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Mórocz M, Qorri E, Pekker E, Tick G, Haracska L. Exploring RAD18-dependent replication of damaged DNA and discontinuities: A collection of advanced tools. J Biotechnol 2024; 380:1-19. [PMID: 38072328 DOI: 10.1016/j.jbiotec.2023.12.001] [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: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/21/2023]
Abstract
DNA damage tolerance (DDT) pathways mitigate the effects of DNA damage during replication by rescuing the replication fork stalled at a DNA lesion or other barriers and also repair discontinuities left in the newly replicated DNA. From yeast to mammalian cells, RAD18-regulated translesion synthesis (TLS) and template switching (TS) represent the dominant pathways of DDT. Monoubiquitylation of the polymerase sliding clamp PCNA by HRAD6A-B/RAD18, an E2/E3 protein pair, enables the recruitment of specialized TLS polymerases that can insert nucleotides opposite damaged template bases. Alternatively, the subsequent polyubiquitylation of monoubiquitin-PCNA by Ubc13-Mms2 (E2) and HLTF or SHPRH (E3) can lead to the switching of the synthesis from the damaged template to the undamaged newly synthesized sister strand to facilitate synthesis past the lesion. When immediate TLS or TS cannot occur, gaps may remain in the newly synthesized strand, partly due to the repriming activity of the PRIMPOL primase, which can be filled during the later phases of the cell cycle. The first part of this review will summarize the current knowledge about RAD18-dependent DDT pathways, while the second part will offer a molecular toolkit for the identification and characterization of the cellular functions of a DDT protein. In particular, we will focus on advanced techniques that can reveal single-stranded and double-stranded DNA gaps and their repair at the single-cell level as well as monitor the progression of single replication forks, such as the specific versions of the DNA fiber and comet assays. This collection of methods may serve as a powerful molecular toolkit to monitor the metabolism of gaps, detect the contribution of relevant pathways and molecular players, as well as characterize the effectiveness of potential inhibitors.
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Affiliation(s)
- Mónika Mórocz
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Erda Qorri
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged H-6720, Hungary.
| | - Emese Pekker
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Doctoral School of Interdisciplinary Medicine, University of Szeged, Korányi fasor 10, 6720 Szeged, Hungary.
| | - Gabriella Tick
- Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Lajos Haracska
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; National Laboratory for Drug Research and Development, Magyar tudósok krt. 2. H-1117 Budapest, Hungary.
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Schuermann D, Ziemann C, Barekati Z, Capstick M, Oertel A, Focke F, Murbach M, Kuster N, Dasenbrock C, Schär P. Assessment of Genotoxicity in Human Cells Exposed to Modulated Electromagnetic Fields of Wireless Communication Devices. Genes (Basel) 2020; 11:E347. [PMID: 32218170 PMCID: PMC7230863 DOI: 10.3390/genes11040347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 12/12/2022] Open
Abstract
Modulated electromagnetic fields (wEMFs), as generated by modern communication technologies, have raised concerns about adverse health effects. The International Agency for Research on Cancer (IARC) classifies them as "possibly carcinogenic to humans" (Group 2B), yet, the underlying molecular mechanisms initiating and promoting tumorigenesis remain elusive. Here, we comprehensively assess the impact of technologically relevant wEMF modulations on the genome integrity of cultured human cells, investigating cell type-specificities as well as time- and dose-dependencies. Classical and advanced methodologies of genetic toxicology and DNA repair were applied, and key experiments were performed in two separate laboratories. Overall, we found no conclusive evidence for an induction of DNA damage nor for alterations of the DNA repair capacity in cells exposed to several wEMF modulations (i.e., GSM, UMTS, WiFi, and RFID). Previously reported observations of increased DNA damage after exposure of cells to GSM-modulated signals could not be reproduced. Experimental variables, presumably underlying the discrepant observations, were investigated and are discussed. On the basis of our data, we conclude that the possible carcinogenicity of wEMF modulations cannot be explained by an effect on genome integrity through direct DNA damage. However, we cannot exclude non-genotoxic, indirect, or secondary effects of wEMF exposure that may promote tumorigenesis in other ways.
