enhancers that are deleted or translocated by disease-associated SVs. A total of 16 selected candidate regulatory sequences were tested for enhancer activity in vitro, with 14 found to be functional enhancers. Further analyses of their in vivo activity in zebrafish showed that each of these enhancers has a distinct activity pattern during development, with eight enhancers displaying neuronal activity. In summary, our results disentangle a complex regulatory network governing neuronal MEF2C expression that involves multiple distal enhancers. In addition, the characterized neuronal enhancers pose as novel candidates to screen for mutations in neurodevelopmental disorders, such as Rett-like syndrome.
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Affiliation(s)
- Eva D'haene
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Reut Bar-Yaacov
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beersheba, Israel
| | - Inbar Bariah
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beersheba, Israel
| | - Lies Vantomme
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Sien Van Loo
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Francisco Avila Cobos
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks (BIG N2N), Ghent, Belgium
| | - Karen Verboom
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Reut Eshel
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beersheba, Israel
| | - Rawan Alatawna
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beersheba, Israel
| | - Björn Menten
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Ramon Y Birnbaum
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beersheba, Israel
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
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11
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D'haene E, Bar-Yaacov R, Bariah I, Vantomme L, Van Loo S, Cobos FA, Verboom K, Eshel R, Alatawna R, Menten B, Birnbaum RY, Vergult S. A neuronal enhancer network upstream of MEF2C is compromised in patients with Rett like characteristics. Hum Mol Genet 2020; 29:879-880. [PMID: 32031622 DOI: 10.1093/hmg/ddaa019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Eva D'haene
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Reut Bar-Yaacov
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, 84105 Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, 84105 Beersheba, Israel
| | - Inbar Bariah
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, 84105 Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, 84105 Beersheba, Israel
| | - Lies Vantomme
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Sien Van Loo
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Francisco Avila Cobos
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks (BIG N2N), 9000 Ghent, Belgium
| | - Karen Verboom
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Reut Eshel
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, 84105 Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, 84105 Beersheba, Israel
| | - Rawan Alatawna
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, 84105 Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, 84105 Beersheba, Israel
| | - Björn Menten
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Ramon Y Birnbaum
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, 84105 Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, 84105 Beersheba, Israel
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
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12
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Costain G, Callewaert B, Gabriel H, Tan TY, Walker S, Christodoulou J, Lazar T, Menten B, Orkin J, Sadedin S, Snell M, Vanlander A, Vergult S, White SM, Scherer SW, Hayeems RZ, Blaser S, Wodak SJ, Chitayat D, Marshall CR, Meyn MS. De novo missense variants in RAC3 cause a novel neurodevelopmental syndrome. Genet Med 2018; 21:1021-1026. [DOI: 10.1038/s41436-018-0323-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/06/2018] [Indexed: 11/09/2022] Open
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13
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Basilicata MF, Bruel AL, Semplicio G, Valsecchi CIK, Aktaş T, Duffourd Y, Rumpf T, Morton J, Bache I, Szymanski WG, Gilissen C, Vanakker O, Õunap K, Mittler G, van der Burgt I, El Chehadeh S, Cho MT, Pfundt R, Tan TY, Kirchhoff M, Menten B, Vergult S, Lindstrom K, Reis A, Johnson DS, Fryer A, McKay V, Fisher RB, Thauvin-Robinet C, Francis D, Roscioli T, Pajusalu S, Radtke K, Ganesh J, Brunner HG, Wilson M, Faivre L, Kalscheuer VM, Thevenon J, Akhtar A. De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation. Nat Genet 2018; 50:1442-1451. [PMID: 30224647 DOI: 10.1038/s41588-018-0220-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 08/01/2018] [Indexed: 12/15/2022]
Abstract
The etiological spectrum of ultra-rare developmental disorders remains to be fully defined. Chromatin regulatory mechanisms maintain cellular identity and function, where misregulation may lead to developmental defects. Here, we report pathogenic variations in MSL3, which encodes a member of the chromatin-associated male-specific lethal (MSL) complex responsible for bulk histone H4 lysine 16 acetylation (H4K16ac) in flies and mammals. These variants cause an X-linked syndrome affecting both sexes. Clinical features of the syndrome include global developmental delay, progressive gait disturbance, and recognizable facial dysmorphism. MSL3 mutations affect MSL complex assembly and activity, accompanied by a pronounced loss of H4K16ac levels in vivo. Patient-derived cells display global transcriptome alterations of pathways involved in morphogenesis and cell migration. Finally, we use histone deacetylase inhibitors to rebalance acetylation levels, alleviating some of the molecular and cellular phenotypes of patient cells. Taken together, we characterize a syndrome that allowed us to decipher the developmental importance of MSL3 in humans.
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Affiliation(s)
- M Felicia Basilicata
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Ange-Line Bruel
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - Giuseppe Semplicio
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | | | - Tuğçe Aktaş
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Yannis Duffourd
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - Tobias Rumpf
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's Hospital NHS Foundation Trust, Birmingham, UK
| | - Iben Bache
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Witold G Szymanski
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Olivier Vanakker
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Gerhard Mittler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Ineke van der Burgt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Salima El Chehadeh
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France.,Service de Génétique Médicale, Hôpital de Hautepierre, Strasbourg, France
| | | | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne Department of Paediatrics, Parkville, VIC, Australia
| | - Maria Kirchhoff
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Diana S Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Alan Fryer
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Victoria McKay
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | | | - Richard B Fisher
- Northern Genetics Service, Teesside Genetics Unit, The James Cook University Hospital, Middlesbrough, UK
| | - Christel Thauvin-Robinet
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - David Francis
- Cytogenetic Laboratory, Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Tony Roscioli
- Neuroscience Research Australia, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia.,Department of Medical Genetics, Sydney Children's Hospital, Sydney, New South Wales, Australia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kelly Radtke
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Jaya Ganesh
- Division of Genetics, Cooper University Hospital and Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Disciplines of Genetic Medicine and Child and Adolescent Health, University of Sydney, Sydney, New South Wales, Australia
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Julien Thevenon
- Inserm UMR 1231 GAD, Genetics of Developmental disorders and Centre de Référence Maladies Rares Anomalies du Développement et syndromes malformatifs FHU TRANSLAD, Université de Bourgogne-Franche Comté, Dijon, France. .,CNRS UMR 5309, INSERM, U1209, Institute of Advanced Biosciences, Université Grenoble-Alpes CHU Grenoble, Grenoble, France.
