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Wilson DM, Rieckher M, Williams AB, Schumacher B. Systematic analysis of DNA crosslink repair pathways during development and aging in Caenorhabditis elegans. Nucleic Acids Res 2017; 45:9467-9480. [PMID: 28934497 PMCID: PMC5766164 DOI: 10.1093/nar/gkx660] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/18/2017] [Indexed: 01/12/2023] Open
Abstract
DNA interstrand crosslinks (ICLs) are generated by endogenous sources and chemotherapeutics, and pose a threat to genome stability and cell survival. Using Caenorhabditis elegans mutants, we identify DNA repair factors that protect against the genotoxicity of ICLs generated by trioxsalen/ultraviolet A (TMP/UVA) during development and aging. Mutations in nucleotide excision repair (NER) components (e.g. XPA-1 and XPF-1) imparted extreme sensitivity to TMP/UVA relative to wild-type animals, manifested as developmental arrest, defects in adult tissue morphology and functionality, and shortened lifespan. Compensatory roles for global-genome (XPC-1) and transcription-coupled (CSB-1) NER in ICL sensing were exposed. The analysis also revealed contributions of homologous recombination (BRC-1/BRCA1), the MUS-81, EXO-1, SLX-1 and FAN-1 nucleases, and the DOG-1 (FANCJ) helicase in ICL resolution, influenced by the replicative-status of the cell/tissue. No obvious or critical role in ICL repair was seen for non-homologous end-joining (cku-80) or base excision repair (nth-1, exo-3), the Fanconi-related proteins BRC-2 (BRCA2/FANCD1) and FCD-2 (FANCD2), the WRN-1 or HIM-6 (BLM) helicases, or the GEN-1 or MRT-1 (SNM1) nucleases. Our efforts uncover replication-dependent and -independent ICL repair networks, and establish nematodes as a model for investigating the repair and consequences of DNA crosslinks in metazoan development and in adult post-mitotic and proliferative germ cells.
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Affiliation(s)
- David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Matthias Rieckher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Ashley B Williams
- Institute for Genome Stability in Aging and Disease, Medical Faculty, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
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52
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Doherty A, Kernogitski Y, Kulminski AM, Pedro de Magalhães J. Identification of polymorphisms in cancer patients that differentially affect survival with age. Aging (Albany NY) 2017; 9:2117-2136. [PMID: 29064820 PMCID: PMC5680559 DOI: 10.18632/aging.101305] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/06/2017] [Indexed: 01/08/2023]
Abstract
The World Health Organization predicts that the proportion of the world's population over 60 will almost double from 12% to 22% between 2015 and 2050. Ageing is the biggest risk factor for cancer, which is a leading cause of deaths worldwide. Unfortunately, research describing how genetic variants affect cancer progression commonly neglects to account for the ageing process. Herein is the first systematic analysis that combines a large longitudinal data set with a targeted candidate gene approach to examine the effect of genetic variation on survival as a function of age in cancer patients. Survival was significantly decreased in individuals with heterozygote or rare homozygote (i.e. variant) genotypes compared to those with a common homozygote genotype (i.e. wild type) for two single nucleotide polymorphisms (rs11574358 and rs4147918), one gene (SIRT3) and one pathway (FoxO signalling) in an age-dependent manner. All identified genes and pathways have previously been associated with ageing and cancer. These observations demonstrate that there are ageing-related genetic elements that differentially affect mortality in cancer patients in an age-dependent manner. Understanding the genetic determinants affecting prognosis differently with age will be invaluable to develop age-specific prognostic biomarkers and personalized therapies that may improve clinical outcomes for older individuals.
