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Cecerska-Heryć E, Wiśniewska Z, Serwin N, Polikowska A, Goszka M, Engwert W, Michałów J, Pękała M, Budkowska M, Michalczyk A, Dołęgowska B. Can Compounds of Natural Origin Be Important in Chemoprevention? Anticancer Properties of Quercetin, Resveratrol, and Curcumin-A Comprehensive Review. Int J Mol Sci 2024; 25:4505. [PMID: 38674092 PMCID: PMC11050349 DOI: 10.3390/ijms25084505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Malignant tumors are the second most common cause of death worldwide. More attention is being paid to the link between the body's impaired oxidoreductive balance and cancer incidence. Much attention is being paid to polyphenols derived from plants, as one of their properties is an antioxidant character: the ability to eliminate reactive oxygen and nitrogen species, chelate specific metal ions, modulate signaling pathways affecting inflammation, and raise the level and activity of antioxidant enzymes while lowering those with oxidative effects. The following three compounds, resveratrol, quercetin, and curcumin, are polyphenols modulating multiple molecular targets, or increasing pro-apoptotic protein expression levels and decreasing anti-apoptotic protein expression levels. Experiments conducted in vitro and in vivo on animals and humans suggest using them as chemopreventive agents based on antioxidant properties. The advantage of these natural polyphenols is low toxicity and weak adverse effects at higher doses. However, the compounds discussed are characterized by low bioavailability and solubility, which may make achieving the blood concentrations needed for the desired effect challenging. The solution may lie in derivatives of naturally occurring polyphenols subjected to structural modifications that enhance their beneficial effects or work on implementing new ways of delivering antioxidants that improve their solubility and bioavailability.
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Affiliation(s)
- Elżbieta Cecerska-Heryć
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Powstancow Wielkopolskich 72, 70-111 Szczecin, Poland; (Z.W.); (N.S.); (A.P.); (M.G.); (W.E.); (J.M.); (M.P.); (B.D.)
| | - Zofia Wiśniewska
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Powstancow Wielkopolskich 72, 70-111 Szczecin, Poland; (Z.W.); (N.S.); (A.P.); (M.G.); (W.E.); (J.M.); (M.P.); (B.D.)
| | - Natalia Serwin
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Powstancow Wielkopolskich 72, 70-111 Szczecin, Poland; (Z.W.); (N.S.); (A.P.); (M.G.); (W.E.); (J.M.); (M.P.); (B.D.)
| | - Aleksandra Polikowska
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Powstancow Wielkopolskich 72, 70-111 Szczecin, Poland; (Z.W.); (N.S.); (A.P.); (M.G.); (W.E.); (J.M.); (M.P.); (B.D.)
| | - Małgorzata Goszka
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Powstancow Wielkopolskich 72, 70-111 Szczecin, Poland; (Z.W.); (N.S.); (A.P.); (M.G.); (W.E.); (J.M.); (M.P.); (B.D.)
| | - Weronika Engwert
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Powstancow Wielkopolskich 72, 70-111 Szczecin, Poland; (Z.W.); (N.S.); (A.P.); (M.G.); (W.E.); (J.M.); (M.P.); (B.D.)
| | - Jaśmina Michałów
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Powstancow Wielkopolskich 72, 70-111 Szczecin, Poland; (Z.W.); (N.S.); (A.P.); (M.G.); (W.E.); (J.M.); (M.P.); (B.D.)
| | - Maja Pękała
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Powstancow Wielkopolskich 72, 70-111 Szczecin, Poland; (Z.W.); (N.S.); (A.P.); (M.G.); (W.E.); (J.M.); (M.P.); (B.D.)
| | - Marta Budkowska
- Department of Medical Analytics, Pomeranian Medical University of Szczecin, Powstancow Wielkopolskich 72, 70-111 Szczecin, Poland;
| | - Anna Michalczyk
- Department of Psychiatry, Pomeranian Medical University of Szczecin, Broniewskiego 26, 71-460 Szczecin, Poland;
| | - Barbara Dołęgowska
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Powstancow Wielkopolskich 72, 70-111 Szczecin, Poland; (Z.W.); (N.S.); (A.P.); (M.G.); (W.E.); (J.M.); (M.P.); (B.D.)
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2
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Bordin DL, Grooms K, Montaldo NP, Fordyce Martin SL, Sætrom P, Samson LD, Bjørås M, van Loon B. Loss of alkyladenine DNA glycosylase alters gene expression in the developing mouse brain and leads to reduced anxiety and improved memory. DNA Repair (Amst) 2024; 135:103632. [PMID: 38280242 DOI: 10.1016/j.dnarep.2024.103632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 01/29/2024]
Abstract
Neurodevelopment is a tightly coordinated process, during which the genome is exposed to spectra of endogenous agents at different stages of differentiation. Emerging evidence indicates that DNA damage is an important feature of developing brain, tightly linked to gene expression and neuronal activity. Some of the most frequent DNA damage includes changes to DNA bases, which are recognized by DNA glycosylases and repaired through base excision repair (BER) pathway. The only mammalian DNA glycosylase able to remove frequent alkylated DNA based is alkyladenine DNA glycosylase (Aag, aka Mpg). We recently demonstrated that, besides its role in DNA repair, AAG affects expression of neurodevelopmental genes in human cells. Aag was further proposed to act as reader of epigenetic marks, including 5-hydroxymethylcytosine (5hmC), in the mouse brain. Despite the potential Aag involvement in the key brain processes, the impact of Aag loss on developing brain remains unknown. Here, by using Aag knockout (Aag-/-) mice, we show that Aag absence leads to reduced DNA break levels, evident in lowered number of γH2AX foci in postnatal day 5 (P5) hippocampi. This is accompanied by changes in 5hmC signal intensity in different hippocampal regions. Transcriptome analysis of hippocampi and prefrontal cortex, at different developmental stages, indicates that lack of Aag alters gene expression, primarily of genes involved in regulation of response to stress. Across all developmental stages tested aldehyde dehydrogenase 2 (Aldh2) emerged as one of the most prominent genes deregulated in Aag-dependent manner. In line with the changes in hippocampal DNA damage levels and the gene expression, adult Aag-/- mice exhibit altered behavior, evident in decreased anxiety levels determined in the Elevated Zero Maze and increased alternations in the Elevated T Maze tests. Taken together these results suggests that Aag has functions in modulation of genome dynamics during brain development, important for animal behavior.
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Affiliation(s)
- Diana L Bordin
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
| | - Kayla Grooms
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
| | - Nicola P Montaldo
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway; Department of Microbiology, Oslo University Hospital, University of Oslo, Oslo 0372, Norway
| | - Sarah L Fordyce Martin
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway; Bioinformatics core facility - BioCore; Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; Department of Computer Science, Faculty of Information Technology and Electrical Engineering, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Leona D Samson
- Department of Biological Engineering, Department of Biology, David H. Koch Institute of integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway; Department of Microbiology, Oslo University Hospital, University of Oslo, Oslo 0372, Norway
| | - Barbara van Loon
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7049 Trondheim, Norway.
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3
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Fahrer J, Christmann M. DNA Alkylation Damage by Nitrosamines and Relevant DNA Repair Pathways. Int J Mol Sci 2023; 24:ijms24054684. [PMID: 36902118 PMCID: PMC10003415 DOI: 10.3390/ijms24054684] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/17/2023] [Accepted: 02/24/2023] [Indexed: 03/04/2023] Open
Abstract
Nitrosamines occur widespread in food, drinking water, cosmetics, as well as tobacco smoke and can arise endogenously. More recently, nitrosamines have been detected as impurities in various drugs. This is of particular concern as nitrosamines are alkylating agents that are genotoxic and carcinogenic. We first summarize the current knowledge on the different sources and chemical nature of alkylating agents with a focus on relevant nitrosamines. Subsequently, we present the major DNA alkylation adducts induced by nitrosamines upon their metabolic activation by CYP450 monooxygenases. We then describe the DNA repair pathways engaged by the various DNA alkylation adducts, which include base excision repair, direct damage reversal by MGMT and ALKBH, as well as nucleotide excision repair. Their roles in the protection against the genotoxic and carcinogenic effects of nitrosamines are highlighted. Finally, we address DNA translesion synthesis as a DNA damage tolerance mechanism relevant to DNA alkylation adducts.
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Affiliation(s)
- Jörg Fahrer
- Division of Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Erwin-Schrödinger Strasse 52, D-67663 Kaiserslautern, Germany
- Correspondence: (J.F.); (M.C.); Tel.: +496312052974 (J.F.); Tel: +496131179066 (M.C.)
| | - Markus Christmann
- Department of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany
- Correspondence: (J.F.); (M.C.); Tel.: +496312052974 (J.F.); Tel: +496131179066 (M.C.)
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4
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Zhao Z, Yan X, Li L, Shu Y, He J, Wang L, Huang Q, Xie J, Zhao J, Peng S. Proliferating Stem Cells are Acutely Affected by DNA Damage Induced by Sulfur Mustard. DNA Cell Biol 2022; 41:716-726. [PMID: 35834647 DOI: 10.1089/dna.2022.0073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sulfur mustard (SM), a chemical warfare agent, can form adducts with DNA, RNA, and proteins. Reactions with DNA lead to the formation of both DNA monoadducts and interstrand cross-links, resulting in DNA damage, and is an important component of SM toxicity. Our previous in vivo studies indicated that dividing cells such as hematopoietic stem cells and intestinal villi stem cells seemed to have increased sensitivity to SM. Therefore, to compare the sensitivity of somatic and stem cells to SM and to investigate the mechanism of SM cytotoxicity, we isolated human foreskin fibroblasts, reprogrammed them into pluripotent stem cells, and then compared the DNA damage repair pathways involved upon SM treatment. Our results indicated that proliferating stem cells were more sensitive to SM-induced DNA damage, and the damage mainly comprised single-stranded breaks. Furthermore, the pathways involved in DNA repair in stem cells and somatic cells were different.
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Affiliation(s)
- Zengming Zhao
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Xiabei Yan
- Department of Reproductive Medicine, General Hospital of Central Theater Command of the People's Liberation Army, Wuhan, China
| | - Lizhong Li
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Yulei Shu
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Jun He
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Lili Wang
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Qingzhen Huang
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Jianwei Xie
- Institutes of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing, China
| | - Jun Zhao
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
| | - Shuangqing Peng
- Center for Disease Control and Prevention of Chinese People's Liberation Army, Beijing, China
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5
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Milano L, Charlier CF, Andreguetti R, Cox T, Healing E, Thomé MP, Elliott RM, Samson LD, Masson JY, Lenz G, Henriques JAP, Nohturfft A, Meira LB. A DNA repair-independent role for alkyladenine DNA glycosylase in alkylation-induced unfolded protein response. Proc Natl Acad Sci U S A 2022; 119:e2111404119. [PMID: 35197283 PMCID: PMC8892324 DOI: 10.1073/pnas.2111404119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/08/2022] [Indexed: 01/25/2023] Open
Abstract
Alkylating agents damage DNA and proteins and are widely used in cancer chemotherapy. While cellular responses to alkylation-induced DNA damage have been explored, knowledge of how alkylation affects global cellular stress responses is sparse. Here, we examined the effects of the alkylating agent methylmethane sulfonate (MMS) on gene expression in mouse liver, using mice deficient in alkyladenine DNA glycosylase (Aag), the enzyme that initiates the repair of alkylated DNA bases. MMS induced a robust transcriptional response in wild-type liver that included markers of the endoplasmic reticulum (ER) stress/unfolded protein response (UPR) known to be controlled by XBP1, a key UPR effector. Importantly, this response is significantly reduced in the Aag knockout. To investigate how AAG affects alkylation-induced UPR, the expression of UPR markers after MMS treatment was interrogated in human glioblastoma cells expressing different AAG levels. Alkylation induced the UPR in cells expressing AAG; conversely, AAG knockdown compromised UPR induction and led to a defect in XBP1 activation. To verify the requirements for the DNA repair activity of AAG in this response, AAG knockdown cells were complemented with wild-type Aag or with an Aag variant producing a glycosylase-deficient AAG protein. As expected, the glycosylase-defective Aag does not fully protect AAG knockdown cells against MMS-induced cytotoxicity. Remarkably, however, alkylation-induced XBP1 activation is fully complemented by the catalytically inactive AAG enzyme. This work establishes that, besides its enzymatic activity, AAG has noncanonical functions in alkylation-induced UPR that contribute to cellular responses to alkylation.