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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14
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Vantroys E, Smet J, Vanlander AV, Vergult S, De Bruyne R, Roels F, Stepman H, Roeyers H, Menten B, Van Coster R. Severe hepatopathy and neurological deterioration after start of valproate treatment in a 6-year-old child with mitochondrial tryptophanyl-tRNA synthetase deficiency. Orphanet J Rare Dis 2018; 13:80. [PMID: 29783990 PMCID: PMC5963168 DOI: 10.1186/s13023-018-0822-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/08/2018] [Indexed: 01/08/2023] Open
Abstract
Background The first subjects with deficiency of mitochondrial tryptophanyl-tRNA synthetase (WARS2) were reported in 2017. Their clinical characteristics can be subdivided into three phenotypes (neonatal phenotype, severe infantile onset phenotype, Parkinson-like phenotype). Results Here, we report on a subject who presented with early developmental delay, motor weakness and intellectual disability and who was considered during several years as having a non-progressive encephalopathy. At the age of six years, she had an epileptic seizure which was treated with sodium valproate. In the months after treatment was started, she developed acute liver failure and severe progressive encephalopathy. Although valproate was discontinued, she died six months later. Spectrophotometric analysis of the oxidative phosphorylation complexes in liver revealed a deficient activity of complex III and low normal activities of the complexes I and IV. Activity staining in the BN-PAGE gel confirmed the low activities of complex I, III and IV and, in addition, showed the presence of a subcomplex of complex V. Histochemically, a mosaic pattern was seen in hepatocytes after cytochrome c oxidase staining. Using Whole Exome Sequencing two known pathogenic variants were detected in WARS2 (c.797delC, p.Pro266ArgfsTer10/ c.938 A > T, p.Lys313Met). Conclusion This is the first report of severe hepatopathy in a subject with WARS2 deficiency. The hepatopathy occurred soon after start of sodium valproate treatment. In the literature, valproate-induced hepatotoxicity was reported in the subjects with pathogenic mutations in POLG and TWNK. This case report illustrates that the course of the disease in the subjects with a mitochondrial defect can be non-progressive during several years. The subject reported here was first diagnosed as having cerebral palsy. Only after a mitochondriotoxic medication was started, the disease became progressive, and the diagnosis of a mitochondrial defect was made.
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Affiliation(s)
- Elise Vantroys
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Joél Smet
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Arnaud V Vanlander
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Ruth De Bruyne
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Ghent University Hospital, Ghent, Belgium
| | - Frank Roels
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Hedwig Stepman
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Herbert Roeyers
- Department of Experimental Clinical and Health Psychology, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Rudy Van Coster
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium.
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15
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Vantroys E, Larson A, Friederich M, Knight K, Swanson MA, Powell CA, Smet J, Vergult S, De Paepe B, Seneca S, Roeyers H, Menten B, Minczuk M, Vanlander A, Van Hove J, Van Coster R. New insights into the phenotype of FARS2 deficiency. Mol Genet Metab 2017; 122:172-181. [PMID: 29126765 PMCID: PMC5734183 DOI: 10.1016/j.ymgme.2017.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/12/2022]
Abstract
Mutations in FARS2 are known to cause dysfunction of mitochondrial translation due to deficient aminoacylation of the mitochondrial phenylalanine tRNA. Here, we report three novel mutations in FARS2 found in two patients in a compound heterozygous state. The missense mutation c.1082C>T (p.Pro361Leu) was detected in both patients. The mutations c.461C>T (p.Ala154Val) and c.521_523delTGG (p.Val174del) were each detected in one patient. We report abnormal in vitro aminoacylation assays as a functional validation of the molecular genetic findings. Based on the phenotypic data of previously reported subjects and the two subjects reported here, we conclude that FARS2 deficiency can be associated with two phenotypes: (i) an epileptic phenotype, and (ii) a spastic paraplegia phenotype.
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Affiliation(s)
- Elise Vantroys
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Austin Larson
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Marisa Friederich
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kaz Knight
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Michael A Swanson
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Christopher A Powell
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Joél Smet
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Boel De Paepe
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Sara Seneca
- Center for Medical Genetics, UZ Brussel and Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Herbert Roeyers
- Department of Experimental Clinical and Health Psychology, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Arnaud Vanlander
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Johan Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Rudy Van Coster
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium.
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16
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Braun DA, Rao J, Mollet G, Schapiro D, Daugeron MC, Tan W, Gribouval O, Boyer O, Revy P, Jobst-Schwan T, Schmidt JM, Lawson JA, Schanze D, Ashraf S, Ullmann JFP, Hoogstraten CA, Boddaert N, Collinet B, Martin G, Liger D, Lovric S, Furlano M, Guerrera IC, Sanchez-Ferras O, Hu JF, Boschat AC, Sanquer S, Menten B, Vergult S, De Rocker N, Airik M, Hermle T, Shril S, Widmeier E, Gee HY, Choi WI, Sadowski CE, Pabst WL, Warejko JK, Daga A, Basta T, Matejas V, Scharmann K, Kienast SD, Behnam B, Beeson B, Begtrup A, Bruce M, Ch'ng GS, Lin SP, Chang JH, Chen CH, Cho MT, Gaffney PM, Gipson PE, Hsu CH, Kari JA, Ke YY, Kiraly-Borri C, Lai WM, Lemyre E, Littlejohn RO, Masri A, Moghtaderi M, Nakamura K, Ozaltin F, Praet M, Prasad C, Prytula A, Roeder ER, Rump P, Schnur RE, Shiihara T, Sinha MD, Soliman NA, Soulami K, Sweetser DA, Tsai WH, Tsai JD, Topaloglu R, Vester U, Viskochil DH, Vatanavicharn N, Waxler JL, Wierenga KJ, Wolf MTF, Wong SN, Leidel SA, Truglio G, Dedon PC, Poduri A, Mane S, Lifton RP, Bouchard M, Kannu P, Chitayat D, Magen D, Callewaert B, van Tilbeurgh H, Zenker M, Antignac C, Hildebrandt F. Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly. Nat Genet 2017; 49:1529-1538. [PMID: 28805828 DOI: 10.1038/ng.3933] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 07/20/2017] [Indexed: 12/19/2022]
Abstract
Galloway-Mowat syndrome (GAMOS) is an autosomal-recessive disease characterized by the combination of early-onset nephrotic syndrome (SRNS) and microcephaly with brain anomalies. Here we identified recessive mutations in OSGEP, TP53RK, TPRKB, and LAGE3, genes encoding the four subunits of the KEOPS complex, in 37 individuals from 32 families with GAMOS. CRISPR-Cas9 knockout in zebrafish and mice recapitulated the human phenotype of primary microcephaly and resulted in early lethality. Knockdown of OSGEP, TP53RK, or TPRKB inhibited cell proliferation, which human mutations did not rescue. Furthermore, knockdown of these genes impaired protein translation, caused endoplasmic reticulum stress, activated DNA-damage-response signaling, and ultimately induced apoptosis. Knockdown of OSGEP or TP53RK induced defects in the actin cytoskeleton and decreased the migration rate of human podocytes, an established intermediate phenotype of SRNS. We thus identified four new monogenic causes of GAMOS, describe a link between KEOPS function and human disease, and delineate potential pathogenic mechanisms.
