1
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Schoch K, Ruegg MSG, Fellows BJ, Cao J, Uhrig S, Einsele-Scholz S, Biskup S, Hawarden SRA, Salpietro V, Capra V, Brown CM, Accogli A, Shashi V, Bicknell LS. A second hotspot for pathogenic exon-skipping variants in CDC45. Eur J Hum Genet 2024:10.1038/s41431-024-01583-1. [PMID: 38467731 DOI: 10.1038/s41431-024-01583-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Biallelic pathogenic variants in CDC45 are associated with Meier-Gorlin syndrome with craniosynostosis (MGORS type 7), which also includes short stature and absent/hypoplastic patellae. Identified variants act through a hypomorphic loss of function mechanism, to reduce CDC45 activity and impact DNA replication initiation. In addition to missense and premature termination variants, several pathogenic synonymous variants have been identified, most of which cause increased exon skipping of exon 4, which encodes an essential part of the RecJ-orthologue's DHH domain. Here we have identified a second cohort of families segregating CDC45 variants, where patients have craniosynostosis and a reduction in height, alongside common facial dysmorphisms, including thin eyebrows, consistent with MGORS7. Skipping of exon 15 is a consequence of two different variants, including a shared synonymous variant that is enriched in individuals of East Asian ancestry, while other variants in trans are predicted to alter key intramolecular interactions in α/β domain II, or cause retention of an intron within the 3'UTR. Our cohort and functional data confirm exon skipping is a relatively common pathogenic mechanism in CDC45, and highlights the need for alternative splicing events, such as exon skipping, to be especially considered for variants initially predicted to be less likely to cause the phenotype, particularly synonymous variants.
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Affiliation(s)
- Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Mischa S G Ruegg
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Bridget J Fellows
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Joseph Cao
- Division of Pediatric Radiology, Department of Radiology Duke University School of Medicine, Durham, NC, USA
| | - Sabine Uhrig
- Institute of Clinical Genetics, Klinikum Stuttgart, Stuttgart, Germany
| | | | - Saskia Biskup
- Center for Human Genetics Tuebingen and CeGaT GmbH, Tuebingen, Germany
| | - Samuel R A Hawarden
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Vincenzo Salpietro
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Valeria Capra
- Genomics and Clinical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Andrea Accogli
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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2
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Fellows BJ, Tolezano GC, Pires SF, Ruegg MSG, Knapp KM, Krepischi ACV, Bicknell LS. A novel KNL1 intronic splicing variant likely destabilizes the KMN complex, causing primary microcephaly. Am J Med Genet A 2024; 194:e63468. [PMID: 37937525 DOI: 10.1002/ajmg.a.63468] [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: 09/12/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023]
Abstract
Primary microcephaly (MCPH) is an autosomal recessive disorder characterized by head circumference of at least two standard deviations below the mean. Biallelic variants in the kinetochore gene KNL1 is a known cause of MCPH4. KNL1 is the central component of the KNL1-MIS12-NSL1 (KMN) network, which acts as the signaling hub of the kinetochore and is required for correct chromosomal segregation during mitosis. We identified biallelic KNL1 variants in two siblings from a non-consanguineous family with microcephaly and intellectual disability. The two siblings carry a frameshift variant predicted to prematurely truncate the transcript and undergo nonsense mediated decay, and an intronic single nucleotide variant (SNV) predicted to disrupt splicing. An in vitro splicing assay and qPCR from blood-derived RNA confirmed that the intronic variant skips exon 23, significantly reducing levels of the canonical transcript. Protein modeling confirmed that absence of exon 23, an inframe exon, would disrupt a key interaction within the KMN network and likely destabilize the kinetochore signaling hub, disrupting mitosis. Therefore, this splicing variant is pathogenic and, in trans with a frameshift variant, causes the MCPH phenotype associated with KLN1. This finding furthers the association of splicing variants as a common pathogenic variant class for KNL1.
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Affiliation(s)
- Bridget J Fellows
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Giovanna Cantini Tolezano
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Sara Ferreira Pires
- Human Genome and Stem Cell Research Center, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Mischa S G Ruegg
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Karen M Knapp
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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3
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Mulligan MR, Bicknell LS. The molecular genetics of nELAVL in brain development and disease. Eur J Hum Genet 2023; 31:1209-1217. [PMID: 37697079 PMCID: PMC10620143 DOI: 10.1038/s41431-023-01456-z] [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: 07/06/2023] [Revised: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Embryonic development requires tight control of gene expression levels, activity, and localisation. This control is coordinated by multiple levels of regulation on DNA, RNA and protein. RNA-binding proteins (RBPs) are recognised as key regulators of post-transcriptional gene regulation, where their binding controls splicing, polyadenylation, nuclear export, mRNA stability, translation rate and decay. In brain development, the ELAVL family of RNA binding proteins undertake essential functions across spatiotemporal windows to help regulate and specify transcriptomic programmes for cell specialisation. Despite their recognised importance in neural tissues, their molecular roles and connections to pathology are less explored. Here we provide an overview of the neuronal ELAVL family, noting commonalities and differences amongst different species, their molecular characteristics, and roles in the cell. We bring together the available molecular genetics evidence to link different ELAVL proteins to phenotypes and disease, in both the brain and beyond, including ELAVL2, which is the least studied ELAVL family member. We find that ELAVL-related pathology shares a common neurological theme, but different ELAVL proteins are more strongly connected to different phenotypes, reflecting their specialised expression across time and space.
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Affiliation(s)
- Meghan R Mulligan
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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4
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Nielsen-Dandoroff E, Ruegg MSG, Bicknell LS. The expanding genetic and clinical landscape associated with Meier-Gorlin syndrome. Eur J Hum Genet 2023:10.1038/s41431-023-01359-z. [PMID: 37059840 PMCID: PMC10400559 DOI: 10.1038/s41431-023-01359-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/26/2023] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
High-throughput sequencing has become a standard first-tier approach for both diagnostics and research-based genetic testing. Consequently, this hypothesis-free testing manner has revealed the true breadth of clinical features for many established genetic disorders, including Meier-Gorlin syndrome (MGORS). Previously known as ear-patella short stature syndrome, MGORS is characterized by growth delay, microtia, and patella hypo/aplasia, as well as genital abnormalities, and breast agenesis in females. Following the initial identification of genetic causes in 2011, a total of 13 genes have been identified to date associated with MGORS. In this review, we summarise the genetic and clinical findings of each gene associated with MGORS and highlight molecular insights that have been made through studying patient variants. We note interesting observations arising across this group of genes as the number of patients has increased, such as the unusually high number of synonymous variants affecting splicing in CDC45 and a subgroup of genes that also cause craniosynostosis. We focus on the complicated molecular genetics for DONSON, where we examine potential genotype-phenotype patterns using the first 3D structural model of DONSON. The canonical role of all proteins associated with MGORS are involved in different stages of DNA replication and in addition to summarising how patient variants impact on this process, we discuss the potential contribution of non-canonical roles of these proteins to the pathophysiology of MGORS.
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Affiliation(s)
| | - Mischa S G Ruegg
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
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5
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Carter S, Fellows BJ, Gibson K, Bicknell LS. Extending the PAX1 spectrum: a dominantly inherited variant causes oculo-auriculo-vertebral syndrome. Eur J Hum Genet 2022; 30:1178-1181. [PMID: 35879406 PMCID: PMC9553880 DOI: 10.1038/s41431-022-01154-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/25/2022] [Revised: 06/17/2022] [Accepted: 07/07/2022] [Indexed: 12/15/2022] Open
Abstract
Oculo-auriculo-vertebral syndrome (OAVS) is a clinically heterogeneous disorder, with both genetic and environmental contributors. Multiple genes have been associated with OAVS and common molecular pathways, such as retinoic acid and the PAX-SIX-EYA-DACH (PSED) network, are being implicated in the disease pathophysiology. Biallelic homozygous nonsense or hypomorphic missense mutations in PAX1 cause otofaciocervical syndrome type 2 (OTFCS2), a similar but more severe multi-system disorder that can be accompanied by severe combined immunodeficiency due to thymic aplasia. Here we have identified a multi-generational family with mild features of OAVS segregating a heterozygous frameshift in PAX1. The four base duplication is expected to result in nonsense-mediated decay, and therefore cause a null allele. While there was full penetrance of the variant, expressivity of facial and ear features were variable. Our findings indicate there can be monoallelic and biallelic disorders associated with PAX1, and further implicate the PSED network in OAVS.