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Affiliation(s)
- Aoife Doherty
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, United Kingdom
| | - Yelena Kernogitski
- Biodemography of Aging Research Unit (BARU), Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit (BARU), Social Science Research Institute, Duke University, Durham, NC 27708, USA
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, L7 8TX, United Kingdom
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53
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Rochester JD, Tanner PC, Sharp CS, Andralojc KM, Updike DL. PQN-75 is expressed in the pharyngeal gland cells of Caenorhabditiselegans and is dispensable for germline development. Biol Open 2017; 6:1355-1363. [PMID: 28916707 PMCID: PMC5612245 DOI: 10.1242/bio.027987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Caenorhabditis elegans, five pharyngeal gland cells reside in the terminal bulb of the pharynx and extend anterior processes to five contact points in the pharyngeal lumen. Pharyngeal gland cells secrete mucin-like proteins thought to facilitate digestion, hatching, molting and assembly of the surface coat of the cuticle, but supporting evidence has been sparse. Here we show pharyngeal gland cell expression of PQN-75, a unique protein containing an N-terminal signal peptide, nucleoporin (Nup)-like phenylalanine/glycine (FG) repeats, and an extensive polyproline repeat domain with similarities to human basic salivary proline-rich pre-protein PRB2. Imaging of C-terminal tagged PQN-75 shows localization throughout pharyngeal gland cell processes but not the pharyngeal lumen; instead, aggregates of PQN-75 are occasionally found throughout the pharynx, suggesting secretion from pharyngeal gland cells into the surrounding pharyngeal muscle. PQN-75 does not affect fertility and brood size in C. elegans but confers some degree of stress resistance and thermotolerance through unknown mechanisms. Summary: PQN-75 is expressed in pharyngeal gland cells and shares similarity with human basic salivary proline-rich protein PBR2, suggesting evolutionary conservation between gland cells in the upper digestive tract.
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Affiliation(s)
- Jesse D Rochester
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
| | - Paige C Tanner
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
| | - Catherine S Sharp
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
| | | | - Dustin L Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA
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Rieckher M, Bujarrabal A, Doll MA, Soltanmohammadi N, Schumacher B. A simple answer to complex questions: Caenorhabditis elegans as an experimental model for examining the DNA damage response and disease genes. J Cell Physiol 2017; 233:2781-2790. [PMID: 28463453 DOI: 10.1002/jcp.25979] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 01/31/2023]
Abstract
The genetic information is constantly challenged by genotoxic attacks. DNA repair mechanisms evolved early in evolution and recognize and remove the various lesions. A complex network of DNA damage responses (DDR) orchestrates a variety of physiological adaptations to the presence of genome instability. Erroneous repair or malfunctioning of the DDR causes cancer development and the accumulation of DNA lesions drives the aging process. For understanding the complex DNA repair and DDR mechanisms it is pivotal to employ simple metazoan as model systems. The nematode Caenorhabditis elegans has become a well-established and popular experimental organism that allows dissecting genome stability mechanisms in dynamic and differentiated tissues and under physiological conditions. We provide an overview of the distinct advantages of the nematode system for studying DDR and provide a range of currently applied methodologies.
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Affiliation(s)
- Matthias Rieckher
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Arturo Bujarrabal
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Markus A Doll
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Najmeh Soltanmohammadi
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD), and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
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55
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Lee S, Dong HH. FoxO integration of insulin signaling with glucose and lipid metabolism. J Endocrinol 2017; 233:R67-R79. [PMID: 28213398 PMCID: PMC5480241 DOI: 10.1530/joe-17-0002] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 02/17/2017] [Indexed: 12/19/2022]
Abstract
The forkhead box O family consists of FoxO1, FoxO3, FoxO4 and FoxO6 proteins in mammals. Expressed ubiquitously in the body, the four FoxO isoforms share in common the amino DNA-binding domain, known as 'forkhead box' domain. They mediate the inhibitory action of insulin or insulin-like growth factor on key functions involved in cell metabolism, growth, differentiation, oxidative stress, senescence, autophagy and aging. Genetic mutations in FoxO genes or abnormal expression of FoxO proteins are associated with metabolic disease, cancer or altered lifespan in humans and animals. Of the FoxO family, FoxO6 is the least characterized member and is shown to play pivotal roles in the liver, skeletal muscle and brain. Altered FoxO6 expression is associated with the pathogenesis of insulin resistance, dietary obesity and type 2 diabetes and risk of neurodegeneration disease. FoxO6 is evolutionally divergent from other FoxO isoforms. FoxO6 mediates insulin action on target genes in a mechanism that is fundamentally different from other FoxO members. Here, we focus our review on the role of FoxO6, in contrast with other FoxO isoforms, in health and disease. We review the distinctive mechanism by which FoxO6 integrates insulin signaling to hepatic glucose and lipid metabolism. We highlight the importance of FoxO6 dysregulation in the dual pathogenesis of fasting hyperglycemia and hyperlipidemia in diabetes. We review the role of FoxO6 in memory consolidation and its contribution to neurodegeneration disease and aging. We discuss the potential therapeutic option of pharmacological FoxO6 inhibition for improving glucose and lipid metabolism in diabetes.