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Affiliation(s)
- Daniela A Braun
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jia Rao
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Geraldine Mollet
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - David Schapiro
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marie-Claire Daugeron
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Weizhen Tan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Olivier Gribouval
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Olivia Boyer
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Pediatric Nephrology, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Patrick Revy
- Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,INSERM, U1163, Imagine Institute, Laboratory of Genome Dynamics in the Immune system, Paris, France
| | - Tilman Jobst-Schwan
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Johanna Magdalena Schmidt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer A Lawson
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Denny Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Shazia Ashraf
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeremy F P Ullmann
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte A Hoogstraten
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nathalie Boddaert
- Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,INSERM, U1163, Imagine Institute, Laboratory of Molecular and Pathophysiological Bases of Cognitive Disorders, and INSERM U1000, Paris, France.,Department of Pediatric Radiology, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,Sorbonne Universités UPMC, UFR 927, Sciences de la Vie, Paris, France.,Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie UMR 7590, Sorbonne Universités, UPMC, Université Paris 06, Paris, France
| | - Gaëlle Martin
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Svjetlana Lovric
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Monica Furlano
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Nephrology Department, Fundació Puigvert, IIB Sant Pau, Universitat Autònoma de Barcelona and REDINREN, Barcelona, Spain
| | - I Chiara Guerrera
- Proteomics platform 3P5-Necker, Université Paris Descartes-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Oraly Sanchez-Ferras
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jennifer F Hu
- Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Sylvia Sanquer
- Department of Metabolomic and Proteomic Biochemistry, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM UMR-S1124, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Nina De Rocker
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Merlin Airik
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tobias Hermle
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medicine, Renal Division, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heon Yung Gee
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Won-Il Choi
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Carolin E Sadowski
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Werner L Pabst
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jillian K Warejko
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ankana Daga
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tamara Basta
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Verena Matejas
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Karin Scharmann
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Sandra D Kienast
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Babak Behnam
- Department of Medical Genetics and Molecular Biology, Iran University of Medical Sciences (IUMS), Tehran, Iran.,Medical Genetics Branch, National Human Genome Research Institute (NHGRI), Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland, USA
| | - Brendan Beeson
- Department of Diagnostic Imaging, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia
| | | | - Malcolm Bruce
- Department of Diagnostic Imaging, Princess Margaret and King Edward Memorial Hospitals, Perth, Western Australia, Australia
| | - Gaik-Siew Ch'ng
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Shuan-Pei Lin
- Department of Pediatric Genetics, MacKay Children's Hospital, Taipei, Taiwan.,Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
| | - Jui-Hsing Chang
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Chao-Huei Chen
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | | | - Patrick M Gaffney
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Patrick E Gipson
- Internal Medicine and Pediatrics Divisions of Adult and Pediatric Nephrology, University of Michigan, Ann Arbor, Michigan, USA
| | - Chyong-Hsin Hsu
- Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan
| | - Jameela A Kari
- Pediatric Nephrology Center of Excellence and Pediatric Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yu-Yuan Ke
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Cathy Kiraly-Borri
- Genetic Services of Western Australia, Princess Margaret Hospital for Children and King Edward Memorial Hospital for Women, Subiaco, Western Australia, Australia
| | - Wai-Ming Lai
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Emmanuelle Lemyre
- Service de Génétique Médicale, Département de Pédiatrie, CHU Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Rebecca Okashah Littlejohn
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Amira Masri
- Department of Pediatrics, Division of Child Neurology, Faculty of Medicine, University of Jordan, Amman, Jordan
| | - Mastaneh Moghtaderi
- Chronic Kidney Disease Research Center, Tehran University of Medical Science, Tehran, Iran
| | - Kazuyuki Nakamura
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Fatih Ozaltin
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey.,Nephrogenetics Laboratory, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey.,Hacettepe University Center for Biobanking and Genomics, Hacettepe University, Ankara, Turkey
| | - Marleen Praet
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Chitra Prasad
- Department of Genetics, Metabolism and Pediatrics, Western University, London Health Sciences Centre, London, Ontario, Canada
| | | | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Patrick Rump
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Takashi Shiihara
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Manish D Sinha
- Department of Paediatric Nephrology, Kings College London, Evelina London Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology &Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt.,Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Kenza Soulami
- Department of Nephrology, Ibn Rochd University Hospital, Casablanca, Morocco
| | - David A Sweetser
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Wen-Hui Tsai
- Division of Genetics and Metabolism, Department of Pediatrics, Chi Mei Medical Center, Tainan, Taiwan
| | - Jeng-Daw Tsai
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan.,Department of Pediatrics, MacKay Children's Hospital, Taipei, Taiwan.,Department of Pediatrics, Taipei Medical University Hospital, Taipei, Taiwan.,Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Rezan Topaloglu
- Department of Pediatric Nephrology, Hacettepe University Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Udo Vester
- Department of Pediatrics II, University Hospital Essen, Essen, Germany
| | - David H Viskochil
- Department of Pediatrics, Division of Medical Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Nithiwat Vatanavicharn
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jessica L Waxler
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Klaas J Wierenga
- Department of Pediatrics, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, Oklahoma, USA
| | - Matthias T F Wolf
- Division of Pediatric Nephrology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sik-Nin Wong
- Department of Pediatrics and Adolescent Medicine, Tuen Mun Hospital, Tuen Mun, Hong Kong, China
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany.,Medical Faculty, University of Muenster, Muenster, Germany
| | - Gessica Truglio
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Singapore-MIT Alliance for Research and Technology, Infectious Disease IRG, Singapore
| | - Annapurna Poduri
- Epilepsy Genetics Program and F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York, USA
| | - Maxime Bouchard
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Peter Kannu
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Daniella Magen
- Pediatric Nephrology Institute, Rambam Health Care Campus, Haifa, Israel
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Corinne Antignac
- Laboratory of Hereditary Kidney Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France.,Department of Genetics, Necker Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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17
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Vantroys E, Smet J, Vanlander A, De Paepe B, Vergult S, Sante T, Menten B, Van Coster R. Mild early epileptic encephalopathy evolving to spastic paraplegia, neurogenic bladder and generalized slow colon transit in an 18-year old patient with pathogenic mutations in FARS2. Neuromuscul Disord 2016. [DOI: 10.1016/j.nmd.2016.06.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Coppieters F, Ascari G, Dannhausen K, Nikopoulos K, Peelman F, Karlstetter M, Xu M, Brachet C, Meunier I, Tsilimbaris M, Tsika C, Blazaki S, Vergult S, Farinelli P, Van Laethem T, Bauwens M, De Bruyne M, Chen R, Langmann T, Sui R, Meire F, Rivolta C, Hamel C, Leroy B, De Baere E. Isolated and Syndromic Retinal Dystrophy Caused by Biallelic Mutations in RCBTB1, a Gene Implicated in Ubiquitination. Am J Hum Genet 2016; 99:470-80. [PMID: 27486781 PMCID: PMC4974088 DOI: 10.1016/j.ajhg.2016.06.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 06/20/2016] [Indexed: 11/24/2022] Open
Abstract
Inherited retinal dystrophies (iRDs) are a group of genetically and clinically heterogeneous conditions resulting from mutations in over 250 genes. Here, homozygosity mapping and whole-exome sequencing (WES) in a consanguineous family revealed a homozygous missense mutation, c.973C>T (p.His325Tyr), in RCBTB1. In affected individuals, it was found to segregate with retinitis pigmentosa (RP), goiter, primary ovarian insufficiency, and mild intellectual disability. Subsequent analysis of WES data in different cohorts uncovered four additional homozygous missense mutations in five unrelated families in whom iRD segregates with or without syndromic features. Ocular phenotypes ranged from typical RP starting in the second decade to chorioretinal dystrophy with a later age of onset. The five missense mutations affect highly conserved residues either in the sixth repeat of the RCC1 domain or in the BTB1 domain. A founder haplotype was identified for mutation c.919G>A (p.Val307Met), occurring in two families of Mediterranean origin. We showed ubiquitous mRNA expression of RCBTB1 and demonstrated predominant RCBTB1 localization in human inner retina. RCBTB1 was very recently shown to be involved in ubiquitination, more specifically as a CUL3 substrate adaptor. Therefore, the effect on different components of the CUL3 and NFE2L2 (NRF2) pathway was assessed in affected individuals’ lymphocytes, revealing decreased mRNA expression of NFE2L2 and several NFE2L2 target genes. In conclusion, our study puts forward mutations in RCBTB1 as a cause of autosomal-recessive non-syndromic and syndromic iRD. Finally, our data support a role for impaired ubiquitination in the pathogenetic mechanism of RCBTB1 mutations.