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Affiliation(s)
- Shannon Carter
- grid.414299.30000 0004 0614 1349Genetic Health Service New Zealand, Christchurch Hospital, Christchurch, New Zealand
| | - Bridget J. Fellows
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Kate Gibson
- grid.414299.30000 0004 0614 1349Genetic Health Service New Zealand, Christchurch Hospital, Christchurch, New Zealand
| | - Louise S. Bicknell
- grid.29980.3a0000 0004 1936 7830Department of Biochemistry, University of Otago, Dunedin, New Zealand
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6
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Tessadori F, Duran K, Knapp K, Fellner M, Smithson S, Beleza Meireles A, Elting MW, Waisfisz Q, O’Donnell-Luria A, Nowak C, Douglas J, Ronan A, Brunet T, Kotzaeridou U, Svihovec S, Saenz MS, Thiffault I, Del Viso F, Devine P, Rego S, Tenney J, van Haeringen A, Ruivenkamp CA, Koene S, Robertson SP, Deshpande C, Pfundt R, Verbeek N, van de Kamp JM, Weiss JM, Ruiz A, Gabau E, Banne E, Pepler A, Bottani A, Laurent S, Guipponi M, Bijlsma E, Bruel AL, Sorlin A, Willis M, Powis Z, Smol T, Vincent-Delorme C, Baralle D, Colin E, Revencu N, Calpena E, Wilkie AO, Chopra M, Cormier-Daire V, Keren B, Afenjar A, Niceta M, Terracciano A, Specchio N, Tartaglia M, Rio M, Barcia G, Rondeau S, Colson C, Bakkers J, Mace PD, Bicknell LS, van Haaften G, van Haaften G. Recurrent de novo missense variants across multiple histone H4 genes underlie a neurodevelopmental syndrome. Am J Hum Genet 2022; 109:750-758. [PMID: 35202563 PMCID: PMC9069069 DOI: 10.1016/j.ajhg.2022.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/24/2021] [Accepted: 02/03/2022] [Indexed: 12/12/2022] Open
Abstract
Chromatin is essentially an array of nucleosomes, each of which consists of the DNA double-stranded fiber wrapped around a histone octamer. This organization supports cellular processes such as DNA replication, DNA transcription, and DNA repair in all eukaryotes. Human histone H4 is encoded by fourteen canonical histone H4 genes, all differing at the nucleotide level but encoding an invariant protein. Here, we present a cohort of 29 subjects with de novo missense variants in six H4 genes (H4C3, H4C4, H4C5, H4C6, H4C9, and H4C11) identified by whole-exome sequencing and matchmaking. All individuals present with neurodevelopmental features of intellectual disability and motor and/or gross developmental delay, while non-neurological features are more variable. Ten amino acids are affected, six recurrently, and are all located within the H4 core or C-terminal tail. These variants cluster to specific regions of the core H4 globular domain, where protein-protein interactions occur with either other histone subunits or histone chaperones. Functional consequences of the identified variants were evaluated in zebrafish embryos, which displayed abnormal general development, defective head organs, and reduced body axis length, providing compelling evidence for the causality of the reported disorder(s). While multiple developmental syndromes have been linked to chromatin-associated factors, missense-bearing histone variants (e.g., H3 oncohistones) are only recently emerging as a major cause of pathogenicity. Our findings establish a broader involvement of H4 variants in developmental syndromes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gijs van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 Utrecht, the Netherlands.
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7
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Shelling AN, Bicknell LS, Bohlander SS, Cox MP, Filoche SK, Fraser HG, Gamet K, Lacaze P, Murphy R, Snell RG, Sporle A, Te Aika B, Purcell RV, Tiller JM. Genomic discrimination in New Zealand health and life insurance. AGenDA: Against Genomic Discrimination in Aotearoa. N Z Med J 2022; 135:7-12. [PMID: 35728166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Andrew N Shelling
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, University of Auckland, Auckland
| | | | - Stefan S Bohlander
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North
| | - Sara K Filoche
- Department of Obstetrics, Gynaecology and Women's Health, University of Otago Wellington, Wellington
| | | | | | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Rinki Murphy
- Department of Medicine, School of Medicine, University of Auckland, Auckland
| | - Russell G Snell
- Centre for Brain Research and School of Biological Sciences, University of Auckland, Auckland
| | - Andrew Sporle
- Department of Statistics, University of Auckland, Auckland
| | - Ben Te Aika
- Genomics Aotearoa, University of Otago, Dunedin
| | | | - Jane M Tiller
- School of Public Health and Preventive Medicine, Monash University, Faculty of Medicine, Nursing and Health Sciences, Melbourne, Australia
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8
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Knapp KM, Jenkins DE, Sullivan R, Harms FL, von Elsner L, Ockeloen CW, de Munnik S, Bongers EMHF, Murray J, Pachter N, Denecke J, Kutsche K, Bicknell LS. MCM complex members MCM3 and MCM7 are associated with a phenotypic spectrum from Meier-Gorlin syndrome to lipodystrophy and adrenal insufficiency. Eur J Hum Genet 2021; 29:1110-1120. [PMID: 33654309 PMCID: PMC8298597 DOI: 10.1038/s41431-021-00839-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 10/21/2020] [Revised: 02/06/2021] [Accepted: 02/17/2021] [Indexed: 12/30/2022] Open
Abstract
The MCM2-7 helicase is a heterohexameric complex with essential roles as part of both the pre-replication and pre-initiation complexes in the early stages of DNA replication. Meier-Gorlin syndrome, a rare primordial dwarfism, is strongly associated with disruption to the pre-replication complex, including a single case described with variants in MCM5. Conversely, a biallelic pathogenic variant in MCM4 underlies immune deficiency with growth retardation, features also seen in individuals with pathogenic variants in other pre-initiation complex encoding genes such as GINS1, MCM10, and POLE. Through exome and chromium genome sequencing, supported by functional studies, we identify biallelic pathogenic variants in MCM7 and a strong candidate biallelic pathogenic variant in MCM3. We confirm variants in MCM7 are deleterious and through interfering with MCM complex formation, impact efficiency of S phase progression. The associated phenotypes are striking; one patient has typical Meier-Gorlin syndrome, whereas the second case has a multi-system disorder with neonatal progeroid appearance, lipodystrophy and adrenal insufficiency. We provide further insight into the developmental complexity of disrupted MCM function, highlighted by two patients with a similar variant profile in MCM7 but disparate clinical features. Our results build on other genetic findings linked to disruption of the pre-replication and pre-initiation complexes, and the replisome, and expand the complex clinical genetics landscape emerging due to disruption of DNA replication.
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Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Danielle E Jenkins
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Rosie Sullivan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leonie von Elsner
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Charlotte W Ockeloen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sonja de Munnik
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ernie M H F Bongers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jennie Murray
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- South East Scotland Clinical Genetics Service, NHS Lothian, Western General Hospital, Edinburgh, UK
| | - Nicholas Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, Australia
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
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9
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Blakes AJM, Gaul E, Lam W, Shannon N, Knapp KM, Bicknell LS, Jackson MR, Wade EM, Robertson S, White SM, Heller R, Chase A, Baralle D, Douglas AGL. Pathogenic variants causing ABL1 malformation syndrome cluster in a myristoyl-binding pocket and increase tyrosine kinase activity. Eur J Hum Genet 2021; 29:593-603. [PMID: 33223528 PMCID: PMC8115115 DOI: 10.1038/s41431-020-00766-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/19/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 11/24/2022] Open
Abstract
ABL1 is a proto-oncogene encoding a nonreceptor tyrosine kinase, best known in the somatic BCR-ABL fusion gene associated with chronic myeloid leukaemia. Recently, germline missense variants in ABL1 have been found to cause an autosomal dominant developmental syndrome with congenital heart disease, skeletal malformations and characteristic facies. Here, we describe a series of six new unrelated individuals with heterozygous missense variants in ABL1 (including four novel variants) identified via whole exome sequencing. All the affected individuals in this series recapitulate the phenotype of the ABL1 developmental syndrome and additionally we affirm that hearing impairment is a common feature of the condition. Four of the variants cluster in the myristoyl-binding pocket of ABL1, a region critical for auto-inhibitory regulation of the kinase domain. Bio-informatic analysis of transcript-wide conservation and germline/somatic variation reveals that this pocket region is subject to high missense constraint and evolutionary conservation. Functional work to investigate ABL1 kinase activity in vitro by transient transfection of HEK293T cells with variant ABL1 plasmid constructs revealed increased phosphorylation of ABL1-specific substrates compared to wild-type. The increased tyrosine kinase activity was suppressed by imatinib treatment. This case series of six new patients with germline heterozygous ABL1 missense variants further delineates the phenotypic spectrum of this condition and recognises microcephaly as a common finding. Our analysis supports an ABL1 gain-of-function mechanism due to loss of auto-inhibition, and demonstrates the potential for pharmacological inhibition using imatinib.
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Affiliation(s)
- Alexander J M Blakes
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Emily Gaul
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wayne Lam
- South East of Scotland Clinical Genetics Service, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Nora Shannon
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Hucknall Road, Nottingham, UK
| | - Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Meremaihi R Jackson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Emma M Wade
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Stephen Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Raoul Heller
- Genetic Health Service NZ - Northern Hub, Auckland District Health Board, Auckland City Hospital, Auckland, New Zealand
| | - Andrew Chase
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Diana Baralle
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew G L Douglas
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.
