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Longman D, Jackson-Jones KA, Maslon MM, Murphy LC, Young RS, Stoddart JJ, Hug N, Taylor MS, Papadopoulos DK, Cáceres JF. Identification of a localized nonsense-mediated decay pathway at the endoplasmic reticulum. Genes Dev 2020; 34:1075-1088. [PMID: 32616520 PMCID: PMC7397857 DOI: 10.1101/gad.338061.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/05/2020] [Indexed: 12/25/2022]
Abstract
Nonsense-mediated decay (NMD) is a translation-dependent RNA quality control mechanism that occurs in the cytoplasm. However, it is unknown how NMD regulates the stability of RNAs translated at the endoplasmic reticulum (ER). Here, we identify a localized NMD pathway dedicated to ER-translated mRNAs. We previously identified NBAS, a component of the Syntaxin 18 complex involved in Golgi-to-ER trafficking, as a novel NMD factor. Furthermore, we show that NBAS fulfills an independent function in NMD. This ER-NMD pathway requires the interaction of NBAS with the core NMD factor UPF1, which is partially localized at the ER in the proximity of the translocon. NBAS and UPF1 coregulate the stability of ER-associated transcripts, in particular those associated with the cellular stress response. We propose a model where NBAS recruits UPF1 to the membrane of the ER and activates an ER-dedicated NMD pathway, thus providing an ER-protective function by ensuring quality control of ER-translated mRNAs.
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Affiliation(s)
- Dasa Longman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Kathryn A Jackson-Jones
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Magdalena M Maslon
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Robert S Young
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Jack J Stoddart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Martin S Taylor
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Dimitrios K Papadopoulos
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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2
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Khoreva A, Pomerantseva E, Belova N, Povolotskaya I, Konovalov F, Kaimonov V, Gavrina A, Zimin S, Pershin D, Davydova N, Burlakov V, Viktorova E, Roppelt A, Kalinina E, Novichkova G, Shcherbina A. Complex Multisystem Phenotype With Immunodeficiency Associated With NBAS Mutations: Reports of Three Patients and Review of the Literature. Front Pediatr 2020; 8:577. [PMID: 33042920 PMCID: PMC7522312 DOI: 10.3389/fped.2020.00577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 08/06/2020] [Indexed: 11/20/2022] Open
Abstract
Objectives: Mutations in the neuroblastoma-amplified sequence (NBAS) gene were originally described in patients with skeletal dysplasia or isolated liver disease of variable severity. Subsequent publications reported a more complex phenotype. Among multisystemic clinical symptoms, we were particularly interested in the immunological consequences of the NBAS deficiency. Methods: Clinical and laboratory data of 3 patients ages 13, 6, and 5 in whom bi-allelic NBAS mutations had been detected via next-generation sequencing were characterized. Literature review of 23 publications describing 74 patients was performed. Results: We report three Russian patients with compound heterozygous mutations of the NBAS gene who had combined immunodeficiency characterized by hypogammaglobulinemia, low T-cells, and near-absent B-cells, along with liver disease, skeletal dysplasia, optic-nerve atrophy, and dysmorphic features. Analysis of the data of 74 previously reported patients who carried various NBAS mutations demonstrated that although the most severe form of liver disease seems to require disruption of the N-terminal or middle part of NBAS, mutations of variable localizations in the gene have been associated with some form of liver disease, as well as immunological disorders. Conclusions: NBAS deficiency has a broad phenotype, and referral to an immunologist should be made in order to screen for immunodeficiency.
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Affiliation(s)
- Anna Khoreva
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | | | | | - Inna Povolotskaya
- Genetics and Reproductive Medicine Center "GENETICO" Ltd., Moscow, Russia.,Veltischev Research and Clinical Institute of Pediatrics, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Vladimir Kaimonov
- Genetics and Reproductive Medicine Center "GENETICO" Ltd., Moscow, Russia
| | - Alena Gavrina
- Center of Inborn Pathology, GMS Clinic, Moscow, Russia
| | | | - Dmitrii Pershin
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | | | - Vasilii Burlakov
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Ekaterina Viktorova
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Roppelt
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Ekaterina Kalinina
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Galina Novichkova
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Shcherbina
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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3
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Palagano E, Zuccarini G, Prontera P, Borgatti R, Stangoni G, Elisei S, Mantero S, Menale C, Forlino A, Uva P, Oppo M, Vezzoni P, Villa A, Merlo GR, Sobacchi C. Mutations in the Neuroblastoma Amplified Sequence gene in a family affected by Acrofrontofacionasal Dysostosis type 1. Bone 2018; 114:125-136. [PMID: 29929043 DOI: 10.1016/j.bone.2018.06.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 06/14/2018] [Accepted: 06/17/2018] [Indexed: 11/24/2022]
Abstract
Acrofrontofacionasal Dysostosis type 1 (AFFND1) is an extremely rare, autosomal recessive syndrome, comprising facial and skeletal abnormalities, short stature and intellectual disability. We analyzed an Indian family with two affected siblings by exome sequencing and identified a novel homozygous truncating mutation in the Neuroblastoma-Amplified Sequence (NBAS) gene in the patients' genome. Mutations in the NBAS gene have recently been associated with different phenotypes mainly involving skeletal formation, liver and cognitive development. The NBAS protein has been implicated in two key cellular processes, namely the non-sense mediated decay and the Golgi-to-Endoplasmic Reticulum retrograde traffic. Both functions were impaired in HEK293T cells overexpressing the truncated NBAS protein, as assessed by Real-Time PCR, Western blot analysis, co-immunoprecipitation, and immunofluorescence analysis. We examined the expression of NBAS protein in mouse embryos at various developmental stages by immunohistochemistry, and detected expression in developing chondrogenic and osteogenic structures of the skeleton as well as in the cortex, hippocampus and cerebellum, which is compatible with a role in bone and brain development. Functional genetics in the zebrafish model showed that depletion of endogenous z-nbas in fish embryos results in defective morphogenesis of chondrogenic cranial skeletal elements. Overall, our data point to a conserved function of NBAS in skeletal morphogenesis during development, support the hypothesis of a causative role of the mutated NBAS gene in the pathogenesis of AFFND1 and extend the spectrum of phenotypes associated with defects in this gene.