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19
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Dheedene A, Sante T, De Smet M, Vanbellinghen JF, Grisart B, Vergult S, Janssens S, Menten B. Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory. Prenat Diagn 2016; 36:699-707. [PMID: 27176606 PMCID: PMC5108441 DOI: 10.1002/pd.4841] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/15/2016] [Accepted: 05/10/2016] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To implement non-invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15-month experience on clinical samples. METHODS We validated a NIPT protocol for cell-free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemented in the workflow. One thousand eighty-one clinical NIPT samples were analysed, following the described protocol. RESULTS Non-invasive prenatal testing was successfully implemented and validated on 201 normal and 74 aneuploid samples. From 1081 clinical samples, 17 samples showed an abnormal result: 14 trisomy 21 samples, one trisomy 18 and one trisomy 16 were detected. Also a maternal copy number variation on chromosome 13 was observed, which could potentially lead to a false positive trisomy 13 result. One sex discordant result was reported, possibly attributable to a vanishing twin. Moreover, our combined fetal fraction calculation enabled a more reliable risk estimate for trisomy 13, 18 and 21. CONCLUSIONS Non-invasive prenatal testing for trisomy 21, 18 and 13 has a very high specificity and sensitivity. Because of several biological phenomena, diagnostic invasive confirmation of abnormal results remains required. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Annelies Dheedene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Matthias De Smet
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Jean-François Vanbellinghen
- Plateforme de Biologie Moléculaire, Département des Laboratoires, Cliniques Universitaires Saint-Luc, Bruxelles, Belgium
| | - Bernard Grisart
- Centre de Génétique Humaine, Institut de Pathologie et Génétique, Charleroi, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sandra Janssens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
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20
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D'haene E, Jacobs EZ, Volders PJ, De Meyer T, Menten B, Vergult S. Identification of long non-coding RNAs involved in neuronal development and intellectual disability. Sci Rep 2016; 6:28396. [PMID: 27319317 PMCID: PMC4913242 DOI: 10.1038/srep28396] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/01/2016] [Indexed: 12/15/2022] Open
Abstract
Recently, exome sequencing led to the identification of causal mutations in 16–31% of patients with intellectual disability (ID), leaving the underlying cause for many patients unidentified. In this context, the noncoding part of the human genome remains largely unexplored. For many long non-coding RNAs (lncRNAs) a crucial role in neurodevelopment and hence the human brain is anticipated. Here we aimed at identifying lncRNAs associated with neuronal development and ID. Therefore, we applied an integrated genomics approach, harnessing several public epigenetic datasets. We found that the presence of neuron-specific H3K4me3 confers the highest specificity for genes involved in neurodevelopment and ID. Based on the presence of this feature and GWAS hits for CNS disorders, we identified 53 candidate lncRNA genes. Extensive expression profiling on human brain samples and other tissues, followed by Gene Set Enrichment Analysis indicates that at least 24 of these lncRNAs are indeed implicated in processes such as synaptic transmission, nervous system development and neurogenesis. The bidirectional or antisense overlapping orientation relative to multiple coding genes involved in neuronal processes supports these results. In conclusion, we identified several lncRNA genes putatively involved in neurodevelopment and CNS disorders, providing a resource for functional studies.
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Affiliation(s)
- Eva D'haene
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Eva Z Jacobs
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Pieter-Jan Volders
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.,Dept. of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
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21
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Vanlander AV, Menten B, Smet J, De Meirleir L, Sante T, De Paepe B, Seneca S, Pearce SF, Powell CA, Vergult S, Michotte A, De Latter E, Vantomme L, Minczuk M, Van Coster R. Two siblings with homozygous pathogenic splice-site variant in mitochondrial asparaginyl-tRNA synthetase (NARS2). Hum Mutat 2015; 36:222-31. [PMID: 25385316 DOI: 10.1002/humu.22728] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/28/2014] [Indexed: 12/13/2022]
Abstract
A homozygous missense mutation (c.822G>C) was found in the gene encoding the mitochondrial asparaginyl-tRNA synthetase (NARS2) in two siblings born to consanguineous parents. These siblings presented with different phenotypes: one had mild intellectual disability and epilepsy in childhood, whereas the other had severe myopathy. Biochemical analysis of the oxidative phosphorylation (OXPHOS) complexes in both siblings revealed a combined complex I and IV deficiency in skeletal muscle. In-gel activity staining after blue native-polyacrylamide gel electrophoresis confirmed the decreased activity of complex I and IV, and, in addition, showed the presence of complex V subcomplexes. Considering the consanguineous descent, homozygosity mapping and whole-exome sequencing were combined revealing the presence of one single missense mutation in the shared homozygous region. The c.822G>C variant affects the 3' splice site of exon 7, leading to skipping of the whole exon 7 and a part of exon 8 in the NARS2 mRNA. In EBV-transformed lymphoblasts, a specific decrease in the amount of charged mt-tRNA(Asn) was demonstrated as compared with controls. This confirmed the pathogenic nature of the variant. To conclude, the reported variant in NARS2 results in a combined OXPHOS complex deficiency involving complex I and IV, making NARS2 a new member of disease-associated aaRS2.