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10
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Knapp KM, Fellows B, Aggarwal S, Dalal A, Bicknell LS. A synonymous variant in a non-canonical exon of CDC45 disrupts splicing in two affected sibs with Meier-Gorlin syndrome with craniosynostosis. Eur J Med Genet 2021; 64:104182. [PMID: 33639314 DOI: 10.1016/j.ejmg.2021.104182] [Citation(s) in RCA: 7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 12/10/2020] [Accepted: 01/23/2021] [Indexed: 11/30/2022]
Abstract
Disruption of the initiation of DNA replication is significantly associated with Meier-Gorlin syndrome (MGORS), an autosomal recessive condition of reduced growth, microtia and patellar a/hypoplasia. Biallelic mutations in CDC45, a member of the pre-initiation complex in DNA replication, cause a spectrum of phenotypes ranging from MGORS with craniosynostosis, through to isolated short stature and craniosynostosis. Here we report two affected sibs with MGORS and craniosynostosis, with biallelic variants in CDC45 identified by 10X Chromium whole genome sequencing. One variant is a frameshift mutation, predicted to be pathogenic, and is inherited in trans with a synonymous variant in a non-canonical exon (exon 7) of CDC45. An in vitro splicing assay showed that while the canonical CDC45 exon 6-exon 8 transcript (with skipping of exon 7; numbering as per NM001178010.2) remained as the predominant transcript, the variant allele induced the use of novel splice acceptor sites in intron 6, all of which produced transcripts harbouring premature stop codons. This perturbation of canonical splicing provides evidence that this synonymous variant is indeed a deleterious alteration in this family. This report adds to the initial patient cohort in which several synonymous variants were also described, further highlighting the contribution of this variant type in CDC45. It also reiterates the true potential pathogenicity of synonymous variants, which is a mutation type that is commonly ignored in variant prioritization strategies.
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Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Bridget Fellows
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Ashwin Dalal
- Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India; Department of Medical Genetics, Kasturba Medical College, Manipal, Karnataka, India
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
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11
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Knapp KM, Murray J, Temple IK, Bicknell LS. Successful pregnancies in an adult with Meier-Gorlin syndrome harboring biallelic CDT1 variants. Am J Med Genet A 2020; 185:871-876. [PMID: 33338304 DOI: 10.1002/ajmg.a.62016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/21/2020] [Revised: 11/18/2020] [Accepted: 11/27/2020] [Indexed: 01/16/2023]
Abstract
Meier-Gorlin syndrome is an autosomal recessively inherited disorder of growth retardation, accompanied by microtia and patellae a/hypoplasia and characteristic facies. Pathogenic variants in genes associated with the initiation of DNA replication underlie the condition, with biallelic variants in CDT1 the most common cause. Using 10× Chromium genome sequencing, we report CDT1 variants in an adult female, with an inframe amino acid deletion inherited in trans with a deep intronic variant which likely serves as the branchpoint site in Intron 8. Splicing defects arising from this variant were confirmed through in vitro analysis. At 49 years, she represents the oldest patient with a molecular diagnosis described in the literature and is the first reported patient with Meier-Gorlin syndrome to have carried a successful pregnancy to term. Both of her pregnancies were complicated by postpartum hemorrhage and upon subsequent necessary hysterectomy, revealed uterine abnormalities. There is scant knowledge on reproductive ability and success in patients with Meier-Gorlin syndrome. Successful pregnancies among other clinically recognizable forms of primordial dwarfism have also not been described previously. This case is therefore of clinical interest for many forms of inherited growth retardation, and will assist in providing more information and clinical guidance for females of reproductive age.
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Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Jennie Murray
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,South East Scotland Clinical Genetics Service, NHS Lothian, Western General Hospital, Edinburgh, UK
| | - I Karen Temple
- Human Development and Health, Faculty of Medicine University of Southampton, Southampton, UK.,Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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12
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Knapp KM, Luu R, Baerenfaenger M, Zijlstra F, Wessels HJCT, Jenkins D, Lefeber DJ, Neas K, Bicknell LS. Biallelic variants in SLC35C1 as a cause of isolated short stature with intellectual disability. J Hum Genet 2020; 65:743-750. [PMID: 32313197 DOI: 10.1038/s10038-020-0764-4] [Citation(s) in RCA: 11] [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: 12/12/2019] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 11/09/2022]
Abstract
Variants in SLC35C1 underlie leucocyte adhesion deficiency (LADII) or congenital disorder of glycosylation type 2c (CDGIIc), an autosomal recessive disorder of fucosylation. This immunodeficiency syndrome is generally characterized by severe recurrent infections, Bombay blood group, reduced growth and intellectual disability (ID). Features are all caused by an inability to generate key fucosylated molecules due to a defective transport of GDP-fucose into the Golgi. Here we report the use of exome sequencing to identify biallelic variants in SLC35C1 (c.501_503delCTT, p.(Phe168del) and c.891T > G, p.(Asn297Lys)) in an individual with short stature and ID. Retrospective clinical examination based on the genetic findings revealed increased otitis media as the only immunological feature present in this child. Biochemical analysis of patient serum identified a clear but mild decrease in protein fucosylation. Modelling all described missense mutations on a SLC35C1 protein model showed pathogenic substitutions localise to close to the dimer interface, providing insight into the possible pathophysiology of non-synonymous causative variants identified in patients. Our evidence confirms this is the second family presenting with only a subset of features and broadens the clinical presentation of this syndrome. Of note, both families segregated a common allele (p.Phe168del), suggesting there could be an associated genotype-phenotype relationship for specific variants. Based on two out of 14 reported families not presenting with the characteristic features of SLC35C1-CDG, we suggest there is clinical utility in considering this gene in patients with short stature and ID.
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Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Rebecca Luu
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Melissa Baerenfaenger
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Fokje Zijlstra
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hans J C T Wessels
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Danielle Jenkins
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, Netherlands.,Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Katherine Neas
- Genetic Health Services New Zealand, Wellington, New Zealand
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
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13
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Knapp KM, Sullivan R, Murray J, Gimenez G, Arn P, D'Souza P, Gezdirici A, Wilson WG, Jackson AP, Ferreira C, Bicknell LS. Linked-read genome sequencing identifies biallelic pathogenic variants in DONSON as a novel cause of Meier-Gorlin syndrome. J Med Genet 2019; 57:195-202. [PMID: 31784481 PMCID: PMC7042968 DOI: 10.1136/jmedgenet-2019-106396] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 06/26/2019] [Revised: 09/16/2019] [Accepted: 09/20/2019] [Indexed: 11/20/2022]
Abstract
Material Linked-read whole genome sequencing (WGS) presents a new opportunity for cost-efficient singleton sequencing in place of traditional trio-based designs while generating informative-phased variants, effective for recessive disorders when parental DNA is unavailable. Methods We have applied linked-read WGS to identify novel causes of Meier-Gorlin syndrome (MGORS), a condition recognised by short stature, microtia and patella hypo/aplasia. There are eight genes associated with MGORS to date, all encoding essential components involved in establishing and initiating DNA replication. Results Our successful phasing of linked-read data led to the identification of biallelic rare variants in four individuals (24% of our cohort) in DONSON, a recently established DNA replication fork surveillance factor. The variants include five novel missense and one deep intronic variant. All were demonstrated to be deleterious to function; the missense variants all disrupted the nuclear localisation of DONSON, while the intronic variant created a novel splice site that generated an out-of-frame transcript with no residual canonical transcript produced. Conclusion Variants in DONSON have previously been associated with extreme microcephaly, short stature and limb anomalies and perinatal lethal microcephaly-micromelia syndrome. Our novel genetic findings extend the complicated spectrum of phenotypes associated with DONSON variants and promote novel hypotheses for the role of DONSON in DNA replication. While our findings reiterate that MGORS is a disorder of DNA replication, the pathophysiology is obviously complex. This successful identification of a novel disease gene for MGORS highlights the utility of linked-read WGS as a successful technology to be considered in the genetic studies of recessive conditions.
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Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Rosie Sullivan
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Jennie Murray
- MRC HGU, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | - Gregory Gimenez
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Pamela Arn
- Nemours Children's Clinic, Jacksonville, Florida, USA
| | - Precilla D'Souza
- Office of the Clinical Director, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - William G Wilson
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Andrew P Jackson
- MRC HGU, Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | - Carlos Ferreira
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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14
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Tarnauskaitė Ž, Bicknell LS, Marsh JA, Murray JE, Parry DA, Logan CV, Bober MB, de Silva DC, Duker AL, Sillence D, Wise C, Jackson AP, Murina O, Reijns MAM. Biallelic variants in DNA2 cause microcephalic primordial dwarfism. Hum Mutat 2019; 40:1063-1070. [PMID: 31045292 PMCID: PMC6773220 DOI: 10.1002/humu.23776] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 12/03/2018] [Revised: 03/15/2019] [Accepted: 04/28/2019] [Indexed: 11/11/2022]
Abstract
Microcephalic primordial dwarfism (MPD) is a group of rare single-gene disorders characterized by the extreme reduction in brain and body size from early development onwards. Proteins encoded by MPD-associated genes play important roles in fundamental cellular processes, notably genome replication and repair. Here we report the identification of four MPD individuals with biallelic variants in DNA2, which encodes an adenosine triphosphate (ATP)-dependent helicase/nuclease involved in DNA replication and repair. We demonstrate that the two intronic variants (c.1764-38_1764-37ins(53) and c.74+4A>C) found in these individuals substantially impair DNA2 transcript splicing. Additionally, we identify a missense variant (c.1963A>G), affecting a residue of the ATP-dependent helicase domain that is highly conserved between humans and yeast, with the resulting substitution (p.Thr655Ala) predicted to directly impact ATP/ADP (adenosine diphosphate) binding by DNA2. Our findings support the pathogenicity of these variants as biallelic hypomorphic mutations, establishing DNA2 as an MPD disease gene.