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Affiliation(s)
- Eleonora Palagano
- Humanitas Clinical and Research Institute, via Manzoni 113, 20089 Rozzano, Italy; Department of Medical Biotechnologies and Translational Medicine, University of Milan, Via Vanvitelli 32, 20133 Milan, Italy
| | - Giulia Zuccarini
- Department Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy
| | - Paolo Prontera
- Centro di Riferimento Regionale di Genetica Medica, Azienda Ospedaliera di Perugia, Piazzale Menghini 8/9, 06129 Perugia, Italy
| | - Renato Borgatti
- Child Neuropsychiatry and Neurorehabilitation Department, Scientific Institute Eugenio Medea, La Nostra Famiglia, Via Don Luigi Monza 20, 23842 Bosisio Parini, Italy
| | - Gabriela Stangoni
- Centro di Riferimento Regionale di Genetica Medica, Azienda Ospedaliera di Perugia, Piazzale Menghini 8/9, 06129 Perugia, Italy
| | - Sandro Elisei
- Istituto Serafico di Assisi, Viale Guglielmo Marconi 6, 06081 Assisi, Italy
| | - Stefano Mantero
- Humanitas Clinical and Research Institute, via Manzoni 113, 20089 Rozzano, Italy; CNR-IRGB, Milan Unit, via Fantoli 16/15, 20138 Milan, Italy
| | - Ciro Menale
- Humanitas Clinical and Research Institute, via Manzoni 113, 20089 Rozzano, Italy; CNR-IRGB, Milan Unit, via Fantoli 16/15, 20138 Milan, Italy
| | - Antonella Forlino
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, Via Taramelli 3/B, 27100 Pavia, Italy
| | - Paolo Uva
- CRS4, Science and Technology Park Polaris, Loc. Piscina Manna, 09010 Pula, Italy
| | - Manuela Oppo
- CRS4, Science and Technology Park Polaris, Loc. Piscina Manna, 09010 Pula, Italy
| | - Paolo Vezzoni
- Humanitas Clinical and Research Institute, via Manzoni 113, 20089 Rozzano, Italy; CNR-IRGB, Milan Unit, via Fantoli 16/15, 20138 Milan, Italy
| | - Anna Villa
- Humanitas Clinical and Research Institute, via Manzoni 113, 20089 Rozzano, Italy; CNR-IRGB, Milan Unit, via Fantoli 16/15, 20138 Milan, Italy
| | - Giorgio R Merlo
- Department Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126 Turin, Italy
| | - Cristina Sobacchi
- Humanitas Clinical and Research Institute, via Manzoni 113, 20089 Rozzano, Italy; CNR-IRGB, Milan Unit, via Fantoli 16/15, 20138 Milan, Italy.
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4
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Cardenas V, DiPaola F, Adams SD, Holtz AM, Ahmad A. Acute Liver Failure Secondary to Neuroblastoma Amplified Sequence Deficiency. J Pediatr 2017; 186:179-182. [PMID: 28410752 DOI: 10.1016/j.jpeds.2017.03.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/03/2017] [Accepted: 03/15/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Vanessa Cardenas
- Division of Gastroenterology, Department of Pediatrics and Communicable Diseases, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI.
| | - Frank DiPaola
- Division of Gastroenterology, Department of Pediatrics and Communicable Diseases, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI
| | - Stacie D Adams
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics and Communicable Diseases, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI
| | - Alexander M Holtz
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI
| | - Ayesha Ahmad
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics and Communicable Diseases, C.S. Mott Children's Hospital, University of Michigan, Ann Arbor, MI
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5
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Balasubramanian M, Hurst J, Brown S, Bishop NJ, Arundel P, DeVile C, Pollitt RC, Crooks L, Longman D, Caceres JF, Shackley F, Connolly S, Payne JH, Offiah AC, Hughes D, Parker MJ, Hide W, Skerry TM. Compound heterozygous variants in NBAS as a cause of atypical osteogenesis imperfecta. Bone 2017; 94:65-74. [PMID: 27789416 PMCID: PMC6067660 DOI: 10.1016/j.bone.2016.10.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/17/2016] [Accepted: 10/21/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Osteogenesis imperfecta (OI), the commonest inherited bone fragility disorder, affects 1 in 15,000 live births resulting in frequent fractures and reduced mobility, with significant impact on quality of life. Early diagnosis is important, as therapeutic advances can lead to improved clinical outcome and patient benefit. REPORT Whole exome sequencing in patients with OI identified, in two patients with a multi-system phenotype, compound heterozygous variants in NBAS (neuroblastoma amplified sequence). Patient 1: NBAS c.5741G>A p.(Arg1914His); c.3010C>T p.(Arg1004*) in a 10-year old boy with significant short stature, bone fragility requiring treatment with bisphosphonates, developmental delay and immunodeficiency. Patient 2: NBAS c.5741G>A p.(Arg1914His); c.2032C>T p.(Gln678*) in a 5-year old boy with similar presenting features, bone fragility, mild developmental delay, abnormal liver function tests and immunodeficiency. DISCUSSION Homozygous missense NBAS variants cause SOPH syndrome (short stature; optic atrophy; Pelger-Huet anomaly), the same missense variant was found in our patients on one allele and a nonsense variant in the other allele. Recent literature suggests a multi-system phenotype. In this study, patient fibroblasts have shown reduced collagen expression, compared to control cells and RNAseq studies, in bone cells show that NBAS is expressed in osteoblasts and osteocytes of rodents and primates. These findings provide proof-of-concept that NBAS mutations have mechanistic effects in bone, and that NBAS variants are a novel cause of bone fragility, which is distinguishable from 'Classical' OI. CONCLUSIONS Here we report on variants in NBAS, as a cause of bone fragility in humans, and expand the phenotypic spectrum associated with NBAS. We explore the mechanism underlying NBAS and the striking skeletal phenotype in our patients.