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Affiliation(s)
- Sojin Lee
- Division of Endocrinology and DiabetesDepartment of Pediatrics, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - H Henry Dong
- Division of Endocrinology and DiabetesDepartment of Pediatrics, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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56
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Son HG, Seo M, Ham S, Hwang W, Lee D, An SWA, Artan M, Seo K, Kaletsky R, Arey RN, Ryu Y, Ha CM, Kim YK, Murphy CT, Roh TY, Nam HG, Lee SJV. RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans. Nat Commun 2017; 8:14749. [PMID: 28276441 PMCID: PMC5347137 DOI: 10.1038/ncomms14749] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 01/30/2017] [Indexed: 12/14/2022] Open
Abstract
Long-lived organisms often feature more stringent protein and DNA quality control. However, whether RNA quality control mechanisms, such as nonsense-mediated mRNA decay (NMD), which degrades both abnormal as well as some normal transcripts, have a role in organismal aging remains unexplored. Here we show that NMD mediates longevity in C. elegans strains with mutations in daf-2/insulin/insulin-like growth factor 1 receptor. We find that daf-2 mutants display enhanced NMD activity and reduced levels of potentially aberrant transcripts. NMD components, including smg-2/UPF1, are required to achieve the longevity of several long-lived mutants, including daf-2 mutant worms. NMD in the nervous system of the animals is particularly important for RNA quality control to promote longevity. Furthermore, we find that downregulation of yars-2/tyrosyl-tRNA synthetase, an NMD target transcript, by daf-2 mutations contributes to longevity. We propose that NMD-mediated RNA surveillance is a crucial quality control process that contributes to longevity conferred by daf-2 mutations.
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Affiliation(s)
- Heehwa G. Son
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Mihwa Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
- Center for Plant Aging Research, Institute for Basic Science, Daegu 42988, South Korea
| | - Seokjin Ham
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Wooseon Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Dongyeop Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Seon Woo A. An
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Murat Artan
- Information Technology Convergence Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Keunhee Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Rachel Kaletsky
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Rachel N. Arey
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Youngjae Ryu
- Research Division, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Chang Man Ha
- Research Division, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, South Korea
- Division of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Coleen T. Murphy
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science, Daegu 42988, South Korea
- Department of New Biology, DGIST, Daegu 42988, South Korea
| | - Seung-Jae V. Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
- Information Technology Convergence Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
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57
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Barzilai A, Schumacher B, Shiloh Y. Genome instability: Linking ageing and brain degeneration. Mech Ageing Dev 2017; 161:4-18. [DOI: 10.1016/j.mad.2016.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/23/2016] [Accepted: 03/26/2016] [Indexed: 02/06/2023]
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58
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Altintas O, Park S, Lee SJV. The role of insulin/IGF-1 signaling in the longevity of model invertebrates, C. elegans and D. melanogaster. BMB Rep 2016; 49:81-92. [PMID: 26698870 PMCID: PMC4915121 DOI: 10.5483/bmbrep.2016.49.2.261] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 01/08/2023] Open
Abstract
Insulin/insulin-like growth factor (IGF)-1 signaling (IIS) pathway regulates
aging in many organisms, ranging from simple invertebrates to mammals, including
humans. Many seminal discoveries regarding the roles of IIS in aging and
longevity have been made by using the roundworm Caenorhabditis
elegans and the fruit fly Drosophila melanogaster. In this
review, we describe the mechanisms by which various IIS components regulate
aging in C. elegans and D. melanogaster. We
also cover systemic and tissue-specific effects of the IIS components on the
regulation of lifespan. We further discuss IIS-mediated physiological processes
other than aging and their effects on human disease models focusing on
C. elegans studies. As both C. elegans and
D. melanogaster have been essential for key findings
regarding the effects of IIS on organismal aging in general, these invertebrate
models will continue to serve as workhorses to help our understanding of
mammalian aging. [BMB Reports 2016; 49(2): 81-92]
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Affiliation(s)
- Ozlem Altintas
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Sangsoon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Seung-Jae V Lee
- School of Interdisciplinary Bioscience and Bioengineering, Department of Life Sciences, and Information Technology Convergence Engineering, Pohang University of Science and Technology, Pohang 37673, Korea
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59
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Targeting transcription-coupled nucleotide excision repair overcomes resistance in chronic lymphocytic leukemia. Leukemia 2016; 31:1177-1186. [DOI: 10.1038/leu.2016.294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 12/31/2022]
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60
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Williams AB, Schumacher B. DNA damage responses and stress resistance: Concepts from bacterial SOS to metazoan immunity. Mech Ageing Dev 2016; 165:27-32. [PMID: 27687175 DOI: 10.1016/j.mad.2016.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/20/2016] [Accepted: 09/25/2016] [Indexed: 11/26/2022]
Abstract
The critical need for species preservation has driven the evolution of mechanisms that integrate stress signals from both exogenous and endogenous sources. Past research has been largely focused on cell-autonomous stress responses; however, recently their systemic outcomes within an organism and their implications at the ecological and species levels have emerged. Maintenance of species depends on the high fidelity transmission of the genome over infinite generations; thus, many pathways exist to monitor and restore the integrity of the genome and to coordinate DNA repair with other cellular processes, such as cell division and growth. The specifics of these DNA damage responses (DDRs) vary vastly but some general themes are conserved from ancient organisms, such as bacteria and archaea, to humans. Despite decades of research, however, DDRs still have many layers of complexity and some surprises left to be discovered. One of the most interesting current research topics is the link between DNA damage and stress resistance: the outcomes of DDRs can protect the organism from other secondary challenges. At this time, these types of responses are best characterized in bacteria and the simple metazoan model, Caenorhabditis elegans, but it is becoming clear that similar processes also exist in higher organisms.