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Affiliation(s)
- David Schuermann
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland; (Z.B.); (F.F.); (P.S.)
| | - Christina Ziemann
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs-Strasse 1, D-30625 Hannover, Germany; (A.O.); (C.D.)
| | - Zeinab Barekati
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland; (Z.B.); (F.F.); (P.S.)
| | - Myles Capstick
- IT’IS Foundation, Zeughausstrasse 43, CH-8004 Zurich, Switzerland; (M.C.); (M.M.); (N.K.)
| | - Antje Oertel
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs-Strasse 1, D-30625 Hannover, Germany; (A.O.); (C.D.)
| | - Frauke Focke
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland; (Z.B.); (F.F.); (P.S.)
| | - Manuel Murbach
- IT’IS Foundation, Zeughausstrasse 43, CH-8004 Zurich, Switzerland; (M.C.); (M.M.); (N.K.)
| | - Niels Kuster
- IT’IS Foundation, Zeughausstrasse 43, CH-8004 Zurich, Switzerland; (M.C.); (M.M.); (N.K.)
- Department of Information Technology and Electrical Engineering, Swiss Federal Institute of Technology (ETH), CH-8092 Zurich, Switzerland
| | - Clemens Dasenbrock
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Nikolai-Fuchs-Strasse 1, D-30625 Hannover, Germany; (A.O.); (C.D.)
| | - Primo Schär
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland; (Z.B.); (F.F.); (P.S.)
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Xiang C, Wu X, Zhao Z, Feng X, Bai X, Liu X, Zhao J, Takeda S, Qing Y. Nonhomologous end joining and homologous recombination involved in luteolin-induced DNA damage in DT40 cells. Toxicol In Vitro 2020; 65:104825. [PMID: 32169435 DOI: 10.1016/j.tiv.2020.104825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/08/2020] [Accepted: 03/08/2020] [Indexed: 02/05/2023]
Abstract
Luteolin (3',4',5,7-tetrahydroxyflavone), a naturally occurring flavonoid, has been shown to have anticancer activity in many types of cancer cell lines. The anticancer capacity of luteolin may be related to its ability to induce DNA double-strand breaks (DSBs). Here, we used DT40 cells to determine whether nonhomologous end joining (NHEJ) and homologous recombination (HR) are involved in the repair mechanism of luteolin-induced DNA damage. Cells defective in Ku70 (an enzyme associated with NHEJ) or Rad54 (an enzyme essential for HR) were hypersensitive and presented more apoptosis in response to luteolin. Moreover, the sensitivity and apoptosis of Ku70-/- and Rad54-/- cells were associated with increased DNA damage when the numbers of γ-H2AX foci and chromosomal aberrations (CAs) were compared with those from WT cells. Additionally, after treatment with luteolin, Ku70-/- cells presented more Top2 covalent cleavage complexes (Top2cc). These results indicated that luteolin induced DSBs in DT40 cells and demonstrated that both NHEJ and HR participated in the repair of luteolin-induced DSBs, which might be related to the inhibition of topoisomerases. These results imply that simultaneous inhibition of NHEJ and HR with luteolin treatment would provide a powerful protocol in cancer chemotherapy.
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Affiliation(s)
- Cuifang Xiang
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xiaohua Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zilu Zhao
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoyu Feng
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xin Bai
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xin Liu
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Jingxia Zhao
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yong Qing
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China.
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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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5
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Nishihara K, Shahane SA, Xia M. Determination of Histone H2AX Phosphorylation in DT40 Cells. Methods Mol Biol 2018; 1473:71-6. [PMID: 27518625 DOI: 10.1007/978-1-4939-6346-1_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Visualization of DNA damage response protein recruitment to DNA damage sites enables measurement of the DNA damage. DNA double-strand breaks (DSBs) and blocked replication forks induce the phosphorylation of H2AX at serine 139 (γH2AX), and accumulate γH2AX which can then be detected as foci. The detection of γH2AX foci by immunostaining with antibodies that recognize γH2AX is an indicator of DSBs presence. This chapter describes the measurement of γH2AX immunostaining using a high-content imaging platform in chicken DT40 B-lymphocyte cell lines.
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Affiliation(s)
- Kana Nishihara
- National Center for Advancing Translational Sciences, National Institutes of Health, Building C, MSC: 3375, 9800 Medical Center Drive, Bethesda, MD, 20892, USA
| | - Sampada A Shahane
- National Center for Advancing Translational Sciences, National Institutes of Health, Building C, MSC: 3375, 9800 Medical Center Drive, Bethesda, MD, 20892, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Building C, MSC: 3375, 9800 Medical Center Drive, Bethesda, MD, 20892, USA.