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Affiliation(s)
- M Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, UK; Highly Specialised Service for Severe, Complex and Atypical OI, UK.
| | - J Hurst
- NE Thames Clinical Genetics Service, Great Ormond Street Hospital, UK
| | - S Brown
- Sheffield RNAi Screening Facility, Department of Biomedical Sciences, University of Sheffield, UK
| | - N J Bishop
- Highly Specialised Service for Severe, Complex and Atypical OI, UK; Academic Unit of Child Health, University of Sheffield, UK
| | - P Arundel
- Highly Specialised Service for Severe, Complex and Atypical OI, UK
| | - C DeVile
- Highly Specialised Service for Severe, Complex and Atypical OI, UK
| | - R C Pollitt
- Academic Unit of Child Health, University of Sheffield, UK; Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, UK
| | - L Crooks
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, UK; Department of Biosciences and Chemistry, Sheffield Hallam University, UK
| | - D Longman
- MRC Human Genetics Unit, IGMM, University of Edinburgh, UK
| | - J F Caceres
- MRC Human Genetics Unit, IGMM, University of Edinburgh, UK
| | - F Shackley
- Department of Paediatric Immunology, Sheffield Children's NHS Foundation Trust, UK
| | - S Connolly
- Department of Paediatric Hepatology, Sheffield Children's NHS Foundation Trust, UK
| | - J H Payne
- Department of Paediatric Haematology, Sheffield Children's NHS Foundation Trust, UK
| | - A C Offiah
- Highly Specialised Service for Severe, Complex and Atypical OI, UK; Academic Unit of Child Health, University of Sheffield, UK
| | - D Hughes
- Department of Histopathology, Sheffield Teaching Hospitals NHS Foundation Trust, UK
| | - M J Parker
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, UK
| | - W Hide
- Centre for Computational Biology, Sheffield Institute of Translational Neuroscience, University of Sheffield, UK
| | - T M Skerry
- Mellanby Bone Research Centre, Department of Oncology & Metabolism, University of Sheffield, UK
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6
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Hug N, Longman D, Cáceres JF. Mechanism and regulation of the nonsense-mediated decay pathway. Nucleic Acids Res 2016; 44:1483-95. [PMID: 26773057 PMCID: PMC4770240 DOI: 10.1093/nar/gkw010] [Citation(s) in RCA: 322] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/31/2015] [Indexed: 12/11/2022] Open
Abstract
The Nonsense-mediated mRNA decay (NMD) pathway selectively degrades mRNAs harboring premature termination codons (PTCs) but also regulates the abundance of a large number of cellular RNAs. The central role of NMD in the control of gene expression requires the existence of buffering mechanisms that tightly regulate the magnitude of this pathway. Here, we will focus on the mechanism of NMD with an emphasis on the role of RNA helicases in the transition from NMD complexes that recognize a PTC to those that promote mRNA decay. We will also review recent strategies aimed at uncovering novel trans-acting factors and their functional role in the NMD pathway. Finally, we will describe recent progress in the study of the physiological role of the NMD response.
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Affiliation(s)
- Nele Hug
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Dasa Longman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Javier F Cáceres
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
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7
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Capo-Chichi JM, Mehawej C, Delague V, Caillaud C, Khneisser I, Hamdan FF, Michaud JL, Kibar Z, Mégarbané A. Neuroblastoma Amplified Sequence (NBAS) mutation in recurrent acute liver failure: Confirmatory report in a sibship with very early onset, osteoporosis and developmental delay. Eur J Med Genet 2015; 58:637-41. [PMID: 26578240 DOI: 10.1016/j.ejmg.2015.11.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/06/2015] [Accepted: 11/07/2015] [Indexed: 02/08/2023]
Abstract
BACKGROUND Recently, biallelic mutations in the Neuroblastoma Amplified Sequence NBAS gene have been identified in ten patients that present recurrent acute liver failure (RALF) in early infancy. In addition to severe liver dysfunction, some of these individuals also suffered from other comorbidities including cardiomyopathy, neurologic phenotypes and gastrointestinal immune defects. Here we report on a consanguineous Lebanese family with three siblings affected by RALF. Of note, neonatal spontaneous fractures, developmental delay, prominent eyes, generalized hirsutism, gum hypertrophy, and hepato-splenomegaly were also present. METHODS Whole-genome SNP genotyping in all the patients, followed by exome sequencing was performed in one of the affected siblings. RESULTS A homozygous c.409C > T (p.Arg137Trp) missense mutation in NBAS was identified in all patients. CONCLUSION Overall, our findings confirm the involvement of NBAS in the pathogenesis of this condition characterized by severe liver dysfunction and help expand its phenotypical spectrum.