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Affiliation(s)
- Ashley B Williams
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
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61
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Non-transcriptional Function of FOXO1/DAF-16 Contributes to Translesion DNA Synthesis. Mol Cell Biol 2016; 36:2755-2766. [PMID: 27550812 DOI: 10.1128/mcb.00265-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Forkhead box O (FOXO; DAF-16 in nematode) transcription factors activate a program of genes that control stress resistance, metabolism, and lifespan. Given the adverse impact of the stochastic DNA damage on organismal development and ageing, we examined the role of FOXO/DAF-16 in UV-induced DNA-damage response. Knockdown of FOXO1, but not FOXO3a, increases sensitivity to UV irradiation when exposed during S phase, suggesting a contribution of FOXO1 to translesion DNA synthesis (TLS), a replicative bypass of UV-induced DNA lesions. Actually, FOXO1 depletion results in a sustained activation of the ATR-Chk1 signaling and a reduction of PCNA monoubiquitination following UV irradiation. FOXO1 does not alter the expression of TLS-related genes but binds to the protein replication protein A (RPA1) that coats single-stranded DNA and acts as a scaffold for TLS. In Caenorhabditis elegans, daf-16 null mutants show UV-induced retardation in larval development and are rescued by overexpressing DAF-16 mutant lacking transactivation domain, but not substitution mutant unable to interact with RPA-1. Thus, our findings demonstrate that FOXO1/DAF-16 is a functional component in TLS independently of its transactivation activity.
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62
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Rieckher M. Light Sheet Microscopy to Measure Protein Dynamics. J Cell Physiol 2016; 232:27-35. [DOI: 10.1002/jcp.25451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/07/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Matthias Rieckher
- Institute for Genome Stability in Ageing and Disease; Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
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63
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Ribezzo F, Shiloh Y, Schumacher B. Systemic DNA damage responses in aging and diseases. Semin Cancer Biol 2016; 37-38:26-35. [PMID: 26773346 PMCID: PMC4886830 DOI: 10.1016/j.semcancer.2015.12.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 12/28/2015] [Accepted: 12/31/2015] [Indexed: 01/09/2023]
Abstract
The genome is constantly attacked by a variety of genotoxic insults. The causal role for DNA damage in aging and cancer is exemplified by genetic defects in DNA repair that underlie a broad spectrum of acute and chronic human disorders that are characterized by developmental abnormalities, premature aging, and cancer predisposition. The disease symptoms are typically tissue-specific with uncertain genotype-phenotype correlation. The cellular DNA damage response (DDR) has been extensively investigated ever since yeast geneticists discovered DNA damage checkpoint mechanisms, several decades ago. In recent years, it has become apparent that not only cell-autonomous but also systemic DNA damage responses determine the outcome of genome instability in organisms. Understanding the mechanisms of non-cell-autonomous DNA damage responses will provide important new insights into the role of genome instability in human aging and a host of diseases including cancer and might better explain the complex phenotypes caused by genome instability.
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Affiliation(s)
- Flavia Ribezzo
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD) Research Center, Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Yosef Shiloh
- The David and Inez Myers Laboratory for Genetic Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD) Research Center, Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany.