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De La Rosa VY, Asfaha J, Fasullo M, Loguinov A, Li P, Moore LE, Rothman N, Nakamura J, Swenberg JA, Scelo G, Zhang L, Smith MT, Vulpe CD. Editor's Highlight: High-Throughput Functional Genomics Identifies Modulators of TCE Metabolite Genotoxicity and Candidate Susceptibility Genes. Toxicol Sci 2017; 160:111-120. [PMID: 28973557 PMCID: PMC5837773 DOI: 10.1093/toxsci/kfx159] [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] [Indexed: 11/13/2022] Open
Abstract
Trichloroethylene (TCE), an industrial chemical and environmental contaminant, is a human carcinogen. Reactive metabolites are implicated in renal carcinogenesis associated with TCE exposure, yet the toxicity mechanisms of these metabolites and their contribution to cancer and other adverse effects remain unclear. We employed an integrated functional genomics approach that combined functional profiling studies in yeast and avian DT40 cell models to provide new insights into the specific mechanisms contributing to toxicity associated with TCE metabolites. Genome-wide profiling studies in yeast identified the error-prone translesion synthesis (TLS) pathway as an import mechanism in response to TCE metabolites. The role of TLS DNA repair was further confirmed by functional profiling in DT40 avian cell lines, but also revealed that TLS and homologous recombination DNA repair likely play competing roles in cellular susceptibility to TCE metabolites in higher eukaryotes. These DNA repair pathways are highly conserved between yeast, DT40, and humans. We propose that in humans, mutagenic TLS is favored over homologous recombination repair in response to TCE metabolites. The results of these studies contribute to the body of evidence supporting a mutagenic mode of action for TCE-induced renal carcinogenesis mediated by reactive metabolites in humans. Our approach illustrates the potential for high-throughput in vitro functional profiling in yeast to elucidate toxicity pathways (molecular initiating events, key events) and candidate susceptibility genes for focused study.
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Affiliation(s)
- Vanessa Y. De La Rosa
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720
| | - Jonathan Asfaha
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720
| | - Michael Fasullo
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, New York 12205
| | - Alex Loguinov
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720
| | - Peng Li
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Lee E. Moore
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jun Nakamura
- Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina
| | | | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Luoping Zhang
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California 94720
| | - Martyn T. Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California 94720
| | - Chris D. Vulpe
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720
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Liu Y, Wu X, Hu X, Chen Z, Liu H, Takeda S, Qing Y. Multiple repair pathways mediate cellular tolerance to resveratrol-induced DNA damage. Toxicol In Vitro 2017; 42:130-138. [PMID: 28431926 DOI: 10.1016/j.tiv.2017.04.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/01/2017] [Accepted: 04/12/2017] [Indexed: 02/05/2023]
Abstract
Resveratrol (RSV) has been reported to exert health benefits for the prevention and treatment of many diseases, including cancer. The anticancer mechanisms of RSV seem to be complex and may be associated with genotoxic potential. To better understand the genotoxic mechanisms, we used wild-type (WT) and a panel of isogenic DNA-repair deficient DT40 cell lines to identify the DNA damage effects and molecular mechanisms of cellular tolerance to RSV. Our results showed that RSV induced significant formation of γ-H2AX foci and chromosome aberrations (CAs) in WT cells, suggesting direct DNA damage effects. Comparing the survival of WT with isogenic DNA-repair deficient DT40 cell lines demonstrated that single strand break repair (SSBR) deficient cell lines of Parp1-/-, base excision repair (BER) deficient cell lines of Polβ-/-, homologous recombination (HR) mutants of Brca1-/- and Brca2-/- and translesion DNA synthesis (TLS) mutants of Rev3-/- and Rad18-/- were more sensitive to RSV. The sensitivities of cells were associated with enhanced DNA damage comparing the accumulation of γ-H2AX foci and number of CAs of isogenic DNA-repair deficient DT40 cell lines with WT cells. These results clearly demonstrated that RSV-induced DNA damage in DT40 cells, and multiple repair pathways including BER, SSBR, HR and TLS, play critical roles in response to RSV- induced genotoxicity.