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Affiliation(s)
| | - Cybel Mehawej
- Unité de Génétique Médicale, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon.
| | - Valerie Delague
- Inserm, UMR_S 910, 13385 Marseille, France; Aix Marseille Université, GMGF, 13385 Marseille, France.
| | - Catherine Caillaud
- Service de Biochimie Médicale, Hôpital Necker Enfants Malades, Paris 75015, France.
| | - Issam Khneisser
- Unité de Génétique Médicale, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon.
| | - Fadi F Hamdan
- CHU Sainte-Justine Research Center, Montreal H3T 1C5, Canada.
| | - Jacques L Michaud
- CHU Sainte-Justine Research Center, Montreal H3T 1C5, Canada; Department of Pediatrics and Department of Neurosciences, Université de Montreal, Montreal, Canada.
| | - Zoha Kibar
- CHU Sainte-Justine Research Center, Montreal H3T 1C5, Canada.
| | - André Mégarbané
- Unité de Génétique Médicale, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon; Institut Jérôme Lejeune, Paris, France.
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8
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Segarra NG, Ballhausen D, Crawford H, Perreau M, Campos-Xavier B, van Spaendonck-Zwarts K, Vermeer C, Russo M, Zambelli PY, Stevenson B, Royer-Bertrand B, Rivolta C, Candotti F, Unger S, Munier FL, Superti-Furga A, Bonafé L. NBAS mutations cause a multisystem disorder involving bone, connective tissue, liver, immune system, and retina. Am J Med Genet A 2015; 167A:2902-12. [PMID: 26286438 DOI: 10.1002/ajmg.a.37338] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 08/10/2015] [Indexed: 11/09/2022]
Abstract
We report two unrelated patients with a multisystem disease involving liver, eye, immune system, connective tissue, and bone, caused by biallelic mutations in the neuroblastoma amplified sequence (NBAS) gene. Both presented as infants with recurrent episodes triggered by fever with vomiting, dehydration, and elevated transaminases. They had frequent infections, hypogammaglobulinemia, reduced natural killer cells, and the Pelger-Huët anomaly of their granulocytes. Their facial features were similar with a pointed chin and proptosis; loose skin and reduced subcutaneous fat gave them a progeroid appearance. Skeletal features included short stature, slender bones, epiphyseal dysplasia with multiple phalangeal pseudo-epiphyses, and small C1-C2 vertebrae causing cervical instability and myelopathy. Retinal dystrophy and optic atrophy were present in one patient. NBAS is a component of the synthaxin-18 complex and is involved in nonsense-mediated mRNA decay control. Putative loss-of-function mutations in NBAS are already known to cause disease in humans. A specific founder mutation has been associated with short stature, optic nerve atrophy and Pelger-Huët anomaly of granulocytes (SOPH) in the Siberian Yakut population. A more recent report associates NBAS mutations with recurrent acute liver failure in infancy in a group of patients of European descent. Our observations indicate that the phenotypic spectrum of NBAS deficiency is wider than previously known and includes skeletal, hepatic, metabolic, and immunologic aspects. Early recognition of the skeletal phenotype is important for preventive management of cervical instability.
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Affiliation(s)
- Nuria Garcia Segarra
- Center for Molecular Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Diana Ballhausen
- Center for Molecular Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Heather Crawford
- Clinical Metabolic Genetics, Cook Children's Health Care System, Fort Worth, Texas, USA
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland
| | | | | | - Cees Vermeer
- VitaK and Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Michel Russo
- Pediatric Service, Centre Hospitalier du Centre Valais, Sion, Switzerland
| | - Pierre-Yves Zambelli
- Service of Pediatric Surgery, Lausanne University Hospital, Lausanne, Switzerland
| | - Brian Stevenson
- Vital-IT group, Swiss Institute of Bioinformatics, University of Lausanne, Switzerland
| | - Beryl Royer-Bertrand
- Department of Medical Genetics, Lausanne University Hospital, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Medical Genetics, Lausanne University Hospital, Lausanne, Switzerland
| | - Fabio Candotti
- Division of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland
| | - Sheila Unger
- Department of Medical Genetics, Lausanne University Hospital, Lausanne, Switzerland
| | | | | | - Luisa Bonafé
- Center for Molecular Diseases, Lausanne University Hospital, Lausanne, Switzerland
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Tagaya M, Arasaki K, Inoue H, Kimura H. Moonlighting functions of the NRZ (mammalian Dsl1) complex. Front Cell Dev Biol 2014; 2:25. [PMID: 25364732 PMCID: PMC4206994 DOI: 10.3389/fcell.2014.00025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/20/2014] [Indexed: 12/31/2022] Open
Abstract
The yeast Dsl1 complex, which comprises Dsl1, Tip20, and Sec39/Dsl3, has been shown to participate, as a vesicle-tethering complex, in retrograde trafficking from the Golgi apparatus to the endoplasmic reticulum. Its metazoan counterpart NRZ complex, which comprises NAG, RINT1, and ZW10, is also involved in Golgi-to-ER retrograde transport, but each component of the complex has diverse cellular functions including endosome-to-Golgi transport, cytokinesis, cell cycle checkpoint, autophagy, and mRNA decay. In this review, we summarize the current knowledge of the metazoan NRZ complex and discuss the "moonlighting" functions and intercorrelation of their subunits.
