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Copy number variants associated with epilepsy from gene expression microarrays. J Clin Neurosci 2015; 22:1907-10. [PMID: 26275332 DOI: 10.1016/j.jocn.2015.05.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/20/2015] [Accepted: 05/09/2015] [Indexed: 11/21/2022]
Abstract
We aimed to identify novel copy number variations (CNV) that might contribute to the pathogenesis of epilepsy. Epilepsy is a common brain disorder characterized by recurring seizures and various serious comorbidities, including respiratory, cardiovascular, and neurologic dysfunction. CNV have recently been considered as important risk factors for epilepsy. With public gene expression data from brain tissue of 23 epilepsy patients and 23 healthy controls, we detected CNV using the R language package CAFÉ. Real-time quantitative polymerase chain reaction validation was performed in a further nine patients and 10 controls. Functional analyses of the genes in the validated CNV were also carried out, using Ingenuity pathway analysis. Three copy number abnormalities (19q13.33, 19q13.11 and 4q35.1) were detected with the gene expression data. The duplication in 19q13.33 (approximately 1.22 million bases) was further validated in three additional epilepsy patients, and the deletion in 19q13.11 (approximately 855 kilobases) was further validated in another two epilepsy patients. The functional analyses of the genes in these two CNV suggested that they may be involved in the pathogenesis of epilepsy. The CNV that we detected may be common genetic etiological factors of epilepsy, and there is potential for the identification of a novel biomarker for treatment from these CNV regions.
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Bras J, Alonso I, Barbot C, Costa M, Darwent L, Orme T, Sequeiros J, Hardy J, Coutinho P, Guerreiro R. Mutations in PNKP cause recessive ataxia with oculomotor apraxia type 4. Am J Hum Genet 2015; 96:474-9. [PMID: 25728773 PMCID: PMC4375449 DOI: 10.1016/j.ajhg.2015.01.005] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/09/2015] [Indexed: 11/13/2022] Open
Abstract
Hereditary autosomal-recessive cerebellar ataxias are a genetically and clinically heterogeneous group of disorders. We used homozygosity mapping and exome sequencing to study a cohort of nine Portuguese families who were identified during a nationwide, population-based, systematic survey as displaying a consistent phenotype of recessive ataxia with oculomotor apraxia (AOA). The integration of data from these analyses led to the identification of the same homozygous PNKP (polynucleotide kinase 3′-phosphatase) mutation, c.1123G>T (p.Gly375Trp), in three of the studied families. When analyzing this particular gene in the exome sequencing data from the remaining cohort, we identified homozygous or compound-heterozygous mutations in five other families. PNKP is a dual-function enzyme with a key role in different pathways of DNA-damage repair. Mutations in this gene have previously been associated with an autosomal-recessive syndrome characterized by microcephaly; early-onset, intractable seizures; and developmental delay (MCSZ). The finding of PNKP mutations associated with recessive AOA extends the phenotype associated with this gene and identifies a fourth locus that causes AOA. These data confirm that MCSZ and some forms of ataxia share etiological features, most likely reflecting the role of PNKP in DNA-repair mechanisms.
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Chatterjee A, Saha S, Chakraborty A, Silva-Fernandes A, Mandal SM, Neves-Carvalho A, Liu Y, Pandita RK, Hegde ML, Hegde PM, Boldogh I, Ashizawa T, Koeppen AH, Pandita TK, Maciel P, Sarkar PS, Hazra TK. The role of the mammalian DNA end-processing enzyme polynucleotide kinase 3'-phosphatase in spinocerebellar ataxia type 3 pathogenesis. PLoS Genet 2015; 11:e1004749. [PMID: 25633985 PMCID: PMC4310589 DOI: 10.1371/journal.pgen.1004749] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 09/11/2014] [Indexed: 01/09/2023] Open
Abstract
DNA strand-breaks (SBs) with non-ligatable ends are generated by ionizing radiation, oxidative stress, various chemotherapeutic agents, and also as base excision repair (BER) intermediates. Several neurological diseases have already been identified as being due to a deficiency in DNA end-processing activities. Two common dirty ends, 3'-P and 5'-OH, are processed by mammalian polynucleotide kinase 3'-phosphatase (PNKP), a bifunctional enzyme with 3'-phosphatase and 5'-kinase activities. We have made the unexpected observation that PNKP stably associates with Ataxin-3 (ATXN3), a polyglutamine repeat-containing protein mutated in spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph Disease (MJD). This disease is one of the most common dominantly inherited ataxias worldwide; the defect in SCA3 is due to CAG repeat expansion (from the normal 14-41 to 55-82 repeats) in the ATXN3 coding region. However, how the expanded form gains its toxic function is still not clearly understood. Here we report that purified wild-type (WT) ATXN3 stimulates, and by contrast the mutant form specifically inhibits, PNKP's 3' phosphatase activity in vitro. ATXN3-deficient cells also show decreased PNKP activity. Furthermore, transgenic mice conditionally expressing the pathological form of human ATXN3 also showed decreased 3'-phosphatase activity of PNKP, mostly in the deep cerebellar nuclei, one of the most affected regions in MJD patients' brain. Finally, long amplicon quantitative PCR analysis of human MJD patients' brain samples showed a significant accumulation of DNA strand breaks. Our results thus indicate that the accumulation of DNA strand breaks due to functional deficiency of PNKP is etiologically linked to the pathogenesis of SCA3/MJD.