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Affiliation(s)
- Larissa Milano
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7WG Guildford, United Kingdom
- Center of Biotechnology, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Québec City, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Center, Quebec City, QC G1V 0A6, Canada
| | - Clara F Charlier
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7WG Guildford, United Kingdom
| | - Rafaela Andreguetti
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7WG Guildford, United Kingdom
| | - Thomas Cox
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7WG Guildford, United Kingdom
| | - Eleanor Healing
- Department of Nutritional Sciences, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, United Kingdom
| | - Marcos P Thomé
- Department of Biophysics, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
| | - Ruan M Elliott
- Department of Nutritional Sciences, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, United Kingdom
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Quebec Research Center, HDQ Pavilion, Oncology Axis, Québec City, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Center, Quebec City, QC G1V 0A6, Canada
| | - Guido Lenz
- Center of Biotechnology, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
- Department of Biophysics, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
| | - João Antonio P Henriques
- Center of Biotechnology, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
- Department of Biophysics, Federal University of Rio Grande do Sul, 91501-970 Porto Alegre, Brazil
| | - Axel Nohturfft
- Molecular and Clinical Sciences Research Institute, St. George's University of London, SW17 0RE London, United Kingdom
| | - Lisiane B Meira
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, GU2 7WG Guildford, United Kingdom;
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6
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Franklin A, Steele EJ. RNA-directed DNA repair and antibody somatic hypermutation. Trends Genet 2021; 38:426-436. [PMID: 34740453 DOI: 10.1016/j.tig.2021.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/03/2021] [Accepted: 10/04/2021] [Indexed: 10/19/2022]
Abstract
Somatic hypermutation at antibody loci affects both deoxyadenosine-deoxythymidine (A/T) and deoxycytidine-deoxyguanosine (C/G) pairs. Deamination of C to deoxyuridine (U) by activation-induced deaminase (AID) explains how mutation at C/G pairs is potentiated. Mutation at A/T pairs is triggered during the initial stages of repair of AID-generated U lesions and occurs through an as yet unknown mechanism in which polymerase η has a major role. Recent evidence confirms that human polymerase η can act as a reverse transcriptase. Here, we compare the popular suggestion of mutation at A/T pairs through nucleotide mispairing (owing to polymerase error) during short-patch repair synthesis with the alternative proposal of mutation at A/T pairs through RNA editing and RNA-directed DNA repair.
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Affiliation(s)
- Andrew Franklin
- Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland.
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7
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Engelward BP. Implications of an epidemiological study showing an association between in utero NDMA exposure and childhood cancer. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2021; 62:288-292. [PMID: 33963777 PMCID: PMC8361697 DOI: 10.1002/em.22434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 05/10/2023]
Abstract
Exposure to N-nitrosodimethylamine (NDMA) has recently been linked to a childhood cancer cluster in Wilmington, MA, which is home to the Olin Chemical Superfund Site. When it was discovered in the 1990's that 22 children in a town of under 22,000 people got cancer, the community took action and pressed for an investigation into the possibility that chemicals from the Olin Chemical site had contaminated their water. This led to the eventual discovery that NDMA was present in the town water supply. NDMA has long been known for its potent carcinogenicity in animal models, and so the community pointed to NDMA as a possible cause. This led to an investigation by the Massachusetts Department of Public Health, which, in 2021, released its findings showing an association between NDMA exposure in utero and childhood cancer. The mission of the NIEHS Superfund Research Program is to protect human health from hazardous substances. In 2017, in response to community concerns, a team at MIT created the MIT Superfund Research Program Center with a focus on research related to NDMA. Just 1 week prior to the release of the Department of Public Health study, the MIT Superfund Research Program Center published a manuscript in Cell Reports that identifies the Alkyladenine DNA glycosylase (AAG) as a possible genetic susceptibility factor. This commentary provides an author's perspective on the context and implications of this and related research.
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Affiliation(s)
- Bevin P. Engelward
- MIT Superfund Research Program, Department of Biological Engineering, Center for Environmental Health SciencesMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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8
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Kay JE, Corrigan JJ, Armijo AL, Nazari IS, Kohale IN, Torous DK, Avlasevich SL, Croy RG, Wadduwage DN, Carrasco SE, Dertinger SD, White FM, Essigmann JM, Samson LD, Engelward BP. Excision of mutagenic replication-blocking lesions suppresses cancer but promotes cytotoxicity and lethality in nitrosamine-exposed mice. Cell Rep 2021; 34:108864. [PMID: 33730582 PMCID: PMC8527524 DOI: 10.1016/j.celrep.2021.108864] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/05/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
N-Nitrosodimethylamine (NDMA) is a DNA-methylating agent that has been discovered to contaminate water, food, and drugs. The alkyladenine DNA glycosylase (AAG) removes methylated bases to initiate the base excision repair (BER) pathway. To understand how gene-environment interactions impact disease susceptibility, we study Aag-knockout (Aag-/-) and Aag-overexpressing mice that harbor increased levels of either replication-blocking lesions (3-methyladenine [3MeA]) or strand breaks (BER intermediates), respectively. Remarkably, the disease outcome switches from cancer to lethality simply by changing AAG levels. To understand the underlying basis for this observation, we integrate a suite of molecular, cellular, and physiological analyses. We find that unrepaired 3MeA is somewhat toxic, but highly mutagenic (promoting cancer), whereas excess strand breaks are poorly mutagenic and highly toxic (suppressing cancer and promoting lethality). We demonstrate that the levels of a single DNA repair protein tip the balance between blocks and breaks and thus dictate the disease consequences of DNA damage.
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Affiliation(s)
- Jennifer E Kay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Joshua J Corrigan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Amanda L Armijo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Ilana S Nazari
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Ishwar N Kohale
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | | | | | - Robert G Croy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Dushan N Wadduwage
- The John Harvard Distinguished Science Fellows Program, Harvard University, Cambridge, MA 02138, USA; Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA
| | - Sebastian E Carrasco
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | | | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - John M Essigmann
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 01239, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 01239, USA.
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9
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Caffrey PJ, Delaney S. Chromatin and other obstacles to base excision repair: potential roles in carcinogenesis. Mutagenesis 2021; 35:39-50. [PMID: 31612219 DOI: 10.1093/mutage/gez029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/13/2019] [Indexed: 12/29/2022] Open
Abstract
DNA is comprised of chemically reactive nucleobases that exist under a constant barrage from damaging agents. Failure to repair chemical modifications to these nucleobases can result in mutations that can cause various diseases, including cancer. Fortunately, the base excision repair (BER) pathway can repair modified nucleobases and prevent these deleterious mutations. However, this pathway can be hindered through several mechanisms. For instance, mutations to the enzymes in the BER pathway have been identified in cancers. Biochemical characterisation of these mutants has elucidated various mechanisms that inhibit their activity. Furthermore, the packaging of DNA into chromatin poses another obstacle to the ability of BER enzymes to function properly. Investigations of BER in the base unit of chromatin, the nucleosome core particle (NCP), have revealed that the NCP acts as a complex substrate for BER enzymes. The constituent proteins of the NCP, the histones, also have variants that can further impact the structure of the NCP and may modulate access of enzymes to the packaged DNA. These histone variants have also displayed significant clinical effects both in carcinogenesis and patient prognosis. This review focuses on the underlying molecular mechanisms that present obstacles to BER and the relationship of these obstacles to cancer. In addition, several chemotherapeutics induce DNA damage that can be repaired by the BER pathway and understanding obstacles to BER can inform how resistance and/or sensitivity to these therapies may occur. With the understanding of these molecular mechanisms, current chemotherapeutic treatment regiments may be improved, and future therapies developed.
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Affiliation(s)
- Paul J Caffrey
- Department of Chemistry, Brown University, Providence, RI
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI
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10
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Bordin DL, Lirussi L, Nilsen H. Cellular response to endogenous DNA damage: DNA base modifications in gene expression regulation. DNA Repair (Amst) 2021; 99:103051. [PMID: 33540225 DOI: 10.1016/j.dnarep.2021.103051] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/19/2022]
Abstract
The integrity of the genetic information is continuously challenged by numerous genotoxic insults, most frequently in the form of oxidation, alkylation or deamination of the bases that result in DNA damage. These damages compromise the fidelity of the replication, and interfere with the progression and function of the transcription machineries. The DNA damage response (DDR) comprises a series of strategies to deal with DNA damage, including transient transcriptional inhibition, activation of DNA repair pathways and chromatin remodeling. Coordinated control of transcription and DNA repair is required to safeguardi cellular functions and identities. Here, we address the cellular responses to endogenous DNA damage, with a particular focus on the role of DNA glycosylases and the Base Excision Repair (BER) pathway, in conjunction with the DDR factors, in responding to DNA damage during the transcription process. We will also discuss functions of newly identified epigenetic and regulatory marks, such as 5-hydroxymethylcytosine and its oxidative products and 8-oxoguanine, that were previously considered only as DNA damages. In light of these resultsthe classical perception of DNA damage as detrimental for cellular processes are changing. and a picture emerges whereDNA glycosylases act as dynamic regulators of transcription, placing them at the intersection of DNA repair and gene expression modulation.
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Affiliation(s)
- Diana L Bordin
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway
| | - Lisa Lirussi
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, 0318, Oslo, Norway; Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478, Lørenskog, Norway.
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11
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Peng Y, Pei H. DNA alkylation lesion repair: outcomes and implications in cancer chemotherapy. J Zhejiang Univ Sci B 2021; 22:47-62. [PMID: 33448187 DOI: 10.1631/jzus.b2000344] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Alkylated DNA lesions, induced by both exogenous chemical agents and endogenous metabolites, represent a major form of DNA damage in cells. The repair of alkylation damage is critical in all cells because such damage is cytotoxic and potentially mutagenic. Alkylation chemotherapy is a major therapeutic modality for many tumors, underscoring the importance of the repair pathways in cancer cells. Several different pathways exist for alkylation repair, including base excision and nucleotide excision repair, direct reversal by methyl-guanine methyltransferase (MGMT), and dealkylation by the AlkB homolog (ALKBH) protein family. However, maintaining a proper balance between these pathways is crucial for the favorable response of an organism to alkylating agents. Here, we summarize the progress in the field of DNA alkylation lesion repair and describe the implications for cancer chemotherapy.
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Affiliation(s)
- Yihan Peng
- Department of Biochemistry and Molecular Medicine, the George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA.,GW Cancer Center, the George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Huadong Pei
- Department of Biochemistry and Molecular Medicine, the George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA. .,GW Cancer Center, the George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA.