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Affiliation(s)
- Žygimantė Tarnauskaitė
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Louise S. Bicknell
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Joseph A. Marsh
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Jennie E. Murray
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - David A. Parry
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Clare V. Logan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Michael B. Bober
- Division of Genetics, Department of PediatricsNemours/Alfred I. duPont Hospital for ChildrenWilmingtonDelaware
| | - Deepthi C. de Silva
- Department of Physiology, Faculty of MedicineUniversity of KelaniyaColomboSri Lanka
| | - Angela L. Duker
- Division of Genetics, Department of PediatricsNemours/Alfred I. duPont Hospital for ChildrenWilmingtonDelaware
| | - David Sillence
- Discipline of Genomic Medicine, Faculty of Medicine and HealthUniversity of SydneySydneyAustralia
- Western Sydney Genetics ProgramSydney Children's Hospitals NetworkWestmeadAustralia
| | - Carol Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal ResearchTexas Scottish, Rite Hospital for ChildrenDallasTexas
- McDermott Center for Human Growth and DevelopmentUniversity of Texas, Southwestern Medical CenterDallasTexas
- Department of Orthopaedic SurgeryUniversity of Texas Southwestern Medical CenterDallasTexas
- Department of PediatricsUniversity of Texas Southwestern Medical CenterDallasTexas
| | - Andrew P. Jackson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Olga Murina
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Martin A. M. Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
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15
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Knapp KM, Poke G, Jenkins D, Truter W, Bicknell LS. Expanding the phenotypic spectrum associated with DPF2: A new case report. Am J Med Genet A 2019; 179:1637-1641. [PMID: 31207137 DOI: 10.1002/ajmg.a.61262] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 11/29/2018] [Revised: 03/26/2019] [Accepted: 06/01/2019] [Indexed: 11/07/2022]
Abstract
Coffin-Siris syndrome (CSS) is a clinically and genetically heterogeneous developmental disorder, linked to disruption of the BAF chromatin-remodeling complex. Recently, de novo missense and truncating variants have been reported in DPF2 in patients sharing some of the common features of CSS. Here we report a further individual harboring a novel de novo missense DPF2 variant, c.1066T>G, p.Cys356Gly. Structural modeling indicated that the predicted amino acid substitution affects a core residue required for zinc ion coordination and would likely alter the PHD2 domain structure of DPF2. The clinical presentation of Pierre Robin sequence and diaphragmatic hernia did not immediately suggest CSS, with the more common CSS features of hypoplastic toenails and characteristic facial features very subtle. This individual further broadens the phenotypic features of DPF2-related CSS, as well as CSS more generally.
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Affiliation(s)
- Karen M Knapp
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Gemma Poke
- Genetic Health Service New Zealand, Wellington, New Zealand
| | - Danielle Jenkins
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Werner Truter
- Department of Child Health, MidCentral District Health Board, Palmerston North, New Zealand
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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16
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Logan CV, Murray JE, Parry DA, Robertson A, Bellelli R, Tarnauskaitė Ž, Challis R, Cleal L, Borel V, Fluteau A, Santoyo-Lopez J, Aitman T, Barroso I, Basel D, Bicknell LS, Goel H, Hu H, Huff C, Hutchison M, Joyce C, Knox R, Lacroix AE, Langlois S, McCandless S, McCarrier J, Metcalfe KA, Morrissey R, Murphy N, Netchine I, O’Connell SM, Olney AH, Paria N, Rosenfeld JA, Sherlock M, Syverson E, White PC, Wise C, Yu Y, Zacharin M, Banerjee I, Reijns M, Bober MB, Semple RK, Boulton SJ, Rios JJ, Jackson AP, Aitman TJ, Biankin AV, Cooke SL, Humphrey WI, Martin S, Mennie L, Meynert A, Miedzybrodzka Z, Murphy F, Nourse C, Santoyo-Lopez J, Semple CA, Williams N. DNA Polymerase Epsilon Deficiency Causes IMAGe Syndrome with Variable Immunodeficiency. Am J Hum Genet 2018; 103:1038-1044. [PMID: 30503519 PMCID: PMC6288413 DOI: 10.1016/j.ajhg.2018.10.024] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/26/2018] [Indexed: 01/19/2023] Open
Abstract
During genome replication, polymerase epsilon (Pol ε) acts as the major leading-strand DNA polymerase. Here we report the identification of biallelic mutations in POLE, encoding the Pol ε catalytic subunit POLE1, in 15 individuals from 12 families. Phenotypically, these individuals had clinical features closely resembling IMAGe syndrome (intrauterine growth restriction [IUGR], metaphyseal dysplasia, adrenal hypoplasia congenita, and genitourinary anomalies in males), a disorder previously associated with gain-of-function mutations in CDKN1C. POLE1-deficient individuals also exhibited distinctive facial features and variable immune dysfunction with evidence of lymphocyte deficiency. All subjects shared the same intronic variant (c.1686+32C>G) as part of a common haplotype, in combination with different loss-of-function variants in trans. The intronic variant alters splicing, and together the biallelic mutations lead to cellular deficiency of Pol ε and delayed S-phase progression. In summary, we establish POLE as a second gene in which mutations cause IMAGe syndrome. These findings add to a growing list of disorders due to mutations in DNA replication genes that manifest growth restriction alongside adrenal dysfunction and/or immunodeficiency, consolidating these as replisome phenotypes and highlighting a need for future studies to understand the tissue-specific development roles of the encoded proteins.
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17
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Llorens-Agost M, Luessing J, van Beneden A, Eykelenboom J, O’Reilly D, Bicknell LS, Reynolds JJ, van Koegelenberg M, Hurles ME, Brady AF, Jackson AP, Stewart GS, Lowndes NF. Analysis of novel missense ATR mutations reveals new splicing defects underlying Seckel syndrome. Hum Mutat 2018; 39:1847-1853. [PMID: 30199583 PMCID: PMC7615757 DOI: 10.1002/humu.23648] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 08/17/2018] [Accepted: 09/06/2018] [Indexed: 01/01/2023]
Abstract
Ataxia Telangiectasia and Rad3 related (ATR) is one of the main regulators of the DNA damage response. It coordinates cell cycle checkpoint activation, replication fork stability, restart and origin firing to maintain genome integrity. Mutations of the ATR gene have been reported in Seckel patients, who suffer from a rare genetic disease characterized by severe microcephaly and growth retardation. Here, we report the case of a Seckel patient with compound heterozygous mutations in ATR. One allele has an intronic mutation affecting splicing of neighboring exons, the other an exonic missense mutation, producing the variant p.Lys1665Asn, of unknown pathogenicity. We have modeled this novel missense mutation, as well as a previously described missense mutation p.Met1159Ile, and assessed their effect on ATR function. Interestingly, our data indicate that both missense mutations have no direct effect on protein function, but rather result in defective ATR splicing. These results emphasize the importance of splicing mutations in Seckel Syndrome.
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Affiliation(s)
- Marta Llorens-Agost
- Centre for Chromosome Biology, National University of Ireland in Galway, Galway, Ireland
| | - Janna Luessing
- Centre for Chromosome Biology, National University of Ireland in Galway, Galway, Ireland
| | - Amandine van Beneden
- Centre for Chromosome Biology, National University of Ireland in Galway, Galway, Ireland
| | - John Eykelenboom
- Centre for Chromosome Biology, National University of Ireland in Galway, Galway, Ireland
- School of Life Sciences, University of Dundee, Dundee, Scotland
| | - Dawn O’Reilly
- Oxford Stem Cell Institute, University of Oxford, Oxford, UK
| | - Louise S Bicknell
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - John J Reynolds
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Angela F Brady
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, UK
| | - Andrew P Jackson
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburg, Scotland
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Noel F Lowndes
- Centre for Chromosome Biology, National University of Ireland in Galway, Galway, Ireland
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18
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McGlasson S, Rannikmäe K, Bevan S, Logan C, Bicknell LS, Jury A, Jackson AP, Markus HS, Sudlow C, Hunt DPJ. Rare variants of the 3'-5' DNA exonuclease TREX1 in early onset small vessel stroke. Wellcome Open Res 2017; 2:106. [PMID: 29387804 PMCID: PMC5717473 DOI: 10.12688/wellcomeopenres.12631.1] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2017] [Indexed: 11/20/2022] Open
Abstract
Background: Monoallelic and biallelic mutations in the exonuclease TREX1 cause monogenic small vessel diseases (SVD). Given recent evidence for genetic and pathophysiological overlap between monogenic and polygenic forms of SVD, evaluation of TREX1 in small vessel stroke is warranted. Methods: We sequenced the TREX1 gene in an exploratory cohort of patients with lacunar stroke (Edinburgh Stroke Study, n=290 lacunar stroke cases). We subsequently performed a fully blinded case-control study of early onset MRI-confirmed small vessel stroke within the UK Young Lacunar Stroke Resource (990 cases, 939 controls). Results: No patients with canonical disease-causing mutations of TREX1 were identified in cases or controls. Analysis of an exploratory cohort identified a potential association between rare variants of TREX1 and patients with lacunar stroke. However, subsequent controlled and blinded evaluation of TREX1 in a larger and MRI-confirmed patient cohort, the UK Young Lacunar Stroke Resource, identified heterozygous rare variants in 2.1% of cases and 2.3% of controls. No association was observed with stroke risk (odds ratio = 0.90; 95% confidence interval, 0.49-1.65 p=0.74). Similarly no association was seen with rare TREX1 variants with predicted deleterious effects on enzyme function (odds ratio = 1.05; 95% confidence interval, 0.43-2.61 p=0.91). Conclusions: No patients with early-onset lacunar stroke had genetic evidence of a TREX1-associated monogenic microangiopathy. These results show no evidence of association between rare variants of TREX1 and early onset lacunar stroke. This includes rare variants that significantly affect protein and enzyme function. Routine sequencing of the TREX1 gene in patients with early onset lacunar stroke is therefore unlikely to be of diagnostic utility, in the absence of syndromic features or family history.
