151
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Exploring Splicing-Switching Molecules For Seckel Syndrome Therapy. Biochim Biophys Acta Mol Basis Dis 2016; 1863:15-20. [PMID: 27639833 DOI: 10.1016/j.bbadis.2016.09.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/05/2016] [Accepted: 09/13/2016] [Indexed: 12/31/2022]
Abstract
The c.2101A>G synonymous change (p.G674G) in the gene for ATR, a key player in the DNA-damage response, has been the first identified genetic cause of Seckel Syndrome (SS), an orphan disease characterized by growth and mental retardation. This mutation mainly causes exon 9 skipping, through an ill-defined mechanism. Through ATR minigene expression studies, we demonstrated that the detrimental effect of this mutation (6±1% of correct transcripts only) depends on the poor exon 9 definition (47±4% in the ATRwt context), because the change was ineffective when the weak 5' or the 3' splice sites (ss) were strengthened (scores from 0.54 to 1) by mutagenesis. Interestingly, the exonic c.2101A nucleotide is conserved across species, and the SS-causing mutation is predicted to concurrently strengthen a Splicing Silencer (ESS) and weaken a Splicing Enhancer (ESE). Consistently, the artificial c.2101A>C change, predicted to weaken the ESE only, moderately impaired exon inclusion (28±7% of correct transcripts). The observation that an antisense oligonucleotide (AONATR) targeting the c.2101A position recovers exon inclusion in the mutated context supports a major role of the underlying ESS. A U1snRNA variant (U1ATR) designed to perfectly base-pair the weak 5'ss, rescued exon inclusion (63±3%) in the ATRSS-allele. Most importantly, upon lentivirus-mediated delivery, the U1ATR partially rescued ATR mRNA splicing (from ~19% to ~54%) and protein (from negligible to ~6%) in embryonic fibroblasts derived from humanized ATRSS mice. Altogether these data elucidate the molecular mechanisms of the ATR c.2101A>G mutation and identify two potential complementary RNA-based therapies for Seckel syndrome.
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152
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Low doses of X-rays induce prolonged and ATM-independent persistence of γH2AX foci in human gingival mesenchymal stem cells. Oncotarget 2016; 6:27275-87. [PMID: 26314960 PMCID: PMC4694989 DOI: 10.18632/oncotarget.4739] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/10/2015] [Indexed: 12/11/2022] Open
Abstract
Diagnostic imaging delivering low doses of radiation often accompany human mesenchymal stem cells (MSCs)-based therapies. However, effects of low dose radiation on MSCs are poorly characterized. Here we examine patterns of phosphorylated histone H2AX (γH2AX) and phospho-S1981 ATM (pATM) foci formation in human gingiva-derived MSCs exposed to X-rays in time-course and dose-response experiments. Both γH2AX and pATM foci accumulated linearly with dose early after irradiation (5–60 min), with a maximum induction observed at 30–60 min (37 ± 3 and 32 ± 3 foci/cell/Gy for γH2AX and pATM, respectively). The number of γH2AX foci produced by intermediate doses (160 and 250 mGy) significantly decreased (40–60%) between 60 and 240 min post-irradiation, indicating rejoining of DNA double-strand breaks. In contrast, γH2AX foci produced by low doses (20–80 mGy) did not change after 60 min. The number of pATM foci between 60 and 240 min decreased down to control values in a dose-independent manner. Similar kinetics was observed for pATM foci co-localized with γH2AX foci. Collectively, our results suggest differential DNA double-strand break signaling and processing in response to low vs. intermediate doses of X-rays in human MSCs. Furthermore, mechanisms governing the prolonged persistence of γH2AX foci in these cells appear to be ATM-independent.
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153
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Taniguchi JB, Kondo K, Fujita K, Chen X, Homma H, Sudo T, Mao Y, Watase K, Tanaka T, Tagawa K, Tamura T, Muramatsu SI, Okazawa H. RpA1 ameliorates symptoms of mutant ataxin-1 knock-in mice and enhances DNA damage repair. Hum Mol Genet 2016; 25:4432-4447. [DOI: 10.1093/hmg/ddw272] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/08/2016] [Accepted: 08/05/2016] [Indexed: 01/05/2023] Open
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154
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Zhang S, Pondarre C, Pennarun G, Labussiere-Wallet H, Vera G, France B, Chansel M, Rouvet I, Revy P, Lopez B, Soulier J, Bertrand P, Callebaut I, de Villartay JP. A nonsense mutation in the DNA repair factor Hebo causes mild bone marrow failure and microcephaly. J Exp Med 2016; 213:1011-28. [PMID: 27185855 PMCID: PMC4886357 DOI: 10.1084/jem.20151183] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 04/12/2016] [Indexed: 11/05/2022] Open
Abstract
de Villartay et al. describe a patient with a DNA repair factor mutation that leads to an increased sensitivity to DNA-damaging agents and, ultimately, to mild bone marrow failure and microcephaly. Inherited bone marrow failure syndromes are human conditions in which one or several cell lineages of the hemopoietic system are affected. They are present at birth or may develop progressively. They are sometimes accompanied by other developmental anomalies. Three main molecular causes have been recognized to result in bone marrow failure syndromes: (1) defects in the Fanconi anemia (FA)/BRCA DNA repair pathway, (2) defects in telomere maintenance, and (3) abnormal ribosome biogenesis. We analyzed a patient with mild bone marrow failure and microcephaly who did not present with the typical FA phenotype. Cells from this patient showed increased sensitivity to ionizing radiations and phleomycin, attesting to a probable DNA double strand break (dsb) repair defect. Linkage analysis and whole exome sequencing revealed a homozygous nonsense mutation in the ERCC6L2 gene. We identified a new ERCC6L2 alternative transcript encoding the DNA repair factor Hebo, which is critical for complementation of the patient’s DNAdsb repair defect. Sequence analysis revealed three structured regions within Hebo: a TUDOR domain, an adenosine triphosphatase domain, and a new domain, HEBO, specifically present in Hebo direct orthologues. Hebo is ubiquitously expressed, localized in the nucleus, and rapidly recruited to DNAdsb’s in an NBS1-dependent manner.
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Affiliation(s)
- Shu Zhang
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Corinne Pondarre
- Institut d'Hématologie et d'Oncologie Pédiatrique, 69008 Lyon, France
| | - Gaelle Pennarun
- Commisariat à l'Energie Atomique, Division des Sciences du Vivant, Institut National de la Santé et de la Recherche Médicale, UMR 967 CEA, Université Paris Diderot, 75013 Paris, France Institut de Radiobiologie Cellulaire et Moléculaire Fontenay-aux-Roses, Université Paris Sud, 91400 Orsay, France
| | - Helene Labussiere-Wallet
- Service d'Hématologie, Groupement Hospitalier Lyon Sud, Hospices Civils de Lyon, 69002 Lyon, France
| | - Gabriella Vera
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Benoit France
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Marie Chansel
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Isabelle Rouvet
- Biotechnology Department, Hospices Civils de Lyon, 69002 Lyon, France
| | - Patrick Revy
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - Bernard Lopez
- Institut de Cancérologie Gustave Roussy, Centre National de la Recherche Scientifique, UMR 8200, Université Paris Sud, 91400 Orsay, France
| | - Jean Soulier
- Institute of Hematology, Institut National de la Santé et de la Recherche Médicale, UMR 944, Centre National de la Recherche Scientifique, UMR 7212, Saint-Louis Hospital and Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Pascale Bertrand
- Commisariat à l'Energie Atomique, Division des Sciences du Vivant, Institut National de la Santé et de la Recherche Médicale, UMR 967 CEA, Université Paris Diderot, 75013 Paris, France
| | - Isabelle Callebaut
- Centre National de la Recherche Scientifique, UMR 7590, Université Pierre et Marie Curie, Museum National d'Histoire Naturelle, Institut de recherche pour le développement, Institut Universitaire de Cancérologie, Sorbonne Universités, 75005 Paris, France
| | - Jean-Pierre de Villartay
- Genome Dynamics in the Immune System Laboratory, Institut National de la Santé et de la Recherche Médicale, UMR 1163, Institut Imagine, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
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155
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Abstract
ATR (Ataxia Telangiectasia and Rad3-related) is a member of the Phosphatidylinositol 3-kinase-related kinases (PIKKs) family, amongst six other vertebrate proteins known so far. ATR is indispensable for cell survival and its essential role is in sensing DNA damage and initiating appropriate repair responses. In this review we highlight emerging and recent observations connecting ATR to alternative roles in controlling the nuclear envelope, nucleolus, centrosome and other organelles in response to both internal and external stress conditions. We propose that ATR functions control cell plasticity by sensing structural deformations of different cellular components, including DNA and initiating appropriate repair responses, most of which are yet to be understood completely.
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Affiliation(s)
- Gururaj Rao Kidiyoor
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy
| | - Amit Kumar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, M.G. Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), India
| | - Marco Foiani
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy.
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156
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Dumitrache LC, McKinnon PJ. Polynucleotide kinase-phosphatase (PNKP) mutations and neurologic disease. Mech Ageing Dev 2016; 161:121-129. [PMID: 27125728 DOI: 10.1016/j.mad.2016.04.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/12/2016] [Accepted: 04/24/2016] [Indexed: 12/30/2022]
Abstract
A variety of human neurologic diseases are caused by inherited defects in DNA repair. In many cases, these syndromes almost exclusively impact the nervous system, underscoring the critical requirement for genome stability in this tissue. A striking example of this is defective enzymatic activity of polynucleotide kinase-phosphatase (PNKP), leading to microcephaly or neurodegeneration. Notably, the broad neural impact of mutations in PNKP can result in markedly different disease entities, even when the inherited mutation is the same. For example microcephaly with seizures (MCSZ) results from various hypomorphic PNKP mutations, as does ataxia with oculomotor apraxia 4 (AOA4). Thus, other contributing factors influence the neural phenotype when PNKP is disabled. Here we consider the role for PNKP in maintaining brain function and how perturbation in its activity can account for the varied pathology of neurodegeneration or microcephaly present in MCSZ and AOA4 respectively.