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Affiliation(s)
- Arnaud V Vanlander
- Department of Pediatric Neurology and Metabolism, Ghent University Hospital, Belgium
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22
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Sante T, Vergult S, Volders PJ, Kloosterman WP, Trooskens G, De Preter K, Dheedene A, Speleman F, De Meyer T, Menten B. ViVar: a comprehensive platform for the analysis and visualization of structural genomic variation. PLoS One 2014; 9:e113800. [PMID: 25503062 PMCID: PMC4264741 DOI: 10.1371/journal.pone.0113800] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/20/2014] [Indexed: 01/06/2023] Open
Abstract
Structural genomic variations play an important role in human disease and phenotypic diversity. With the rise of high-throughput sequencing tools, mate-pair/paired-end/single-read sequencing has become an important technique for the detection and exploration of structural variation. Several analysis tools exist to handle different parts and aspects of such sequencing based structural variation analyses pipelines. A comprehensive analysis platform to handle all steps, from processing the sequencing data, to the discovery and visualization of structural variants, is missing. The ViVar platform is built to handle the discovery of structural variants, from Depth Of Coverage analysis, aberrant read pair clustering to split read analysis. ViVar provides you with powerful visualization options, enables easy reporting of results and better usability and data management. The platform facilitates the processing, analysis and visualization, of structural variation based on massive parallel sequencing data, enabling the rapid identification of disease loci or genes. ViVar allows you to scale your analysis with your work load over multiple (cloud) servers, has user access control to keep your data safe and is easy expandable as analysis techniques advance. URL: https://www.cmgg.be/vivar/
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Affiliation(s)
- Tom Sante
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Pieter-Jan Volders
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Wigard P. Kloosterman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Geert Trooskens
- BioBix, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
| | - Tim De Meyer
- BioBix, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, Gent, Belgium
- * E-mail:
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23
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van Heesch S, Simonis M, van Roosmalen MJ, Pillalamarri V, Brand H, Kuijk EW, de Luca KL, Lansu N, Braat AK, Menelaou A, Hao W, Korving J, Snijder S, van der Veken LT, Hochstenbach R, Knegt AC, Duran K, Renkens I, Alekozai N, Jager M, Vergult S, Menten B, de Bruijn E, Boymans S, Ippel E, van Binsbergen E, Talkowski ME, Lichtenbelt K, Cuppen E, Kloosterman WP. Genomic and functional overlap between somatic and germline chromosomal rearrangements. Cell Rep 2014; 9:2001-10. [PMID: 25497101 DOI: 10.1016/j.celrep.2014.11.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 10/20/2014] [Accepted: 11/15/2014] [Indexed: 12/17/2022] Open
Abstract
Genomic rearrangements are a common cause of human congenital abnormalities. However, their origin and consequences are poorly understood. We performed molecular analysis of two patients with congenital disease who carried de novo genomic rearrangements. We found that the rearrangements in both patients hit genes that are recurrently rearranged in cancer (ETV1, FOXP1, and microRNA cluster C19MC) and drive formation of fusion genes similar to those described in cancer. Subsequent analysis of a large set of 552 de novo germline genomic rearrangements underlying congenital disorders revealed enrichment for genes rearranged in cancer and overlap with somatic cancer breakpoints. Breakpoints of common (inherited) germline structural variations also overlap with cancer breakpoints but are depleted for cancer genes. We propose that the same genomic positions are prone to genomic rearrangements in germline and soma but that timing and context of breakage determines whether developmental defects or cancer are promoted.
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Affiliation(s)
- Sebastiaan van Heesch
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Marieke Simonis
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Markus J van Roosmalen
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Vamsee Pillalamarri
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Harrison Brand
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ewart W Kuijk
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Kim L de Luca
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Nico Lansu
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - A Koen Braat
- Department of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, the Netherlands
| | - Androniki Menelaou
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Wensi Hao
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jeroen Korving
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Simone Snijder
- Department of Clinical Genetics, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Lars T van der Veken
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Ron Hochstenbach
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Alida C Knegt
- Department of Clinical Genetics, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Karen Duran
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Ivo Renkens
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Najla Alekozai
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Myrthe Jager
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Ewart de Bruijn
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Sander Boymans
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Elly Ippel
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Michael E Talkowski
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Klaske Lichtenbelt
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Edwin Cuppen
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
| | - Wigard P Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
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24
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De Rocker N, Vergult S, Koolen D, Jacobs E, Hoischen A, Zeesman S, Bang B, Béna F, Bockaert N, Bongers EM, de Ravel T, Devriendt K, Giglio S, Faivre L, Joss S, Maas S, Marle N, Novara F, Nowaczyk MJM, Peeters H, Polstra A, Roelens F, Rosenberg C, Thevenon J, Tümer Z, Vanhauwaert S, Varvagiannis K, Willaert A, Willemsen M, Willems M, Zuffardi O, Coucke P, Speleman F, Eichler EE, Kleefstra T, Menten B. Refinement of the critical 2p25.3 deletion region: the role of MYT1L in intellectual disability and obesity. Genet Med 2014; 17:460-6. [PMID: 25232846 DOI: 10.1038/gim.2014.124] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/07/2014] [Indexed: 01/04/2023] Open
Abstract
PURPOSE Submicroscopic deletions of chromosome band 2p25.3 are associated with intellectual disability and/or central obesity. Although MYT1L is believed to be a critical gene responsible for intellectual disability, so far no unequivocal data have confirmed this hypothesis. METHODS In this study we evaluated a cohort of 22 patients (15 sporadic patients and two families) with a 2p25.3 aberration to further refine the clinical phenotype and to delineate the role of MYT1L in intellectual disability and obesity. In addition, myt1l spatiotemporal expression in zebrafish embryos was analyzed by quantitative polymerase chain reaction and whole-mount in situ hybridization. RESULTS Complete MYT1L deletion, intragenic deletion, or duplication was observed in all sporadic patients, in addition to two patients with a de novo point mutation in MYT1L. The familial cases comprise a 6-Mb deletion in a father and his three children and a 5' MYT1L overlapping duplication in a father and his two children. Expression analysis in zebrafish embryos shows specific myt1l expression in the developing brain. CONCLUSION Our data strongly strengthen the hypothesis that MYT1L is the causal gene for the observed syndromal intellectual disability. Moreover, because 17 patients present with obesity/overweight, haploinsufficiency of MYT1L might predispose to weight problems with childhood onset.Genet Med 17 6, 460-466.
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Affiliation(s)
- Nina De Rocker
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - David Koolen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Eva Jacobs
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Susan Zeesman
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Birgitte Bang
- Paediatric Department, Copenhagen University Hospital, Herlev, Denmark
| | - Frédérique Béna
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Nele Bockaert
- Center for Developmental Disorders, Ghent University Hospital, Ghent, Belgium
| | - Ernie M Bongers
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Thomy de Ravel
- Center for Human Genetics, Leuven University Hospitals, KU Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Center for Human Genetics, Leuven University Hospitals, KU Leuven, Leuven, Belgium
| | - Sabrina Giglio
- Medical Genetics Unit, Meyer Children's University Hospital, Florence, Italy
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Shelagh Joss
- West of Scotland Regional Genetics Service, NHS Greater Glasgow and Clyde, Southern General Hospital, Glasgow, UK
| | - Saskia Maas
- Department of Clinical Genetics, Academic Medical Center, UVA, Amsterdam, The Netherlands
| | - Nathalie Marle
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Francesca Novara
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Malgorzata J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Hilde Peeters
- Center for Human Genetics, Leuven University Hospitals, KU Leuven, Leuven, Belgium
| | - Abeltje Polstra
- Department of Clinical Genetics, Academic Medical Center, UVA, Amsterdam, The Netherlands
| | - Filip Roelens
- Heilig Hart Ziekenhuis Roeselare-Menen, Roeselare, Belgium
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Zeynep Tümer
- Center for Applied Human Molecular Genetics, Kennedy Center, University of Copenhagen, Glostrup, Denmark
| | | | | | - Andy Willaert
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Marjolein Willemsen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Marjolaine Willems
- Département de Génétique Clinique, CHRU de Montpellier, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Paul Coucke
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Evan E Eichler
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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25
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Vulto-van Silfhout AT, Rajamanickam S, Jensik PJ, Vergult S, de Rocker N, Newhall KJ, Raghavan R, Reardon SN, Jarrett K, McIntyre T, Bulinski J, Ownby SL, Huggenvik JI, McKnight GS, Rose GM, Cai X, Willaert A, Zweier C, Endele S, de Ligt J, van Bon BWM, Lugtenberg D, de Vries PF, Veltman JA, van Bokhoven H, Brunner HG, Rauch A, de Brouwer APM, Carvill GL, Hoischen A, Mefford HC, Eichler EE, Vissers LELM, Menten B, Collard MW, de Vries BBA. Mutations affecting the SAND domain of DEAF1 cause intellectual disability with severe speech impairment and behavioral problems. Am J Hum Genet 2014; 94:649-61. [PMID: 24726472 DOI: 10.1016/j.ajhg.2014.03.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/18/2014] [Indexed: 11/29/2022] Open
Abstract
Recently, we identified in two individuals with intellectual disability (ID) different de novo mutations in DEAF1, which encodes a transcription factor with an important role in embryonic development. To ascertain whether these mutations in DEAF1 are causative for the ID phenotype, we performed targeted resequencing of DEAF1 in an additional cohort of over 2,300 individuals with unexplained ID and identified two additional individuals with de novo mutations in this gene. All four individuals had severe ID with severely affected speech development, and three showed severe behavioral problems. DEAF1 is highly expressed in the CNS, especially during early embryonic development. All four mutations were missense mutations affecting the SAND domain of DEAF1. Altered DEAF1 harboring any of the four amino acid changes showed impaired transcriptional regulation of the DEAF1 promoter. Moreover, behavioral studies in mice with a conditional knockout of Deaf1 in the brain showed memory deficits and increased anxiety-like behavior. Our results demonstrate that mutations in DEAF1 cause ID and behavioral problems, most likely as a result of impaired transcriptional regulation by DEAF1.