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Affiliation(s)
- Sarah McGlasson
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Kristiina Rannikmäe
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Steven Bevan
- Stroke Research Group, Department of Clinical Neurosciences, Cambridge University, Cambridge, CB2 2PY , UK.,Joseph Banks Laboratories, University of Lincoln, Lincoln, LN6 7DL, UK
| | - Clare Logan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Louise S Bicknell
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Alexa Jury
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | | | - Andrew P Jackson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Hugh S Markus
- Stroke Research Group, Department of Clinical Neurosciences, Cambridge University, Cambridge, CB2 2PY , UK
| | - Cathie Sudlow
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David P J Hunt
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
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19
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Martin CA, Murray JE, Carroll P, Leitch A, MacKenzie KJ, Halachev M, Fetit AE, Keith C, Bicknell LS, Fluteau A, Gautier P, Hall EA, Joss S, Soares G, Silva J, Bober MB, Duker A, Wise CA, Quigley AJ, Phadke SR, Wood AJ, Vagnarelli P, Jackson AP. Corrigendum: Mutations in genes encoding condensins cause microcephaly through decatenation failure at mitosis. Genes Dev 2017; 31:953. [DOI: 10.1101/gad.300871.117] [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: 11/24/2022]
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20
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Martin CA, Murray JE, Carroll P, Leitch A, Mackenzie KJ, Halachev M, Fetit AE, Keith C, Bicknell LS, Fluteau A, Gautier P, Hall EA, Joss S, Soares G, Silva J, Bober MB, Duker A, Wise CA, Quigley AJ, Phadke SR, Wood AJ, Vagnarelli P, Jackson AP. Mutations in genes encoding condensin complex proteins cause microcephaly through decatenation failure at mitosis. Genes Dev 2016; 30:2158-2172. [PMID: 27737959 PMCID: PMC5088565 DOI: 10.1101/gad.286351.116] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [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: 06/29/2016] [Accepted: 09/09/2016] [Indexed: 11/24/2022]
Abstract
Martin et al. report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of condensin complexes, cause microcephaly. Frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis are the consequence of failed sister chromatid disentanglement during chromosome compaction. Compaction of chromosomes is essential for accurate segregation of the genome during mitosis. In vertebrates, two condensin complexes ensure timely chromosome condensation, sister chromatid disentanglement, and maintenance of mitotic chromosome structure. Here, we report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of these complexes, cause microcephaly. In addition, hypomorphic Ncaph2 mice have significantly reduced brain size, with frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis. Such DNA bridges also arise in condensin-deficient patient cells, where they are the consequence of failed sister chromatid disentanglement during chromosome compaction. This results in chromosome segregation errors, leading to micronucleus formation and increased aneuploidy in daughter cells. These findings establish “condensinopathies” as microcephalic disorders, with decatenation failure as an additional disease mechanism for microcephaly, implicating mitotic chromosome condensation as a key process ensuring mammalian cerebral cortex size.
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Affiliation(s)
- Carol-Anne Martin
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Jennie E Murray
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Paula Carroll
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Andrea Leitch
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Karen J Mackenzie
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Mihail Halachev
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Ahmed E Fetit
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Charlotte Keith
- South East Scotland Cytogenetics Service, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Louise S Bicknell
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.,Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Adeline Fluteau
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Emma A Hall
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Shelagh Joss
- West of Scotland Genetic Service, Southern General Hospital, Glasgow G51 4TF, United Kingdom
| | - Gabriela Soares
- Centro de Genética Médica Doutor Jacinto Magalhães, Centro Hospitalar do Porto, 4099-028 Porto, Portugal
| | - João Silva
- Instituto de Biologia Molecular e Celular (IBMC), 4150 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Michael B Bober
- Division of Genetics, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Angela Duker
- Division of Genetics, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,Department of Orthopedic Surgery, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,Department of Pediatrics, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas 75350, USA
| | - Alan J Quigley
- Department of Radiology, Royal Hospital for Sick Children, Edinburgh EH9 1LF, United Kingdom
| | - Shubha R Phadke
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh 226014, India
| | | | - Andrew J Wood
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Paola Vagnarelli
- Biosciences, Research Institute for Health and Environment, Brunel University, London UB8 3PH, United Kingdom
| | - Andrew P Jackson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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21
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Fenwick AL, Kliszczak M, Cooper F, Murray J, Sanchez-Pulido L, Twigg SRF, Goriely A, McGowan SJ, Miller KA, Taylor IB, Logan C, Bozdogan S, Danda S, Dixon J, Elsayed SM, Elsobky E, Gardham A, Hoffer MJV, Koopmans M, McDonald-McGinn DM, Santen GWE, Savarirayan R, de Silva D, Vanakker O, Wall SA, Wilson LC, Yuregir OO, Zackai EH, Ponting CP, Jackson AP, Wilkie AOM, Niedzwiedz W, Bicknell LS. Mutations in CDC45, Encoding an Essential Component of the Pre-initiation Complex, Cause Meier-Gorlin Syndrome and Craniosynostosis. Am J Hum Genet 2016; 99:125-38. [PMID: 27374770 PMCID: PMC5005452 DOI: 10.1016/j.ajhg.2016.05.019] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [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: 03/30/2016] [Accepted: 05/09/2016] [Indexed: 11/19/2022] Open
Abstract
DNA replication precisely duplicates the genome to ensure stable inheritance of genetic information. Impaired licensing of origins of replication during the G1 phase of the cell cycle has been implicated in Meier-Gorlin syndrome (MGS), a disorder defined by the triad of short stature, microtia, and a/hypoplastic patellae. Biallelic partial loss-of-function mutations in multiple components of the pre-replication complex (preRC; ORC1, ORC4, ORC6, CDT1, or CDC6) as well as de novo stabilizing mutations in the licensing inhibitor, GMNN, cause MGS. Here we report the identification of mutations in CDC45 in 15 affected individuals from 12 families with MGS and/or craniosynostosis. CDC45 encodes a component of both the pre-initiation (preIC) and CMG helicase complexes, required for initiation of DNA replication origin firing and ongoing DNA synthesis during S-phase itself, respectively, and hence is functionally distinct from previously identified MGS-associated genes. The phenotypes of affected individuals range from syndromic coronal craniosynostosis to severe growth restriction, fulfilling diagnostic criteria for Meier-Gorlin syndrome. All mutations identified were biallelic and included synonymous mutations altering splicing of physiological CDC45 transcripts, as well as amino acid substitutions expected to result in partial loss of function. Functionally, mutations reduce levels of full-length transcripts and protein in subject cells, consistent with partial loss of CDC45 function and a predicted limited rate of DNA replication and cell proliferation. Our findings therefore implicate the preIC as an additional protein complex involved in the etiology of MGS and connect the core cellular machinery of genome replication with growth, chondrogenesis, and cranial suture homeostasis.
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Affiliation(s)
- Aimee L Fenwick
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Maciej Kliszczak
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Fay Cooper
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jennie Murray
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Luis Sanchez-Pulido
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Anne Goriely
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Simon J McGowan
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Kerry A Miller
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Indira B Taylor
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Clare Logan
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sevcan Bozdogan
- Department of Medical Genetics, Mersin University, Mersin, 33343 Cukurova, Turkey
| | - Sumita Danda
- Department of Clinical Genetics, Christian Medical College and Hospital, Vellore, Tamil Nadu 632004, India
| | - Joanne Dixon
- Genetic Health Service NZ-South Island Hub, Christchurch Hospital, Christchurch, Canterbury 8140, New Zealand
| | - Solaf M Elsayed
- Children's Hospital, Ain Shams University, Cairo 11566, Egypt
| | - Ezzat Elsobky
- Children's Hospital, Ain Shams University, Cairo 11566, Egypt
| | - Alice Gardham
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Mariette J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Marije Koopmans
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Donna M McDonald-McGinn
- Clinical Genetics, The Children's Hospital of Philadelphia, 34th & Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Deepthi de Silva
- Department of Physiology, Faculty of Medicine, University of Kelaniya, Ragama, Gampaha GQ 11010, Sri Lanka
| | - Olivier Vanakker
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Steven A Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Louise C Wilson
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Ozge Ozalp Yuregir
- Genetic Diagnosis Center, Adana Numune Training and Research Hospital, Cukurova, Adana, 01170, Turkey
| | - Elaine H Zackai
- Clinical Genetics, The Children's Hospital of Philadelphia, 34th & Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Chris P Ponting
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew P Jackson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Wojciech Niedzwiedz
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Louise S Bicknell
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh EH4 2XU, UK; Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, Otago 9016, New Zealand.