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Affiliation(s)
- Lavinia C Dumitrache
- Dept. of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J McKinnon
- Dept. of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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157
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Stiff T, Casar Tena T, O'Driscoll M, Jeggo PA, Philipp M. ATR promotes cilia signalling: links to developmental impacts. Hum Mol Genet 2016; 25:1574-87. [PMID: 26908596 PMCID: PMC4805311 DOI: 10.1093/hmg/ddw034] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/05/2016] [Indexed: 01/18/2023] Open
Abstract
Mutations in ATR(ataxia telangiectasia and RAD3-related) cause Seckel syndrome (ATR-SS), a microcephalic primordial dwarfism disorder. Hitherto, the clinical manifestation of ATR deficiency has been attributed to its canonical role in DNA damage response signalling following replication fork stalling/collapse. Here, we show that ATR regulates cilia-dependent signalling in a manner that can be uncoupled from its function during replication. ATR-depleted or patient-derived ATR-SS cells form cilia of slightly reduced length but are dramatically impaired in cilia-dependent signalling functions, including growth factor and Sonic hedgehog signalling. To better understand the developmental impact of ATR loss of function, we also used zebrafish as a model. Zebrafish embryos depleted of Atr resembled ATR-SS morphology, showed a modest but statistically significant reduction in cilia length and other morphological features indicative of cilia dysfunction. Additionally, they displayed defects in left-right asymmetry including ambiguous expression of southpaw, incorrectly looped hearts and randomized localization of internal organs including the pancreas, features typically conferred by cilia dysfunction. Our findings reveal a novel role for ATR in cilia signalling distinct from its canonical function during replication and strengthen emerging links between cilia function and development.
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Affiliation(s)
- Tom Stiff
- Double Strand Break Repair Laboratory and
| | - Teresa Casar Tena
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Mark O'Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK and
| | | | - Melanie Philipp
- Institute for Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
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158
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Zheng Y, Mennella V, Marks S, Wildonger J, Elnagdi E, Agard D, Megraw TL. The Seckel syndrome and centrosomal protein Ninein localizes asymmetrically to stem cell centrosomes but is not required for normal development, behavior, or DNA damage response in Drosophila. Mol Biol Cell 2016; 27:1740-52. [PMID: 27053665 PMCID: PMC4884065 DOI: 10.1091/mbc.e15-09-0655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 03/28/2016] [Indexed: 12/21/2022] Open
Abstract
Ninein associates with the microtubule regulator γ-tubulin, regulates microtubule assembly, and localizes to centrosomes and noncentrosomal microtubule-organizing centers in Drosophila. Ninein localizes to stem cell centrosomes asymmetrically, with a bias for the daughter centrosome. Remarkably, Ninein is dispensable for development, fertility, or viability. Ninein (Nin) is a centrosomal protein whose gene is mutated in Seckel syndrome (SCKL, MIM 210600), an inherited recessive disease that results in primordial dwarfism, cognitive deficiencies, and increased sensitivity to genotoxic stress. Nin regulates neural stem cell self-renewal, interkinetic nuclear migration, and microtubule assembly in mammals. Nin is evolutionarily conserved, yet its role in cell division and development has not been investigated in a model organism. Here we characterize the single Nin orthologue in Drosophila. Drosophila Nin localizes to the periphery of the centrosome but not at centriolar structures as in mammals. However, Nin shares the property of its mammalian orthologue of promoting microtubule assembly. In neural and germline stem cells, Nin localizes asymmetrically to the younger (daughter) centrosome, yet it is not required for the asymmetric division of stem cells. In wing epithelia and muscle, Nin localizes to noncentrosomal microtubule-organizing centers. Surprisingly, loss of nin expression from a nin mutant does not significantly affect embryonic and brain development, fertility, or locomotor performance of mutant flies or their survival upon exposure to DNA-damaging agents. Although it is not essential, our data suggest that Nin plays a supportive role in centrosomal and extracentrosomal microtubule organization and asymmetric stem cell division.
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Affiliation(s)
- Yiming Zheng
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306-4300
| | - Vito Mennella
- Department of Biochemistry, University of Toronto, Toronto, M5G 0A4, Canada Cell Biology Program, The Hospital for Sick Children, Toronto, M5G 1X8, Canada
| | - Steven Marks
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306-4300
| | - Jill Wildonger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Esraa Elnagdi
- Department of Biochemistry, University of Toronto, Toronto, M5G 0A4, Canada Cell Biology Program, The Hospital for Sick Children, Toronto, M5G 1X8, Canada
| | - David Agard
- The Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143-2240
| | - Timothy L Megraw
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306-4300
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159
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Jackson RA, Wu JS, Chen ES. C1D family proteins in coordinating RNA processing, chromosome condensation and DNA damage response. Cell Div 2016; 11:2. [PMID: 27030795 PMCID: PMC4812661 DOI: 10.1186/s13008-016-0014-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/22/2016] [Indexed: 12/02/2022] Open
Abstract
Research on the involvement of C1D and its yeast homologues Rrp47 (S. cerevisiae) and Cti1 (S. pombe) in DNA damage repair and RNA processing has remained mutually exclusive, with most studies predominantly concentrating on Rrp47. This review will look to reconcile the functions of these proteins in their involvement with the RNA exosome, in the regulation of chromatin architecture, and in the repair of DNA double-strand breaks, focusing on non-homologous end joining and homologous recombination. We propose that C1D is situated in a central position to maintain genomic stability at highly transcribed gene loci by coordinating these processes through the timely recruitment of relevant regulatory factors. In the event that the damage is beyond repair, C1D induces apoptosis in a p53-dependent manner.
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Affiliation(s)
- Rebecca A Jackson
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore
| | - Jocelyn Shumei Wu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore ; National University Health System (NUHS), Singapore, 119228 Singapore ; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119228 Singapore
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160
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Terré B, Piergiovanni G, Segura-Bayona S, Gil-Gómez G, Youssef SA, Attolini CSO, Wilsch-Bräuninger M, Jung C, Rojas AM, Marjanović M, Knobel PA, Palenzuela L, López-Rovira T, Forrow S, Huttner WB, Valverde MA, de Bruin A, Costanzo V, Stracker TH. GEMC1 is a critical regulator of multiciliated cell differentiation. EMBO J 2016; 35:942-60. [PMID: 26933123 DOI: 10.15252/embj.201592821] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 02/05/2016] [Indexed: 11/09/2022] Open
Abstract
The generation of multiciliated cells (MCCs) is required for the proper function of many tissues, including the respiratory tract, brain, and germline. Defects in MCC development have been demonstrated to cause a subclass of mucociliary clearance disorders termed reduced generation of multiple motile cilia (RGMC). To date, only two genes, Multicilin (MCIDAS) and cyclin O (CCNO) have been identified in this disorder in humans. Here, we describe mice lacking GEMC1 (GMNC), a protein with a similar domain organization as Multicilin that has been implicated in DNA replication control. We have found that GEMC1-deficient mice are growth impaired, develop hydrocephaly with a high penetrance, and are infertile, due to defects in the formation of MCCs in the brain, respiratory tract, and germline. Our data demonstrate that GEMC1 is a critical regulator of MCC differentiation and a candidate gene for human RGMC or related disorders.
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Affiliation(s)
- Berta Terré
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Sandra Segura-Bayona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Gabriel Gil-Gómez
- IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Barcelona, Spain
| | - Sameh A Youssef
- Dutch Molecular Pathology Center, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Carole Jung
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ana M Rojas
- Computational Biology and Bioinformatics Group, Institute of Biomedicine of Seville, Campus Hospital Universitario Virgen del Rocio, Seville, Spain
| | - Marko Marjanović
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Philip A Knobel
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Lluís Palenzuela
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Teresa López-Rovira
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stephen Forrow
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Miguel A Valverde
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Alain de Bruin
- Dutch Molecular Pathology Center, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
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161
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Hettne KM, Thompson M, van Haagen HHHBM, van der Horst E, Kaliyaperumal R, Mina E, Tatum Z, Laros JFJ, van Mulligen EM, Schuemie M, Aten E, Li TS, Bruskiewich R, Good BM, Su AI, Kors JA, den Dunnen J, van Ommen GJB, Roos M, ‘t Hoen PA, Mons B, Schultes EA. The Implicitome: A Resource for Rationalizing Gene-Disease Associations. PLoS One 2016; 11:e0149621. [PMID: 26919047 PMCID: PMC4769089 DOI: 10.1371/journal.pone.0149621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/03/2016] [Indexed: 11/19/2022] Open
Abstract
High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases. Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease relations. Here, we use concept profile technology to expose from the biomedical literature both explicitly stated gene-disease relations (the explicitome) and a much larger set of implied gene-disease associations (the implicitome). Implicit relations are largely unknown to, or are even unintended by the original authors, but they vastly extend the reach of existing biomedical knowledge for identification and interpretation of gene-disease associations. The implicitome can be used in conjunction with experimental data resources to rationalize both known and novel associations. We demonstrate the usefulness of the implicitome by rationalizing known and novel gene-disease associations, including those from GWAS. To facilitate the re-use of implicit gene-disease associations, we publish our data in compliance with FAIR Data Publishing recommendations [https://www.force11.org/group/fairgroup] using nanopublications. An online tool (http://knowledge.bio) is available to explore established and potential gene-disease associations in the context of other biomedical relations.
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Affiliation(s)
- Kristina M. Hettne
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
| | - Mark Thompson
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Eelke van der Horst
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Rajaram Kaliyaperumal
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Eleni Mina
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Zuotian Tatum
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen F. J. Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik M. van Mulligen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical Informatics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martijn Schuemie
- Department of Medical Informatics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Emmelien Aten
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tong Shu Li
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | | | - Benjamin M. Good
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Andrew I. Su
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Jan A. Kors
- Department of Medical Informatics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gert-Jan B. van Ommen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marco Roos
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A.C. ‘t Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Barend Mons
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Dutch Techcentre for Life Sciences, Utrecht, The Netherlands
| | - Erik A. Schultes
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Institute for Advanced Computer Science, Leiden, The Netherlands
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162
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Samadder P, Aithal R, Belan O, Krejci L. Cancer TARGETases: DSB repair as a pharmacological target. Pharmacol Ther 2016; 161:111-131. [PMID: 26899499 DOI: 10.1016/j.pharmthera.2016.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cancer is a disease attributed to the accumulation of DNA damages due to incapacitation of DNA repair pathways resulting in genomic instability and a mutator phenotype. Among the DNA lesions, double stranded breaks (DSBs) are the most toxic forms of DNA damage which may arise as a result of extrinsic DNA damaging agents or intrinsic replication stress in fast proliferating cancer cells. Accurate repair of DSBs is therefore paramount to the cell survival, and several classes of proteins such as kinases, nucleases, helicases or core recombinational proteins have pre-defined jobs in precise execution of DSB repair pathways. On one hand, the proper functioning of these proteins ensures maintenance of genomic stability in normal cells, and on the other hand results in resistance to various drugs employed in cancer therapy and therefore presents a suitable opportunity for therapeutic targeting. Higher relapse and resistance in cancer patients due to non-specific, cytotoxic therapies is an alarming situation and it is becoming more evident to employ personalized treatment based on the genetic landscape of the cancer cells. For the success of personalized treatment, it is of immense importance to identify more suitable targetable proteins in DSB repair pathways and also to explore new synthetic lethal interactions with these pathways. Here we review the various alternative approaches to target the various protein classes termed as cancer TARGETases in DSB repair pathway to obtain more beneficial and selective therapy.