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12
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Kim DV, Makarova AV, Miftakhova RR, Zharkov DO. Base Excision DNA Repair Deficient Cells: From Disease Models to Genotoxicity Sensors. Curr Pharm Des 2020; 25:298-312. [PMID: 31198112 DOI: 10.2174/1381612825666190319112930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/13/2019] [Indexed: 12/29/2022]
Abstract
Base excision DNA repair (BER) is a vitally important pathway that protects the cell genome from many kinds of DNA damage, including oxidation, deamination, and hydrolysis. It involves several tightly coordinated steps, starting from damaged base excision and followed by nicking one DNA strand, incorporating an undamaged nucleotide, and DNA ligation. Deficiencies in BER are often embryonic lethal or cause morbid diseases such as cancer, neurodegeneration, or severe immune pathologies. Starting from the early 1980s, when the first mammalian cell lines lacking BER were produced by spontaneous mutagenesis, such lines have become a treasure trove of valuable information about the mechanisms of BER, often revealing unexpected connections with other cellular processes, such as antibody maturation or epigenetic demethylation. In addition, these cell lines have found an increasing use in genotoxicity testing, where they provide increased sensitivity and representativity to cell-based assay panels. In this review, we outline current knowledge about BER-deficient cell lines and their use.
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Affiliation(s)
- Daria V Kim
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., Moscow 123182, Russian Federation
| | - Regina R Miftakhova
- Kazan Federal University, 18 Kremlevsakaya St., Kazan 420008, Russian Federation
| | - Dmitry O Zharkov
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation.,SB RAS Institute of Chemical Biology and Fu ndamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russian Federation
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13
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Alkyladenine DNA glycosylase deficiency uncouples alkylation-induced strand break generation from PARP-1 activation and glycolysis inhibition. Sci Rep 2020; 10:2209. [PMID: 32042007 PMCID: PMC7010680 DOI: 10.1038/s41598-020-59072-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/16/2020] [Indexed: 01/07/2023] Open
Abstract
DNA alkylation damage is repaired by base excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG). Despite its role in DNA repair, AAG-initiated BER promotes cytotoxicity in a process dependent on poly (ADP-ribose) polymerase-1 (PARP-1); a NAD+-consuming enzyme activated by strand break intermediates of the AAG-initiated repair process. Importantly, PARP-1 activation has been previously linked to impaired glycolysis and mitochondrial dysfunction. However, whether alkylation affects cellular metabolism in the absence of AAG-mediated BER initiation is unclear. To address this question, we temporally profiled repair and metabolism in wild-type and Aag−/− cells treated with the alkylating agent methyl methanesulfonate (MMS). We show that, although Aag−/− cells display similar levels of alkylation-induced DNA breaks as wild type, PARP-1 activation is undetectable in AAG-deficient cells. Accordingly, Aag−/− cells are protected from MMS-induced NAD+ depletion and glycolysis inhibition. MMS-induced mitochondrial dysfunction, however, is AAG-independent. Furthermore, treatment with FK866, a selective inhibitor of the NAD+ salvage pathway enzyme nicotinamide phosphoribosyltransferase (NAMPT), synergizes with MMS to induce cytotoxicity and Aag−/− cells are resistant to this combination FK866 and MMS treatment. Thus, AAG plays an important role in the metabolic response to alkylation that could be exploited in the treatment of conditions associated with NAD+ dysregulation.
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14
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de Barrios O, Sanchez-Moral L, Cortés M, Ninfali C, Profitós-Pelejà N, Martínez-Campanario MC, Siles L, Del Campo R, Fernández-Aceñero MJ, Darling DS, Castells A, Maurel J, Salas A, Dean DC, Postigo A. ZEB1 promotes inflammation and progression towards inflammation-driven carcinoma through repression of the DNA repair glycosylase MPG in epithelial cells. Gut 2019; 68:2129-2141. [PMID: 31366457 DOI: 10.1136/gutjnl-2018-317294] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Chronic inflammation is a risk factor in colorectal cancer (CRC) and reactive oxygen species (ROS) released by the inflamed stroma elicit DNA damage in epithelial cells. We sought to identify new drivers of ulcerative colitis (UC) and inflammatory CRC. DESIGN The study uses samples from patients with UC, mouse models of colitis and CRC and mice deficient for the epithelial-to-mesenchymal transition factor ZEB1 and the DNA repair glycosylase N-methyl-purine glycosylase (MPG). Samples were analysed by immunostaining, qRT-PCR, chromatin immunoprecipitation assays, microbiota next-generation sequencing and ROS determination. RESULTS ZEB1 was induced in the colonic epithelium of UC and of mouse models of colitis. Compared with wild-type counterparts, Zeb1-deficient mice were partially protected from experimental colitis and, in a model of inflammatory CRC, they developed fewer tumours and exhibited lower levels of DNA damage (8-oxo-dG) and higher expression of MPG. Knockdown of ZEB1 in CRC cells inhibited 8-oxo-dG induction by oxidative stress (H2O2) and inflammatory cytokines (interleukin (IL)1β). ZEB1 bound directly to the MPG promoter whose expression inhibited. This molecular mechanism was validated at the genetic level and the crossing of Zeb1-deficient and Mpg-deficient mice reverted the reduced inflammation and tumourigenesis in the former. ZEB1 expression in CRC cells induced ROS and IL1β production by macrophages that, in turn, lowered MPG in CRC cells thus amplifying a positive loop between both cells to promote DNA damage and inhibit DNA repair. CONCLUSIONS ZEB1 promotes colitis and inflammatory CRC through the inhibition of MPG in epithelial cells, thus offering new therapeutic strategies to modulate inflammation and inflammatory cancer.
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Affiliation(s)
- Oriol de Barrios
- Group of Transcriptional Regulation of Gene Expression, Dept of Oncology and Hematology, IDIBAPS, Barcelona, Spain
| | - Lidia Sanchez-Moral
- Group of Transcriptional Regulation of Gene Expression, Dept of Oncology and Hematology, IDIBAPS, Barcelona, Spain
| | - Marlies Cortés
- Group of Transcriptional Regulation of Gene Expression, Dept of Oncology and Hematology, IDIBAPS, Barcelona, Spain
| | - Chiara Ninfali
- Group of Transcriptional Regulation of Gene Expression, Dept of Oncology and Hematology, IDIBAPS, Barcelona, Spain
| | - Nuria Profitós-Pelejà
- Group of Transcriptional Regulation of Gene Expression, Dept of Oncology and Hematology, IDIBAPS, Barcelona, Spain
| | - M C Martínez-Campanario
- Group of Transcriptional Regulation of Gene Expression, Dept of Oncology and Hematology, IDIBAPS, Barcelona, Spain
| | - Laura Siles
- Group of Transcriptional Regulation of Gene Expression, Dept of Oncology and Hematology, IDIBAPS, Barcelona, Spain
| | - Rosa Del Campo
- Dept of Microbiology, Hospital Ramon y Cajal Health Research Institute (IRYCIS), Spanish Network of Infectious Diseases (REIPI), National Health Institute Carlos III (ISCIII), Madrid, Spain
| | | | - Douglas S Darling
- Dept of Oral Immunology and Infectious Diseases and Center for Genetics and Molecular Medicine, University of Louisville, Louisville, Kentucky, USA
| | - Antoni Castells
- Dept of Gastroenterology, Hospital Clínic and IDIBAPS, Barcelona, Spain.,Gastrointestinal and Pancreatic Oncology Team, CIBERehd, Barcelona, Spain
| | - Joan Maurel
- Group of Translational Genomics and Targeted Therapeutics in Solid Tumours, Dept of Medical Oncology, Hospital Clínic and IDIBAPS, Barcelona, Spain
| | - Azucena Salas
- Dept of Gastroenterology, Hospital Clínic and IDIBAPS, Barcelona, Spain
| | - Douglas C Dean
- Dept of Ophthalmology and Visual Sciences and Birth Defects Center, University of Louisville, Louisville, Kentucky, USA.,Molecular Targets Program, James G. Brown Cancer Center, Louisville, Kentucky, USA
| | - Antonio Postigo
- Group of Transcriptional Regulation of Gene Expression, Dept of Oncology and Hematology, IDIBAPS, Barcelona, Spain.,Molecular Targets Program, James G. Brown Cancer Center, Louisville, Kentucky, USA.,ICREA, Barcelona, Spain
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15
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Kay J, Thadhani E, Samson L, Engelward B. Inflammation-induced DNA damage, mutations and cancer. DNA Repair (Amst) 2019; 83:102673. [PMID: 31387777 DOI: 10.1016/j.dnarep.2019.102673] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 06/15/2019] [Accepted: 07/18/2019] [Indexed: 12/22/2022]
Abstract
The relationships between inflammation and cancer are varied and complex. An important connection linking inflammation to cancer development is DNA damage. During inflammation reactive oxygen and nitrogen species (RONS) are created to combat pathogens and to stimulate tissue repair and regeneration, but these chemicals can also damage DNA, which in turn can promote mutations that initiate and promote cancer. DNA repair pathways are essential for preventing DNA damage from causing mutations and cytotoxicity, but RONS can interfere with repair mechanisms, reducing their efficacy. Further, cellular responses to DNA damage, such as damage signaling and cytotoxicity, can promote inflammation, creating a positive feedback loop. Despite coordination of DNA repair and oxidative stress responses, there are nevertheless examples whereby inflammation has been shown to promote mutagenesis, tissue damage, and ultimately carcinogenesis. Here, we discuss the DNA damage-mediated associations between inflammation, mutagenesis and cancer.
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Affiliation(s)
- Jennifer Kay
- Department of Biological Engineering, United States.
| | | | - Leona Samson
- Department of Biological Engineering, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
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16
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Allocca M, Corrigan JJ, Mazumder A, Fake KR, Samson LD. Inflammation, necrosis, and the kinase RIP3 are key mediators of AAG-dependent alkylation-induced retinal degeneration. Sci Signal 2019; 12:12/568/eaau9216. [PMID: 30755477 DOI: 10.1126/scisignal.aau9216] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA-alkylating agents are commonly used to kill cancer cells, but the base excision repair (BER) pathway they trigger can also produce toxic intermediates that cause tissue damage, such as retinal degeneration (RD). Apoptosis, a process of programmed cell death, is assumed to be the main mechanism of this alkylation-induced photoreceptor (PR) cell death in RD. Here, we studied the involvement of necroptosis (another programmed cell death process) and inflammation in alkylation-induced RD. Male mice exposed to a methylating agent exhibited a reduced number of PR cell rows, active gliosis, and cytokine induction and macrophage infiltration in the retina. Dying PRs exhibited a necrotic morphology, increased 8-hydroxyguanosine abundance (an oxidative damage marker), and overexpression of the necroptosis-associated genes Rip1 and Rip3 The activity of PARP1, which mediates BER, cell death, and inflammation, was increased in PR cells and associated with the release of proinflammatory chemokine HMGB1 from PR nuclei. Mice lacking the anti-inflammatory cytokine IL-10 exhibited more severe RD, whereas deficiency of RIP3 (also known as RIPK3) conferred partial protection. Female mice were partially protected from alkylation-induced RD, showing reduced necroptosis and inflammation compared to males. PRs in mice lacking the BER-initiating DNA glycosylase AAG did not exhibit alkylation-induced necroptosis or inflammation. Our findings show that AAG-initiated BER at alkylated DNA bases induces sex-dependent RD primarily by triggering necroptosis and activating an inflammatory response that amplifies the original damage and, furthermore, reveal new potential targets to prevent this side effect of chemotherapy.