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22
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Harley ME, Murina O, Leitch A, Higgs MR, Bicknell LS, Yigit G, Blackford AN, Zlatanou A, Mackenzie KJ, Reddy K, Halachev M, McGlasson S, Reijns MAM, Fluteau A, Martin CA, Sabbioneda S, Elcioglu NH, Altmüller J, Thiele H, Greenhalgh L, Chessa L, Maghnie M, Salim M, Bober MB, Nürnberg P, Jackson SP, Hurles ME, Wollnik B, Stewart GS, Jackson AP. TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism. Nat Genet 2016; 48:36-43. [PMID: 26595769 PMCID: PMC4697364 DOI: 10.1038/ng.3451] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/26/2015] [Indexed: 12/11/2022]
Abstract
DNA lesions encountered by replicative polymerases threaten genome stability and cell cycle progression. Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism. We establish that TRAIP relocalizes to sites of DNA damage, where it is required for optimal phosphorylation of H2AX and RPA2 during S-phase in response to ultraviolet (UV) irradiation, as well as fork progression through UV-induced DNA lesions. TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes. Human genetics thus identifies TRAIP as a component of the DNA damage response to replication-blocking DNA lesions.
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Affiliation(s)
- Margaret E Harley
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Olga Murina
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrea Leitch
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Louise S Bicknell
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Gökhan Yigit
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | | | - Anastasia Zlatanou
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Karen J Mackenzie
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Kaalak Reddy
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Mihail Halachev
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah McGlasson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Martin A M Reijns
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Adeline Fluteau
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Carol-Anne Martin
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | | | - Nursel H Elcioglu
- Department of Pediatric Genetics, Marmara University Pendik Hospital, Istanbul, Turkey
| | - Janine Altmüller
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Lynn Greenhalgh
- Cheshire and Merseyside Clinical Genetics Service, Liverpool Women's Hospital, Liverpool, L12 2AP, UK
| | - Luciana Chessa
- Department of Clinical and Molecular Medicine, University Sapienza, A.O.S. Andrea, I-00189 Roma, Italy
| | - Mohamad Maghnie
- Department of Pediatrics, IRCCS, Giannina Gaslini, University of Genova, 16147 Genova, Italy
| | - Mahmoud Salim
- Department of Pediatric Genetics, Marmara University Pendik Hospital, Istanbul, Turkey
| | - Michael B Bober
- Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Stephen P Jackson
- The Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | | | - Bernd Wollnik
- Institute of Human Genetics, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
- Institute of Human Genetics, University Medical Centre Göttingen, 37073 Göttingen, Germany
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Andrew P Jackson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK
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23
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Murray JE, Bicknell LS, Yigit G, Duker AL, van Kogelenberg M, Haghayegh S, Wieczorek D, Kayserili H, Albert MH, Wise CA, Brandon J, Kleefstra T, Warris A, van der Flier M, Bamforth JS, Doonanco K, Adès L, Ma A, Field M, Johnson D, Shackley F, Firth H, Woods CG, Nürnberg P, Gatti RA, Hurles M, Bober MB, Wollnik B, Jackson AP. Extreme growth failure is a common presentation of ligase IV deficiency. Hum Mutat 2013; 35:76-85. [PMID: 24123394 PMCID: PMC3995017 DOI: 10.1002/humu.22461] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [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: 03/25/2013] [Accepted: 09/24/2013] [Indexed: 12/20/2022]
Abstract
Ligase IV syndrome is a rare differential diagnosis for Nijmegen breakage syndrome owing to a shared predisposition to lympho-reticular malignancies, significant microcephaly, and radiation hypersensitivity. Only 16 cases with mutations in LIG4 have been described to date with phenotypes varying from malignancy in developmentally normal individuals, to severe combined immunodeficiency and early mortality. Here, we report the identification of biallelic truncating LIG4 mutations in 11 patients with microcephalic primordial dwarfism presenting with restricted prenatal growth and extreme postnatal global growth failure (average OFC -10.1 s.d., height -5.1 s.d.). Subsequently, most patients developed thrombocytopenia and leucopenia later in childhood and many were found to have previously unrecognized immunodeficiency following molecular diagnosis. None have yet developed malignancy, though all patients tested had cellular radiosensitivity. A genotype-phenotype correlation was also noted with position of truncating mutations corresponding to disease severity. This work extends the phenotypic spectrum associated with LIG4 mutations, establishing that extreme growth retardation with microcephaly is a common presentation of bilallelic truncating mutations. Such growth failure is therefore sufficient to consider a diagnosis of LIG4 deficiency and early recognition of such cases is important as bone marrow failure, immunodeficiency, and sometimes malignancy are long term sequelae of this disorder.
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Affiliation(s)
- Jennie E Murray
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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24
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Lancaster MA, Renner M, Martin CA, Wenzel D, Bicknell LS, Hurles ME, Homfray T, Penninger JM, Jackson AP, Knoblich JA. Cerebral organoids model human brain development and microcephaly. Nature 2013; 501:373-9. [PMID: 23995685 PMCID: PMC3817409 DOI: 10.1038/nature12517] [Citation(s) in RCA: 3038] [Impact Index Per Article: 276.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 08/02/2013] [Indexed: 02/06/2023]
Abstract
The complexity of the human brain has made it difficult to study many brain disorders in model organisms, highlighting the need for an in vitro model of human brain development. Here we have developed a human pluripotent stem cell-derived three-dimensional organoid culture system, termed cerebral organoids, that develop various discrete, although interdependent, brain regions. These include a cerebral cortex containing progenitor populations that organize and produce mature cortical neuron subtypes. Furthermore, cerebral organoids are shown to recapitulate features of human cortical development, namely characteristic progenitor zone organization with abundant outer radial glial stem cells. Finally, we use RNA interference and patient-specific induced pluripotent stem cells to model microcephaly, a disorder that has been difficult to recapitulate in mice. We demonstrate premature neuronal differentiation in patient organoids, a defect that could help to explain the disease phenotype. Together, these data show that three-dimensional organoids can recapitulate development and disease even in this most complex human tissue.
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Affiliation(s)
- Madeline A Lancaster
- Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna 1030, Austria
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25
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Uzak AS, Jackson AP, Murray JE, Bicknell LS, Dundar M. A de novo SRCAP mutation associated with Floating-Harbor syndrome. Curr Opin Biotechnol 2013. [DOI: 10.1016/j.copbio.2013.05.302] [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: 11/25/2022]
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26
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Meynert AM, Bicknell LS, Hurles ME, Jackson AP, Taylor MS. Quantifying single nucleotide variant detection sensitivity in exome sequencing. BMC Bioinformatics 2013; 14:195. [PMID: 23773188 PMCID: PMC3695811 DOI: 10.1186/1471-2105-14-195] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [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: 01/15/2013] [Accepted: 06/10/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The targeted capture and sequencing of genomic regions has rapidly demonstrated its utility in genetic studies. Inherent in this technology is considerable heterogeneity of target coverage and this is expected to systematically impact our sensitivity to detect genuine polymorphisms. To fully interpret the polymorphisms identified in a genetic study it is often essential to both detect polymorphisms and to understand where and with what probability real polymorphisms may have been missed. RESULTS Using down-sampling of 30 deeply sequenced exomes and a set of gold-standard single nucleotide variant (SNV) genotype calls for each sample, we developed an empirical model relating the read depth at a polymorphic site to the probability of calling the correct genotype at that site. We find that measured sensitivity in SNV detection is substantially worse than that predicted from the naive expectation of sampling from a binomial. This calibrated model allows us to produce single nucleotide resolution SNV sensitivity estimates which can be merged to give summary sensitivity measures for any arbitrary partition of the target sequences (nucleotide, exon, gene, pathway, exome). These metrics are directly comparable between platforms and can be combined between samples to give "power estimates" for an entire study. We estimate a local read depth of 13X is required to detect the alleles and genotype of a heterozygous SNV 95% of the time, but only 3X for a homozygous SNV. At a mean on-target read depth of 20X, commonly used for rare disease exome sequencing studies, we predict 5-15% of heterozygous and 1-4% of homozygous SNVs in the targeted regions will be missed. CONCLUSIONS Non-reference alleles in the heterozygote state have a high chance of being missed when commonly applied read coverage thresholds are used despite the widely held assumption that there is good polymorphism detection at these coverage levels. Such alleles are likely to be of functional importance in population based studies of rare diseases, somatic mutations in cancer and explaining the "missing heritability" of quantitative traits.
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Affiliation(s)
- Alison M Meynert
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK.