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Affiliation(s)
- Pounami Samadder
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, 60200 Brno, Czech Republic
| | - Rakesh Aithal
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; Department of Biology, Masaryk University, 62500 Brno, Czech Republic
| | - Ondrej Belan
- Department of Biology, Masaryk University, 62500 Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, 60200 Brno, Czech Republic; Department of Biology, Masaryk University, 62500 Brno, Czech Republic.
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163
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ATRIP Deacetylation by SIRT2 Drives ATR Checkpoint Activation by Promoting Binding to RPA-ssDNA. Cell Rep 2016; 14:1435-1447. [PMID: 26854234 DOI: 10.1016/j.celrep.2016.01.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 11/16/2015] [Accepted: 01/02/2016] [Indexed: 11/22/2022] Open
Abstract
The ataxia telangiectasia-mutated and Rad3-related (ATR) kinase checkpoint pathway maintains genome integrity; however, the role of the sirtuin 2 (SIRT2) acetylome in regulating this pathway is not clear. We found that deacetylation of ATR-interacting protein (ATRIP), a regulatory partner of ATR, by SIRT2 potentiates the ATR checkpoint. SIRT2 interacts with and deacetylates ATRIP at lysine 32 (K32) in response to replication stress. SIRT2 deacetylation of ATRIP at K32 drives ATR autophosphorylation and signaling and facilitates DNA replication fork progression and recovery of stalled replication forks. K32 deacetylation by SIRT2 further promotes ATRIP accumulation to DNA damage sites and binding to replication protein A-coated single-stranded DNA (RPA-ssDNA). Collectively, these results support a model in which ATRIP deacetylation by SIRT2 promotes ATR-ATRIP binding to RPA-ssDNA to drive ATR activation and thus facilitate recovery from replication stress, outlining a mechanism by which the ATR checkpoint is regulated by SIRT2 through deacetylation.
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164
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Kmochova A, Tichy A, Zarybnicka L, Sinkorova Z, Vavrova J, Rehacek V, Durisova K, Kubelkova K, Pejchal J, Kuca K. Modulation of ionizing radiation-induced effects by NU7441, KU55933 and VE821 in peripheral blood lymphocytes. J Appl Biomed 2016. [DOI: 10.1016/j.jab.2015.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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165
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Botting C, Lu X, Triezenberg SJ. H2AX phosphorylation and DNA damage kinase activity are dispensable for herpes simplex virus replication. Virol J 2016; 13:15. [PMID: 26817608 PMCID: PMC4728825 DOI: 10.1186/s12985-016-0470-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/19/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Herpes simplex virus type 1 (HSV-1) can establish both lytic and latent infections in humans. The phosphorylation of histone H2AX, a common marker of DNA damage, during lytic infection by HSV-1 is well established. However, the role(s) of H2AX phosphorylation in lytic infection remain unclear. METHODS Following infection of human foreskin fibroblasts by HSV-1 or HSV-2, we assayed the phosphorylation of H2AX in the presence of inhibitors of transcription, translation, or viral DNA replication, or in the presence of inhibitors of ATM and ATR kinases (KU-55933 and VE-821, respectively). We also assayed viral replication in fibroblasts in the presence of the kinase inhibitors or siRNAs specific for ATM and ATR, as well as in cell lines deficient for either ATR or ATM. RESULTS The expression of viral immediate-early and early proteins (including the viral DNA polymerase), but not viral DNA replication or late protein expression, were required for H2AX phosphorylation following HSV-1 infection. Inhibition of ATM kinase activity prevented HSV-stimulated H2AX phosphorylation but had only a minor effect on DNA replication and virus yield in HFF cells. These results differ from previous reports of a dramatic reduction in viral yield following chemical inhibition of ATM in oral keratinocytes or following infection of ATM(-/-) cells. Inhibition of the closely related kinase ATR (whether by chemical inhibitor or siRNA disruption) had no effect on H2AX phosphorylation and reduced viral DNA replication only moderately. During infection by HSV-2, H2AX phosphorylation was similarly dispensable but was dependent on both ATM activity and viral DNA replication. CONCLUSION H2AX phosphorylation represents a cell type-specific and virus type-specific host response to HSV infection with little impact on viral infection.
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Affiliation(s)
- Carolyn Botting
- Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA.
| | - Xu Lu
- Department of Biology, University of Findlay, 1000 N Main St, Findlay, OH, 45840, USA.
| | - Steven J Triezenberg
- Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI, 49503, USA.
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166
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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] [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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167
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Beyaert M, Starczewska E, Van Den Neste E, Bontemps F. A crucial role for ATR in the regulation of deoxycytidine kinase activity. Biochem Pharmacol 2016; 100:40-50. [DOI: 10.1016/j.bcp.2015.11.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/20/2015] [Indexed: 11/15/2022]
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169
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Yigit G, Rosin N, Wollnik B. Molekulare Grundlagen der autosomal-rezessiven primären Mikrozephalie. MED GENET-BERLIN 2015. [DOI: 10.1007/s11825-015-0068-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Zusammenfassung
Die primäre autosomal-rezessive Mikrozephalie (MCPH) ist eine genetisch sehr heterogene Erkrankung, die klinisch definiert wird durch das Vorliegen einer kongenitalen, nicht progressiven Mikrozephalie, einer mentalen Retardierung variablen Ausmaßes bei weitgehend normaler Körpergröße und das Fehlen von zusätzlichen Fehlbildungen und weiteren neurologischen Befunden. Bislang konnten Mutationen in 14 verschiedenen Genen identifiziert werden, deren Produkte auf zellulärer Ebene insbesondere bei Vorgängen der Zellteilung, der Zellzyklusregulierung und bei der Aktivierung von DNA-Reparaturmechanismen nach DNA-Schädigungen eine wichtige Rolle spielen. Darüber hinaus sind auch syndromale Formen der Mikrozephalie bekannt, zu denen u. a. das Seckel-Syndrom sowie der mikrozephale osteodysplastische primordiale Kleinwuchs Typ II (MOPD II) zählen.
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Affiliation(s)
- Gökhan Yigit
- Aff1 grid.411097.a 000000008852305X Institut für Humangenetik Uniklinik Köln Köln Deutschland
- Aff2 grid.411984.1 0000000104825331 Institut für Humangenetik Universitätsmedizin Göttingen Heinrich-Düker-Weg 12 37073 Göttingen Deutschland
| | - Nadine Rosin
- Aff1 grid.411097.a 000000008852305X Institut für Humangenetik Uniklinik Köln Köln Deutschland
- Aff2 grid.411984.1 0000000104825331 Institut für Humangenetik Universitätsmedizin Göttingen Heinrich-Düker-Weg 12 37073 Göttingen Deutschland
| | - Bernd Wollnik
- Aff1 grid.411097.a 000000008852305X Institut für Humangenetik Uniklinik Köln Köln Deutschland
- Aff2 grid.411984.1 0000000104825331 Institut für Humangenetik Universitätsmedizin Göttingen Heinrich-Düker-Weg 12 37073 Göttingen Deutschland
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170
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Xiao G, Kue P, Bhosle R, Bargonetti J. Decarbamoyl mitomycin C (DMC) activates p53-independent ataxia telangiectasia and rad3 related protein (ATR) chromatin eviction. Cell Cycle 2015; 14:744-54. [PMID: 25565400 PMCID: PMC4418290 DOI: 10.1080/15384101.2014.997517] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Interstrand crosslinks induce DNA replication fork stalling that in turn activates the ATR-dependent checkpoint and DNA repair on nuclear chromatin. Mitomycin C (MC) and Decarbamoyl Mitomycin C (DMC) induce different types of DNA crosslinks with DMC being a more cytotoxic agent. We previously reported that the novel DMC induced β–interstrand DNA crosslinks induce a p53-independent form of cell death. The p53-independent DMC cytotoxicity associates with the activation, and subsequent depletion, of Chk1. In this study we further dissect the novel DMC signal transduction pathway and asked how it influences chromatin-associated proteins. We found that treatment with DMC, but not MC, stimulated the disassociation of ATR from chromatin and re-localization of ATR to the cytoplasm. The chromatin eviction of ATR was coupled with the formation of nuclear Rad51 foci and the phosphorylation of Chk1. Furthermore, DMC but not MC, activated expression of gadd45α mRNA. Importantly, knocking down p53 via shRNA did not inhibit the DMC-induced disassociation of ATR from chromatin or reduce the activation of transcription of gadd45α. Our results suggest that DMC induces a p53-independent disassociation of ATR from chromatin that facilitates Chk1 checkpoint activation and Rad51 chromatin recruitment. Our findings provide evidence that ATR chromatin eviction in breast cancer cells is an area of study that should be focused on for inducing p53-independent cell death.
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Key Words
- ATR
- ATR, Ataxia Telangiectasia and Rad3 Related
- Cdc25, cell division cycle 25.
- ChIP, chromatin immunoprecipitation
- Chk1, checkpoint serine/threonine protein kinase 1
- DDR, DNA damage response
- DMC, Decarbamoyl Mitomycin C
- DOX, doxycycline
- HR, homologous recombination
- ICLs, interstrand cross-links
- MC, Mitomycin C
- NER, nuclear excision repair
- PCNA, Proliferating Cell Nuclear Antigen
- RPA, replication protein A
- TNBCs, triple negative breast cancers
- breast cancer
- cell death
- chromatin
- interstrand crosslink
- mitomycin C
- p53
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Affiliation(s)
- Gu Xiao
- a Department of Biological Sciences; Hunter College and The Graduate Center Biology Program ; City University of New York ; New York , NY USA
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171
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DNA Damage Signalling and Repair Inhibitors: The Long-Sought-After Achilles' Heel of Cancer. Biomolecules 2015; 5:3204-59. [PMID: 26610585 PMCID: PMC4693276 DOI: 10.3390/biom5043204] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/09/2015] [Indexed: 12/16/2022] Open
Abstract
For decades, radiotherapy and chemotherapy were the two only approaches exploiting DNA repair processes to fight against cancer. Nowadays, cancer therapeutics can be a major challenge when it comes to seeking personalized targeted medicine that is both effective and selective to the malignancy. Over the last decade, the discovery of new targeted therapies against DNA damage signalling and repair has offered the possibility of therapeutic improvements in oncology. In this review, we summarize the current knowledge of DNA damage signalling and repair inhibitors, their molecular and cellular effects, and future therapeutic use.