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64
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Du L, Tracy S, Rifkin SA. Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements. Dev Biol 2016; 412:160-170. [PMID: 26896592 PMCID: PMC4814310 DOI: 10.1016/j.ydbio.2016.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/03/2016] [Accepted: 02/10/2016] [Indexed: 10/22/2022]
Abstract
Cis-regulatory elements (CREs) are crucial links in developmental gene regulatory networks, but in many cases, it can be difficult to discern whether similar CREs are functionally equivalent. We found that despite similar conservation and binding capability to upstream activators, different GATA cis-regulatory motifs within the promoter of the C. elegans endoderm regulator elt-2 play distinctive roles in activating and modulating gene expression throughout development. We fused wild-type and mutant versions of the elt-2 promoter to a gfp reporter and inserted these constructs as single copies into the C. elegans genome. We then counted early embryonic gfp transcripts using single-molecule RNA FISH (smFISH) and quantified gut GFP fluorescence. We determined that a single primary dominant GATA motif located 527bp upstream of the elt-2 start codon was necessary for both embryonic activation and later maintenance of transcription, while nearby secondary GATA motifs played largely subtle roles in modulating postembryonic levels of elt-2. Mutation of the primary activating site increased low-level spatiotemporally ectopic stochastic transcription, indicating that this site acts repressively in non-endoderm cells. Our results reveal that CREs with similar GATA factor binding affinities in close proximity can play very divergent context-dependent roles in regulating the expression of a developmentally critical gene in vivo.
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Affiliation(s)
- Lawrence Du
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States
| | - Sharon Tracy
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States
| | - Scott A Rifkin
- Section of Ecology, Behavior, and Evolution, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0116, United States.
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Babu V, Schumacher B. A C. elegans homolog for the UV-hypersensitivity syndrome disease gene UVSSA. DNA Repair (Amst) 2016; 41:8-15. [PMID: 27043179 DOI: 10.1016/j.dnarep.2016.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/27/2016] [Accepted: 03/24/2016] [Indexed: 01/27/2023]
Abstract
The transcription-coupled repair pathway (TC-NER) plays a vital role in removing transcription-blocking DNA lesions, particularly UV-induced damage. Clinical symptoms of the two TC-NER-deficiency syndromes, Cockayne syndrome (CS) and UV-hypersensitivity syndrome (UVSS) are dissimilar and the underlying molecular mechanism causing this difference in disease pathology is not yet clearly understood. UV-stimulated scaffold protein A (UVSSA) has been identified recently as a new causal gene for UVSS. Here we describe a functional homolog of the human UVSSA gene in the nematode Caenorhabditis elegans, uvs-1 (UVSSA-like-1). Mutations in uvs-1 render the animals hypersensitive to UV-B irradiation and transcription-blocking lesion-inducing illudin-M, similar to mutations in TC-NER deficient mutants. Moreover, we demonstrate that TC-NER factors including UVS-1 are required for the survival of the adult animals after UV-treatment.
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Affiliation(s)
- Vipin Babu
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Research Center and Centre for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Research Center and Centre for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
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Affiliation(s)
- Laia Castells-Roca
- a Institute for Genome Stability in Ageing and Disease; Medical Faculty ; University of Cologne ; Cologne , Germany
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Local and long-range activation of innate immunity by infection and damage in C. elegans. Curr Opin Immunol 2015; 38:1-7. [PMID: 26517153 DOI: 10.1016/j.coi.2015.09.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/30/2015] [Indexed: 01/14/2023]
Abstract
The nematode worm Caenorhabditis elegans lends itself naturally to investigation of innate immunity, from the scale of molecules to the whole animal. Numerous studies have begun to reveal the complex interplay of signalling mechanisms that underlie host defence in C. elegans. We discuss here research that illustrates the connection between cell and tissue-level homeostatic mechanisms and the activation of innate immune signalling pathways. These are woven together to provide a comprehensive organismal protection against perceived threats.
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Ermolaeva MA, Dakhovnik A, Schumacher B. Quality control mechanisms in cellular and systemic DNA damage responses. Ageing Res Rev 2015; 23:3-11. [PMID: 25560147 DOI: 10.1016/j.arr.2014.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/21/2014] [Accepted: 12/23/2014] [Indexed: 11/30/2022]
Abstract
The maintenance of the genome is of pivotal importance for the functional integrity of cells and tissues. The gradual accumulation of DNA damage is thought to contribute to the functional decline of tissues and organs with ageing. Defects in multiple genome maintenance systems cause human disorders characterized by cancer susceptibility, developmental failure, and premature ageing. The complex pathological consequences of genome instability are insufficiently explained by cell-autonomous DNA damage responses (DDR) alone. Quality control pathways play an important role in DNA repair and cellular DDR pathways. Recent years have revealed non-cell autonomous effects of DNA damage that impact the physiological adaptations during ageing. We will discuss the role of quality assurance pathways in cell-autonomous and systemic responses to genome instability.