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Affiliation(s)
- Mitsuo Tagaya
- Department of Molecular Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences Hachioji, Japan
| | - Kohei Arasaki
- Department of Molecular Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences Hachioji, Japan
| | - Hiroki Inoue
- Department of Molecular Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences Hachioji, Japan
| | - Hana Kimura
- Department of Molecular Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences Hachioji, Japan
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10
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Longman D, Hug N, Keith M, Anastasaki C, Patton EE, Grimes G, Cáceres JF. DHX34 and NBAS form part of an autoregulatory NMD circuit that regulates endogenous RNA targets in human cells, zebrafish and Caenorhabditis elegans. Nucleic Acids Res 2013; 41:8319-31. [PMID: 23828042 PMCID: PMC3783168 DOI: 10.1093/nar/gkt585] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway selectively degrades mRNAs harboring premature termination codons but also regulates the abundance of cellular RNAs. We sought to identify transcripts that are regulated by two novel NMD factors, DHX34 and neuroblastoma amplified sequence (NBAS), which were identified in a genome-wide RNA interference screen in Caenorhabditis elegans and later shown to mediate NMD in vertebrates. We performed microarray expression profile analysis in human cells, zebrafish embryos and C. elegans that were individually depleted of these factors. Our analysis revealed that a significant proportion of genes are co-regulated by DHX34, NBAS and core NMD factors in these three organisms. Further analysis indicates that NMD modulates cellular stress response pathways and membrane trafficking across species. Interestingly, transcripts encoding different NMD factors were sensitive to DHX34 and NBAS depletion, suggesting that these factors participate in a conserved NMD negative feedback regulatory loop, as was recently described for core NMD factors. In summary, we find that DHX34 and NBAS act in concert with core NMD factors to co-regulate a large number of endogenous RNA targets. Furthermore, the conservation of a mechanism to tightly control NMD homeostasis across different species highlights the importance of the NMD response in the control of gene expression.
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Affiliation(s)
- Dasa Longman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
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Anastasaki C, Longman D, Capper A, Patton EE, Cáceres JF. Dhx34 and Nbas function in the NMD pathway and are required for embryonic development in zebrafish. Nucleic Acids Res 2011; 39:3686-94. [PMID: 21227923 PMCID: PMC3089463 DOI: 10.1093/nar/gkq1319] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway is a highly conserved surveillance mechanism that is present in all eukaryotes. It prevents the synthesis of truncated proteins by selectively degrading mRNAs harbouring premature termination codons (PTCs). The core NMD effectors were originally identified in genetic screens in Saccharomyces cerevisae and in the nematode Caenorhabditis elegans, and subsequently by homology searches in other metazoans. A genome-wide RNAi screen in C. elegans resulted in the identification of two novel NMD genes that are essential for proper embryonic development. Their human orthologues, DHX34 and NAG/NBAS, are required for NMD in human cells. Here, we find that the zebrafish genome encodes orthologues of DHX34 and NAG/NBAS. We show that the morpholino-induced depletion of zebrafish Dhx34 and Nbas proteins results in severe developmental defects and reduced embryonic viability. We also found that Dhx34 and Nbas are required for degradation of PTC-containing mRNAs in zebrafish embryos. The phenotypes observed in both Dhx34 and Nbas morphants are similar to defects in Upf1, Smg-5- or Smg-6- depleted embryos, suggesting that these factors affect the same pathway and confirming that zebrafish embryogenesis requires an active NMD pathway.
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Affiliation(s)
- Corina Anastasaki
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh EH4 2XU, UK
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12
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Maksimova N, Hara K, Nikolaeva I, Chun-Feng T, Usui T, Takagi M, Nishihira Y, Miyashita A, Fujiwara H, Oyama T, Nogovicina A, Sukhomyasova A, Potapova S, Kuwano R, Takahashi H, Nishizawa M, Onodera O. Neuroblastoma amplified sequence gene is associated with a novel short stature syndrome characterised by optic nerve atrophy and Pelger-Huët anomaly. J Med Genet 2010; 47:538-48. [PMID: 20577004 PMCID: PMC2921285 DOI: 10.1136/jmg.2009.074815] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Background Hereditary short stature syndromes are clinically and genetically heterogeneous disorders and the cause have not been fully identified. Yakuts are a population isolated in Asia; they live in the far east of the Russian Federation and have a high prevalence of hereditary short stature syndrome including 3-M syndrome. A novel short stature syndrome in Yakuts is reported here, which is characterised by autosomal recessive inheritance, severe postnatal growth retardation, facial dysmorphism with senile face, small hands and feet, normal intelligence, Pelger-Huët anomaly of leucocytes, and optic atrophy with loss of visual acuity and colour vision. This new syndrome is designated as short stature with optic atrophy and Pelger-Huët anomaly (SOPH) syndrome. Aims To identify a causative gene for SOPH syndrome. Methods Genomewide homozygosity mapping was conducted in 33 patients in 30 families. Results The disease locus was mapped to the 1.1 Mb region on chromosome 2p24.3, including the neuroblastoma amplified sequence (NBAS) gene. Subsequently, 33 of 34 patients were identified with SOPH syndrome and had a 5741G/A nucleotide substitution (resulting in the amino acid substitution R1914H) in the NBAS gene in the homozygous state. None of the 203 normal Yakuts individuals had this substitution in the homozygous state. Immunohistochemical analysis revealed that the NBAS protein is well expressed in retinal ganglion cells, epidermal skin cells, and leucocyte cytoplasm in controls as well as a patient with SOPH syndrome. Conclusion These findings suggest that function of NBAS may associate with the pathogenesis of short stature syndrome as well as optic atrophy and Pelger-Huët anomaly.