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172
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Menolfi D, Delamarre A, Lengronne A, Pasero P, Branzei D. Essential Roles of the Smc5/6 Complex in Replication through Natural Pausing Sites and Endogenous DNA Damage Tolerance. Mol Cell 2015; 60:835-46. [PMID: 26698660 PMCID: PMC4691243 DOI: 10.1016/j.molcel.2015.10.023] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/02/2015] [Accepted: 10/09/2015] [Indexed: 02/07/2023]
Abstract
The essential functions of the conserved Smc5/6 complex remain elusive. To uncover its roles in genome maintenance, we established Saccharomyces cerevisiae cell-cycle-regulated alleles that enable restriction of Smc5/6 components to S or G2/M. Unexpectedly, the essential functions of Smc5/6 segregated fully and selectively to G2/M. Genetic screens that became possible with generated alleles identified processes that crucially rely on Smc5/6 specifically in G2/M: metabolism of DNA recombination structures triggered by endogenous replication stress, and replication through natural pausing sites located in late-replicating regions. In the first process, Smc5/6 modulates remodeling of recombination intermediates, cooperating with dissolution activities. In the second, Smc5/6 prevents chromosome fragility and toxic recombination instigated by prolonged pausing and the fork protection complex, Tof1-Csm3. Our results thus dissect Smc5/6 essential roles and reveal that combined defects in DNA damage tolerance and pausing site-replication cause recombination-mediated DNA lesions, which we propose to drive developmental and cancer-prone disorders. Cell-cycle-regulated alleles reveal Smc5/6-essential functions to segregate in G2/M Genetic screen with new hypomorphic allele identifies processes relying on Smc5/6 Smc5/6 acts on recombination structures triggered by endogenous replication stress Smc5/6 prevents fragility and mediates replication through natural pausing sites
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Affiliation(s)
- Demis Menolfi
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Axel Delamarre
- IGH, Institute of Human Genetics CNRS UPR 1142, 141 rue de la Cardonille F-34396 Cedex 5, Montpellier, France
| | - Armelle Lengronne
- IGH, Institute of Human Genetics CNRS UPR 1142, 141 rue de la Cardonille F-34396 Cedex 5, Montpellier, France
| | - Philippe Pasero
- IGH, Institute of Human Genetics CNRS UPR 1142, 141 rue de la Cardonille F-34396 Cedex 5, Montpellier, France
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy.
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173
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Abstract
ATM and ATR signaling pathways are well conserved throughout evolution and are central to the maintenance of genome integrity. Although the role of both ATM and ATR in DNA repair, cell cycle regulation and apoptosis have been well studied, both still remain in the focus of current research activities owing to their role in cancer. Recent advances in the field suggest that these proteins have an additional function in maintaining cellular homeostasis under both stressed and non-stressed conditions. In this Cell Science at a Glance article and the accompanying poster, we present an overview of recent advances in ATR and ATM research with emphasis on that into the modes of ATM and ATR activation, the different signaling pathways they participate in - including those that do not involve DNA damage - and highlight their relevance in cancer.
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Affiliation(s)
- Poorwa Awasthi
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, M.G. Marg 80, Lucknow 226001, India Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR campus, Lucknow 226001, India
| | - Marco Foiani
- IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), IFOM-IEO Campus Via Adamello 16, Milan 20139, Italy DSBB-Università degli Studi di Milano, Milan 20133, Italy
| | - Amit Kumar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, M.G. Marg 80, Lucknow 226001, India Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR campus, Lucknow 226001, India
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174
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Wanrooij PH, Tannous E, Kumar S, Navadgi-Patil VM, Burgers PM. Probing the Mec1ATR Checkpoint Activation Mechanism with Small Peptides. J Biol Chem 2015; 291:393-401. [PMID: 26499799 DOI: 10.1074/jbc.m115.687145] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Indexed: 01/16/2023] Open
Abstract
Yeast Mec1, the ortholog of human ATR, is the apical protein kinase that initiates the cell cycle checkpoint in response to DNA damage and replication stress. The basal activity of Mec1 kinase is activated by cell cycle phase-specific activators. Three distinct activators stimulate Mec1 kinase using an intrinsically disordered domain of the protein. These are the Ddc1 subunit of the 9-1-1 checkpoint clamp (ortholog of human and Schizosaccharomyces pombe Rad9), the replication initiator Dpb11 (ortholog of human TopBP1 and S. pombe Cut5), and the multifunctional nuclease/helicase Dna2. Here, we use small peptides to determine the requirements for Mec1 activation. For Ddc1, we identify two essential aromatic amino acids in a hydrophobic environment that when fused together are proficient activators. Using this increased insight, we have been able to identify homologous motifs in S. pombe Rad9 that can activate Mec1. Furthermore, we show that a 9-amino acid Dna2-based peptide is sufficient for Mec1 activation. Studies with mutant activators suggest that binding of an activator to Mec1 is a two-step process, the first step involving the obligatory binding of essential aromatic amino acids to Mec1, followed by an enhancement in binding energy through interactions with neighboring sequences.
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Affiliation(s)
- Paulina H Wanrooij
- From the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden, and
| | - Elias Tannous
- From the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Sandeep Kumar
- From the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030
| | - Vasundhara M Navadgi-Patil
- From the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Peter M Burgers
- From the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110,
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175
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Geister KA, Brinkmeier ML, Cheung LY, Wendt J, Oatley MJ, Burgess DL, Kozloff KM, Cavalcoli JD, Oatley JM, Camper SA. LINE-1 Mediated Insertion into Poc1a (Protein of Centriole 1 A) Causes Growth Insufficiency and Male Infertility in Mice. PLoS Genet 2015; 11:e1005569. [PMID: 26496357 PMCID: PMC4619696 DOI: 10.1371/journal.pgen.1005569] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 09/15/2015] [Indexed: 11/19/2022] Open
Abstract
Skeletal dysplasias are a common, genetically heterogeneous cause of short stature that can result from disruptions in many cellular processes. We report the identification of the lesion responsible for skeletal dysplasia and male infertility in the spontaneous, recessive mouse mutant chagun. We determined that Poc1a, encoding protein of the centriole 1a, is disrupted by the insertion of a processed Cenpw cDNA, which is flanked by target site duplications, suggestive of a LINE-1 retrotransposon-mediated event. Mutant fibroblasts have impaired cilia formation and multipolar spindles. Male infertility is caused by defective spermatogenesis early in meiosis and progressive germ cell loss. Spermatogonial stem cell transplantation studies revealed that Poc1a is essential for normal function of both Sertoli cells and germ cells. The proliferative zone of the growth plate is small and disorganized because chondrocytes fail to re-align after cell division and undergo increased apoptosis. Poc1a and several other genes associated with centrosome function can affect the skeleton and lead to skeletal dysplasias and primordial dwarfisms. This mouse mutant reveals how centrosome dysfunction contributes to defects in skeletal growth and male infertility.
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Affiliation(s)
- Krista A. Geister
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Michelle L. Brinkmeier
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Leonard Y. Cheung
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jennifer Wendt
- Roche NimbleGen, Inc., Research and Development, Madison, Wisconsin, United States of America
| | - Melissa J. Oatley
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Daniel L. Burgess
- Roche NimbleGen, Inc., Research and Development, Madison, Wisconsin, United States of America
| | - Kenneth M. Kozloff
- Department of Orthopedic Surgery, University of Michigan, Ann Arbor, Michigan, United States of America
| | - James D. Cavalcoli
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jon M. Oatley
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
| | - Sally A. Camper
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Beumer JH, Fu KY, Anyang BN, Siegfried JM, Bakkenist CJ. Functional analyses of ATM, ATR and Fanconi anemia proteins in lung carcinoma : ATM, ATR and FA in lung carcinoma. BMC Cancer 2015; 15:649. [PMID: 26438152 PMCID: PMC4595318 DOI: 10.1186/s12885-015-1649-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 09/11/2015] [Indexed: 11/10/2022] Open
Abstract
Background ATM and ATR are kinases implicated in a myriad of DNA-damage responses. ATM kinase inhibition radiosensitizes cells and selectively kills cells with Fanconi anemia (FA) gene mutations. ATR kinase inhibition sensitizes cells to agents that induce replication stress and selectively kills cells with ATM and TP53 mutations. ATM mutations and FANCF promoter-methylation are reported in lung carcinomas. Methods We undertook functional analyses of ATM, ATR, Chk1 and FA proteins in lung cancer cell lines. We included Calu6 that is reported to be FANCL-deficient. In addition, the cancer genome atlas (TCGA) database was interrogated for alterations in: 1) ATM, MRE11A, RAD50 and NBN; 2) ATR, ATRIP and TOPBP1; and 3) 15 FA genes. Results No defects in ATM, ATR or Chk1 kinase activation, or FANCD2 monoubiquitination were identified in the lung cancer cell lines examined, including Calu6, and major alterations in these pathways were not identified in the TCGA database. Cell lines were radiosensitized by ATM kinase inhibitor KU60019, but no cell killing by ATM kinase inhibitor alone was observed. While no synergy between gemcitabine or carboplatin and ATR kinase inhibitor ETP-46464 was observed, synergy between gemcitabine and Chk1 kinase inhibitor UCN-01 was observed in 54 T, 201 T and H460, and synergy between carboplatin and Chk1 kinase inhibitor was identified in 201 T and 239 T. No interactions between ATM, ATR and FA activation were observed by either ATM or ATR kinase inhibition in the lung cancer cell lines. Conclusions Analyses of ATM serine 1981 and Chk1 serine 345 phosphorylation, and FANCD2 monoubiquitination revealed that ATM and ATR kinase activation and FA pathway signaling are intact in the lung cancer cell lines examined. As such, these posttranslational modifications may have utility as biomarkers for the integrity of DNA damage signaling pathways in lung cancer. Different sensitization profiles between gemcitabine and carboplatin and ATR kinase inhibitor ETP-46464 and Chk1 kinase inhibitor UCN-01 were observed and this should be considered in the rationale for Phase I clinical trial design with ATR kinase inhibitors. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1649-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jan H Beumer
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA. .,Molecular Therapeutics Drug Discovery Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.
| | - Katherine Y Fu
- Department of Radiation Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Bean N Anyang
- Molecular Therapeutics Drug Discovery Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA.
| | - Jill M Siegfried
- Department of Pharmacology, Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN, USA.
| | - Christopher J Bakkenist
- Department of Radiation Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Hillman Cancer Center, Research Pavilion, Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA, 15213-1863, USA.