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Affiliation(s)
| | - Shivakumar Rajamanickam
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Philip J Jensik
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Nina de Rocker
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Kathryn J Newhall
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Ramya Raghavan
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sara N Reardon
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Kelsey Jarrett
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Tara McIntyre
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Joseph Bulinski
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Stacy L Ownby
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Jodi I Huggenvik
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - G Stanley McKnight
- Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Gregory M Rose
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA; Department of Anatomy, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Xiang Cai
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Andy Willaert
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Sabine Endele
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Joep de Ligt
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Bregje W M van Bon
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Dorien Lugtenberg
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Petra F de Vries
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neurosciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8603 Schwerzenbach-Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich, 8603 Schwerzenbach-Zurich, Switzerland; Zurich Center of Integrative Human Physiology, University of Zurich, 8603 Schwerzenbach-Zurich, Switzerland
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neurosciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Gemma L Carvill
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent 9000, Belgium
| | - Michael W Collard
- Department of Physiology and Center for Integrated Research in Cognitive & Neural Sciences, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
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26
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Bustin SA, Benes V, Garson J, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley G, Wittwer CT, Schjerling P, Day PJ, Abreu M, Aguado B, Beaulieu JF, Beckers A, Bogaert S, Browne JA, Carrasco-Ramiro F, Ceelen L, Ciborowski K, Cornillie P, Coulon S, Cuypers A, De Brouwer S, De Ceuninck L, De Craene J, De Naeyer H, De Spiegelaere W, Deckers K, Dheedene A, Durinck K, Ferreira-Teixeira M, Fieuw A, Gallup JM, Gonzalo-Flores S, Goossens K, Heindryckx F, Herring E, Hoenicka H, Icardi L, Jaggi R, Javad F, Karampelias M, Kibenge F, Kibenge M, Kumps C, Lambertz I, Lammens T, Markey A, Messiaen P, Mets E, Morais S, Mudarra-Rubio A, Nakiwala J, Nelis H, Olsvik PA, Pérez-Novo C, Plusquin M, Remans T, Rihani A, Rodrigues-Santos P, Rondou P, Sanders R, Schmidt-Bleek K, Skovgaard K, Smeets K, Tabera L, Toegel S, Van Acker T, Van den Broeck W, Van der Meulen J, Van Gele M, Van Peer G, Van Poucke M, Van Roy N, Vergult S, Wauman J, Tshuikina-Wiklander M, Willems E, Zaccara S, Zeka F, Vandesompele J. The need for transparency and good practices in the qPCR literature. Nat Methods 2013; 10:1063-7. [PMID: 24173381 DOI: 10.1038/nmeth.2697] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Two surveys of over 1,700 publications whose authors use quantitative real-time PCR (qPCR) reveal a lack of transparent and comprehensive reporting of essential technical information. Reporting standards are significantly improved in publications that cite the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, although such publications are still vastly outnumbered by those that do not.
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Affiliation(s)
- Stephen A Bustin
- Postgraduate Medical Institute, Anglia Ruskin University, Chelmsford, UK
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27
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Vergult S, Van Binsbergen E, Sante T, Nowak S, Vanakker O, Claes K, Poppe B, Van der Aa N, van Roosmalen MJ, Duran K, Tavakoli-Yaraki M, Swinkels M, van den Boogaard MJ, van Haelst M, Roelens F, Speleman F, Cuppen E, Mortier G, Kloosterman WP, Menten B. Mate pair sequencing for the detection of chromosomal aberrations in patients with intellectual disability and congenital malformations. Eur J Hum Genet 2013; 22:652-9. [PMID: 24105367 DOI: 10.1038/ejhg.2013.220] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 08/13/2013] [Accepted: 08/29/2013] [Indexed: 12/20/2022] Open
Abstract
Recently, microarrays have replaced karyotyping as a first tier test in patients with idiopathic intellectual disability and/or multiple congenital abnormalities (ID/MCA) in many laboratories. Although in about 14-18% of such patients, DNA copy-number variants (CNVs) with clinical significance can be detected, microarrays have the disadvantage of missing balanced rearrangements, as well as providing no information about the genomic architecture of structural variants (SVs) like duplications and complex rearrangements. Such information could possibly lead to a better interpretation of the clinical significance of the SV. In this study, the clinical use of mate pair next-generation sequencing was evaluated for the detection and further characterization of structural variants within the genomes of 50 ID/MCA patients. Thirty of these patients carried a chromosomal aberration that was previously detected by array CGH or karyotyping and suspected to be pathogenic. In the remaining 20 patients no causal SVs were found and only benign aberrations were detected by conventional techniques. Combined cluster and coverage analysis of the mate pair data allowed precise breakpoint detection and further refinement of previously identified balanced and (complex) unbalanced aberrations, pinpointing the causal gene for some patients. We conclude that mate pair sequencing is a powerful technology that can provide rapid and unequivocal characterization of unbalanced and balanced SVs in patient genomes and can be essential for the clinical interpretation of some SVs.