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Affiliation(s)
- Nadezda Maksimova
- Department of Molecular Genetics, Yakut Scientific Center of Complex Medical Problems, Siberian Department of Russian Academy of Medical Science, Yakutsk, Russia
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13
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Fujita K, Sanada M, Harada H, Mori H, Niikura H, Omine M, Inazawa J, Imoto I. Molecular cloning of t(2;7)(p24.3;p14.2), a novel chromosomal translocation in myelodysplastic syndrome-derived acute myeloid leukemia. J Hum Genet 2009; 54:355-9. [DOI: 10.1038/jhg.2009.40] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Aoki T, Ichimura S, Itoh A, Kuramoto M, Shinkawa T, Isobe T, Tagaya M. Identification of the neuroblastoma-amplified gene product as a component of the syntaxin 18 complex implicated in Golgi-to-endoplasmic reticulum retrograde transport. Mol Biol Cell 2009; 20:2639-49. [PMID: 19369418 DOI: 10.1091/mbc.e08-11-1104] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Syntaxin 18, a soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor (SNARE) protein implicated in endoplasmic reticulum (ER) membrane fusion, forms a complex with other SNAREs (BNIP1, p31, and Sec22b) and several peripheral membrane components (Sly1, ZW10, and RINT-1). In the present study, we showed that a peripheral membrane protein encoded by the neuroblastoma-amplified gene (NAG) is a subunit of the syntaxin 18 complex. NAG encodes a protein of 2371 amino acids, which exhibits weak similarity to yeast Dsl3p/Sec39p, an 82-kDa component of the complex containing the yeast syntaxin 18 orthologue Ufe1p. Under conditions favoring SNARE complex disassembly, NAG was released from syntaxin 18 but remained in a p31-ZW10-RINT-1 subcomplex. Binding studies showed that the extreme N-terminal region of p31 is responsible for the interaction with NAG and that the N- and the C-terminal regions of NAG interact with p31 and ZW10-RINT-1, respectively. Knockdown of NAG resulted in a reduction in the expression of p31, confirming their intimate relationship. NAG depletion did not substantially affect Golgi morphology and protein export from the ER, but it caused redistribution of Golgi recycling proteins accompanied by a defect in protein glycosylation. These results together suggest that NAG links between p31 and ZW10-RINT-1 and is involved in Golgi-to-ER transport.
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Affiliation(s)
- Takehiro Aoki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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15
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Stock C, Bozsaky E, Watzinger F, Poetschger U, Orel L, Lion T, Kowalska A, Ambros PF. Genes proximal and distal to MYCN are highly expressed in human neuroblastoma as visualized by comparative expressed sequence hybridization. THE AMERICAN JOURNAL OF PATHOLOGY 2007; 172:203-14. [PMID: 18165268 DOI: 10.2353/ajpath.2008.061263] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
MYCN amplification is associated with poor prognosis in neuroblastoma disease. To improve our understanding of the influence of the MYCN amplicon and its corresponding expression, we investigated the 2p expression pattern of MYCN amplified (n = 13) and nonamplified (n = 4) cell lines and corresponding primary tumors (n = 3) using the comparative expressed sequence hybridization technique. All but one MYCN amplified cell line displayed overexpression at 2p. Expression peaks were observed frequently at 2pter and less frequently at 2p24 (MYCN locus), 2p23.3-23.2, and/or 2p23.1. Importantly, cell lines and two corresponding primary tumors displayed expression peaks at similar loci. No significant 2p24 expression level was observed for those cell lines displaying a low amplification rate (n = 3) by comparative genomic hybridization. Only the cell lines with an enhanced peak at 2p23.2-23.3 displayed coamplification of the ALK gene (2p23.2), reported to be associated with unfavorable prognosis. Finally, two of four cell lines without MYCN amplification, both derived from patients with poor outcome, also showed an expression peak at 2p23.2. These data indicate that, besides MYCN, other genes proximal and distal to MYCN are highly expressed in neuroblastoma. The prognostic significance of expression peaks at 2p23.2-23.3, independent of MYCN and ALK status, remains to be investigated.