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Castella M, Jacquemont C, Thompson EL, Yeo JE, Cheung RS, Huang JW, Sobeck A, Hendrickson EA, Taniguchi T. FANCI Regulates Recruitment of the FA Core Complex at Sites of DNA Damage Independently of FANCD2. PLoS Genet 2015; 11:e1005563. [PMID: 26430909 PMCID: PMC4592014 DOI: 10.1371/journal.pgen.1005563] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/10/2015] [Indexed: 12/31/2022] Open
Abstract
The Fanconi anemia (FA)-BRCA pathway mediates repair of DNA interstrand crosslinks. The FA core complex, a multi-subunit ubiquitin ligase, participates in the detection of DNA lesions and monoubiquitinates two downstream FA proteins, FANCD2 and FANCI (or the ID complex). However, the regulation of the FA core complex itself is poorly understood. Here we show that the FA core complex proteins are recruited to sites of DNA damage and form nuclear foci in S and G2 phases of the cell cycle. ATR kinase activity, an intact FA core complex and FANCM-FAAP24 were crucial for this recruitment. Surprisingly, FANCI, but not its partner FANCD2, was needed for efficient FA core complex foci formation. Monoubiquitination or ATR-dependent phosphorylation of FANCI were not required for the FA core complex recruitment, but FANCI deubiquitination by USP1 was. Additionally, BRCA1 was required for efficient FA core complex foci formation. These findings indicate that FANCI functions upstream of FA core complex recruitment independently of FANCD2, and alter the current view of the FA-BRCA pathway. Fanconi anemia is a genetic disease characterized by bone marrow failure, congenital malformations and cancer predisposition. Cells derived from Fanconi anemia patients have a dysfunctional FA-BRCA pathway and are deficient in the repair of a specific form of DNA damage, DNA interstrand-crosslinks, that are induced by certain chemotherapeutic drugs. Therefore, the study of FA-BRCA pathway regulation is essential for developing new treatments for Fanconi anemia patients and cancer patients in general. One of the first steps in the pathway is the detection of DNA lesions by the FA core complex. We have optimized a method to visualize the recruitment of the FA core complex to sites of DNA damage and, for the first time, explored how this process occurs. We have uncovered several factors that are required for this recruitment. Among them is a FA core complex substrate, FANCI. We report that non-phosphorylated FANCI, previously believed to be an inactive form, has an important role in the recruitment of the FA core complex and DNA interstrand-crosslink repair. Our findings change the current view of the FA-BRCA pathway and have implications for potential clinical strategies aimed at activating or inhibiting the FA-BRCA pathway.
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Affiliation(s)
- Maria Castella
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Celine Jacquemont
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Elizabeth L. Thompson
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Jung Eun Yeo
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Ronald S. Cheung
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jen-Wei Huang
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Alexandra Sobeck
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Eric A. Hendrickson
- Biochemistry, Molecular Biology, and Biophysics Department, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Toshiyasu Taniguchi
- Howard Hughes Medical Institute, Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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178
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Yard B, Chie EK, Adams DJ, Peacock C, Abazeed ME. Radiotherapy in the Era of Precision Medicine. Semin Radiat Oncol 2015; 25:227-36. [DOI: 10.1016/j.semradonc.2015.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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179
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De Cicco M, Rahim MSA, Dames SA. Regulation of the Target of Rapamycin and Other Phosphatidylinositol 3-Kinase-Related Kinases by Membrane Targeting. MEMBRANES 2015; 5:553-75. [PMID: 26426064 PMCID: PMC4703999 DOI: 10.3390/membranes5040553] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/24/2015] [Indexed: 01/05/2023]
Abstract
Phosphatidylinositol 3-kinase-related kinases (PIKKs) play vital roles in the regulation of cell growth, proliferation, survival, and consequently metabolism, as well as in the cellular response to stresses such as ionizing radiation or redox changes. In humans six family members are known to date, namely mammalian/mechanistic target of rapamycin (mTOR), ataxia-telangiectasia mutated (ATM), ataxia- and Rad3-related (ATR), DNA-dependent protein kinase catalytic subunit (DNA-PKcs), suppressor of morphogenesis in genitalia-1 (SMG-1), and transformation/transcription domain-associated protein (TRRAP). All fulfill rather diverse functions and most of them have been detected in different cellular compartments including various cellular membranes. It has been suggested that the regulation of the localization of signaling proteins allows for generating a locally specific output. Moreover, spatial partitioning is expected to improve the reliability of biochemical signaling. Since these assumptions may also be true for the regulation of PIKK function, the current knowledge about the regulation of the localization of PIKKs at different cellular (membrane) compartments by a network of interactions is reviewed. Membrane targeting can involve direct lipid-/membrane interactions as well as interactions with membrane-anchored regulatory proteins, such as, for example, small GTPases, or a combination of both.
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Affiliation(s)
- Maristella De Cicco
- Department of Chemistry, Biomolecular NMR Spectroscopy, Technische Universität München, Lichtenbergstr. 4, Garching 85747, Germany.
| | - Munirah S Abd Rahim
- Department of Chemistry, Biomolecular NMR Spectroscopy, Technische Universität München, Lichtenbergstr. 4, Garching 85747, Germany.
| | - Sonja A Dames
- Department of Chemistry, Biomolecular NMR Spectroscopy, Technische Universität München, Lichtenbergstr. 4, Garching 85747, Germany.
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.
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180
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Shaheen R, Abdel-Salam GMH, Guy MP, Alomar R, Abdel-Hamid MS, Afifi HH, Ismail SI, Emam BA, Phizicky EM, Alkuraya FS. Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism. Genome Biol 2015; 16:210. [PMID: 26416026 PMCID: PMC4587777 DOI: 10.1186/s13059-015-0779-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/14/2015] [Indexed: 04/13/2023] Open
Abstract
Background Primordial dwarfism is a state of extreme prenatal and postnatal growth deficiency, and is characterized by marked clinical and genetic heterogeneity. Results Two presumably unrelated consanguineous families presented with an apparently novel form of primordial dwarfism in which severe growth deficiency is accompanied by distinct facial dysmorphism, brain malformation (microcephaly, agenesis of corpus callosum, and simplified gyration), and severe encephalopathy with seizures. Combined autozygome/exome analysis revealed a novel missense mutation in WDR4 as the likely causal variant. WDR4 is the human ortholog of the yeast Trm82, an essential component of the Trm8/Trm82 holoenzyme that effects a highly conserved and specific (m7G46) methylation of tRNA. The human mutation and the corresponding yeast mutation result in a significant reduction of m7G46 methylation of specific tRNA species, which provides a potential mechanism for primordial dwarfism associated with this lesion, since reduced m7G46 modification causes a growth deficiency phenotype in yeast. Conclusion Our study expands the number of biological pathways underlying primordial dwarfism and adds to a growing list of human diseases linked to abnormal tRNA modification. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0779-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Michael P Guy
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Current address: Department of Chemistry, Northern Kentucky University, Highland Heights, KY, USA
| | - Rana Alomar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Hanan H Afifi
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Samira I Ismail
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Bayoumi A Emam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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181
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Specks J, Nieto-Soler M, Lopez-Contreras AJ, Fernandez-Capetillo O. Modeling the study of DNA damage responses in mice. Methods Mol Biol 2015; 1267:413-37. [PMID: 25636482 DOI: 10.1007/978-1-4939-2297-0_21] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Damaged DNA has a profound impact on mammalian health and overall survival. In addition to being the source of mutations that initiate cancer, the accumulation of toxic amounts of DNA damage can cause severe developmental diseases and accelerate aging. Therefore, understanding how cells respond to DNA damage has become one of the most intense areas of biomedical research in the recent years. However, whereas most mechanistic studies derive from in vitro or in cellulo work, the impact of a given mutation on a living organism is largely unpredictable. For instance, why BRCA1 mutations preferentially lead to breast cancer whereas mutations compromising mismatch repair drive colon cancer is still not understood. In this context, evaluating the specific physiological impact of mutations that compromise genome integrity has become crucial for a better dimensioning of our knowledge. We here describe the various technologies that can be used for modeling mutations in mice and provide a review of the genes and pathways that have been modeled so far in the context of DNA damage responses.
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Affiliation(s)
- Julia Specks
- Genomic Instability Group, Spanish National Cancer Research Center (CNIO), C/Melchor Fernandez Almagro, 3, E-28029, Madrid, Spain
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182
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Karnitz LM, Zou L. Molecular Pathways: Targeting ATR in Cancer Therapy. Clin Cancer Res 2015; 21:4780-5. [PMID: 26362996 DOI: 10.1158/1078-0432.ccr-15-0479] [Citation(s) in RCA: 181] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 08/12/2015] [Indexed: 12/19/2022]
Abstract
The human ATR gene encodes a kinase that is activated by DNA damage and replication stress as a central transducer of a checkpoint signaling pathway. Once activated, ATR phosphorylates multiple substrates, including the kinase Chk1, to regulate cell-cycle progression, replication fork stability, and DNA repair. These events promote cell survival during replication stress and in cells with DNA damage. Accordingly, there has been the tantalizing possibility that ATR inhibitors would be therapeutically useful, especially if they were more effective in tumor versus normal cells. Indeed, multiple studies have demonstrated that alterations that promote tumorigenesis, such as defects in the ATM-p53 pathway, constitutive oncogene activation, and acquisition of the alternative lengthening of telomeres pathway, render tumor cells sensitive to ATR inhibitor monotherapy and/or increase the synergy between ATR inhibitors and genotoxic chemotherapies. Now, nearly two decades after the discovery of ATR, two highly selective and potent ATR inhibitors, AZD6738 and VX-970, are in early-phase clinical trials either as monotherapies or paired with a variety of genotoxic chemotherapies. These trials will generate important insights into the effects of ATR inhibition in humans and the potential role of inhibiting this kinase in the treatment of human malignancies.
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Affiliation(s)
- Larry M Karnitz
- Division of Oncology Research and Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Department of Pathology, Harvard Medical School, Boston, Massachusetts
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183
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Primordial dwarfism: overview of clinical and genetic aspects. Mol Genet Genomics 2015; 291:1-15. [PMID: 26323792 DOI: 10.1007/s00438-015-1110-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 08/21/2015] [Indexed: 01/16/2023]
Abstract
Primordial dwarfism is a group of genetic disorders which include Seckel Syndrome, Silver-Russell Syndrome, Microcephalic Osteodysplastic Primordial Dwarfism types I/III, II and Meier-Gorlin Syndrome. This genetic disorder group is characterized by intra-uterine growth retardation and post-natal growth abnormalities which occur as a result of disorganized molecular and genomic changes in embryonic stage and, thus, it represents a unique area to study growth and developmental abnormalities. Lot of research has been carried out on different aspects; however, a consolidated review that discusses an overall spectrum of this disorder is not accessible. Recent research in this area points toward important molecular and cellular mechanisms in human body that regulate the complexity of growth process. Studies have emerged that have clearly associated with a number of abnormal chromosomal, genetic and epigenetic alterations that can predispose an embryo to develop PD-associated developmental defects. Finding and associating such fundamental changes to its subtypes will help in re-examination of alleged functions at both cellular and developmental levels and thus reveal the intrinsic mechanism that leads to a balanced growth. Although such findings have unraveled a subtle understanding of growth process, we further require active research in terms of identification of reliable biomarkers for different subtypes as an immediate requirement for clinical utilization. It is hoped that further study will advance the understanding of basic mechanisms regulating growth relevant to human health. Therefore, this review has been written with an aim to present an overview of chromosomal, molecular and epigenetic modifications reported to be associated with different subtypes of this heterogenous disorder. Further, latest findings with respect to clinical and molecular genetics research have been summarized to aid the medical fraternity in their clinical utility, for diagnosing disorders where there are overlapping physical attributes and simultaneously inform about the latest developments in PD biology.