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27
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de Munnik SA, Otten BJ, Schoots J, Bicknell LS, Aftimos S, Al-Aama JY, van Bever Y, Bober MB, Borm GF, Clayton-Smith J, Deal CL, Edrees AY, Feingold M, Fryer A, van Hagen JM, Hennekam RC, Jansweijer MCE, Johnson D, Kant SG, Opitz JM, Ramadevi AR, Reardon W, Ross A, Sarda P, Schrander-Stumpel CTRM, Sluiter AE, Temple IK, Terhal PA, Toutain A, Wise CA, Wright M, Skidmore DL, Samuels ME, Hoefsloot LH, Knoers NVAM, Brunner HG, Jackson AP, Bongers EMHF. Meier-Gorlin syndrome: growth and secondary sexual development of a microcephalic primordial dwarfism disorder. Am J Med Genet A 2012; 158A:2733-42. [PMID: 23023959 DOI: 10.1002/ajmg.a.35681] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 09/03/2012] [Indexed: 11/09/2022]
Abstract
Meier-Gorlin syndrome (MGS) is a rare autosomal recessive disorder characterized by primordial dwarfism, microtia, and patellar aplasia/hypoplasia. Recently, mutations in the ORC1, ORC4, ORC6, CDT1, and CDC6 genes, encoding components of the pre-replication complex, have been identified. This complex is essential for DNA replication and therefore mutations are expected to impair cell proliferation and consequently could globally reduce growth. However, detailed growth characteristics of MGS patients have not been reported, and so this is addressed here through study of 45 MGS patients, the largest cohort worldwide. Here, we report that growth velocity (length) is impaired in MGS during pregnancy and first year of life, but, thereafter, height increases in paralleled normal reference centiles, resulting in a mean adult height of -4.5 standard deviations (SD). Height is dependent on ethnic background and underlying molecular cause, with ORC1 and ORC4 mutations causing more severe short stature and microcephaly. Growth hormone therapy (n = 9) was generally ineffective, though in two patients with significantly reduced IGF1 levels, growth was substantially improved by GH treatment, with 2SD and 3.8 SD improvement in height. Growth parameters for monitoring growth in future MGS patients are provided and as well we highlight that growth is disproportionately affected in certain structures, with growth related minor genital abnormalities (42%) and mammary hypoplasia (100%) frequently present, in addition to established effects on ears and patellar growth.
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Affiliation(s)
- Sonja A de Munnik
- Department of Human Genetics, Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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28
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Pagnamenta AT, Murray JE, Yoon G, Sadighi Akha E, Harrison V, Bicknell LS, Ajilogba K, Stewart H, Kini U, Taylor JC, Keays DA, Jackson AP, Knight SJL. A novel nonsense CDK5RAP2 mutation in a Somali child with primary microcephaly and sensorineural hearing loss. Am J Med Genet A 2012; 158A:2577-82. [PMID: 22887808 PMCID: PMC3470702 DOI: 10.1002/ajmg.a.35558] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [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: 05/01/2012] [Accepted: 06/20/2012] [Indexed: 12/15/2022]
Abstract
Primary microcephaly is a genetically heterogeneous condition characterized by reduced head circumference (-3 SDS or more) and mild-to-moderate learning disability. Here, we describe clinical and molecular investigations of a microcephalic child with sensorineural hearing loss. Although consanguinity was unreported initially, detection of 13.7 Mb of copy neutral loss of heterozygosity (cnLOH) on chromosome 9 implicated the CDK5RAP2 gene. Targeted sequencing identified a homozygous E234X mutation, only the third mutation to be described in CDK5RAP2, the first in an individual of non-Pakistani descent. Sensorineural hearing loss is not generally considered to be consistent with autosomal recessive microcephaly and therefore it seems likely that the deafness in this individual is caused by the co-occurrence of a further gene mutation, independent of CDK5RAP2. Nevertheless, further detailed clinical descriptions of rare CDK5RAP2 patients, including hearing assessments will be needed to resolve fully the phenotypic range associated with mutations in this gene. This study also highlights the utility of SNP-array testing to guide disease gene identification where an autosomal recessive condition is plausible.
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Affiliation(s)
- Alistair T Pagnamenta
- NIHR Biomedical Research Centre, Oxford and Wellcome Trust Centre for Human Genetics, University of Oxford, UK
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29
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Bober MB, Niiler T, Duker AL, Murray JE, Ketterer T, Harley ME, Alvi S, Flora C, Rustad C, Bongers EMHF, Bicknell LS, Wise C, Jackson AP. Growth in individuals with Majewski osteodysplastic primordial dwarfism type II caused by pericentrin mutations. Am J Med Genet A 2012; 158A:2719-25. [PMID: 22821869 DOI: 10.1002/ajmg.a.35447] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 04/08/2012] [Indexed: 11/09/2022]
Abstract
Microcephalic primordial dwarfism (MPD) is a class of disorders characterized by intrauterine growth restriction (IUGR), impaired postnatal growth and microcephaly. Majewski osteodysplastic primordial dwarfism type II (MOPD II) is one of the more common conditions within this group. MOPD II is caused by truncating mutations in pericentrin (PCNT) and is inherited in an autosomal recessive manner. Detailed growth curves for length, weight, and OFC are presented here and derived from retrospective data from 26 individuals with MOPD II confirmed by molecular or functional studies. Severe pre- and postnatal growth failure is evident in MOPD II patients. The length, weight, and OFC at term (when corrected for gestational age) were -7.0, -3.9, and -4.6 standard deviation (SD) below the population mean and equivalent to the 50th centile of a 28-29-, 31-32-, and 30-31-week neonate, respectively. While at skeletal maturity, the height, weight, and OFC were -10.3, -14.3, and -8.5 SD below the population mean and equivalent to the size of 3-year 10- to 11-month-old, a 5-year 2- to 3-month-old, and 5- to 6-month-old, respectively. During childhood, MOPD II patients grow with slowed, but fairly constant growth velocities and show no evidence of any pubertal growth spurt. Treatment with human growth hormone (n = 11) did not lead to any significant improvement in final stature. The growth charts presented here will be of assistance with diagnosis and management of MOPD II, and should have particular utility in nutritional management of MOPD II during infancy.
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Affiliation(s)
- Michael B Bober
- Division of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, Delaware 19083, USA.
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30
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Leung JW, Leitch A, Wood JL, Shaw-Smith C, Metcalfe K, Bicknell LS, Jackson AP, Chen J. SET nuclear oncogene associates with microcephalin/MCPH1 and regulates chromosome condensation. J Biol Chem 2011; 286:21393-400. [PMID: 21515671 DOI: 10.1074/jbc.m110.208793] [Citation(s) in RCA: 26] [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] [Indexed: 11/06/2022] Open
Abstract
Primary microcephaly is an autosomal recessive disorder characterized by marked reduction in human brain size. Microcephalin (MCPH1), one of the genes mutated in primary microcephaly, plays an important role in DNA damage checkpoint control and mitotic entry. Additionally, MCPH1 ensures the proper temporal activation of chromosome condensation during mitosis, by acting as a negative regulator of the condensin II complex. We previously found that deletion of the of the MCPH1 N terminus leads to the premature chromosome condensation (PCC) phenotype. In the present study, we unexpectedly observed that a truncated form of MCPH1 appears to be expressed in MCPH1(S25X/S25X) patient cells. This likely results from utilization of an alternative translational start codon, which would produce a mutant MCPH1 protein with a small deletion of its N-terminal BRCT domain. Furthermore, missense mutations in the MCPH1 cluster at its N terminus, suggesting that intact function of this BRCT protein-interaction domain is required both for coordinating chromosome condensation and human brain development. Subsequently, we identified the SET nuclear oncogene as a direct binding partner of the MCPH1 N-terminal BRCT domain. Cells with SET knockdown exhibited abnormal condensed chromosomes similar to those observed in MCPH1-deficient mouse embryonic fibroblasts. Condensin II knockdown rescued the abnormal chromosome condensation phenotype in SET-depleted cells. In addition, MCPH1 V50G/I51V missense mutations, impair binding to SET and fail to fully rescue the abnormal chromosome condensation phenotype in Mcph1(-/-) mouse embryonic fibroblasts. Collectively, our findings suggest that SET is an important regulator of chromosome condensation/decondensation and that disruption of the MCPH1-SET interaction might be important for the pathogenesis of primary microcephaly.
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Affiliation(s)
- Justin W Leung
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
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31
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Huang-Doran I, Bicknell LS, Finucane FM, Rocha N, Porter KM, Tung YL, Szekeres F, Krook A, Nolan JJ, O’Driscoll M, Bober M, O’Rahilly S, Jackson AP, Semple RK. Genetic defects in human pericentrin are associated with severe insulin resistance and diabetes. Diabetes 2011; 60:925-35. [PMID: 21270239 PMCID: PMC3046854 DOI: 10.2337/db10-1334] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Accepted: 12/13/2010] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Genetic defects in human pericentrin (PCNT), encoding the centrosomal protein pericentrin, cause a form of osteodysplastic primordial dwarfism that is sometimes reported to be associated with diabetes. We thus set out to determine the prevalence of diabetes and insulin resistance among patients with PCNT defects and examined the effects of pericentrin depletion on insulin action using 3T3-L1 adipocytes as a model system. RESEARCH DESIGN AND METHODS A cross-sectional metabolic assessment of 21 patients with PCNT mutations was undertaken. Pericentrin expression in human tissues was profiled using quantitative real-time PCR. The effect of pericentrin knockdown on insulin action and adipogenesis in 3T3-L1 adipocytes was determined using Oil red O staining, gene-expression analysis, immunoblotting, and glucose uptake assays. Pericentrin expression and localization also was determined in skeletal muscle. RESULTS Of 21 patients with genetic defects in PCNT, 18 had insulin resistance, which was severe in the majority of subjects. Ten subjects had confirmed diabetes (mean age of onset 15 years [range 5-28]), and 13 had metabolic dyslipidemia. All patients without insulin resistance were younger than 4 years old. Knockdown of pericentrin in adipocytes had no effect on proximal insulin signaling but produced a twofold impairment in insulin-stimulated glucose uptake, approximately commensurate with an associated defect in cell proliferation and adipogenesis. Pericentrin was highly expressed in human skeletal muscle, where it showed a perinuclear distribution. CONCLUSIONS Severe insulin resistance and premature diabetes are common features of PCNT deficiency but are not congenital. Partial failure of adipocyte differentiation may contribute to this, but pericentrin deficiency does not impair proximal insulin action in adipocytes.