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Affiliation(s)
- Mariacarmela Allocca
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Joshua J Corrigan
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Aprotim Mazumder
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kimberly R Fake
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. .,Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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17
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Gruber CC, Walker GC. Incomplete base excision repair contributes to cell death from antibiotics and other stresses. DNA Repair (Amst) 2018; 71:108-117. [PMID: 30181041 DOI: 10.1016/j.dnarep.2018.08.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Numerous lethal stresses in bacteria including antibiotics, thymineless death, and MalE-LacZ expression trigger an increase in the production of reactive oxygen species. This results in the oxidation of the nucleotide pool by radicals produced by Fenton chemistry. Following the incorporation of these oxidized nucleotides into the genome, the cell's unsuccessful attempt to repair these lesions through base excision repair (BER) contributes causally to the lethality of these stresses. We review the evidence for this phenomenon of incomplete BER-mediated cell death and discuss how better understanding this pathway could contribute to the development of new antibiotics.
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Affiliation(s)
- Charley C Gruber
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States.
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18
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Parrish MC, Chaim IA, Nagel ZD, Tannenbaum SR, Samson LD, Engelward BP. Nitric oxide induced S-nitrosation causes base excision repair imbalance. DNA Repair (Amst) 2018; 68:25-33. [PMID: 29929044 DOI: 10.1016/j.dnarep.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/20/2018] [Accepted: 04/30/2018] [Indexed: 02/05/2023]
Abstract
It is well established that inflammation leads to the creation of potent DNA damaging chemicals, including reactive oxygen and nitrogen species. Nitric oxide can react with glutathione to create S-nitrosoglutathione (GSNO), which can in turn lead to S-nitrosated proteins. Of particular interest is the impact of GSNO on the function of DNA repair enzymes. The base excision repair (BER) pathway can be initiated by the alkyl-adenine DNA glycosylase (AAG), a monofunctional glycosylase that removes methylated bases. After base removal, an abasic site is formed, which then gets cleaved by AP endonuclease and processed by downstream BER enzymes. Interestingly, using the Fluorescence-based Multiplexed Host Cell Reactivation Assay (FM-HCR), we show that GSNO actually enhances AAG activity, which is consistent with the literature. This raised the possibility that there might be imbalanced BER when cells are challenged with a methylating agent. To further explore this possibility, we confirmed that GSNO can cause AP endonuclease to translocate from the nucleus to the cytoplasm, which might further exacerbate imbalanced BER by increasing the levels of AP sites. Analysis of abasic sites indeed shows GSNO induces an increase in the level of AP sites. Furthermore, analysis of DNA damage using the CometChip (a higher throughput version of the comet assay) shows an increase in the levels of BER intermediates. Finally, we found that GSNO exposure is associated with an increase in methylation-induced cytotoxicity. Taken together, these studies support a model wherein GSNO increases BER initiation while processing of AP sites is decreased, leading to a toxic increase in BER intermediates. This model is also supported by additional studies performed in our laboratory showing that inflammation in vivo leads to increased large-scale sequence rearrangements. Taken together, this work provides new evidence that inflammatory chemicals can drive cytotoxicity and mutagenesis via BER imbalance.
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Affiliation(s)
- Marcus C Parrish
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Zachary D Nagel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Steven R Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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19
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Calvo JA, Allocca M, Fake KR, Muthupalani S, Corrigan JJ, Bronson RT, Samson LD. Parp1 protects against Aag-dependent alkylation-induced nephrotoxicity in a sex-dependent manner. Oncotarget 2018; 7:44950-44965. [PMID: 27391435 PMCID: PMC5216697 DOI: 10.18632/oncotarget.10440] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 06/06/2016] [Indexed: 11/25/2022] Open
Abstract
Nephrotoxicity is a common toxic side-effect of chemotherapeutic alkylating agents. Although the base excision repair (BER) pathway is essential in repairing DNA alkylation damage, under certain conditions the initiation of BER produces toxic repair intermediates that damage healthy tissues. We have shown that the alkyladenine DNA glycosylase, Aag (a.k.a. Mpg), an enzyme that initiates BER, mediates alkylation-induced whole-animal lethality and cytotoxicity in the pancreas, spleen, retina, and cerebellum, but not in the kidney. Cytotoxicity in both wild-type and Aag-transgenic mice (AagTg) was abrogated in the absence of Poly(ADP-ribose) polymerase-1 (Parp1). Here we report that Parp1-deficient mice expressing increased Aag (AagTg/Parp1−/−) develop sex-dependent kidney failure upon exposure to the alkylating agent, methyl methanesulfonate (MMS), and suffer increased whole-animal lethality compared to AagTg and wild-type mice. Macroscopic, histological, electron microscopic and immunohistochemical analyses revealed morphological kidney damage including dilated tubules, proteinaceous casts, vacuolation, collapse of the glomerular tuft, and deterioration of podocyte structure. Moreover, mice exhibited clinical signs of kidney disease indicating functional damage, including elevated blood nitrogen urea and creatinine, hypoproteinemia and proteinuria. Pharmacological Parp inhibition in AagTg mice also resulted in sensitivity to MMS-induced nephrotoxicity. These findings provide in vivo evidence that Parp1 modulates Aag-dependent MMS-induced nephrotoxicity in a sex-dependent manner and highlight the critical roles that Aag-initiated BER and Parp1 may play in determining the side-effects of chemotherapeutic alkylating agents.
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Affiliation(s)
- Jennifer A Calvo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mariacarmela Allocca
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kimberly R Fake
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Joshua J Corrigan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.,The David H. Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology, Cambridge, MA, USA
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20
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Bj Rås KØ, Sousa MML, Sharma A, Fonseca DM, S Gaard CK, Bj Rås M, Otterlei M. Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication. Nucleic Acids Res 2017; 45:8291-8301. [PMID: 28575236 PMCID: PMC5737410 DOI: 10.1093/nar/gkx476] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 05/15/2017] [Indexed: 12/03/2022] Open
Abstract
Base lesions in DNA can stall the replication machinery or induce mutations if bypassed. Consequently, lesions must be repaired before replication or in a post-replicative process to maintain genomic stability. Base excision repair (BER) is the main pathway for repair of base lesions and is known to be associated with DNA replication, but how BER is organized during replication is unclear. Here we coupled the iPOND (isolation of proteins on nascent DNA) technique with targeted mass-spectrometry analysis, which enabled us to detect all proteins required for BER on nascent DNA and to monitor their spatiotemporal orchestration at replication forks. We demonstrate that XRCC1 and other BER/single-strand break repair (SSBR) proteins are enriched in replisomes in unstressed cells, supporting a cellular capacity of post-replicative BER/SSBR. Importantly, we identify for the first time the DNA glycosylases MYH, UNG2, MPG, NTH1, NEIL1, 2 and 3 on nascent DNA. Our findings suggest that a broad spectrum of DNA base lesions are recognized and repaired by BER in a post-replicative process.
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Affiliation(s)
- Karine Ø Bj Rås
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Mirta M L Sousa
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway.,The Central Norway Regional Health Authority, N-7501 Stj⊘rdal, Norway
| | - Animesh Sharma
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway.,The Central Norway Regional Health Authority, N-7501 Stj⊘rdal, Norway.,Proteomics and Metabolomics Core Facility (PROMEC), Department of Cancer Research and Molecular Medicine, NTNU, N-7491 Trondheim, Norway
| | - Davi M Fonseca
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway.,The Central Norway Regional Health Authority, N-7501 Stj⊘rdal, Norway.,Proteomics and Metabolomics Core Facility (PROMEC), Department of Cancer Research and Molecular Medicine, NTNU, N-7491 Trondheim, Norway
| | - Caroline K S Gaard
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Magnar Bj Rås
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway.,Department of Microbiology, Oslo University Hospital and University of Oslo, N-0027 Oslo, Norway
| | - Marit Otterlei
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
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21
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Hendershot JM, O'Brien PJ. Search for DNA damage by human alkyladenine DNA glycosylase involves early intercalation by an aromatic residue. J Biol Chem 2017; 292:16070-16080. [PMID: 28747435 PMCID: PMC5625039 DOI: 10.1074/jbc.m117.782813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/19/2017] [Indexed: 01/22/2023] Open
Abstract
DNA repair enzymes recognize and remove damaged bases that are embedded in the duplex. To gain access, most enzymes use nucleotide flipping, whereby the target nucleotide is rotated 180° into the active site. In human alkyladenine DNA glycosylase (AAG), the enzyme that initiates base excision repair of alkylated bases, the flipped-out nucleotide is stabilized by intercalation of the side chain of tyrosine 162 that replaces the lesion nucleobase. Previous kinetic studies provided evidence for the formation of a transient complex that precedes the stable flipped-out complex, but it is not clear how this complex differs from nonspecific complexes. We used site-directed mutagenesis and transient-kinetic approaches to investigate the timing of Tyr162 intercalation for AAG. The tryptophan substitution (Y162W) appeared to be conservative, because the mutant protein retained a highly favorable equilibrium constant for flipping the 1,N6-ethenoadenine (ϵA) lesion, and the rate of N-glycosidic bond cleavage was identical to that of the wild-type enzyme. We assigned the tryptophan fluorescence signal from Y162W by removing two native tryptophan residues (W270A/W284A). Stopped-flow experiments then demonstrated that the change in tryptophan fluorescence of the Y162W mutant is extremely rapid upon binding to either damaged or undamaged DNA, much faster than the lesion-recognition and nucleotide flipping steps that were independently determined by monitoring the ϵA fluorescence. These observations suggest that intercalation by this aromatic residue is one of the earliest steps in the search for DNA damage and that this interaction is important for the progression of AAG from nonspecific searching to specific-recognition complexes.
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Affiliation(s)
- Jenna M Hendershot
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
| | - Patrick J O'Brien
- From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0600
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22
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Chaim IA, Gardner A, Wu J, Iyama T, Wilson DM, Samson LD. A novel role for transcription-coupled nucleotide excision repair for the in vivo repair of 3,N4-ethenocytosine. Nucleic Acids Res 2017; 45:3242-3252. [PMID: 28115629 PMCID: PMC5389632 DOI: 10.1093/nar/gkx015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/20/2017] [Indexed: 12/13/2022] Open
Abstract
Etheno (ε) DNA base adducts are highly mutagenic lesions produced endogenously via reactions with lipid peroxidation (LPO) products. Cancer-promoting conditions, such as inflammation, can induce persistent oxidative stress and increased LPO, resulting in the accumulation of ε-adducts in different tissues. Using a recently described fluorescence multiplexed host cell reactivation assay, we show that a plasmid reporter bearing a site-specific 3,N4-ethenocytosine (εC) causes transcriptional blockage. Notably, this blockage is exacerbated in Cockayne Syndrome and xeroderma pigmentosum patient-derived lymphoblastoid and fibroblast cells. Parallel RNA-Seq expression analysis of the plasmid reporter identifies novel transcriptional mutagenesis properties of εC. Our studies reveal that beyond the known pathways, such as base excision repair, the process of transcription-coupled nucleotide excision repair plays a role in the removal of εC from the genome, and thus in the protection of cells and tissues from collateral damage induced by inflammatory responses.