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184
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Abstract
Fanconi anemia (FA) is a rare recessive genetic disease characterized by congenital abnormalities, bone marrow failure and heightened cancer susceptibility in early adulthood. FA is caused by biallelic germ-line mutation of any one of 16 genes. While several functions for the FA proteins have been ascribed, the prevailing hypothesis is that the FA proteins function cooperatively in the FA-BRCA pathway to repair damaged DNA. A pivotal step in the activation of the FA-BRCA pathway is the monoubiquitination of the FANCD2 and FANCI proteins. Despite their importance for DNA repair, the domain structure, regulation, and function of FANCD2 and FANCI remain poorly understood. In this review, we provide an overview of our current understanding of FANCD2 and FANCI, with an emphasis on their posttranslational modification and common and unique functions.
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Key Words
- AML , acute myeloid leukemia
- APC/C, anaphase-promoting complex/cyclosome
- APH, aphidicolin
- ARM, armadillo repeat domain
- AT, ataxia-telangiectasia
- ATM, ataxia-telangiectasia mutated
- ATR, ATM and Rad3-related
- BAC, bacterial-artificial-chromosome
- BS, Bloom syndrome
- CUE, coupling of ubiquitin conjugation to endoplasmic reticulum degradation
- ChIP-seq, CHIP sequencing
- CtBP, C-terminal binding protein
- CtIP, CtBP-interacting protein
- DNA interstrand crosslink repair
- DNA repair
- EPS15, epidermal growth factor receptor pathway substrate 15
- FA, Fanconi anemia
- FAN1, FANCD2-associated nuclease1
- FANCD2
- FANCI
- FISH, fluorescence in situ hybridization
- Fanconi anemia
- HECT, homologous to E6-AP Carboxy Terminus
- HJ, Holliday junction
- HR, homologous recombination
- MCM2-MCM7, minichromosome maintenance 2–7
- MEFs, mouse embryonic fibroblasts
- MMC, mitomycin C
- MRN, MRE11/RAD50/NBS1
- NLS, nuclear localization signal
- PCNA, proliferating cell nuclear antigen
- PIKK, phosphatidylinositol-3-OH-kinase-like family of protein kinases
- PIP-box, PCNA-interacting protein motif
- POL κ, DNA polymerase κ
- RACE, rapid amplification of cDNA ends
- RING, really interesting new gene
- RTK, receptor tyrosine kinase
- SCF, Skp1/Cullin/F-box protein complex
- SCKL1, seckel syndrome
- SILAC, stable isotope labeling with amino acids in cell culture
- SLD1/SLD2, SUMO-like domains
- SLIM, SUMO-like domain interacting motif
- TIP60, 60 kDa Tat-interactive protein
- TLS, Translesion DNA synthesis
- UAF1, USP1-associated factor 1
- UBD, ubiquitin-binding domain
- UBZ, ubiquitin-binding zinc finger
- UFB, ultra-fine DNA bridges
- UIM, ubiquitin-interacting motif
- ULD, ubiquitin-like domain
- USP1, ubiquitin-specific protease 1
- VRR-nuc, virus-type replication repair nuclease
- iPOND, isolation of proteins on nascent DNA
- ubiquitin
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Affiliation(s)
- Rebecca A Boisvert
- a Department of Cell and Molecular Biology ; University of Rhode Island ; Kingston , RI USA
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185
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Bertelsen B, Nazaryan-Petersen L, Sun W, Mehrjouy MM, Xie G, Chen W, Hjermind LE, Taschner PEM, Tümer Z. A germline chromothripsis event stably segregating in 11 individuals through three generations. Genet Med 2015; 18:494-500. [PMID: 26312826 DOI: 10.1038/gim.2015.112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/01/2015] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Parentally transmitted germ-line chromothripsis (G-CTH) has been identified in only a few cases. Most of these rearrangements were stably transmitted, in an unbalanced form, from a healthy mother to her child with congenital abnormalities probably caused by de novo copy-number changes of dosage sensitive genes. We describe a G-CTH transmitted through three generations in 11 healthy carriers. METHODS Conventional cytogenetic analysis, mate-pair sequencing, and polymerase chain reaction (PCR) were used to identify the chromosome rearrangement and characterize the breakpoints in all three generations. RESULTS We identified an apparently balanced translocation t(3;5), later shown to be a G-CTH, in all individuals of a three-generation family. The G-CTH stably segregated without occurrence of additional rearrangements; however, several spontaneous abortions were reported, possibly due to unbalanced transmission. Although seven protein-coding genes are interrupted, no clinical features can be definitively attributed to the affected genes. However, it can be speculated that truncation of one of these genes, encoding ataxia-telangiectasia and Rad3-related protein kinase (ATR), a key component of the DNA damage response, may be related to G-CTH formation. CONCLUSION G-CTH rearrangements are not always associated with abnormal phenotypes and may be misinterpreted as balanced two-way translocations, suggesting that G-CTH is an underdiagnosed phenomenon.Genet Med 18 5, 494-500.
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Affiliation(s)
- Birgitte Bertelsen
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
| | - Lusine Nazaryan-Petersen
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
| | - Wei Sun
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Mana M Mehrjouy
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Gangcai Xie
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Wei Chen
- Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Lena E Hjermind
- Neurogenetics Clinic, Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, and Department of Cellular and Molecular Medicine, Section of Neurogenetics, University of Copenhagen, Copenhagen, Denmark
| | - Peter E M Taschner
- Generade Center of Expertise Genomics; University of Applied Sciences Leiden, Leiden, The Netherlands
| | - Zeynep Tümer
- Department of Clinical Genetics, Applied Human Molecular Genetics, Kennedy Center, Copenhagen University Hospital, Glostrup, Denmark
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186
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CEP63 deficiency promotes p53-dependent microcephaly and reveals a role for the centrosome in meiotic recombination. Nat Commun 2015; 6:7676. [PMID: 26158450 PMCID: PMC4499871 DOI: 10.1038/ncomms8676] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/30/2015] [Indexed: 12/24/2022] Open
Abstract
CEP63 is a centrosomal protein that facilitates centriole duplication and is regulated by the DNA damage response. Mutations in CEP63 cause Seckel syndrome, a human disease characterized by microcephaly and dwarfism. Here we demonstrate that Cep63 deficient mice recapitulate Seckel syndrome pathology. The attrition of neural progenitor cells involves p53-dependent cell death and brain size is rescued by the deletion of p53. Cell death is not the result of an aberrant DNA damage response but is triggered by centrosome-based mitotic errors. In addition, Cep63 loss severely impairs meiotic recombination, leading to profound male infertility. Cep63 deficient spermatocytes display numerical and structural centrosome aberrations, chromosome entanglements and defective telomere clustering, suggesting that a reduction in centrosome-mediated chromosome movements underlies recombination failure. Our results provide novel insight into the molecular pathology of microcephaly and establish a role for the centrosome in meiotic recombination.
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187
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Abstract
Homology-dependent exchange of genetic information between DNA molecules has a profound impact on the maintenance of genome integrity by facilitating error-free DNA repair, replication, and chromosome segregation during cell division as well as programmed cell developmental events. This chapter will focus on homologous mitotic recombination in budding yeast Saccharomyces cerevisiae. However, there is an important link between mitotic and meiotic recombination (covered in the forthcoming chapter by Hunter et al. 2015) and many of the functions are evolutionarily conserved. Here we will discuss several models that have been proposed to explain the mechanism of mitotic recombination, the genes and proteins involved in various pathways, the genetic and physical assays used to discover and study these genes, and the roles of many of these proteins inside the cell.
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188
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Kadamb R, Mittal S, Bansal N, Saluja D. Stress-mediated Sin3B activation leads to negative regulation of subset of p53 target genes. Biosci Rep 2015; 35:e00234. [PMID: 26181367 PMCID: PMC4613689 DOI: 10.1042/bsr20150122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/03/2015] [Accepted: 06/19/2015] [Indexed: 11/28/2022] Open
Abstract
The multiprotein SWI-independent 3 (Sin3)-HDAC (histone deacetylase) corepressor complex mediates gene repression through its interaction with DNA-binding factors and recruitment of chromatin-modifying proteins on to the promoters of target gene. Previously, an increased expression of Sin3B and tumour suppressor protein, p53 has been established upon adriamycin treatment. We, now provide evidence that Sin3B expression is significantly up-regulated under variety of stress conditions and this response is not stress-type specific. We observed that Sin3B expression is significantly up-regulated both at transcript and at protein level upon DNA damage induced by bleomycin drug, a radiomimetic agent. This increase in Sin3B expression upon stress is found to be p53-dependent and is associated with enhanced interaction of Sin3B with Ser(15) phosphorylated p53. Binding of Sin3-HDAC repressor complex on to the promoters of p53 target genes influences gene regulation by altering histone modifications (H3K9me3 and H3K27me3) at target genes. Furthermore, knockdown of Sin3B by shRNA severely compromises p53-mediated gene repression under stress conditions. Taken together, these results suggest that stress-induced Sin3B activation is p53-dependent and is essential for p53-mediated repression of its selective target genes. The present study has an implication in understanding the transrepression mechanism of p53 under DNA damaging conditions.
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Affiliation(s)
- Rama Kadamb
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
| | - Shilpi Mittal
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
| | - Nidhi Bansal
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
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189
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Knittel G, Liedgens P, Reinhardt HC. Targeting ATM-deficient CLL through interference with DNA repair pathways. Front Genet 2015; 6:207. [PMID: 26113859 PMCID: PMC4461826 DOI: 10.3389/fgene.2015.00207] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/28/2015] [Indexed: 11/13/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common form of leukemia in the Western world and accounts for approximately 30% of adult leukemias and 25% of non-Hodgkin lymphomas. The median age at diagnosis is 72 years. During recent years numerous genetic aberrations have been identified that are associated with an aggressive course of the disease and resistance against genotoxic chemotherapies. The DNA damage-responsive proapoptotic ATM-CHK2-p53 signaling pathway is frequently mutationally inactivated in CLL either through large deletions on chromosome 11q (ATM) or 17p (TP53), or through protein-damaging mutations. Here, we focus on the role of ATM signaling for the immediate DNA damage response, DNA repair and leukemogenesis. We further discuss novel therapeutic concepts for the targeted treatment of ATM-defective CLLs. We specifically highlight the potential use of PARP1 and DNA-PKcs inhibitors for the treatment of ATM-mutant CLL clones. Lastly, we briefly discuss the current state of genetically engineered mouse models of the disease and emphasize the use of these preclinical tools as a common platform for the development and validation of novel therapeutic agents.