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Affiliation(s)
- Ying Liu
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaohua Wu
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Xiaoqing Hu
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ziyuan Chen
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hao Liu
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yong Qing
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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8
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Szikriszt B, Póti Á, Pipek O, Krzystanek M, Kanu N, Molnár J, Ribli D, Szeltner Z, Tusnády GE, Csabai I, Szallasi Z, Swanton C, Szüts D. A comprehensive survey of the mutagenic impact of common cancer cytotoxics. Genome Biol 2016; 17:99. [PMID: 27161042 PMCID: PMC4862131 DOI: 10.1186/s13059-016-0963-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic mutations caused by cytotoxic agents used in cancer chemotherapy may cause secondary malignancies as well as contribute to the evolution of treatment-resistant tumour cells. The stable diploid genome of the chicken DT40 lymphoblast cell line, an established DNA repair model system, is well suited to accurately assay genomic mutations. RESULTS We use whole genome sequencing of multiple DT40 clones to determine the mutagenic effect of eight common cytotoxics used for the treatment of millions of patients worldwide. We determine the spontaneous mutagenesis rate at 2.3 × 10(-10) per base per cell division and find that cisplatin, cyclophosphamide and etoposide induce extra base substitutions with distinct spectra. After four cycles of exposure, cisplatin induces 0.8 mutations per Mb, equivalent to the median mutational burden in common leukaemias. Cisplatin-induced mutations, including short insertions and deletions, are mainly located at sites of putative intrastrand crosslinks. We find two of the newly defined cisplatin-specific mutation types as causes of the reversion of BRCA2 mutations in emerging cisplatin-resistant tumours or cell clones. Gemcitabine, 5-fluorouracil, hydroxyurea, doxorubicin and paclitaxel have no measurable mutagenic effect. The cisplatin-induced mutation spectrum shows good correlation with cancer mutation signatures attributed to smoking and other sources of guanine-directed base damage. CONCLUSION This study provides support for the use of cell line mutagenesis assays to validate or predict the mutagenic effect of environmental and iatrogenic exposures. Our results suggest genetic reversion due to cisplatin-induced mutations as a distinct mechanism for developing resistance.
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Affiliation(s)
- Bernadett Szikriszt
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary
| | - Orsolya Pipek
- Department of Physics of Complex Systems, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Marcin Krzystanek
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Nnennaya Kanu
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - János Molnár
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary
| | - Dezső Ribli
- Department of Physics of Complex Systems, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Zoltán Szeltner
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary
| | - Gábor E Tusnády
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Zoltan Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800, Lyngby, Denmark.
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, 02215, USA.
- MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, 1091, Budapest, Hungary.
| | - Charles Swanton
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK.
- Francis Crick Institute, 44 Lincoln's Inn Fields, London, WCA2 3PX, UK.
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117, Budapest, Hungary.
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Jiang L, Wu X, He F, Liu Y, Hu X, Takeda S, Qing Y. Genetic Evidence for Genotoxic Effect of Entecavir, an Anti-Hepatitis B Virus Nucleotide Analog. PLoS One 2016; 11:e0147440. [PMID: 26800464 PMCID: PMC4723259 DOI: 10.1371/journal.pone.0147440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/04/2016] [Indexed: 02/05/2023] Open
Abstract
Nucleoside analogues (NAs) have been the most frequently used treatment option for chronic hepatitis B patients. However, they may have genotoxic potentials due to their interference with nucleic acid metabolism. Entecavir, a deoxyguanosine analog, is one of the most widely used oral antiviral NAs against hepatitis B virus. It has reported that entecavir gave positive responses in both genotoxicity and carcinogenicity assays. However the genotoxic mechanism of entecavir remains elusive. To evaluate the genotoxic mechanisms, we analyzed the effect of entecavir on a panel of chicken DT40 B-lymphocyte isogenic mutant cell line deficient in DNA repair and damage tolerance pathways. Our results showed that Parp1-/- mutant cells defective in single-strand break (SSB) repair were the most sensitive to entecavir. Brca1-/-, Ubc13-/- and translesion-DNA-synthesis deficient cells including Rad18-/- and Rev3-/- were hypersensitive to entecavir. XPA-/- mutant deficient in nucleotide excision repair was also slightly sensitive to entecavir. γ-H2AX foci forming assay confirmed the existence of DNA damage by entecavir in Parp1-/-, Rad18-/- and Brca1-/- mutants. Karyotype assay further showed entecavir-induced chromosomal aberrations, especially the chromosome gaps in Parp1-/-, Brca1-/-, Rad18-/- and Rev3-/- cells when compared with wild-type cells. These genetic comprehensive studies clearly identified the genotoxic potentials of entecavir and suggested that SSB and postreplication repair pathways may suppress entecavir-induced genotoxicity.