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Affiliation(s)
- Maria A Ermolaeva
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
| | - Alexander Dakhovnik
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Systems Biology of Ageing Cologne, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
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Genome Instability in Development and Aging: Insights from Nucleotide Excision Repair in Humans, Mice, and Worms. Biomolecules 2015; 5:1855-69. [PMID: 26287260 PMCID: PMC4598778 DOI: 10.3390/biom5031855] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/06/2015] [Accepted: 08/07/2015] [Indexed: 12/12/2022] Open
Abstract
DNA damage causally contributes to aging and cancer. Congenital defects in nucleotide excision repair (NER) lead to distinct cancer-prone and premature aging syndromes. The genetics of NER mutations have provided important insights into the distinct consequences of genome instability. Recent work in mice and C. elegans has shed new light on the mechanisms through which developing and aging animals respond to persistent DNA damage. The various NER mouse mutants have served as important disease models for Xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD), while the traceable genetics of C. elegans have allowed the mechanistic delineation of the distinct outcomes of genome instability in metazoan development and aging. Intriguingly, highly conserved longevity assurance mechanisms respond to transcription-blocking DNA lesions in mammals as well as in worms and counteract the detrimental consequences of persistent DNA damage. The insulin-like growth factor signaling (IIS) effector transcription factor DAF-16 could indeed overcome DNA damage-driven developmental growth delay and functional deterioration even when DNA damage persists. Longevity assurance mechanisms might thus delay DNA damage-driven aging by raising the threshold when accumulating DNA damage becomes detrimental for physiological tissue functioning.
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Abstract
The various symptoms associated with hereditary defects in the DNA damage response (DDR), which range from developmental and neurological abnormalities and immunodeficiency to tissue-specific cancers and accelerated aging, suggest that DNA damage affects tissues differently. Mechanistic DDR studies are, however, mostly performed in vitro, in unicellular model systems or cultured cells, precluding a clear and comprehensive view of the DNA damage response of multicellular organisms. Studies performed in intact, multicellular animals models suggest that DDR can vary according to the type, proliferation and differentiation status of a cell. The nematode Caenorhabditis elegans has become an important DDR model and appears to be especially well suited to understand in vivo tissue-specific responses to DNA damage as well as the impact of DNA damage on development, reproduction and health of an entire multicellular organism. C. elegans germ cells are highly sensitive to DNA damage induction and respond via classical, evolutionary conserved DDR pathways aimed at efficient and error-free maintenance of the entire genome. Somatic tissues, however, respond differently to DNA damage and prioritize DDR mechanisms that promote growth and function. In this mini-review, we describe tissue-specific differences in DDR mechanisms that have been uncovered utilizing C. elegans as role model.
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Affiliation(s)
- Hannes Lans
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.
| | - Wim Vermeulen
- Department of Genetics, Cancer Genomics Netherlands, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.
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Frommolt P, Schumacher B. Wormpath: searching for molecular interaction networks in Caenorhabditis elegans. SOURCE CODE FOR BIOLOGY AND MEDICINE 2015; 10:5. [PMID: 25866556 PMCID: PMC4392734 DOI: 10.1186/s13029-015-0034-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/12/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND High-throughput transcriptional profiling using Next-Generation Sequencing (RNA-Seq) or microarray technology have become standard tools in molecular biology. Successful investigations of gene regulatory mechanisms from these data typically employ mathematical models of biological networks. RESULTS We have developed Wormpath, a software for molecular network discovery which operates on the genetic and physical interaction data of the Wormbase, a comprehensive resource of molecular data on Caenorhabditis elegans. We use Wormpath to show that the insulin/insulin-like growth factor signalling (IIS) pathway responds to UV-induced DNA damage during development. CONCLUSIONS Our software provides highly facilitated access to C. elegans interaction data and is capable of identifying essential molecular networks within a list of differentially expressed genes.
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Affiliation(s)
- Peter Frommolt
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany ; Cologne Center for Genomics, University of Cologne, Cologne, Germany ; Systems Biology of Aging Cologne (SyBACol), University of Cologne, Cologne, Germany
| | - Björn Schumacher
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany ; Systems Biology of Aging Cologne (SyBACol), University of Cologne, Cologne, Germany ; Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Cologne, Germany ; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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