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Affiliation(s)
- Gero Knittel
- Department of Internal Medicine, University Hospital of CologneCologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of CologneCologne, Germany
| | - Paul Liedgens
- Department of Internal Medicine, University Hospital of CologneCologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of CologneCologne, Germany
| | - Hans C. Reinhardt
- Department of Internal Medicine, University Hospital of CologneCologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases, University of CologneCologne, Germany
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190
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Yigit G, Brown KE, Kayserili H, Pohl E, Caliebe A, Zahnleiter D, Rosser E, Bögershausen N, Uyguner ZO, Altunoglu U, Nürnberg G, Nürnberg P, Rauch A, Li Y, Thiel CT, Wollnik B. Mutations in CDK5RAP2 cause Seckel syndrome. Mol Genet Genomic Med 2015; 3:467-80. [PMID: 26436113 PMCID: PMC4585455 DOI: 10.1002/mgg3.158] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/22/2015] [Accepted: 04/22/2015] [Indexed: 11/08/2022] Open
Abstract
Seckel syndrome is a heterogeneous, autosomal recessive disorder marked by prenatal proportionate short stature, severe microcephaly, intellectual disability, and characteristic facial features. Here, we describe the novel homozygous splice-site mutations c.383+1G>C and c.4005-9A>G in CDK5RAP2 in two consanguineous families with Seckel syndrome. CDK5RAP2 (CEP215) encodes a centrosomal protein which is known to be essential for centrosomal cohesion and proper spindle formation and has been shown to be causally involved in autosomal recessive primary microcephaly. We establish CDK5RAP2 as a disease-causing gene for Seckel syndrome and show that loss of functional CDK5RAP2 leads to severe defects in mitosis and spindle organization, resulting in cells with abnormal nuclei and centrosomal pattern, which underlines the important role of centrosomal and mitotic proteins in the pathogenesis of the disease. Additionally, we present an intriguing case of possible digenic inheritance in Seckel syndrome: A severely affected child of nonconsanguineous German parents was found to carry heterozygous mutations in CDK5RAP2 and CEP152. This finding points toward a potential additive genetic effect of mutations in CDK5RAP2 and CEP152.
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Affiliation(s)
- Gökhan Yigit
- Institute of Human Genetics, University of Cologne Cologne, Germany ; Center for Molecular Medicine Cologne (CMMC), University of Cologne Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne Cologne, Germany
| | - Karen E Brown
- Chromosome Biology Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital London, W12 0NN, UK
| | - Hülya Kayserili
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University Istanbul, Turkey
| | - Esther Pohl
- Institute of Human Genetics, University of Cologne Cologne, Germany ; Center for Molecular Medicine Cologne (CMMC), University of Cologne Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne Cologne, Germany
| | - Almuth Caliebe
- Institute of Human Genetics, Christian-Albrechts-University of Kiel Kiel, Germany
| | - Diana Zahnleiter
- Institute of Human Genetics, Friedrich-Alexander University Erlangen-Nuremberg Erlangen, Germany
| | - Elisabeth Rosser
- Department of Clinical Genetics, Great Ormond Street Hospital for Children London, WC1N 3EH, UK
| | - Nina Bögershausen
- Institute of Human Genetics, University of Cologne Cologne, Germany ; Center for Molecular Medicine Cologne (CMMC), University of Cologne Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne Cologne, Germany
| | - Zehra Oya Uyguner
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University Istanbul, Turkey
| | - Umut Altunoglu
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University Istanbul, Turkey
| | - Gudrun Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne Cologne, Germany ; Cologne Center for Genomics, University of Cologne Cologne, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne Cologne, Germany ; Cologne Center for Genomics, University of Cologne Cologne, Germany
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich Schwerzenbach-Zurich, Switzerland
| | - Yun Li
- Institute of Human Genetics, University of Cologne Cologne, Germany ; Center for Molecular Medicine Cologne (CMMC), University of Cologne Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne Cologne, Germany
| | - Christian Thomas Thiel
- Institute of Human Genetics, Friedrich-Alexander University Erlangen-Nuremberg Erlangen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University of Cologne Cologne, Germany ; Center for Molecular Medicine Cologne (CMMC), University of Cologne Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne Cologne, Germany
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191
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Thiffault I, Saunders C, Jenkins J, Raje N, Canty K, Sharma M, Grote L, Welsh HI, Farrow E, Twist G, Miller N, Zwick D, Zellmer L, Kingsmore SF, Safina NP. A patient with polymerase E1 deficiency (POLE1): clinical features and overlap with DNA breakage/instability syndromes. BMC MEDICAL GENETICS 2015; 16:31. [PMID: 25948378 PMCID: PMC4630961 DOI: 10.1186/s12881-015-0177-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/24/2015] [Indexed: 12/21/2022]
Abstract
Background Chromosome instability syndromes are a group of inherited conditions associated with chromosomal instability and breakage, often leading to immunodeficiency, growth retardation and increased risk of malignancy. Case presentation We performed exome sequencing on a girl with a suspected chromosome instability syndrome that manifested as growth retardation, microcephaly, developmental delay, dysmorphic features, poikiloderma, immune deficiency with pancytopenia, and myelodysplasia. She was homozygous for a previously reported splice variant, c.4444 + 3A > G in the POLE1 gene, which encodes the catalytic subunit of DNA polymerase E. Conclusion This is the second family with POLE1-deficency, with the affected individual demonstrating a more severe phenotype than previously described. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0177-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA. .,Department of Pathology and Laboratory Medicine, Childrens Mercy Hospitals, Kansas City, MO, 64108, USA.
| | - Carol Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA. .,Department of Pathology and Laboratory Medicine, Childrens Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
| | - Janda Jenkins
- Division of Clinical Genetics, Childrens Mercy Hospital, 2420 Pershing Road, Suite 421, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
| | - Nikita Raje
- Pediatric Allergy, Asthma and Immunology Clinic, Children's Mercy Hospitals, Kansas City, MO, 64108, USA.
| | - Kristi Canty
- Dermatology Clinic, Children's Mercy Hospitals, Kansas City, MO, 64108, USA.
| | - Mukta Sharma
- Department of Hematology and Oncology, Children's Mercy Hospitals, Kansas City, MO, 64108, USA.
| | - Lauren Grote
- Division of Clinical Genetics, Childrens Mercy Hospital, 2420 Pershing Road, Suite 421, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
| | - Holly I Welsh
- Division of Clinical Genetics, Childrens Mercy Hospital, 2420 Pershing Road, Suite 421, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
| | - Emily Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA.
| | - Greyson Twist
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA.
| | - Neil Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA.
| | - David Zwick
- Department of Pathology and Laboratory Medicine, Childrens Mercy Hospitals, Kansas City, MO, 64108, USA.
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA.
| | - Stephen F Kingsmore
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, 64108, USA. .,Department of Pathology and Laboratory Medicine, Childrens Mercy Hospitals, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
| | - Nicole P Safina
- Division of Clinical Genetics, Childrens Mercy Hospital, 2420 Pershing Road, Suite 421, Kansas City, MO, 64108, USA. .,Department of Pediatrics, Children's Mercy Hospitals, Kansas City, MO, 64108, USA. .,University of Missouri, Kansas City School of Medicine, Kansas City, MO, USA.
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192
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Abstract
Mec1 (ATR in humans) is the principal kinase responsible for checkpoint activation in response to replication stress and DNA damage in Saccharomyces cerevisiae. Checkpoint initiation requires stimulation of Mec1 kinase activity by specific activators. The complexity of checkpoint initiation in yeast increases with the complexity of chromosomal states during the different phases of the cell cycle. In G1 phase, the checkpoint clamp 9-1-1 is both necessary and sufficient for full activation of Mec1 kinase whereas in G2/M, robust checkpoint function requires both 9-1-1 and the replisome assembly protein Dpb11 (human TopBP1). A third activator, Dna2, is employed specifically during S phase to stimulate Mec1 kinase and to initiate the replication checkpoint. Dna2 is an essential nuclease-helicase that is required for proper Okazaki fragment maturation, for double-strand break repair, and for protecting stalled replication forks. Remarkably, all three Mec1 activators use an unstructured region of the protein, containing two critically important aromatic residues, in order to activate Mec1. A role for these checkpoint activators in channeling aberrant replication structures into checkpoint complexes is discussed.
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Affiliation(s)
- Paulina H Wanrooij
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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193
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Abstract
In order to maintain genomic stability, cells have developed sophisticated signalling pathways to enable DNA damage or DNA replication stress to be resolved. Key mediators of this DNA damage response (DDR) are the ATM and ATR kinases, which induce cell cycle arrest and facilitate DNA repair via their downstream targets. Inhibiting the DDR has become an attractive therapeutic concept in cancer therapy, since (i) resistance to genotoxic therapies has been associated with increased DDR signalling, and (ii) many cancers have defects in certain components of the DDR rendering them highly dependent on the remaining DDR pathways for survival. ATM and ATR act as the apical regulators of the response to DNA double strand breaks and replication stress, respectively, with overlapping but non-redundant activities. Highly selective small molecule inhibitors of ATM and ATR are currently in preclinical and clinical development, respectively. Preclinical data have provided a strong rationale for clinical testing of these compounds both in combination with radio- or chemotherapy, and in synthetic lethal approaches to treat tumours with deficiencies in certain DDR components. Whole genome sequencing studies have reported that mutations in DDR genes occur with a high frequency in many common tumour types, suggesting that a synthetic lethal approach with ATM or ATR inhibitors could have widespread utility, providing that appropriate biomarkers are developed.
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Affiliation(s)
- Anika Maria Weber
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, The Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Anderson Joseph Ryan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, The Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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194
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Abstract
Genome instability is a hallmark of cancer, and DNA replication is the most vulnerable cellular process that can lead to it. Any condition leading to high levels of DNA damage will result in replication stress, which is a source of genome instability and a feature of pre-cancerous and cancerous cells. Therefore, understanding the molecular basis of replication stress is crucial to the understanding of tumorigenesis. Although a negative aspect of replication stress is its prominent role in tumorigenesis, a positive aspect is that it provides a potential target for cancer therapy. In this Review, we discuss the link between persistent replication stress and tumorigenesis, with the goal of shedding light on the mechanisms underlying the initiation of an oncogenic process, which should open up new possibilities for cancer diagnostics and treatment.