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Affiliation(s)
- Isabel Huang-Doran
- Institute of Metabolic Science, Addenbrooke’s Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, U.K
| | - Louise S. Bicknell
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, U.K
| | - Francis M. Finucane
- Metabolic Research Unit, St. James Hospital, Trinity College, Dublin, Ireland
| | - Nuno Rocha
- Institute of Metabolic Science, Addenbrooke’s Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, U.K
| | - Keith M. Porter
- Institute of Metabolic Science, Addenbrooke’s Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, U.K
| | - Y.C. Loraine Tung
- Institute of Metabolic Science, Addenbrooke’s Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, U.K
| | - Ferenc Szekeres
- Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Anna Krook
- Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - John J. Nolan
- Metabolic Research Unit, St. James Hospital, Trinity College, Dublin, Ireland
| | - Mark O’Driscoll
- Human DNA Damage Response Disorders Group, University of Sussex, Brighton, U.K
| | - Michael Bober
- Division of Genetics, Department of Pediatrics, Alfred I. DuPont Hospital for Children, Wilmington, Delaware
| | - Stephen O’Rahilly
- Institute of Metabolic Science, Addenbrooke’s Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, U.K
| | - Andrew P. Jackson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, U.K
| | - Robert K. Semple
- Institute of Metabolic Science, Addenbrooke’s Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, U.K
| | - for the Majewski Osteodysplastic Primordial Dwarfism Study Group
- Institute of Metabolic Science, Addenbrooke’s Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, U.K
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, U.K
- Metabolic Research Unit, St. James Hospital, Trinity College, Dublin, Ireland
- Integrative Physiology, Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
- Human DNA Damage Response Disorders Group, University of Sussex, Brighton, U.K
- Division of Genetics, Department of Pediatrics, Alfred I. DuPont Hospital for Children, Wilmington, Delaware
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Bicknell LS, Walker S, Klingseisen A, Stiff T, Leitch A, Kerzendorfer C, Martin CA, Yeyati P, Al Sanna N, Bober M, Johnson D, Wise C, Jackson AP, O'Driscoll M, Jeggo PA. Mutations in ORC1, encoding the largest subunit of the origin recognition complex, cause microcephalic primordial dwarfism resembling Meier-Gorlin syndrome. Nat Genet 2011; 43:350-5. [PMID: 21358633 DOI: 10.1038/ng.776] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 01/25/2011] [Indexed: 11/09/2022]
Abstract
Studies into disorders of extreme growth failure (for example, Seckel syndrome and Majewski osteodysplastic primordial dwarfism type II) have implicated fundamental cellular processes of DNA damage response signaling and centrosome function in the regulation of human growth. Here we report that mutations in ORC1, encoding a subunit of the origin recognition complex, cause microcephalic primordial dwarfism resembling Meier-Gorlin syndrome. We establish that these mutations disrupt known ORC1 functions including pre-replicative complex formation and origin activation. ORC1 deficiency perturbs S-phase entry and S-phase progression. Additionally, we show that Orc1 depletion in zebrafish is sufficient to markedly reduce body size during rapid embryonic growth. Our data suggest a model in which ORC1 mutations impair replication licensing, slowing cell cycle progression and consequently impeding growth during development, particularly at times of rapid proliferation. These findings establish a novel mechanism for the pathogenesis of microcephalic dwarfism and show a surprising but important developmental impact of impaired origin licensing.
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Affiliation(s)
- Louise S Bicknell
- Medical Research Council (MRC) Human Genetics Unit (HGU), Institute for Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
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Bicknell LS, Pitt J, Aftimos S, Ramadas R, Maw MA, Robertson SP. A missense mutation in ALDH18A1, encoding Δ1-pyrroline-5-carboxylate synthase (P5CS), causes an autosomal recessive neurocutaneous syndrome. Eur J Hum Genet 2008; 16:1176-86. [DOI: 10.1038/ejhg.2008.91] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Farrington-Rock C, Firestein MH, Bicknell LS, Superti-Furga A, Bacino CA, Cormier-Daire V, Le Merrer M, Baumann C, Roume J, Rump P, Verheij JBGM, Sweeney E, Rimoin DL, Lachman RS, Robertson SP, Cohn DH, Krakow D. Mutations in two regions of FLNB result in atelosteogenesis I and III. Hum Mutat 2006; 27:705-10. [PMID: 16752402 DOI: 10.1002/humu.20348] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [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] [Indexed: 11/08/2022]
Abstract
The filamins are a family of cytoplasmic proteins that bind to and organize actin filaments, link membrane proteins to the cytoskeleton, and provide a scaffold for signaling molecules. Mutations in the gene encoding filamin B (FLNB) cause a spectrum of osteochondrodysplasias, including atelosteogenesis type I (AOI) and atelosteogenesis type III (AOIII). AOI and AOIII are autosomal dominant lethal skeletal dysplasias characterized by overlapping clinical findings that include vertebral abnormalities, disharmonious skeletal maturation, hypoplastic long bones, and joint dislocations. Previous studies have shown that heterozygosity for missense mutations that alter the CH2 domain and repeat 6 region of filamin B produce AOI and AOIII. In this study, 14 novel missense mutations in FLNB were found in 15 unrelated patients with AOI and AOIII. The majority of the mutations resided in exon 2 and exon 3, which encode the CH2 domain of the actin-binding region of filamin B. The remaining mutations were found in exon 28 and exon 29, which encode repeats 14 and 15 of filamin B. These results show that clustering of mutations in two regions of FLNB produce AOI/AOIII, and highlight the important role of this cytoskeletal protein in normal skeletogenesis.
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Affiliation(s)
- Claire Farrington-Rock
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
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Bicknell LS, Farrington-Rock C, Shafeghati Y, Rump P, Alanay Y, Alembik Y, Al-Madani N, Firth H, Karimi-Nejad MH, Kim CA, Leask K, Maisenbacher M, Moran E, Pappas JG, Prontera P, de Ravel T, Fryns JP, Sweeney E, Fryer A, Unger S, Wilson LC, Lachman RS, Rimoin DL, Cohn DH, Krakow D, Robertson SP. A molecular and clinical study of Larsen syndrome caused by mutations in FLNB. J Med Genet 2006; 44:89-98. [PMID: 16801345 PMCID: PMC2598053 DOI: 10.1136/jmg.2006.043687] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Larsen syndrome is an autosomal dominant osteochondrodysplasia characterised by large-joint dislocations and craniofacial anomalies. Recently, Larsen syndrome was shown to be caused by missense mutations or small inframe deletions in FLNB, encoding the cytoskeletal protein filamin B. To further delineate the molecular causes of Larsen syndrome, 20 probands with Larsen syndrome together with their affected relatives were evaluated for mutations in FLNB and their phenotypes studied. METHODS Probands were screened for mutations in FLNB using a combination of denaturing high-performance liquid chromatography, direct sequencing and restriction endonuclease digestion. Clinical and radiographical features of the patients were evaluated. RESULTS AND DISCUSSION The clinical signs most frequently associated with a FLNB mutation are the presence of supernumerary carpal and tarsal bones and short, broad, spatulate distal phalanges, particularly of the thumb. All individuals with Larsen syndrome-associated FLNB mutations are heterozygous for either missense or small inframe deletions. Three mutations are recurrent, with one mutation, 5071G-->A, observed in 6 of 20 subjects. The distribution of mutations within the FLNB gene is non-random, with clusters of mutations leading to substitutions in the actin-binding domain and filamin repeats 13-17 being the most common cause of Larsen syndrome. These findings collectively define autosomal dominant Larsen syndrome and demonstrate clustering of causative mutations in FLNB.
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Affiliation(s)
- Louise S Bicknell
- Department of Paediatrics and Child Health, University of Otago, Dunedin, New Zealand
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Bicknell LS, Morgan T, Bonafé L, Wessels MW, Bialer MG, Willems PJ, Cohn DH, Krakow D, Robertson SP. Mutations in FLNB cause boomerang dysplasia. J Med Genet 2006; 42:e43. [PMID: 15994868 PMCID: PMC1736093 DOI: 10.1136/jmg.2004.029967] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Boomerang dysplasia (BD) is a perinatal lethal osteochondrodysplasia, characterised by absence or underossification of the limb bones and vertebrae. The BD phenotype is similar to a group of disorders including atelosteogenesis I, atelosteogenesis III, and dominantly inherited Larsen syndrome that we have recently shown to be associated with mutations in FLNB, the gene encoding the actin binding cytoskeletal protein, filamin B. We report the identification of mutations in FLNB in two unrelated individuals with boomerang dysplasia. The resultant substitutions, L171R and S235P, lie within the calponin homology 2 region of the actin binding domain of filamin B and occur at sites that are evolutionarily well conserved. These findings expand the phenotypic spectrum resulting from mutations in FLNB and underline the central role this protein plays during skeletogenesis in humans.
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