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Affiliation(s)
- Lei Jiang
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaohua Wu
- Regenerative Medicine Research Center, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Fang He
- Center of Infectious Diseases, Division of Molecular Biology of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ying Liu
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaoqing Hu
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, 606–8501, Japan
| | - Yong Qing
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
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Chibwe L, Geier MC, Nakamura J, Tanguay RL, Aitken MD, Simonich SLM. Aerobic Bioremediation of PAH Contaminated Soil Results in Increased Genotoxicity and Developmental Toxicity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015. [PMID: 26200254 PMCID: PMC4666737 DOI: 10.1021/acs.est.5b00499] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The formation of more polar and toxic polycyclic aromatic hydrocarbon (PAH) transformation products is one of the concerns associated with the bioremediation of PAH-contaminated soils. Soil contaminated with coal tar (prebioremediation) from a former manufactured gas plant (MGP) site was treated in a laboratory scale bioreactor (postbioremediation) and extracted using pressurized liquid extraction. The soil extracts were fractionated, based on polarity, and analyzed for 88 PAHs (unsubstituted, oxygenated, nitrated, and heterocyclic PAHs). The PAH concentrations in the soil tested, postbioremediation, were lower than their regulatory maximum allowable concentrations (MACs), with the exception of the higher molecular weight PAHs (BaA, BkF, BbF, BaP, and IcdP), most of which did not undergo significant biodegradation. The soil extract fractions were tested for genotoxicity using the DT40 chicken lymphocyte bioassay and developmental toxicity using the embryonic zebrafish (Danio rerio) bioassay. A statistically significant increase in genotoxicity was measured in the unfractionated soil extract, as well as in four polar soil extract fractions, postbioremediation (p < 0.05). In addition, a statistically significant increase in developmental toxicity was measured in one polar soil extract fraction, postbioremediation (p < 0.05). A series of morphological abnormalities, including peculiar caudal fin malformations and hyperpigmentation in the tail, were measured in several soil extract fractions in embryonic zebrafish, both pre- and postbioremediation. The increased toxicity measured postbioremediation is not likely due to the 88 PAHs measured in this study (including quinones), because most were not present in the toxic polar fractions and/or because their concentrations did not increase postbioremediation. However, the increased toxicity measured postbioremediation is likely due to hydroxylated and carboxylated transformation products of the 3- and 4-ring PAHs (PHE, 1MPHE, 2MPHE, PRY, BaA, and FLA) that were most degraded.
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Affiliation(s)
- Leah Chibwe
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
| | - Mitra C. Geier
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Jun Nakamura
- Department of Environmental Sciences & Engineering, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert L. Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Michael D. Aitken
- Department of Environmental Sciences & Engineering, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Staci L. Massey Simonich
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
- Corresponding Author Address: 1141 Agricultural and Life Sciences, Corvallis, OR 97331-7301, USA; telephone: (541) 737-9194; fax: (541) 737-0497;
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Nishihara K, Huang R, Zhao J, Shahane SA, Witt KL, Smith-Roe SL, Tice RR, Takeda S, Xia M. Identification of genotoxic compounds using isogenic DNA repair deficient DT40 cell lines on a quantitative high throughput screening platform. Mutagenesis 2015; 31:69-81. [PMID: 26243743 DOI: 10.1093/mutage/gev055] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA repair pathways play a critical role in maintaining cellular homeostasis by repairing DNA damage induced by endogenous processes and xenobiotics, including environmental chemicals. Induction of DNA damage may lead to genomic instability, disruption of cellular homeostasis and potentially tumours. Isogenic chicken DT40 B-lymphocyte cell lines deficient in DNA repair pathways can be used to identify genotoxic compounds and aid in characterising the nature of the induced DNA damage. As part of the US Tox21 program, we previously optimised several different DT40 isogenic clones on a high-throughput screening platform and confirmed the utility of this approach for detecting genotoxicants by measuring differential cytotoxicity in wild-type and DNA repair-deficient clones following chemical exposure. In the study reported here, we screened the Tox21 10K compound library against two isogenic DNA repair-deficient DT40 cell lines (KU70 (-/-) /RAD54 (-/-) and REV3 (-/-) ) and the wild-type cell line using a cell viability assay that measures intracellular adenosine triphosphate levels. KU70 and RAD54 are genes associated with DNA double-strand break repair processes, and REV3 is associated with translesion DNA synthesis pathways. Active compounds identified in the primary screening included many well-known genotoxicants (e.g. adriamycin, melphalan) and several compounds previously untested for genotoxicity. A subset of compounds was further evaluated by assessing their ability to induce micronuclei and phosphorylated H2AX. Using this comprehensive approach, three compounds with previously undefined genotoxicity-2-oxiranemethanamine, AD-67 and tetraphenylolethane glycidyl ether-were identified as genotoxic. These results demonstrate the utility of this approach for identifying and prioritising compounds that may damage DNA.