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Affiliation(s)
- Cornelia Stock
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Kinderspitalgasse 6, A-1090 Vienna, Austria
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16
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Longman D, Plasterk RH, Johnstone IL, Cáceres JF. Mechanistic insights and identification of two novel factors in the C. elegans NMD pathway. Genes Dev 2007; 21:1075-85. [PMID: 17437990 PMCID: PMC1855233 DOI: 10.1101/gad.417707] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The nonsense-mediated mRNA decay (NMD) pathway selectively degrades mRNAs harboring premature termination codons (PTCs). Seven genes (smg-1-7, for suppressor with morphological effect on genitalia) that are essential for NMD were originally identified in the nematode Caenorhabditis elegans, and orthologs of these genes have been found in several species. Whereas in humans NMD is linked to splicing, PTC definition occurs independently of exon boundaries in Drosophila. Here, we have conducted an analysis of the cis-acting sequences and trans-acting factors that are required for NMD in C. elegans. We show that a PTC codon is defined independently of introns in C. elegans and, consequently, components of the exon junction complex (EJC) are dispensable for NMD. We also show a distance-dependent effect, whereby PTCs that are closer to the 3' end of the mRNA are less sensitive to NMD. We also provide evidence for the existence of previously unidentified components of the NMD pathway that, unlike known smg genes, are essential for viability in C. elegans. A genome-wide RNA interference (RNAi) screen resulted in the identification of two such novel NMD genes, which are essential for proper embryonic development, and as such represent a new class of essential NMD genes in C. elegans that we have termed smgl (for smg lethal). We show that the encoded proteins are conserved throughout evolution and are required for NMD in C. elegans and also in human cells.
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Affiliation(s)
- Dasa Longman
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, Scotland, United Kingdom
| | - Ronald H.A. Plasterk
- Hubrecht Laboratory-Koninklijke Nederlandse Akademie van Wetenschappen (KNAW), 3584 CT Utrecht, The Netherlands
| | - Iain L. Johnstone
- Institute of Biomedical and Life Sciences, Division of Molecular Genetics, University of Glasgow, Anderson College, Glasgow G11 6NU, Scotland, United Kingdom
| | - Javier F. Cáceres
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, Scotland, United Kingdom
- Corresponding author.E-MAIL ; FAX 44-131-467-8456
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Kaneko S, Ohira M, Nakamura Y, Isogai E, Nakagawara A, Kaneko M. Relationship of DDX1 and NAG gene amplification/overexpression to the prognosis of patients with MYCN-amplified neuroblastoma. J Cancer Res Clin Oncol 2006; 133:185-92. [PMID: 17028906 DOI: 10.1007/s00432-006-0156-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 08/28/2006] [Indexed: 10/24/2022]
Abstract
PURPOSE Amplification of the MYCN gene strongly correlates with advanced stage, rapid tumor progression and poor prognosis in neuroblastoma (NB). Several genes in the MYCN amplicon, including the DEAD box polypeptide 1 (DDX1) gene, and neuroblastoma-amplified gene (NAG gene), have been found to be frequently co-amplified with MYCN in NB. The aim of this study was to clarify the prognostic significance of the co-amplification or overexpression of DDX1 and NAG with MYCN. PROCEDURE The gene copy numbers and mRNA expression levels of MYCN, DDX1, and NAG in 113 primary NBs were determined by the real-time quantitative polymerase chain reaction or quantitative reverse transcriptase/polymerase chain reaction assay. The relationships between gene co-amplification/overexpression status and stage, age at diagnosis, and overall survival were analyzed. RESULTS For evaluating the frequency of DDX1 and NAG co-amplification, it proved appropriate to discriminate NBs with <40 copies of MYCN amplification from those with > or =40 copies of MYCN (DDX1, p = 0.00058; NAG, p = 0.0242, chi(2) for independence test). In patients with MYCN-amplified NB aged > or =18 months, those with tumor with enhanced DDX1 expression and low-NAG expression showed a significantly better outcome than those with low-DDX1 expression or enhanced NAG expression (p = 0.0245, log-rank test). None of the gene expression statuses had a significant relation to disease stage or survival for patients <18 months old. No relationship between any gene co-amplification status and disease stage, age at diagnosis, or overall survival was found. CONCLUSIONS Our findings suggest that there may be a subset of NB in which enhanced DDX1 and low-NAG expression consequent to DDX1 co-amplification without NAG amplification contributes to susceptibility to intensive therapy. A larger study using an age cut-off of 18 months will be required.
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Affiliation(s)
- Setsuko Kaneko
- Department of Pediatric Surgery, Institute of Clinical Medicine, University of Tsukuba, Ibaraki 305-8575, Japan.
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Bredel M, Bredel C, Juric D, Harsh GR, Vogel H, Recht LD, Sikic BI. High-resolution genome-wide mapping of genetic alterations in human glial brain tumors. Cancer Res 2005; 65:4088-96. [PMID: 15899798 DOI: 10.1158/0008-5472.can-04-4229] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-resolution genome-wide mapping of exact boundaries of chromosomal alterations should facilitate the localization and identification of genes involved in gliomagenesis and may characterize genetic subgroups of glial brain tumors. We have done such mapping using cDNA microarray-based comparative genomic hybridization technology to profile copy number alterations across 42,000 mapped human cDNA clones, in a series of 54 gliomas of varying histogenesis and tumor grade. This gene-by-gene approach permitted the precise sizing of critical amplicons and deletions and the detection of multiple new genetic aberrations. It has also revealed recurrent patterns of occurrence of distinct chromosomal aberrations as well as their interrelationships and showed that gliomas can be clustered into distinct genetic subgroups. A subset of detected alterations was shown predominantly associated with either astrocytic or oligodendrocytic tumor phenotype. Finally, five novel minimally deleted regions were identified in a subset of tumors, containing putative candidate tumor suppressor genes (TOPORS, FANCG, RAD51, TP53BP1, and BIK) that could have a role in gliomagenesis.
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Affiliation(s)
- Markus Bredel
- Division of Oncology, Center for Clinical Sciences Research, Stanford University School of Medicine, Stanford, California 94305-5151, USA.