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Affiliation(s)
- Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alycia Gardner
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jie Wu
- The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility in the Swanson Biotechnology Center, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Teruaki Iyama
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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PARP inhibitors protect against sex- and AAG-dependent alkylation-induced neural degeneration. Oncotarget 2017; 8:68707-68720. [PMID: 28978150 PMCID: PMC5620290 DOI: 10.18632/oncotarget.19844] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/08/2017] [Indexed: 11/25/2022] Open
Abstract
Alkylating agents are commonly used to treat cancer. Although base excision repair (BER) is a major pathway for repairing DNA alkylation damage, under certain conditions, the initiation of BER produces toxic repair intermediates that damage healthy tissues. The initiation of BER by the alkyladenine DNA glycosylase (AAG, a.k.a. MPG) can mediate alkylation-induced cytotoxicity in specific cells in the retina and cerebellum of male mice. Cytotoxicity in both wild-type and Aag-transgenic (AagTg) mice is abrogated in the absence of Poly(ADP-ribose) polymerase-1 (PARP1). Here, we tested whether PARP inhibitors can also prevent alkylation-induced retinal and cerebellar degeneration in male and female WT and AagTg mice. Importantly, we found that WT mice display sex-dependent alkylation-induced retinal damage (but not cerebellar damage), with WT males being more sensitive than females. Accordingly, estradiol treatment protects males against alkylation-induced retinal degeneration. In AagTg male and female mice, the alkylation-induced tissue damage in both the retina and cerebellum is exacerbated and the sex difference in the retina is abolished. PARP inhibitors, much like Parp1 gene deletion, protect against alkylation-induced AAG-dependent neuronal degeneration in WT and AagTg mice, regardless of the gender, but their efficacy in preventing alkylation-induced neuronal degeneration depends on PARP inhibitor characteristics and doses. The recent surge in the use of PARP inhibitors in combination with cancer chemotherapeutic alkylating agents might represent a powerful tool for obtaining increased therapeutic efficacy while avoiding the collateral effects of alkylating agents in healthy tissues.
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24
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Jordan JJ, Chhim S, Margulies CM, Allocca M, Bronson RT, Klungland A, Samson LD, Fu D. ALKBH7 drives a tissue and sex-specific necrotic cell death response following alkylation-induced damage. Cell Death Dis 2017; 8:e2947. [PMID: 28726787 PMCID: PMC5550884 DOI: 10.1038/cddis.2017.343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/14/2017] [Indexed: 12/12/2022]
Abstract
Regulated necrosis has emerged as a major cell death mechanism in response to different forms of physiological and pharmacological stress. The AlkB homolog 7 (ALKBH7) protein is required for regulated cellular necrosis in response to chemotherapeutic alkylating agents but its role within a whole organism is unknown. Here, we show that ALKBH7 modulates alkylation-induced cellular death through a tissue and sex-specific mechanism. At the whole-animal level, we find that ALKBH7 deficiency confers increased resistance to MMS-induced toxicity in male but not female mice. Moreover, ALKBH7-deficient mice exhibit protection against alkylation-mediated cytotoxicity in retinal photoreceptor and cerebellar granule cells, two cell types that undergo necrotic death through the initiation of the base excision repair pathway and hyperactivation of the PARP1/ARTD1 enzyme. Notably, the protection against alkylation-induced cerebellar degeneration is specific to ALKBH7-deficient male but not female mice. Our results uncover an in vivo role for ALKBH7 in mediating a sexually dimorphic tissue response to alkylation damage that could influence individual responses to chemotherapies based upon alkylating agents.
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Affiliation(s)
- Jennifer J Jordan
- Department of Biological Engineering, Biology, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sophea Chhim
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Carrie M Margulies
- Department of Biological Engineering, Biology, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mariacarmela Allocca
- Department of Biological Engineering, Biology, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Arne Klungland
- Department of Molecular Microbiology A3.3021, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Leona D Samson
- Department of Biological Engineering, Biology, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dragony Fu
- Department of Biology, University of Rochester, Rochester, NY, USA
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25
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Ignatov A, Bondarenko K, Makarova A. Non-bulky Lesions in Human DNA: the Ways of Formation, Repair, and Replication. Acta Naturae 2017; 9:12-26. [PMID: 29104772 PMCID: PMC5662270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 11/06/2022] Open
Abstract
DNA damage is a major cause of replication interruption, mutations, and cell death. DNA damage is removed by several types of repair processes. The involvement of specialized DNA polymerases in replication provides an important mechanism that helps tolerate persistent DNA damage. Specialized DNA polymerases incorporate nucleotides opposite lesions with high efficiency but demonstrate low accuracy of DNA synthesis. In this review, we summarize the types and mechanisms of formation and repair of non-bulky DNA lesions, and we provide an overview of the role of specialized DNA polymerases in translesion DNA synthesis.
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Affiliation(s)
- A.V. Ignatov
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
- Department of Molecular Biology, Faculty of Biology, Moscow State University, Leninskie Gory 1, bldg. 12, Moscow, 119991, Russia
| | - K.A. Bondarenko
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
| | - A.V. Makarova
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, Moscow, 123182 , Russia
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26
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Boiteux S, Coste F, Castaing B. Repair of 8-oxo-7,8-dihydroguanine in prokaryotic and eukaryotic cells: Properties and biological roles of the Fpg and OGG1 DNA N-glycosylases. Free Radic Biol Med 2017; 107:179-201. [PMID: 27903453 DOI: 10.1016/j.freeradbiomed.2016.11.042] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 01/23/2023]
Abstract
Oxidatively damaged DNA results from the attack of sugar and base moieties by reactive oxygen species (ROS), which are formed as byproducts of normal cell metabolism and during exposure to endogenous or exogenous chemical or physical agents. Guanine, having the lowest redox potential, is the DNA base the most susceptible to oxidation, yielding products such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2-6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). In DNA, 8-oxoG was shown to be mutagenic yielding GC to TA transversions upon incorporation of dAMP opposite this lesion by replicative DNA polymerases. In prokaryotic and eukaryotic cells, 8-oxoG is primarily repaired by the base excision repair pathway (BER) initiated by a DNA N-glycosylase, Fpg and OGG1, respectively. In Escherichia coli, Fpg cooperates with MutY and MutT to prevent 8-oxoG-induced mutations, the "GO-repair system". In Saccharomyces cerevisiae, OGG1 cooperates with nucleotide excision repair (NER), mismatch repair (MMR), post-replication repair (PRR) and DNA polymerase η to prevent mutagenesis. Human and mouse cells mobilize all these pathways using OGG1, MUTYH (MutY-homolog also known as MYH), MTH1 (MutT-homolog also known as NUDT1), NER, MMR, NEILs and DNA polymerases η and λ, to prevent 8-oxoG-induced mutations. In fact, mice deficient in both OGG1 and MUTYH develop cancer in different organs at adult age, which points to the critical impact of 8-oxoG repair on genetic stability in mammals. In this review, we will focus on Fpg and OGG1 proteins, their biochemical and structural properties as well as their biological roles. Other DNA N-glycosylases able to release 8-oxoG from damaged DNA in various organisms will be discussed. Finally, we will report on the role of OGG1 in human disease and the possible use of 8-oxoG DNA N-glycosylases as therapeutic targets.
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Affiliation(s)
- Serge Boiteux
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France.
| | - Franck Coste
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France.
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27
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Fahrer J, Kaina B. Impact of DNA repair on the dose-response of colorectal cancer formation induced by dietary carcinogens. Food Chem Toxicol 2016; 106:583-594. [PMID: 27693244 DOI: 10.1016/j.fct.2016.09.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/10/2016] [Accepted: 09/27/2016] [Indexed: 12/30/2022]
Abstract
Colorectal cancer (CRC) is one of the most frequently diagnosed cancers, which is causally linked to dietary habits, notably the intake of processed and red meat. Processed and red meat contain dietary carcinogens, including heterocyclic aromatic amines (HCAs) and N-nitroso compounds (NOC). NOC are agents that induce various N-methylated DNA adducts and O6-methylguanine (O6-MeG), which are removed by base excision repair (BER) and O6-methylguanine-DNA methyltransferase (MGMT), respectively. HCAs such as the highly mutagenic 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) cause bulky DNA adducts, which are removed from DNA by nucleotide excision repair (NER). Both O6-MeG and HCA-induced DNA adducts are linked to the occurrence of KRAS and APC mutations in colorectal tumors of rodents and humans, thereby driving CRC initiation and progression. In this review, we focus on DNA repair pathways removing DNA lesions induced by NOC and HCA and assess their role in protecting against mutagenicity and carcinogenicity in the large intestine. We further discuss the impact of DNA repair on the dose-response relationship in colorectal carcinogenesis in view of recent studies, demonstrating the existence of 'no effect' point of departures (PoDs), i.e. thresholds for genotoxicity and carcinogenicity. The available data support the threshold concept for NOC with DNA repair being causally involved.
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Affiliation(s)
- Jörg Fahrer
- Department of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany.
| | - Bernd Kaina
- Department of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany.
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28
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Ray D, Kidane D. Gut Microbiota Imbalance and Base Excision Repair Dynamics in Colon Cancer. J Cancer 2016; 7:1421-30. [PMID: 27471558 PMCID: PMC4964126 DOI: 10.7150/jca.15480] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/18/2016] [Indexed: 12/15/2022] Open
Abstract
Gut microbiota are required for host nutrition, energy balance, and regulating immune homeostasis, however, in some cases, this mutually beneficial relationship becomes twisted (dysbiosis), and the gut flora can incite pathological disorders including colon cancer. Microbial dysbiosis promotes the release of bacterial genotoxins, metabolites, and causes chronic inflammation, which promote oxidative DNA damage. Oxidized DNA base lesions are removed by base excision repair (BER), however, the role of this altered function of BER, as well as microbiota-mediated genomic instability and colon cancer development, is still poorly understood. In this review article, we will discuss how dysbiotic microbiota induce DNA damage, its impact on base excision repair capacity, the potential link of host BER gene polymorphism, and the risk of dysbiotic microbiota mediated genomic instability and colon cancer.
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Affiliation(s)
- Debolina Ray
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
| | - Dawit Kidane
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd. R1800, Austin, TX 78723, United States
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29
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Aspen Cancer Conference Fellows. Toxicol Pathol 2016. [DOI: 10.1080/01926230490882358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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30
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You C, Wang P, Nay SL, Wang J, Dai X, O’Connor TR, Wang Y. Roles of Aag, Alkbh2, and Alkbh3 in the Repair of Carboxymethylated and Ethylated Thymidine Lesions. ACS Chem Biol 2016; 11:1332-8. [PMID: 26930515 DOI: 10.1021/acschembio.6b00085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Environmental and endogenous genotoxic agents can result in a variety of alkylated and carboxymethylated DNA lesions, including N3-ethylthymidine (N3-EtdT), O(2)-EtdT, and O(4)-EtdT as well as N3-carboxymethylthymidine (N3-CMdT) and O(4)-CMdT. By using nonreplicative double-stranded vectors harboring a site-specifically incorporated DNA lesion, we assessed the potential roles of alkyladenine DNA glycosylase (Aag); alkylation repair protein B homologue 2 (Alkbh2); or Alkbh3 in modulating the effects of N3-EtdT, O(2)-EtdT, O(4)-EtdT, N3-CMdT, or O(4)-CMdT on DNA transcription in mammalian cells. We found that the depletion of Aag did not significantly change the transcriptional inhibitory or mutagenic properties of all five examined lesions, suggesting a negligible role of Aag in the repair of these DNA adducts in mammalian cells. In addition, our results revealed that N3-EtdT, but not other lesions, could be repaired by Alkbh2 and Alkbh3 in mammalian cells. Furthermore, we demonstrated the direct reversal of N3-EtdT by purified human Alkbh2 protein in vitro. These findings provided important new insights into the repair of the carboxymethylated and alkylated thymidine lesions in mammalian cells.