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Affiliation(s)
- Kana Nishihara
- Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo, Kyoto 606-8501, Japan, National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, MSC: 3375 Bethesda, MD 20892, USA and
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, MSC: 3375 Bethesda, MD 20892, USA and
| | - Jinghua Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, MSC: 3375 Bethesda, MD 20892, USA and
| | - Sampada A Shahane
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, MSC: 3375 Bethesda, MD 20892, USA and
| | - Kristine L Witt
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Stephanie L Smith-Roe
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Raymond R Tice
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Shunichi Takeda
- Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo, Kyoto 606-8501, Japan
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, MSC: 3375 Bethesda, MD 20892, USA and
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12
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Fujii Y, Narita T, Tice RR, Takeda S, Yamada R. Isotonic Regression Based-Method in Quantitative High-Throughput Screenings for Genotoxicity. Dose Response 2015; 13:10.2203_dose-response.13-045.Fujii. [PMID: 26673567 PMCID: PMC4674159 DOI: 10.2203/dose-response.13-045.fujii] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Quantitative high-throughput screenings (qHTSs) for genotoxicity are conducted as part of comprehensive toxicology screening projects. The most widely used method is to compare the dose-response data of a wild-type and DNA repair gene knockout mutants, using model-fitting to the Hill equation (HE). However, this method performs poorly when the observed viability does not fit the equation well, as frequently happens in qHTS. More capable methods must be developed for qHTS where large data variations are unavoidable. In this study, we applied an isotonic regression (IR) method and compared its performance with HE under multiple data conditions. When dose-response data were suitable to draw HE curves with upper and lower asymptotes and experimental random errors were small, HE was better than IR, but when random errors were big, there was no difference between HE and IR. However, when the drawn curves did not have two asymptotes, IR showed better performance (p < 0.05, exact paired Wilcoxon test) with higher specificity (65% in HE vs. 96% in IR). In summary, IR performed similarly to HE when dose-response data were optimal, whereas IR clearly performed better in suboptimal conditions. These findings indicate that IR would be useful in qHTS for comparing dose-response data.
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Affiliation(s)
- Yosuke Fujii
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Japan
| | - Takeo Narita
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Japan
| | - Raymond Richard Tice
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, USA
| | - Shunich Takeda
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Japan
| | - Ryo Yamada
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Japan
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13
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Zhang L, McHale CM, Greene N, Snyder RD, Rich IN, Aardema MJ, Roy S, Pfuhler S, Venkatactahalam S. Emerging approaches in predictive toxicology. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:679-688. [PMID: 25044351 PMCID: PMC4749138 DOI: 10.1002/em.21885] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 06/19/2014] [Indexed: 05/29/2023]
Abstract
Predictive toxicology plays an important role in the assessment of toxicity of chemicals and the drug development process. While there are several well-established in vitro and in vivo assays that are suitable for predictive toxicology, recent advances in high-throughput analytical technologies and model systems are expected to have a major impact on the field of predictive toxicology. This commentary provides an overview of the state of the current science and a brief discussion on future perspectives for the field of predictive toxicology for human toxicity. Computational models for predictive toxicology, needs for further refinement and obstacles to expand computational models to include additional classes of chemical compounds are highlighted. Functional and comparative genomics approaches in predictive toxicology are discussed with an emphasis on successful utilization of recently developed model systems for high-throughput analysis. The advantages of three-dimensional model systems and stem cells and their use in predictive toxicology testing are also described.