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19
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Affiliation(s)
- Axel Weber
- Children's Hospital of Marburg, Pediatric Oncology and Hematology, Neuroblastoma Research Laboratory, Marburg, Germany
| | - Patricia Imisch
- Children's Hospital of Marburg, Pediatric Oncology and Hematology, Neuroblastoma Research Laboratory, Marburg, Germany
| | - Eckhard Bergmann
- Children's Hospital of Marburg, Pediatric Oncology and Hematology, Neuroblastoma Research Laboratory, Marburg, Germany
| | - Holger Christiansen
- Children's Hospital of Marburg, Pediatric Oncology and Hematology, Neuroblastoma Research Laboratory, Marburg, Germany
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20
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Weber A, Imisch P, Bergmann E, Christiansen H. Coamplification of DDX1 correlates with an improved survival probability in children with MYCN-amplified human neuroblastoma. J Clin Oncol 2004; 22:2681-90. [PMID: 15226335 DOI: 10.1200/jco.2004.07.192] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
PURPOSE Amplification of the MYCN oncogene at chromosome 2p24-25 identifies an aggressive subtype of human neuroblastoma with a poor clinical outcome. Differences in amplicon structure and coamplification of genes telomeric and centromeric to the MYCN oncogene have previously been described. A relevant role of gene coamplification for neuroblastoma pathogenesis remains elusive. PATIENTS AND METHODS We analyzed 98 primary neuroblastoma tumors with MYCN amplification for coamplification of seven additional genes at chromosome 2p24-25 (DDX1, NAG, NSE1, LPIN1, EST-AA581763, SMC6, and SDC1). Two semiquantitative multiplex polymerase chain reactions were used to obtain the amplification status of the target genes in relation to a reference gene on chromosome 2q (Inhibin-beta-b). Furthermore, mRNA expression pattern of coamplified genes in a subset of tumors was analyzed. RESULTS Our results show that the frequency of gene coamplification on 2p24-25 in neuroblastoma is correlated directly to the physical distance to MYCN. Coamplification is correlated to an upregulated gene expression for DDX1 and NAG. Coamplification of the DDX1 gene within 400kb telomeric to MYCN identifies a subgroup of advanced stage neuroblastoma tumors with a more favorable outcome (P =.027, log-rank test). A high expression level of DDX1 is associated with a trend towards a better survival probability (P =.058, log-rank test). CONCLUSION Our results indicate that DDX1 coamplification correlates with a better prognosis and improved patient survival in MYCN-amplified neurobastoma.
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Affiliation(s)
- Axel Weber
- Children's Hospital, Pedriatric Oncology and Hematology, University of Marburg, Germany
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21
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De Preter K, Pattyn F, Berx G, Strumane K, Menten B, Van Roy F, De Paepe A, Speleman F, Vandesompele J. Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons. BMC Genomics 2004; 5:11. [PMID: 15018647 PMCID: PMC365025 DOI: 10.1186/1471-2164-5-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2003] [Accepted: 02/03/2004] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Activation of proto-oncogenes by DNA amplification is an important mechanism in the development and maintenance of cancer cells. Until recently, identification of the targeted genes relied on labour intensive and time consuming positional cloning methods. In this study, we outline a straightforward and efficient strategy for fast and comprehensive cloning of amplified and overexpressed genes. RESULTS As a proof of principle, we analyzed neuroblastoma cell line IMR-32, with at least two amplification sites along the short arm of chromosome 2. In a first step, overexpressed cDNA clones were isolated using a PCR based subtractive cloning method. Subsequent deposition of these clones on a custom microarray and hybridization with IMR-32 DNA, resulted in the identification of clones that were overexpressed due to gene amplification. Using this approach, amplification of all previously reported amplified genes in this cell line was detected. Furthermore, four additional clones were found to be amplified, including the TEM8 gene on 2p13.3, two anonymous transcripts, and a fusion transcript, resulting from 2p13.3 and 2p24.3 fused sequences. CONCLUSIONS The combinatorial strategy of subtractive cDNA cloning and array CGH analysis allows comprehensive amplicon dissection, which opens perspectives for improved identification of hitherto unknown targeted oncogenes in cancer cells.
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MESH Headings
- Cell Line, Tumor
- Chromosomes, Human, Pair 2/genetics
- Cloning, Molecular/methods
- DEAD-box RNA Helicases
- DNA/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Female
- Gene Amplification
- Gene Expression Profiling/methods
- Homeodomain Proteins/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Male
- Myeloid Ecotropic Viral Integration Site 1 Protein
- N-Myc Proto-Oncogene Protein
- Neoplasm Proteins/genetics
- Nuclear Proteins/genetics
- Nucleic Acid Hybridization/methods
- Oligonucleotide Array Sequence Analysis/methods
- Oncogene Proteins/genetics
- RNA Helicases/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reproducibility of Results
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
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Affiliation(s)
- Katleen De Preter
- Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, 9000 Gent, Belgium
| | - Filip Pattyn
- Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, 9000 Gent, Belgium
| | - Geert Berx
- Department for Molecular Biomedical Research, Flemish Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Kristin Strumane
- Department for Molecular Biomedical Research, Flemish Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, 9000 Gent, Belgium
| | - Frans Van Roy
- Department for Molecular Biomedical Research, Flemish Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Anne De Paepe
- Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, 9000 Gent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, 9000 Gent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University Hospital 1K5, De Pintelaan 185, 9000 Gent, Belgium
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