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Affiliation(s)
- Hélène Gaillard
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Av. Américo Vespucio s/n, Sevilla 41092, Spain
| | - Tatiana García-Muse
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Av. Américo Vespucio s/n, Sevilla 41092, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla, Av. Américo Vespucio s/n, Sevilla 41092, Spain
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195
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de Bruin C, Mericq V, Andrew SF, van Duyvenvoorde HA, Verkaik NS, Losekoot M, Porollo A, Garcia H, Kuang Y, Hanson D, Clayton P, van Gent DC, Wit JM, Hwa V, Dauber A. An XRCC4 splice mutation associated with severe short stature, gonadal failure, and early-onset metabolic syndrome. J Clin Endocrinol Metab 2015; 100:E789-98. [PMID: 25742519 PMCID: PMC4422886 DOI: 10.1210/jc.2015-1098] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
CONTEXT Severe short stature can be caused by defects in numerous biological processes including defects in IGF-1 signaling, centromere function, cell cycle control, and DNA damage repair. Many syndromic causes of short stature are associated with medical comorbidities including hypogonadism and microcephaly. OBJECTIVE To identify an underlying genetic etiology in two siblings with severe short stature and gonadal failure. DESIGN Clinical phenotyping, genetic analysis, complemented by in vitro functional studies of the candidate gene. SETTING An academic pediatric endocrinology clinic. PATIENTS OR OTHER PARTICIPANTS Two adult siblings (male patient [P1] and female patient 2 [P2]) presented with a history of severe postnatal growth failure (adult heights: P1, -6.8 SD score; P2, -4 SD score), microcephaly, primary gonadal failure, and early-onset metabolic syndrome in late adolescence. In addition, P2 developed a malignant gastrointestinal stromal tumor at age 28. INTERVENTION(S) Single nucleotide polymorphism microarray and exome sequencing. RESULTS Combined microarray analysis and whole exome sequencing of the two affected siblings and one unaffected sister identified a homozygous variant in XRCC4 as the probable candidate variant. Sanger sequencing and mRNA studies revealed a splice variant resulting in an in-frame deletion of 23 amino acids. Primary fibroblasts (P1) showed a DNA damage repair defect. CONCLUSIONS In this study we have identified a novel pathogenic variant in XRCC4, a gene that plays a critical role in non-homologous end-joining DNA repair. This finding expands the spectrum of DNA damage repair syndromes to include XRCC4 deficiency causing severe postnatal growth failure, microcephaly, gonadal failure, metabolic syndrome, and possibly tumor predisposition.
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Affiliation(s)
- Christiaan de Bruin
- Cincinnati Center for Growth Disorders (C.d.B., S.F.A., V.H., A.D.), Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229; Institute of Maternal and Child Research (V.M.), Faculty of Medicine, University of Chile, 226-3 Santiago, Chile; Laboratory for Diagnostic Genome Analysis (H.A.v.D., M.L.), Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; Department of Genetics (N.S.V., D.C.v.G.), Erasmus MC, 3015 CE Rotterdam, The Netherlands; Center for Autoimmune Genomics and Etiology (A.P.), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229; Pediatrics Division (H.G.), Faculty of Medicine, Pontificia Universidad Catolica de Chile Santiago, 340 Santiago, Chile; Division of Developmental Biology (Y.K.), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229; Institute of Human Development (D.H., P.C.), University of Manchester and Manchester Academic Health Sciences Centre, Manchester M13 9PL, United Kingdom; and Department of Pediatrics (J.M.W.), Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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196
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HUS1 regulates in vivo responses to genotoxic chemotherapies. Oncogene 2015; 35:662-9. [PMID: 25915840 DOI: 10.1038/onc.2015.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 03/08/2015] [Accepted: 03/10/2015] [Indexed: 12/14/2022]
Abstract
Cells are under constant attack from genotoxins and rely on a multifaceted DNA damage response (DDR) network to maintain genomic integrity. Central to the DDR are the ATM and ATR kinases, which respond primarily to double-strand DNA breaks (DSBs) and replication stress, respectively. Optimal ATR signaling requires the RAD9A-RAD1-HUS1 (9-1-1) complex, a toroidal clamp that is loaded at damage sites and scaffolds signaling and repair factors. Whereas complete ATR pathway inactivation causes embryonic lethality, partial Hus1 impairment has been accomplished in adult mice using hypomorphic (Hus1(neo)) and null (Hus1(Δ1)) Hus1 alleles, and here we use this system to define the tissue- and cell type-specific actions of the HUS1-mediated DDR in vivo. Hus1(neo/Δ1) mice showed hypersensitivity to agents that cause replication stress, including the crosslinking agent mitomycin C (MMC) and the replication inhibitor hydroxyurea, but not the DSB inducer ionizing radiation. Analysis of tissue morphology, genomic instability, cell proliferation and apoptosis revealed that MMC treatment caused severe damage in highly replicating tissues of mice with partial Hus1 inactivation. The role of the 9-1-1 complex in responding to MMC was partially ATR-independent, as a HUS1 mutant that was proficient for ATR-induced checkpoint kinase 1 phosphorylation nevertheless conferred MMC hypersensitivity. To assess the interplay between the ATM and ATR pathways in responding to replication stress in vivo, we used Hus1/Atm double mutant mice. Whereas Hus1(neo/neo) and Atm(-/-) single mutant mice survived low-dose MMC similar to wild-type controls, Hus1(neo/neo)Atm(-/-) double mutants showed striking MMC hypersensitivity, consistent with a model in which MMC exposure in the context of Hus1 dysfunction results in DSBs to which the ATM pathway normally responds. This improved understanding of the inter-dependency between two major DDR mechanisms during the response to a conventional chemotherapeutic illustrates how inhibition of checkpoint factors such as HUS1 may be effective for the treatment of ATM-deficient and other cancers.
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197
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Torgovnick A, Schumacher B. DNA repair mechanisms in cancer development and therapy. Front Genet 2015; 6:157. [PMID: 25954303 PMCID: PMC4407582 DOI: 10.3389/fgene.2015.00157] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/07/2015] [Indexed: 01/18/2023] Open
Abstract
DNA damage has been long recognized as causal factor for cancer development. When erroneous DNA repair leads to mutations or chromosomal aberrations affecting oncogenes and tumor suppressor genes, cells undergo malignant transformation resulting in cancerous growth. Genetic defects can predispose to cancer: mutations in distinct DNA repair systems elevate the susceptibility to various cancer types. However, DNA damage not only comprises a root cause for cancer development but also continues to provide an important avenue for chemo- and radiotherapy. Since the beginning of cancer therapy, genotoxic agents that trigger DNA damage checkpoints have been applied to halt the growth and trigger the apoptotic demise of cancer cells. We provide an overview about the involvement of DNA repair systems in cancer prevention and the classes of genotoxins that are commonly used for the treatment of cancer. A better understanding of the roles and interactions of the highly complex DNA repair machineries will lead to important improvements in cancer therapy.
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Affiliation(s)
- Alessandro Torgovnick
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases Research Center, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases Research Center, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
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198
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Abstract
Skeletal dysplasias result from disruptions in normal skeletal growth and development and are a major contributor to severe short stature. They occur in approximately 1/5,000 births, and some are lethal. Since the most recent publication of the Nosology and Classification of Genetic Skeletal Disorders, genetic causes of 56 skeletal disorders have been uncovered. This remarkable rate of discovery is largely due to the expanded use of high-throughput genomic technologies. In this review, we discuss these recent discoveries and our understanding of the molecular mechanisms behind these skeletal dysplasia phenotypes. We also cover potential therapies, unusual genetic mechanisms, and novel skeletal syndromes both with and without known genetic causes. The acceleration of skeletal dysplasia genetics is truly spectacular, and these advances hold great promise for diagnostics, risk prediction, and therapeutic design.
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199
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Brown JS, Jackson SP. Ubiquitylation, neddylation and the DNA damage response. Open Biol 2015; 5:150018. [PMID: 25833379 PMCID: PMC4422126 DOI: 10.1098/rsob.150018] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/09/2015] [Indexed: 12/19/2022] Open
Abstract
Failure of accurate DNA damage sensing and repair mechanisms manifests as a variety of human diseases, including neurodegenerative disorders, immunodeficiency, infertility and cancer. The accuracy and efficiency of DNA damage detection and repair, collectively termed the DNA damage response (DDR), requires the recruitment and subsequent post-translational modification (PTM) of a complex network of proteins. Ubiquitin and the ubiquitin-like protein (UBL) SUMO have established roles in regulating the cellular response to DNA double-strand breaks (DSBs). A role for other UBLs, such as NEDD8, is also now emerging. This article provides an overview of the DDR, discusses our current understanding of the process and function of PTM by ubiquitin and NEDD8, and reviews the literature surrounding the role of ubiquitylation and neddylation in DNA repair processes, focusing particularly on DNA DSB repair.
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Affiliation(s)
- Jessica S Brown
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
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200
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Çelenk F, Cevizci R, Altınyay Ş, Bayazıt YA. Cochlear Implantation in Extraordinary Cases. Balkan Med J 2015; 32:208-13. [PMID: 26167347 DOI: 10.5152/balkanmedj.2015.15937] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/27/2014] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Although cochlear implantation has been almost a standard otological procedure worldwide, it may still create a dilemma for the surgeon in some unusual instances such as Seckel syndrome, aural atresia and posterior fossa arachnoid cyst. CASE REPORT Three extraordinary cases of cochlear implantation were reported. The first case was a case of Seckel syndrome with a cardiac pacemaker due to complete atrioventricular block. The second case had posterior fossa arachnoid cyst that had retrosigmoid cyst removal and cochlear implantation simultaneously. The last case had cochlear implantation in the ear with congenital aural atresia. All cases could be implanted successfully with full electrode insertion and good audiological outcome. Delayed facial paralysis that occurred in the patient with arachnoid cyst resolved spontaneously. CONCLUSION This study addressed the efficiency of cochlear implantation in cases of Seckel syndrome, complete atrioventricular block managed with cardiac pacemaker, congenital aural atresia and posterior fossa arachnoid cyst. In addition, the retrosigmoid approach and cochlear implantation can be performed simultaneously.
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Affiliation(s)
- Fatih Çelenk
- Department of Otorhinolaryngology, Gaziantep University Faculty of Medicine, Gaziantep, Turkey
| | - Raşit Cevizci
- Department of Otorhinolaryngology, Medipol University Faculty of Medicine, İstanbul, Turkey
| | - Şenay Altınyay
- Audiology Unit, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Yıldırım Ahmet Bayazıt
- Department of Otorhinolaryngology, Medipol University Faculty of Medicine, İstanbul, Turkey
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