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Affiliation(s)
- Luoping Zhang
- Genes and Environment Laboratory, Division of Environmental Health and Sciences, School of Public Health, University of California, Berkeley, California
| | - Cliona M. McHale
- Genes and Environment Laboratory, Division of Environmental Health and Sciences, School of Public Health, University of California, Berkeley, California
| | - Nigel Greene
- Compound Safety Prediction, Worldwide Medicinal Chemistry, Pfizer World-wide R&D, Groton, Connecticut
| | | | | | - Marilyn J. Aardema
- Marilyn Aardema Consulting, LLC, Fairfield Ohio
- Toxicology Division, BioReliance Corporation, Rockville, Maryland
| | - Shambhu Roy
- Toxicology Division, BioReliance Corporation, Rockville, Maryland
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Gaytán BD, Vulpe CD. Functional toxicology: tools to advance the future of toxicity testing. Front Genet 2014; 5:110. [PMID: 24847352 PMCID: PMC4017141 DOI: 10.3389/fgene.2014.00110] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 04/12/2014] [Indexed: 11/16/2022] Open
Abstract
The increased presence of chemical contaminants in the environment is an undeniable concern to human health and ecosystems. Historically, by relying heavily upon costly and laborious animal-based toxicity assays, the field of toxicology has often neglected examinations of the cellular and molecular mechanisms of toxicity for the majority of compounds—information that, if available, would strengthen risk assessment analyses. Functional toxicology, where cells or organisms with gene deletions or depleted proteins are used to assess genetic requirements for chemical tolerance, can advance the field of toxicity testing by contributing data regarding chemical mechanisms of toxicity. Functional toxicology can be accomplished using available genetic tools in yeasts, other fungi and bacteria, and eukaryotes of increased complexity, including zebrafish, fruit flies, rodents, and human cell lines. Underscored is the value of using less complex systems such as yeasts to direct further studies in more complex systems such as human cell lines. Functional techniques can yield (1) novel insights into chemical toxicity; (2) pathways and mechanisms deserving of further study; and (3) candidate human toxicant susceptibility or resistance genes.
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Affiliation(s)
- Brandon D Gaytán
- Department of Nutritional Science and Toxicology, University of California Berkeley Berkeley, CA, USA
| | - Chris D Vulpe
- Department of Nutritional Science and Toxicology, University of California Berkeley Berkeley, CA, USA
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15
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Shekh K, Khan S, Jena G, Kansara BR, Kushwaha S. 3-Aminobenzamide – a PARP inhibitor enhances the sensitivity of peripheral blood micronucleus and comet assays in mice. Toxicol Mech Methods 2014; 24:332-41. [DOI: 10.3109/15376516.2014.898355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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16
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McHale CM, Smith MT, Zhang L. Application of toxicogenomic profiling to evaluate effects of benzene and formaldehyde: from yeast to human. Ann N Y Acad Sci 2014; 1310:74-83. [PMID: 24571325 DOI: 10.1111/nyas.12382] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genetic variation underlies a significant proportion of the individual variation in human susceptibility to toxicants. The primary current approaches to identify gene-environment (GxE) associations, genome-wide association studies and candidate gene association studies, require large exposed and control populations and an understanding of toxicity genes and pathways, respectively. This limits their application in the study of GxE associations for the leukemogens benzene and formaldehyde, whose toxicity has long been a focus of our research. As an alternative approach, our published work has applied innovative in vitro functional genomics testing systems, including unbiased functional screening assays in yeast and a near-haploid human bone marrow cell line. Through comparative genomic and computational analyses of the resulting data, human genes and pathways that may modulate susceptibility to benzene and formaldehyde were identified, and the roles of several genes in mammalian cell models were validated. In populations occupationally exposed to low levels of benzene, we applied peripheral blood mononuclear cell transcriptomics and chromosome-wide aneuploidy studies in lymphocytes. In this review, we describe our comprehensive toxicogenomic approach and the potential mechanisms of toxicity and susceptibility genes identified for benzene and formaldehyde, as well as related studies conducted by other researchers.