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Affiliation(s)
- Arpita Chatterjee
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Saikat Saha
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Anabela Silva-Fernandes
- School of Health Sciences, Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Santi M. Mandal
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Andreia Neves-Carvalho
- School of Health Sciences, Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Yongping Liu
- Department of Neurology and Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Raj K. Pandita
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Muralidhar L. Hegde
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas, United States of America
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Pavana M. Hegde
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas, United States of America
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Istvan Boldogh
- Department of Microbiology & Immunology; University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tetsuo Ashizawa
- Department of Neurology, University of Florida, Gainesville, Florida, United States of America
| | - Arnulf H. Koeppen
- Department of Neurology, Albany Stratton VA Medical Center, Albany, New York, United States of America
| | - Tej K. Pandita
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas, United States of America
| | - Patricia Maciel
- School of Health Sciences, Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Partha S. Sarkar
- Department of Neurology and Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tapas K. Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
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Gao R, Liu Y, Silva-Fernandes A, Fang X, Paulucci-Holthauzen A, Chatterjee A, Zhang HL, Matsuura T, Choudhary S, Ashizawa T, Koeppen AH, Maciel P, Hazra TK, Sarkar PS. Inactivation of PNKP by mutant ATXN3 triggers apoptosis by activating the DNA damage-response pathway in SCA3. PLoS Genet 2015; 11:e1004834. [PMID: 25590633 PMCID: PMC4295939 DOI: 10.1371/journal.pgen.1004834] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 10/16/2014] [Indexed: 12/30/2022] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease (MJD), is an untreatable autosomal dominant neurodegenerative disease, and the most common such inherited ataxia worldwide. The mutation in SCA3 is the expansion of a polymorphic CAG tri-nucleotide repeat sequence in the C-terminal coding region of the ATXN3 gene at chromosomal locus 14q32.1. The mutant ATXN3 protein encoding expanded glutamine (polyQ) sequences interacts with multiple proteins in vivo, and is deposited as aggregates in the SCA3 brain. A large body of literature suggests that the loss of function of the native ATNX3-interacting proteins that are deposited in the polyQ aggregates contributes to cellular toxicity, systemic neurodegeneration and the pathogenic mechanism in SCA3. Nonetheless, a significant understanding of the disease etiology of SCA3, the molecular mechanism by which the polyQ expansions in the mutant ATXN3 induce neurodegeneration in SCA3 has remained elusive. In the present study, we show that the essential DNA strand break repair enzyme PNKP (polynucleotide kinase 3'-phosphatase) interacts with, and is inactivated by, the mutant ATXN3, resulting in inefficient DNA repair, persistent accumulation of DNA damage/strand breaks, and subsequent chronic activation of the DNA damage-response ataxia telangiectasia-mutated (ATM) signaling pathway in SCA3. We report that persistent accumulation of DNA damage/strand breaks and chronic activation of the serine/threonine kinase ATM and the downstream p53 and protein kinase C-δ pro-apoptotic pathways trigger neuronal dysfunction and eventually neuronal death in SCA3. Either PNKP overexpression or pharmacological inhibition of ATM dramatically blocked mutant ATXN3-mediated cell death. Discovery of the mechanism by which mutant ATXN3 induces DNA damage and amplifies the pro-death signaling pathways provides a molecular basis for neurodegeneration due to PNKP inactivation in SCA3, and for the first time offers a possible approach to treatment.