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Affiliation(s)
- Sarah Vergult
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Ellen Van Binsbergen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tom Sante
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Silke Nowak
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | | | - Kathleen Claes
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Nathalie Van der Aa
- Department for Medical Genetics, University Hospital of Antwerp, Antwerp, Belgium
| | - Markus J van Roosmalen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Karen Duran
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Marielle Swinkels
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Mieke van Haelst
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Edwin Cuppen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Geert Mortier
- 1] Center for Medical Genetics, Ghent University, Ghent, Belgium [2] Department for Medical Genetics, University Hospital of Antwerp, Antwerp, Belgium
| | - Wigard P Kloosterman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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28
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Beunders G, Voorhoeve E, Golzio C, Pardo LM, Rosenfeld JA, Talkowski ME, Simonic I, Lionel AC, Vergult S, Pyatt RE, van de Kamp J, Nieuwint A, Weiss MM, Rizzu P, Verwer LENI, van Spaendonk RML, Shen Y, Wu BL, Yu T, Yu Y, Chiang C, Gusella JF, Lindgren AM, Morton CC, van Binsbergen E, Bulk S, van Rossem E, Vanakker O, Armstrong R, Park SM, Greenhalgh L, Maye U, Neill NJ, Abbott KM, Sell S, Ladda R, Farber DM, Bader PI, Cushing T, Drautz JM, Konczal L, Nash P, de Los Reyes E, Carter MT, Hopkins E, Marshall CR, Osborne LR, Gripp KW, Thrush DL, Hashimoto S, Gastier-Foster JM, Astbury C, Ylstra B, Meijers-Heijboer H, Posthuma D, Menten B, Mortier G, Scherer SW, Eichler EE, Girirajan S, Katsanis N, Groffen AJ, Sistermans EA. Exonic deletions in AUTS2 cause a syndromic form of intellectual disability and suggest a critical role for the C terminus. Am J Hum Genet 2013; 92:210-20. [PMID: 23332918 DOI: 10.1016/j.ajhg.2012.12.011] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/06/2012] [Accepted: 12/20/2012] [Indexed: 01/15/2023] Open
Abstract
Genomic rearrangements involving AUTS2 (7q11.22) are associated with autism and intellectual disability (ID), although evidence for causality is limited. By combining the results of diagnostic testing of 49,684 individuals, we identified 24 microdeletions that affect at least one exon of AUTS2, as well as one translocation and one inversion each with a breakpoint within the AUTS2 locus. Comparison of 17 well-characterized individuals enabled identification of a variable syndromic phenotype including ID, autism, short stature, microcephaly, cerebral palsy, and facial dysmorphisms. The dysmorphic features were more pronounced in persons with 3'AUTS2 deletions. This part of the gene is shown to encode a C-terminal isoform (with an alternative transcription start site) expressed in the human brain. Consistent with our genetic data, suppression of auts2 in zebrafish embryos caused microcephaly that could be rescued by either the full-length or the C-terminal isoform of AUTS2. Our observations demonstrate a causal role of AUTS2 in neurocognitive disorders, establish a hitherto unappreciated syndromic phenotype at this locus, and show how transcriptional complexity can underpin human pathology. The zebrafish model provides a valuable tool for investigating the etiology of AUTS2 syndrome and facilitating gene-function analysis in the future.
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Affiliation(s)
- Gea Beunders
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
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29
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Vergult S, Leroy B, Claerhout I, Menten B. Familial cases of a submicroscopic Xp22.2 deletion: genotype-phenotype correlation in microphthalmia with linear skin defects syndrome. Mol Vis 2013; 19:311-8. [PMID: 23401659 PMCID: PMC3566894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 02/04/2013] [Indexed: 12/02/2022] Open
Abstract
PURPOSE Microphthalmia with linear skin defects syndrome (MLS or MIDAS, OMIM #309801) is a rare X-linked male-lethal disorder characterized by microphthalmia or other ocular anomalies and skin lesions limited to the face and neck. However, inter- and intrafamilial variability is high. Here we report a familial case of MLS. METHODS A mother and daughter with MLS underwent a complete ophthalmological examination, and extensive imaging, including anterior segment pictures, corneal topography and keratometry, autofluorescence, infrared reflectance and red free images, as well as spectral-domain optical coherence tomography. The mother also underwent full-field flash electroretinography. In addition, high-resolution array comparative genomic hybridization analysis was performed in both as well as in the maternal grandparents of the proband. RESULTS Microphthalmia and retinal abnormalities were noted in the proband and the mother, whereas only the mother presented with scars of the typical neonatal linear skin defects. Array comparative genomic hybridization analysis revealed a 185-220 kb deletion on chromosome band Xp22.2 including the entire HCCS gene. CONCLUSIONS The identification of a deletion including HCCS led to the diagnosis of MLS in these patients. Retinal abnormalities can be part of the ocular manifestations of MLS.
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Affiliation(s)
- Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital & Ghent University, Ghent, Belgium
| | - Bart Leroy
- Center for Medical Genetics, Ghent University Hospital & Ghent University, Ghent, Belgium,Department of Ophthalmology, Ghent University Hospital & Ghent University, Ghent, Belgium
| | - Ilse Claerhout
- Department of Ophthalmology, Ghent University Hospital & Ghent University, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital & Ghent University, Ghent, Belgium
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30
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Dheedene A, Maes M, Vergult S, Menten B. A de novo POU3F3 Deletion in a Boy with Intellectual Disability and Dysmorphic Features. Mol Syndromol 2013; 5:32-5. [DOI: 10.1159/000356060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2013] [Indexed: 11/19/2022] Open
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31
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Vergult S, Hoogeboom AJM, Bijlsma EK, Sante T, Klopocki E, De Wilde B, Jongmans M, Thiel C, Verheij JBGM, Perez-Aytes A, Van Esch H, Kuechler A, Barge-Schaapveld DQCM, Sznajer Y, Mortier G, Menten B. Complex genetics of radial ray deficiencies: screening of a cohort of 54 patients. Genet Med 2012; 15:195-202. [DOI: 10.1038/gim.2012.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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32
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Kloosterman WP, Tavakoli-Yaraki M, van Roosmalen MJ, van Binsbergen E, Renkens I, Duran K, Ballarati L, Vergult S, Giardino D, Hansson K, Ruivenkamp CAL, Jager M, van Haeringen A, Ippel EF, Haaf T, Passarge E, Hochstenbach R, Menten B, Larizza L, Guryev V, Poot M, Cuppen E. Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms. Cell Rep 2012; 1:648-55. [PMID: 22813740 DOI: 10.1016/j.celrep.2012.05.009] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 02/09/2012] [Accepted: 05/14/2012] [Indexed: 12/20/2022] Open
Abstract
Chromothripsis represents a novel phenomenon in the structural variation landscape of cancer genomes. Here, we analyze the genomes of ten patients with congenital disease who were preselected to carry complex chromosomal rearrangements with more than two breakpoints. The rearrangements displayed unanticipated complexity resembling chromothripsis. We find that eight of them contain hallmarks of multiple clustered double-stranded DNA breaks (DSBs) on one or more chromosomes. In addition, nucleotide resolution analysis of 98 breakpoint junctions indicates that break repair involves nonhomologous or microhomology-mediated end joining. We observed that these eight rearrangements are balanced or contain sporadic deletions ranging in size between a few hundred base pairs and several megabases. The two remaining complex rearrangements did not display signs of DSBs and contain duplications, indicative of rearrangement processes involving template switching. Our work provides detailed insight into the characteristics of chromothripsis and supports a role for clustered DSBs driving some constitutional chromothripsis rearrangements.
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Affiliation(s)
- Wigard P Kloosterman
- Department of Medical Genetics, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands.