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Affiliation(s)
- Changjun You
- Department
of Chemistry, University of California, Riverside, California, United States
| | - Pengcheng Wang
- Environmental
Toxicology Graduate Program, University of California, Riverside, California, United States
| | - Stephanie L. Nay
- Department
of Cancer Biology, Beckman Research Institute, Duarte, California, United States
| | - Jianshuang Wang
- Department
of Chemistry, University of California, Riverside, California, United States
| | - Xiaoxia Dai
- Department
of Chemistry, University of California, Riverside, California, United States
| | - Timothy R. O’Connor
- Department
of Cancer Biology, Beckman Research Institute, Duarte, California, United States
| | - Yinsheng Wang
- Department
of Chemistry, University of California, Riverside, California, United States
- Environmental
Toxicology Graduate Program, University of California, Riverside, California, United States
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31
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Crystal structure and MD simulation of mouse EndoV reveal wedge motif plasticity in this inosine-specific endonuclease. Sci Rep 2016; 6:24979. [PMID: 27108838 PMCID: PMC4842958 DOI: 10.1038/srep24979] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 04/07/2016] [Indexed: 01/06/2023] Open
Abstract
Endonuclease V (EndoV) is an enzyme with specificity for deaminated adenosine (inosine) in nucleic acids. EndoV from Escherichia coli (EcEndoV) acts both on inosines in DNA and RNA, whereas the human homolog cleaves only at inosines in RNA. Inosines in DNA are mutagenic and the role of EndoV in DNA repair is well established. In contrast, the biological function of EndoV in RNA processing is largely unexplored. Here we have characterized a second mammalian EndoV homolog, mouse EndoV (mEndoV), and show that mEndoV shares the same RNA selectivity as human EndoV (hEndoV). Mouse EndoV cleaves the same inosine-containing substrates as hEndoV, but with reduced efficiencies. The crystal structure of mEndoV reveals a conformation different from the hEndoV and prokaryotic EndoV structures, particularly for the conserved tyrosine in the wedge motif, suggesting that this strand separating element has some flexibility. Molecular dynamics simulations of mouse and human EndoV reveal alternative conformations for the invariant tyrosine. The configuration of the active site, on the other hand, is very similar between the prokaryotic and mammalian versions of EndoV.
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32
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Impact of topical application of sulfur mustard on mice skin and distant organs DNA repair enzyme signature. Toxicol Lett 2016; 241:71-81. [DOI: 10.1016/j.toxlet.2015.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/02/2015] [Accepted: 11/02/2015] [Indexed: 11/23/2022]
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33
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Zhang Y, O’Brien PJ. Repair of Alkylation Damage in Eukaryotic Chromatin Depends on Searching Ability of Alkyladenine DNA Glycosylase. ACS Chem Biol 2015; 10:2606-15. [PMID: 26317160 DOI: 10.1021/acschembio.5b00409] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Human alkyladenine DNA glycosylase (AAG) initiates the base excision repair pathway by excising alkylated and deaminated purine lesions. In vitro biochemical experiments demonstrate that AAG uses facilitated diffusion to efficiently search DNA to find rare sites of damage and suggest that electrostatic interactions are critical to the searching process. However, it remains an open question whether DNA searching limits the rate of DNA repair in vivo. We constructed AAG mutants with altered searching ability and measured their ability to protect yeast from alkylation damage in order to address this question. Each of the conserved arginine and lysine residues that are near the DNA binding interface were mutated, and the functional impacts were evaluated using kinetic and thermodynamic analysis. These mutations do not perturb catalysis of N-glycosidic bond cleavage, but they decrease the ability to capture rare lesion sites. Nonspecific and specific DNA binding properties are closely correlated, suggesting that the electrostatic interactions observed in the specific recognition complex are similarly important for DNA searching complexes. The ability of the mutant proteins to complement repair-deficient yeast cells is positively correlated with the ability of the proteins to search DNA in vitro, suggesting that cellular resistance to DNA alkylation is governed by the ability to find and efficiently capture cytotoxic lesions. It appears that chromosomal access is not restricted and toxic sites of alkylation damage are readily accessible to a searching protein.
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Affiliation(s)
- Yaru Zhang
- Chemical
Biology Program, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
| | - Patrick J. O’Brien
- Chemical
Biology Program, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109-2216, United States
- Department
of Biological Chemistry, University of Michigan Medical School, 1150
W. Medical Center Dr., Ann Arbor, Michigan 48109-0600, United States
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34
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Wang Y, Zang W, Du Y, Chen X, Zhao G. The K167I variant of DNA polymerase β that is found in Esophageal Carcinoma patients impairs polymerase activity and BER. Sci Rep 2015; 5:15986. [PMID: 26527528 PMCID: PMC4630582 DOI: 10.1038/srep15986] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 10/02/2015] [Indexed: 12/17/2022] Open
Abstract
DNA polymerase β (pol β) is a key enzyme in DNA base excision repair, and an important factor for maintaining genomic integrity and stability. Esophageal carcinoma (EC) patients who have been identified as carrying the K167I variant of pol β have been shown to have decreased life expectancy. However, it is unknown if the variant affects pol β’s functions and/or how it contributes to the initiation and progression of cancer. In this study, we expressed and purified the K167I variant. Moreover, we found that K167I significantly reduced polymerase activity. As a result, the K167I substitution reduced base excision repair (BER) efficiency when assayed in a reconstitution assay or when using cellular extracts. Finally, we observed EC cells expressing the K167I variant to be sensitive to DNA damaging agents. These results suggest the K167I variant affected pol β biochemical activity resulting in impaired BER function, which might subsequently contribute to genomic instability and cancer development.
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Affiliation(s)
- Yuanyuan Wang
- College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Wenqiao Zang
- College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yuwen Du
- College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaonan Chen
- College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Guoqiang Zhao
- College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
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35
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Taylor EL, O'Brien PJ. Kinetic mechanism for the flipping and excision of 1,N(6)-ethenoadenine by AlkA. Biochemistry 2015; 54:898-908. [PMID: 25537480 PMCID: PMC4310629 DOI: 10.1021/bi501356x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
Escherichia coli 3-methyladenine DNA glycosylase
II (AlkA), an adaptive response glycosylase with a broad substrate
range, initiates base excision repair by flipping a lesion out of
the DNA duplex and hydrolyzing the N-glycosidic bond. We used transient
and steady state kinetics to determine the minimal mechanism for recognition
and excision of 1,N6-ethenoadenine (εA)
by AlkA. The natural fluorescence of this endogenously produced lesion
allowed us to directly monitor the nucleotide flipping step. We found
that AlkA rapidly and reversibly binds and flips out εA prior
to N-glycosidic bond hydrolysis, which is the rate-limiting step of
the reaction. The binding affinity of AlkA for the εA-DNA lesion
is only 40-fold tighter than for a nonspecific site and 20-fold weaker
than for the abasic DNA site. The mechanism of AlkA-catalyzed excision
of εA was compared to that of the human alkyladenine DNA glycosylase
(AAG), an independently evolved glycosylase that recognizes many of
the same substrates. AlkA and AAG both catalyze N-glycosidic bond
hydrolysis to release εA, and their overall rates of reaction
are within 2-fold of each other. Nevertheless, we find dramatic differences
in the kinetics and thermodynamics for binding to εA-DNA. AlkA
catalyzes nucleotide flipping an order of magnitude faster than AAG;
however, the equilibrium for flipping is almost 3 orders of magnitude
more favorable for AAG than for AlkA. These results illustrate how
enzymes that perform the same chemistry can use different substrate
recognition strategies to effectively repair DNA damage.
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Affiliation(s)
- Erin L Taylor
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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Hedglin M, Zhang Y, O'Brien PJ. Probing the DNA structural requirements for facilitated diffusion. Biochemistry 2014; 54:557-66. [PMID: 25495964 PMCID: PMC4303293 DOI: 10.1021/bi5013707] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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DNA glycosylases perform a genome-wide
search to locate damaged
nucleotides among a great excess of undamaged nucleotides. Many glycosylases
are capable of facilitated diffusion, whereby multiple sites along
the DNA are sampled during a single binding encounter. Electrostatic
interactions between positively charged amino acids and the negatively
charged phosphate backbone are crucial for facilitated diffusion,
but the extent to which diffusing proteins rely on the double-helical
structure DNA is not known. Kinetic assays were used to probe the
DNA searching mechanism of human alkyladenine DNA glycosylase (AAG)
and to test the extent to which diffusion requires B-form duplex DNA.
Although AAG excises εA lesions from single-stranded DNA, it
is not processive on single-stranded DNA because dissociation is faster
than N-glycosidic bond cleavage. However, the AAG complex with single-stranded
DNA is sufficiently stable to allow for DNA annealing when a complementary
strand is added. This observation provides evidence of nonspecific
association of AAG with single-stranded DNA. Single-strand gaps, bubbles,
and bent structures do not impede the search by AAG. Instead, these
flexible or bent structures lead to the capture of a nearby site of
damage that is more efficient than that of a continuous B-form duplex.
The ability of AAG to negotiate these helix discontinuities is inconsistent
with a sliding mode of diffusion but can be readily explained by a
hopping mode that involves microscopic dissociation and reassociation.
These experiments provide evidence of relatively long-range hops that
allow a searching protein to navigate around DNA binding proteins
that would serve as obstacles to a sliding protein.
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Affiliation(s)
- Mark Hedglin
- Chemical Biology Program and ‡Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-5606, United States
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Hendershot JM, O'Brien PJ. Critical role of DNA intercalation in enzyme-catalyzed nucleotide flipping. Nucleic Acids Res 2014; 42:12681-90. [PMID: 25324304 PMCID: PMC4227769 DOI: 10.1093/nar/gku919] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/21/2014] [Accepted: 09/22/2014] [Indexed: 11/14/2022] Open
Abstract
Nucleotide flipping is a common feature of DNA-modifying enzymes that allows access to target sites within duplex DNA. Structural studies have identified many intercalating amino acid side chains in a wide variety of enzymes, but the functional contribution of these intercalating residues is poorly understood. We used site-directed mutagenesis and transient kinetic approaches to dissect the energetic contribution of intercalation for human alkyladenine DNA glycosylase, an enzyme that initiates repair of alkylation damage. When AAG flips out a damaged nucleotide, the void in the duplex is filled by a conserved tyrosine (Y162). We find that tyrosine intercalation confers 140-fold stabilization of the extrahelical specific recognition complex, and that Y162 functions as a plug to slow the rate of unflipping by 6000-fold relative to the Y162A mutant. Surprisingly, mutation to the smaller alanine side chain increases the rate of nucleotide flipping by 50-fold relative to the wild-type enzyme. This provides evidence against the popular model that DNA intercalation accelerates nucleotide flipping. In the case of AAG, DNA intercalation contributes to the specific binding of a damaged nucleotide, but this enhanced specificity comes at the cost of reduced speed of nucleotide flipping.