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Affiliation(s)
- Rui Gao
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yongping Liu
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Anabela Silva-Fernandes
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s PT Government Associate Laboratory, Braga/Guimarặes, Portugal
| | - Xiang Fang
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Adriana Paulucci-Holthauzen
- Department of Biomedical Engineering, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Arpita Chatterjee
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Hang L. Zhang
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tohru Matsuura
- Department of Neurology, Jichi Medical School, Shimotsuke, Japan
| | - Sanjeev Choudhary
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tetsuo Ashizawa
- Department of Neurology and McNight Brain Research Institute, University of Florida, Gainesville, Florida, United States of America
| | - Arnulf H. Koeppen
- Department of Neurology, Albany Stratton VA Medical Center, Albany, New York, United States of America
| | - Patricia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s PT Government Associate Laboratory, Braga/Guimarặes, Portugal
| | - Tapas K. Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Partha S. Sarkar
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
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DNA repair abnormalities leading to ataxia: shared neurological phenotypes and risk factors. Neurogenetics 2014; 15:217-28. [PMID: 25038946 DOI: 10.1007/s10048-014-0415-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/11/2014] [Indexed: 02/06/2023]
Abstract
Since identification of mutations in the ATM gene leading to ataxia-telangiectasia, enormous efforts have been devoted to discovering the roles this protein plays in DNA repair as well as other cellular functions. Even before the identification of ATM mutations, it was clear that other diseases with different genomic loci had very similar neurological symptoms. There has been significant progress in understanding why cancer and immunodeficiency occur in ataxia-telangiectasia even though many details remain to be determined, but the field is no closer to determining why the nervous system requires ATM and other DNA repair genes. Even though rodent disease models have similar DNA repair abnormalities as the human diseases, they have no consistent, robust neuropathological phenotype making it difficult to understand the neurological underpinnings of disease. Therefore, it may be useful to reassess the neurological and neuropathological characteristics of ataxia-telangiectasia in human patients to look for potential commonalities in DNA repair diseases that result in ataxia. In doing so, it is clear that ataxia-telangiectasia and similar diseases share neurological features other than merely ataxia, such as length-dependent motor and sensory neuropathies, and that the neuroanatomical localization for these symptoms is understood. Cells affected in ataxia-telangiectasia and similar diseases are some of the largest single nucleated cells in the body. In addition, a subset of these diseases also has extrapyramidal movements and oculomotor apraxia. These neurological and neuropathological similarities may indicate a common DNA repair related pathogenesis with very large cell size as a critical risk factor.
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Causative novel PNKP mutations and concomitant PCDH15 mutations in a patient with microcephaly with early-onset seizures and developmental delay syndrome and hearing loss. J Hum Genet 2014; 59:471-4. [PMID: 24965255 DOI: 10.1038/jhg.2014.51] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/03/2014] [Accepted: 06/05/2014] [Indexed: 12/25/2022]
Abstract
We report on a 1-year-old boy with microcephaly with a simplified gyral pattern, early-onset seizures, congenital hearing loss and a severe developmental delay. Trio-based whole-exome sequencing identified candidate compound heterozygous mutations in two genes: c.163G>T (p.Ala55Ser) and c.874G>A (p.Gly292Arg) in polynucleotide kinase 3'-phosphatase gene (PNKP), and c.195G>A (p.Met65Ile) and c.1210A>C (p.Ser404Arg) in PCDH15. PNKP and PCDH15 mutations have been reported in autosomal recessive microcephaly with early-onset seizures and developmental delay syndrome, and Usher syndrome type 1F, respectively. Our patient showed neurological features similar to reported cases of both syndromes that could be explained by the observed mutations in both PNKP and PCDH15, which therefore appear to be pathogenic in this case.
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58
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Oegema R, Poulton CJ, Mancini GMS. A single strand that links multiple neuropathologies in human disease. Brain 2013; 137:e266. [DOI: 10.1093/brain/awt197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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59
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Reynolds JJ, Stewart GS. Reply: A single strand that links multiple neuropathologies in human disease. Brain 2013; 137:e267. [DOI: 10.1093/brain/awt198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Stracker TH, Roig I, Knobel PA, Marjanović M. The ATM signaling network in development and disease. Front Genet 2013; 4:37. [PMID: 23532176 PMCID: PMC3607076 DOI: 10.3389/fgene.2013.00037] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 03/04/2013] [Indexed: 12/15/2022] Open
Abstract
The DNA damage response (DDR) rapidly recognizes DNA lesions and initiates the appropriate cellular programs to maintain genome integrity. This includes the coordination of cell cycle checkpoints, transcription, translation, DNA repair, metabolism, and cell fate decisions, such as apoptosis or senescence (Jackson and Bartek, 2009). DNA double-strand breaks (DSBs) represent one of the most cytotoxic DNA lesions and defects in their metabolism underlie many human hereditary diseases characterized by genomic instability (Stracker and Petrini, 2011; McKinnon, 2012). Patients with hereditary defects in the DDR display defects in development, particularly affecting the central nervous system, the immune system and the germline, as well as aberrant metabolic regulation and cancer predisposition. Central to the DDR to DSBs is the ataxia-telangiectasia mutated (ATM) kinase, a master controller of signal transduction. Understanding how ATM signaling regulates various aspects of the DDR and its roles in vivo is critical for our understanding of human disease, its diagnosis and its treatment. This review will describe the general roles of ATM signaling and highlight some recent advances that have shed light on the diverse roles of ATM and related proteins in human disease.
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Affiliation(s)
- Travis H. Stracker
- Oncology Programme, Institute for Research in Biomedicine (IRB Barcelona)Barcelona, Spain
| | - Ignasi Roig
- Departament de Biologia Cellular, Fisiologia i Immunologia, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de BarcelonBarcelona, Spain
| | - Philip A. Knobel
- Oncology Programme, Institute for Research in Biomedicine (IRB Barcelona)Barcelona, Spain
| | - Marko Marjanović
- Oncology Programme, Institute for Research in Biomedicine (IRB Barcelona)Barcelona, Spain
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