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Stouffs K, Vandermaelen D, Massart A, Menten B, Vergult S, Tournaye H, Lissens W. Array comparative genomic hybridization in male infertility. Hum Reprod 2012; 27:921-9. [DOI: 10.1093/humrep/der440] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Vergult S, Dauber A, Delle Chiaie B, Van Oudenhove E, Simon M, Rihani A, Loeys B, Hirschhorn J, Pfotenhauer J, Phillips JA, Mohammed S, Ogilvie C, Crolla J, Mortier G, Menten B. 17q24.2 microdeletions: a new syndromal entity with intellectual disability, truncal obesity, mood swings and hallucinations. Eur J Hum Genet 2011; 20:534-9. [PMID: 22166941 DOI: 10.1038/ejhg.2011.239] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Although microdeletions of the long arm of chromosome 17 are being reported with increasing frequency, deletions of chromosome band 17q24.2 are rare. Here we report four patients with a microdeletion encompassing chromosome band 17q24.2 with a smallest region of overlap of 713 kb containing five Refseq genes and one miRNA. The patients share the phenotypic characteristics, such as intellectual disability (4/4), speech delay (4/4), truncal obesity (4/4), seizures (2/4), hearing loss (3/4) and a particular facial gestalt. Hallucinations and mood swings were also noted in two patients. The PRKCA gene is a very interesting candidate gene for many of the observed phenotypic features, as this gene plays an important role in many cellular processes. Deletion of this gene might explain the observed truncal obesity and could also account for the hallucinations and mood swings seen in two patients, whereas deletion of a CACNG gene cluster might be responsible for the seizures observed in two patients. In one of the patients, the PRKAR1A gene responsible for Carney Complex and the KCNJ2 gene causal for Andersen syndrome are deleted. This is the first report of a patient with a whole gene deletion of the KCNJ2 gene.
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Affiliation(s)
- Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Fieuw A, Kumps C, Schramm A, Pattyn F, Menten B, Antonacci F, Sudmant P, Schulte JH, Van Roy N, Vergult S, Buckley PG, De Paepe A, Noguera R, Versteeg R, Stallings R, Eggert A, Vandesompele J, De Preter K, Speleman F. Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas. Int J Cancer 2011; 130:2599-606. [PMID: 21796619 DOI: 10.1002/ijc.26317] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/12/2011] [Indexed: 01/04/2023]
Abstract
Neuroblastoma is an aggressive embryonal tumor that accounts for ∼15% of childhood cancer deaths. Hitherto, despite the availability of comprehensive genomic data on DNA copy number changes in neuroblastoma, relatively little is known about the genes driving neuroblastoma tumorigenesis. In this study, high resolution array comparative genome hybridization (CGH) was performed on 188 primary neuroblastoma tumors and 33 neuroblastoma cell lines to search for previously undetected recurrent DNA copy number gains and losses. A new recurrent distal chromosome 1q deletion (del(1)(q42.2qter)) was detected in seven cases. Further analysis of available array CGH datasets revealed 13 additional similar distal 1q deletions. The majority of all detected 1q deletions was found in high risk 11q deleted tumors without MYCN amplification (Fisher exact test p = 5.61 × 10(-5) ). Using ultra-high resolution (∼115 bp resolution) custom arrays covering the breakpoints on 1q for 11 samples, clustering of nine breakpoints was observed within a 12.5-kb region, of which eight were found in a 7-kb copy number variable region, whereas the remaining two breakpoints were colocated 1.4-Mb proximal. The commonly deleted region contains one miRNA (hsa-mir-1537), four transcribed ultra conserved region elements (uc.43-uc.46) and 130 protein coding genes including at least two bona fide tumor suppressor genes, EGLN1 (or PHD2) and FH. This finding further contributes to the delineation of the genomic profile of aggressive neuroblastoma, offers perspectives for the identification of genes contributing to the disease phenotype and may be relevant in the light of assessment of response to new molecular treatments.
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Affiliation(s)
- Annelies Fieuw
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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36
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Vergult S, Krgovic D, Loeys B, Lyonnet S, Liedén A, Anderlid BM, Sharkey F, Joss S, Mortier G, Menten B. Nasal speech and hypothyroidism are common hallmarks of 12q15 microdeletions. Eur J Hum Genet 2011; 19:1032-7. [PMID: 21505450 DOI: 10.1038/ejhg.2011.67] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The introduction of array CGH in clinical diagnostics has led to the discovery of many new microdeletion/microduplication syndromes. Most of them are rare and often present with a variable range of clinical anomalies. In this study we report three patients with a de novo overlapping microdeletion of chromosome bands 12q15q21.1. The deletions are ∼2.5 Mb in size, with a 1.34-Mb common deleted region containing six RefSeq genes. All three patients present with learning disability or developmental delay, nasal speech and hypothyroidism. In this paper we will further elaborate on the genotype-phenotype correlation associated with this deletion and compare our patients with previously reported cases.
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Affiliation(s)
- Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Buysse K, Vergult S, Mussche S, Groote CCD, Speleman F, Menten B, Lissens W, Van Coster R. Giant axonal neuropathy caused by compound heterozygosity for a maternally inherited microdeletion and a paternal mutation within the GAN gene. Am J Med Genet A 2010; 152A:2802-4. [DOI: 10.1002/ajmg.a.33508] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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De Weer A, Poppe B, Vergult S, Van Vlierberghe P, Petrick M, De Bock R, Benoit Y, Noens L, De Paepe A, Van Roy N, Menten B, Speleman F. Identification of two critically deleted regions within chromosome segment 7q35-q36 in EVI1 deregulated myeloid leukemia cell lines. PLoS One 2010; 5:e8676. [PMID: 20084277 PMCID: PMC2800774 DOI: 10.1371/journal.pone.0008676] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 12/07/2009] [Indexed: 01/19/2023] Open
Abstract
Chromosomal rearrangements involving the EVI1 proto-oncogene are a recurrent finding in myeloid leukemias and are indicative of a poor prognosis. Rearrangements of the EVI1 locus are often associated with monosomy 7 or cytogenetic detectable deletions of part of 7q. As EVI1 overexpression alone is not sufficient to induce leukemia, loss of a 7q tumour suppressor gene might be a required cooperating event. To test this hypothesis, we performed high-resolution array comparative genomic hybridization analysis of twelve EVI1 overexpressing patients and three EVI1 deregulated cell lines to search for 7q submicroscopic deletions. This analysis lead to the delineation of two critical regions, one of 0.39 Mb on 7q35 containing the CNTNAP2 gene and one of 1.33 Mb on chromosome bands 7q35-q36 comprising nine genes in EVI1 deregulated cell lines. These findings open the way to further studies aimed at identifying the culprit EVI1 implicated tumour suppressor genes on 7q.
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Affiliation(s)
- An De Weer
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Bruce Poppe
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | | | - Marjan Petrick
- Department of Radiotherapy, Oncology and Hematology, AZ Sint-Lucas, Ghent, Belgium
| | | | - Yves Benoit
- Department of Pediatric Hemato-Oncology, Ghent University Hospital, Ghent, Belgium
| | - Lucien Noens
- Department of Hematology, Ghent University Hospital, Ghent, Belgium
| | - Anne De Paepe
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Nadine Van Roy
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Frank Speleman
- Centre for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- * E-mail:
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