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Affiliation(s)
- Jenna M Hendershot
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Patrick J O'Brien
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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38
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Meira LB, Calvo JA, Shah D, Klapacz J, Moroski-Erkul CA, Bronson RT, Samson LD. Repair of endogenous DNA base lesions modulate lifespan in mice. DNA Repair (Amst) 2014; 21:78-86. [PMID: 24994062 PMCID: PMC4125484 DOI: 10.1016/j.dnarep.2014.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/30/2014] [Accepted: 05/20/2014] [Indexed: 12/21/2022]
Abstract
The accumulation of DNA damage is thought to contribute to the physiological decay associated with the aging process. Here, we report the results of a large-scale study examining longevity in various mouse models defective in the repair of DNA alkylation damage, or defective in the DNA damage response. We find that the repair of spontaneous DNA damage by alkyladenine DNA glycosylase (Aag/Mpg)-initiated base excision repair and O(6)-methylguanine DNA methyltransferase (Mgmt)-mediated direct reversal contributes to maximum life span in the laboratory mouse. We also uncovered important genetic interactions between Aag, which excises a wide variety of damaged DNA bases, and the DNA damage sensor and signaling protein, Atm. We show that Atm plays a role in mediating survival in the face of both spontaneous and induced DNA damage, and that Aag deficiency not only promotes overall survival, but also alters the tumor spectrum in Atm(-/-) mice. Further, the reversal of spontaneous alkylation damage by Mgmt interacts with the DNA mismatch repair pathway to modulate survival and tumor spectrum. Since these aging studies were performed without treatment with DNA damaging agents, our results indicate that the DNA damage that is generated endogenously accumulates with age, and that DNA alkylation repair proteins play a role in influencing longevity.
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Affiliation(s)
- Lisiane B Meira
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Jennifer A Calvo
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Dharini Shah
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Joanna Klapacz
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Catherine A Moroski-Erkul
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Roderick T Bronson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Rodent Histopathology Core, Harvard Medical School, 126 Goldenson Building, Boston, MA 02115, United States
| | - Leona D Samson
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Biology Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Rodent Histopathology Core, Harvard Medical School, 126 Goldenson Building, Boston, MA 02115, United States.
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39
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Alseth I, Dalhus B, Bjørås M. Inosine in DNA and RNA. Curr Opin Genet Dev 2014; 26:116-23. [PMID: 25173738 DOI: 10.1016/j.gde.2014.07.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/28/2014] [Accepted: 07/30/2014] [Indexed: 12/25/2022]
Abstract
Deamination of the nucleobases in DNA and RNA is a result of spontaneous hydrolysis, endogenous or environmental factors as well as deaminase enzymes. Adenosine is deaminated to inosine which is miscoding and preferentially base pairs with cytosine. In the case of DNA, this is a premutagenic event that is counteracted by DNA repair enzymes specifically engaged in recognition and removal of inosine. However, in RNA, inosine is an essential modification introduced by specialized enzymes in a highly regulated manner to generate transcriptome diversity. Defect editing is seen in various human disease including cancer, viral infections and neurological and psychiatric disorders. Enzymes catalyzing the deaminase reaction are well characterized and recently an unexpected function of Endonuclease V in RNA processing was revealed. Whereas bacterial Endonuclease V enzymes are classified as DNA repair enzymes, it appears that the mammalian enzymes are involved in processing of inosine in RNA. This yields an interesting yet unexplored, link between DNA and RNA processing. Further work is needed to gain understanding of the impact of inosine in DNA and RNA under normal physiology and disease progression.
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Affiliation(s)
- Ingrun Alseth
- Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Bjørn Dalhus
- Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway; Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway; Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Oslo, Norway.
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40
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Kiraly O, Gong G, Roytman MD, Yamada Y, Samson LD, Engelward BP. DNA glycosylase activity and cell proliferation are key factors in modulating homologous recombination in vivo. Carcinogenesis 2014; 35:2495-502. [PMID: 25155011 DOI: 10.1093/carcin/bgu177] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Cancer susceptibility varies between people, affected by genotoxic exposures, genetic makeup and physiological state. Yet, how these factors interact among each other to define cancer risk is largely unknown. Here, we uncover the interactive effects of genetical, environmental and physiological factors on genome rearrangements driven by homologous recombination (HR). Using FYDR mice to quantify HR-driven rearrangements in pancreas tissue, we show that DNA methylation damage (induced by methylnitrosourea) and cell proliferation (induced by thyroid hormone) each induce HR and together act synergistically to induce HR-driven rearrangements in vivo. These results imply that developmental or regenerative proliferation as well as mitogenic exposures may sensitize tissues to DNA damaging exposures. We exploited mice genetically deficient in alkyl-adenine DNA glycosylase (Aag) to analyse the relative contributions of unrepaired DNA base lesions versus intermediates formed during base excision repair (BER). Remarkably, results show that, in the pancreas, Aag is a major driver of spontaneous HR, indicating that BER intermediates (including abasic sites and single strand breaks) are more recombinogenic than the spontaneous base lesions removed by Aag. Given that mammals have about a dozen DNA glycosylases, these results point to BER as a major source of pressure on the HR pathway in vivo. Taken together, methylation damage, cell proliferation and Aag interact to define the risk of HR-driven sequence rearrangements in vivo. These data identify important sources of sequence changes in a cancer-relevant organ, and advance the effort to identify populations at high-risk for cancer.
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Affiliation(s)
- Orsolya Kiraly
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA and
| | - Guanyu Gong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA and
| | - Megan D Roytman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA and
| | - Yoshiyuki Yamada
- Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA and
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA and Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
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41
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Woodrick J, Gupta S, Khatkar P, Sarangi S, Narasimhan G, Trehan A, Adhikari S, Roy R. Slow repair of lipid peroxidation-induced DNA damage at p53 mutation hotspots in human cells caused by low turnover of a DNA glycosylase. Nucleic Acids Res 2014; 42:9033-46. [PMID: 25081213 PMCID: PMC4132702 DOI: 10.1093/nar/gku520] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 05/21/2014] [Accepted: 05/24/2014] [Indexed: 12/16/2022] Open
Abstract
Repair of oxidative stress- and inflammation-induced DNA lesions by the base excision repair (BER) pathway prevents mutation, a form of genomic instability which is often observed in cancer as 'mutation hotspots'. This suggests that some sequences have inherent mutability, possibly due to sequence-related differences in repair. This study has explored intrinsic mutability as a consequence of sequence-specific repair of lipid peroxidation-induced DNA adduct, 1, N(6)-ethenoadenine (εA). For the first time, we observed significant delay in repair of ϵA at mutation hotspots in the tumor suppressor gene p53 compared to non-hotspots in live human hepatocytes and endothelial cells using an in-cell real time PCR-based method. In-cell and in vitro mechanism studies revealed that this delay in repair was due to inefficient turnover of N-methylpurine-DNA glycosylase (MPG), which initiates BER of εA. We determined that the product dissociation rate of MPG at the hotspot codons was ≈5-12-fold lower than the non-hotspots, suggesting a previously unknown mechanism for slower repair at mutation hotspots and implicating sequence-related variability of DNA repair efficiency to be responsible for mutation hotspot signatures.
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Affiliation(s)
- Jordan Woodrick
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington, DC 20057, USA
| | - Suhani Gupta
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington, DC 20057, USA
| | - Pooja Khatkar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington, DC 20057, USA
| | - Sanchita Sarangi
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington, DC 20057, USA
| | - Ganga Narasimhan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington, DC 20057, USA
| | - Akriti Trehan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington, DC 20057, USA
| | - Sanjay Adhikari
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington, DC 20057, USA
| | - Rabindra Roy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical School, Washington, DC 20057, USA
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42
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Fahrer J, Kaina B. O6-methylguanine-DNA methyltransferase in the defense against N-nitroso compounds and colorectal cancer. Carcinogenesis 2013; 34:2435-42. [PMID: 23929436 DOI: 10.1093/carcin/bgt275] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is among the leading causes of cancer death worldwide, involving multiple dietary and non-dietary risk factors. A growing body of evidence suggests that N-nitroso compounds (NOC) play a pivotal role in the etiology of CRC. NOC are present in food and are also formed endogenously in the large intestine. Upon metabolic activation and also spontaneously, they form electrophilic species that methylate the DNA, producing N-methylated purines and O(6)-methylguanine, the latter of which bears high mutagenic and carcinogenic potential. Methylated DNA bases are removed by base excision repair initiated by the alkyladenine-DNA glycosylase, the family of AlkB homologs proteins, and the suicide enzyme O(6)-methylguanine-DNA methyltransferase (MGMT), which is the main focus of this review. We present animal models with a deficiency of MGMT that display a tremendously enhanced sensitivity toward alkylation-induced colorectal carcinogenesis, highlighting its role in the protection against the cytotoxic and mutagenic effects of alkylating agents. In line with these studies, MGMT was linked to the formation of human sporadic CRC. Colorectal tumors and precursor lesions frequently display epigenetic inactivation of MGMT resulting from promoter hypermethylation, which is tightly associated with the occurrence of G:C to A:T transition mutations in the KRAS oncogene. We also discuss clinical data, which identified the MGMT status of CRC patients as promising parameter for the treatment of metastasized CRC using alkylating anticancer drugs such as temozolomide.
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Affiliation(s)
- Jörg Fahrer
- Department of Toxicology, University Medical Center Mainz, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany
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43
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Hedglin M, Zhang Y, O'Brien PJ. Isolating contributions from intersegmental transfer to DNA searching by alkyladenine DNA glycosylase. J Biol Chem 2013; 288:24550-9. [PMID: 23839988 DOI: 10.1074/jbc.m113.477018] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Large genomes pose a challenge to DNA repair pathways because rare sites of damage must be efficiently located from among a vast excess of undamaged sites. Human alkyladenine DNA glycosylase (AAG) employs nonspecific DNA binding interactions and facilitated diffusion to conduct a highly redundant search of adjacent sites. This ensures that every site is searched, but could be a detriment if the protein is trapped in a local segment of DNA. Intersegmental transfer between DNA segments that are transiently in close proximity provides an elegant solution that balances global and local searching processes. It has been difficult to detect intersegmental transfer experimentally; therefore, we developed biochemical assays that allowed us to observe and measure the rates of intersegmental transfer by AAG. AAG has a flexible amino terminus that tunes its affinity for nonspecific DNA, but we find that it is not required for intersegmental transfer. As AAG has only a single DNA binding site, this argues against the bridging model for intersegmental transfer. The rates of intersegmental transfer are strongly dependent on the salt concentration, supporting a jumping mechanism that involves microscopic dissociation and capture by a proximal DNA site. As many DNA-binding proteins have only a single binding site, jumping may be a common mechanism for intersegmental transfer.
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Affiliation(s)
- Mark Hedglin
- Department of Biological Chemistry and the Chemical Biology Doctoral Program, the University of Michigan Medical School, Ann Arbor, Michigan 48109-0600, USA
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44
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Calvo JA, Moroski-Erkul CA, Lake A, Eichinger LW, Shah D, Jhun I, Limsirichai P, Bronson RT, Christiani DC, Meira LB, Samson LD. Aag DNA glycosylase promotes alkylation-induced tissue damage mediated by Parp1. PLoS Genet 2013; 9:e1003413. [PMID: 23593019 PMCID: PMC3617098 DOI: 10.1371/journal.pgen.1003413] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 02/11/2013] [Indexed: 12/21/2022] Open
Abstract
Alkylating agents comprise a major class of front-line cancer chemotherapeutic compounds, and while these agents effectively kill tumor cells, they also damage healthy tissues. Although base excision repair (BER) is essential in repairing DNA alkylation damage, under certain conditions, initiation of BER can be detrimental. Here we illustrate that the alkyladenine DNA glycosylase (AAG) mediates alkylation-induced tissue damage and whole-animal lethality following exposure to alkylating agents. Aag-dependent tissue damage, as observed in cerebellar granule cells, splenocytes, thymocytes, bone marrow cells, pancreatic β-cells, and retinal photoreceptor cells, was detected in wild-type mice, exacerbated in Aag transgenic mice, and completely suppressed in Aag−/− mice. Additional genetic experiments dissected the effects of modulating both BER and Parp1 on alkylation sensitivity in mice and determined that Aag acts upstream of Parp1 in alkylation-induced tissue damage; in fact, cytotoxicity in WT and Aag transgenic mice was abrogated in the absence of Parp1. These results provide in vivo evidence that Aag-initiated BER may play a critical role in determining the side-effects of alkylating agent chemotherapies and that Parp1 plays a crucial role in Aag-mediated tissue damage. Alkylating agents are genotoxic chemicals that induce both toxic and mutagenic DNA damage through addition of an alkyl group to DNA. Alkylating agents are routinely and successfully used as chemotherapeutic therapies for cancer patients, with one major disadvantage being the significant toxicity induced in non-tumor tissues. Accordingly, identifying factors that modify susceptibility to alkylation-induced toxicity will provide valuable information in designing cancer therapeutic regimens. This study used mouse genetic experiments to investigate whether proteins important in the base excision repair pathway modulate susceptibility to alkylating agents. In addition to whole-animal toxicity at high doses, treatment of mice with alkylating agents resulted in severe damage to numerous tissues including the cerebellum, retina, bone marrow, spleen, thymus, and the pancreas. We illustrate that the DNA glycosylase Aag can actually confer, rather than prevent, alkylation sensitivity at both the whole-animal and tissue level; i.e., Aag transgenic animals are more susceptible than wild type, whereas Aag-deficient animals are less susceptible than wild type to alkylation-induced toxicity. Further genetic experiments show that the Aag-mediated alkylation sensitivity is dependent on Parp1. Given that we observe a wide range of human AAG expression among healthy individuals, this and other base excision repair proteins may be important factors modulating alkylation susceptibility.
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Affiliation(s)
- Jennifer A. Calvo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Catherine A. Moroski-Erkul
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Annabelle Lake
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Lindsey W. Eichinger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Dharini Shah
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Iny Jhun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Prajit Limsirichai
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Roderick T. Bronson
- Department of Pathology, Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - David C. Christiani
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Lisiane B. Meira
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Leona D. Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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45
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Adhikary S, Cato MC, McGary KL, Rokas A, Eichman BF. Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe. DNA Repair (Amst) 2012; 12:196-204. [PMID: 23273506 DOI: 10.1016/j.dnarep.2012.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/03/2012] [Accepted: 12/03/2012] [Indexed: 11/15/2022]
Abstract
Schizosaccharomyces pombe contains two paralogous proteins, Mag1 and Mag2, related to the helix-hairpin-helix (HhH) superfamily of alkylpurine DNA glycosylases from yeast and bacteria. Phylogenetic analysis of related proteins from four Schizosaccharomyces and other fungal species shows that the Mag1/Mag2 duplication is unique to the genus Schizosaccharomyces and most likely occurred in its ancestor. Mag1 excises N3- and N7-alkylguanines and 1,N(6)-ethenoadenine from DNA, whereas Mag2 has been reported to have no detectible alkylpurine base excision activity despite high sequence and active site similarity to Mag1. To understand this discrepancy we determined the crystal structure of Mag2 bound to abasic DNA and compared it to our previously determined Mag1-DNA structure. In contrast to Mag1, Mag2 does not flip the abasic moiety into the active site or stabilize the DNA strand 5' to the lesion, suggesting that it is incapable of forming a catalytically competent protein-DNA complex. Subtle differences in Mag1 and Mag2 interactions with the DNA duplex illustrate how Mag2 can stall at damage sites without fully engaging the lesion. We tested our structural predictions by mutational analysis of base excision and found a single amino acid responsible at least in part for Mag2's lack of activity. Substitution of Mag2 Asp56, which caps the helix at the base of the DNA intercalation loop, with the corresponding serine residue in Mag1 endows Mag2 with ɛA excision activity comparable to Mag1. This work provides novel insight into the chemical and physical determinants by which the HhH glycosylases engage DNA in a catalytically productive manner.
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Affiliation(s)
- Suraj Adhikary
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
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Dalhus B, Nilsen L, Korvald H, Huffman J, Forstrøm RJ, McMurray CT, Alseth I, Tainer JA, Bjørås M. Sculpting of DNA at abasic sites by DNA glycosylase homolog mag2. Structure 2012; 21:154-166. [PMID: 23245849 DOI: 10.1016/j.str.2012.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 11/05/2012] [Accepted: 11/06/2012] [Indexed: 11/15/2022]
Abstract
Modifications and loss of bases are frequent types of DNA lesions, often handled by the base excision repair (BER) pathway. BER is initiated by DNA glycosylases, generating abasic (AP) sites that are subsequently cleaved by AP endonucleases, which further pass on nicked DNA to downstream DNA polymerases and ligases. The coordinated handover of cytotoxic intermediates between different BER enzymes is most likely facilitated by the DNA conformation. Here, we present the atomic structure of Schizosaccharomyces pombe Mag2 in complex with DNA to reveal an unexpected structural basis for nonenzymatic AP site recognition with an unflipped AP site. Two surface-exposed loops intercalate and widen the DNA minor groove to generate a DNA conformation previously only found in the mismatch repair MutS-DNA complex. Consequently, the molecular role of Mag2 appears to be AP site recognition and protection, while possibly facilitating damage signaling by structurally sculpting the DNA substrate.
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Affiliation(s)
- Bjørn Dalhus
- Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway
| | - Line Nilsen
- Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway
| | - Hanne Korvald
- Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway
| | - Joy Huffman
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rune Johansen Forstrøm
- Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway
| | - Cynthia T McMurray
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic and Foundation, Rochester, MN 55905, USA; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop: 83R0101, Berkeley, CA 94720, USA
| | - Ingrun Alseth
- Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway.
| | - John A Tainer
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Bioenergy/GTL and Structural Biology, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop: 83R0101, Berkeley, CA 94720, USA.
| | - Magnar Bjørås
- Department of Microbiology, Centre of Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway; Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, N-0424, Oslo, Norway; Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Bosshard M, Markkanen E, van Loon B. Base excision repair in physiology and pathology of the central nervous system. Int J Mol Sci 2012. [PMID: 23203191 PMCID: PMC3546685 DOI: 10.3390/ijms131216172] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Relatively low levels of antioxidant enzymes and high oxygen metabolism result in formation of numerous oxidized DNA lesions in the tissues of the central nervous system. Accumulation of damage in the DNA, due to continuous genotoxic stress, has been linked to both aging and the development of various neurodegenerative disorders. Different DNA repair pathways have evolved to successfully act on damaged DNA and prevent genomic instability. The predominant and essential DNA repair pathway for the removal of small DNA base lesions is base excision repair (BER). In this review we will discuss the current knowledge on the involvement of BER proteins in the maintenance of genetic stability in different brain regions and how changes in the levels of these proteins contribute to aging and the onset of neurodegenerative disorders.
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Affiliation(s)
- Matthias Bosshard
- Institute for Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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Small-molecule inhibitors of DNA damage-repair pathways: an approach to overcome tumor resistance to alkylating anticancer drugs. Future Med Chem 2012; 4:1093-111. [PMID: 22709253 DOI: 10.4155/fmc.12.58] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A major challenge in the future development of cancer therapeutics is the identification of biological targets and pathways, and the subsequent design of molecules to combat the drug-resistant cells hiding in virtually all cancers. This therapeutic approach is justified based upon the limited advances in cancer cures over the past 30 years, despite the development of many novel chemotherapies and earlier detection, which often fail due to drug resistance. Among the various targets to overcome tumor resistance are the DNA repair systems that can reverse the cytotoxicity of many clinically used DNA-damaging agents. Some progress has already been made but much remains to be done. We explore some components of the DNA-repair process, which are involved in repair of alkylation damage of DNA, as targets for the development of novel and effective molecules designed to improve the efficacy of existing anticancer drugs.
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Folate and colorectal cancer in rodents: a model of DNA repair deficiency. JOURNAL OF ONCOLOGY 2012; 2012:105949. [PMID: 23093960 PMCID: PMC3474250 DOI: 10.1155/2012/105949] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 06/07/2012] [Indexed: 12/31/2022]
Abstract
Fortification of grains has resulted in a positive public health outcome vis-a-vis reduced incidence of neural tube defects. Whether folate has a correspondingly beneficial effect on other disease outcomes is less clear. A role for dietary folate in the prevention of colorectal cancer has been established through epidemiological data. Experimental data aiming to further elucidate this relationship has been somewhat equivocal. Studies report that folate depletion increases DNA damage, mutagenesis, and chromosomal instability, all suggesting inhibited DNA repair. While these data connecting folate depletion and inhibition of DNA repair are convincing, we also present data demonstrating that genetic inhibition of DNA repair is protective in the development of preneoplastic colon lesions, both when folate is depleted and when it is not. The purpose of this paper is to (1) give an overview of the data demonstrating a DNA repair defect in response to folate depletion, and (2) critically compare and contrast the experimental designs utilized in folate/colorectal cancer research and the corresponding impact on tissue folate status and critical colorectal cancer endpoints. Our analysis suggests that there is still an important need for a comprehensive evaluation of the impact of differential dietary prescriptions on blood and tissue folate status.
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Srinivasan A, Wang L, Cline CJ, Xie Z, Sobol RW, Xie XQ, Gold B. Identification and characterization of human apurinic/apyrimidinic endonuclease-1 inhibitors. Biochemistry 2012; 51:6246-59. [PMID: 22788932 DOI: 10.1021/bi300490r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The repair of abasic sites that arise in DNA from hydrolytic depurination/depyrimidination of the nitrogenous bases from the sugar-phosphate backbone and the action of DNA glycosylases on deaminated, oxidized, and alkylated bases are critical to cell survival. Apurinic/apyrimidinic endonuclease-1/redox effector factor-1 (APE-1; aka APE1/ref-1) is responsible for the initial removal of abasic lesions as part of the base excision repair pathway. Deletion of APE-1 activity is embryonic lethal in animals and is lethal in cells. Potential inhibitors of the repair function of APE-1 were identified based upon molecular modeling of the crystal structure of the APE-1 protein. We describe the characterization of several unique nanomolar inhibitors using two complementary biochemical screens. The most active molecules all contain a 2-methyl-4-amino-6,7-dioxolo-quinoline structure that is predicted from the modeling to anchor the compounds in the endonuclease site of the protein. The mechanism of action of the selected compounds was probed by fluorescence and competition studies, which indicate, in a specific case, direct interaction between the inhibitor and the active site of the protein. It is demonstrated that the inhibitors induce time-dependent increases in the accumulation of abasic sites in cells at levels that correlate with their potency to inhibit APE-1 endonuclease excision. The inhibitor molecules also potentiate by 5-fold the toxicity of a DNA methylating agent that creates abasic sites. The molecules represent a new class of APE-1 inhibitors that can be used to probe the biology of this critical enzyme and to sensitize resistant tumor cells to the cytotoxicity of clinically used DNA damaging anticancer drugs.
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Affiliation(s)
- Ajay Srinivasan
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
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