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Affiliation(s)
- Cliona M McHale
- Genes and Environment Laboratory, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California
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17
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Smith S, Fox J, Mejia M, Ruangpradit W, Saberi A, Kim S, Choi Y, Oh S, Wang Y, Choi K, Li L, Hendrickson EA, Takeda S, Muller M, Myung K. Histone deacetylase inhibitors selectively target homology dependent DNA repair defective cells and elevate non-homologous endjoining activity. PLoS One 2014; 9:e87203. [PMID: 24466340 PMCID: PMC3900704 DOI: 10.1371/journal.pone.0087203] [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: 06/04/2013] [Accepted: 12/27/2013] [Indexed: 01/08/2023] Open
Abstract
Background We have previously used the ATAD5-luciferase high-throughput screening assay to identify genotoxic compounds with potential chemotherapeutic capabilities. The successful identification of known genotoxic agents, including the histone deacetylase inhibitor (HDACi) trichostatin A (TSA), confirmed the specificity of the screen since TSA has been widely studied for its ability to cause apoptosis in cancer cells. Because many cancers have acquired mutations in DNA damage checkpoints or repair pathways, we hypothesized that these cancers may be susceptible to treatments that target compensatory pathways. Here, we used a panel of isogenic chicken DT40 B lymphocyte mutant and human cell lines to investigate the ability of TSA to define selective pathways that promote HDACi toxicity. Results HDACi induced a DNA damage response and reduced viability in all repair deficient DT40 mutants although ATM-nulls were least affected. The most dramatic sensitivity was observed in mutants lacking the homology dependent repair (HDR) factor BLM or the non-homologous end-joining (NHEJ) and HDR factors, KU/RAD54, suggesting an involvement of either HDR or NHEJ in HDACi-induced cell death. To extend these findings, we measured the frequencies of HDR and NHEJ after HDACi treatment and monitored viability in human cell lines comparably deficient in HDR or NHEJ. Although no difference in HDR frequency was observed between HDACi treated and untreated cells, HDR-defective human cell lines were clearly more sensitive than wild type. Unexpectedly, cells treated with HDACis showed a significantly elevated NHEJ frequency. Conclusions HDACi targeting drugs induced significant increases in NHEJ activity in human cell lines but did not alter HDR frequency. Moreover, HDR is required for cellular resistance to HDACi therapy; therefore, NHEJ does not appear to be a critical axis for HDACi resistance. Rather, HDACi compounds induced DNA damage, most likely double strand breaks (DSBs), and HDR proficiency is correlated with cell survival.
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Affiliation(s)
- Stephanie Smith
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jennifer Fox
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marco Mejia
- Department of Molecular Biology and Microbiology, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Wanvipa Ruangpradit
- Department of Molecular Biology and Microbiology, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Alihossein Saberi
- Department of Radiation Genetics Kyoto University, Medical School, Kyoto, 606-8501 Japan
| | - Sunmi Kim
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Radiation Genetics Kyoto University, Medical School, Kyoto, 606-8501 Japan
- Department of Environmental Health School of Public Hearth, Seoul National University, Seoul, Korea
| | - Yongjun Choi
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sehyun Oh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Yucai Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston Texas, United States of America
| | - Kyungho Choi
- Department of Environmental Health School of Public Hearth, Seoul National University, Seoul, Korea
| | - Lei Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Eric A. Hendrickson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Shunichi Takeda
- Department of Radiation Genetics Kyoto University, Medical School, Kyoto, 606-8501 Japan
| | - Mark Muller
- Department of Molecular Biology and Microbiology, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Kyungjae Myung
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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18
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Torres NP, Lee AY, Giaever G, Nislow C, Brown GW. A high-throughput yeast assay identifies synergistic drug combinations. Assay Drug Dev Technol 2014; 11:299-307. [PMID: 23772551 DOI: 10.1089/adt.2012.503] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Drug combinations are commonly used in the treatment of a range of diseases such as cancer, AIDS, and bacterial infections. Such combinations are less likely to be thwarted by resistance, and they have the desirable potential to be synergistic. Synergistic combinations can have decreased toxicity if lower doses of the constituent agents can be used. Conversely, antagonistic combinations can lead to lower efficacy of a treatment. Unfortunately, practical limitations, including the large number of possible combinations to be tested and the importance of optimizing concentrations and order of addition, discourage systematic studies of compound combinations. To address these limitations, we present a platform to screen drug combinations at multiple concentrations with varying orders of addition in Saccharomyces cerevisiae, at high throughput. In a proof of principle, we screened all possible pairwise combinations of 11 DNA damaging agents and found that of the 66 combinations tested, six were synergistic and three were antagonistic. The strength of two-thirds of these combinations was dependent on the order in which the drugs were added to the cells. We further tested the synergistic and antagonistic combinations in two cancer cell lines and found the combination of mitomycin C and irinotecan to be synergistic in both cell lines. This pilot study demonstrates the utility of using yeast for screening large matrices of drug combinations, and it provides a means to prioritize drug combination tests in human cells. Finally, we underscore the importance of testing the order of addition for assessing drug combinations.
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19
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Lee S, Liu X, Takeda S, Choi K. Genotoxic potentials and related mechanisms of bisphenol A and other bisphenol compounds: a comparison study employing chicken DT40 cells. CHEMOSPHERE 2013; 93:434-440. [PMID: 23791112 DOI: 10.1016/j.chemosphere.2013.05.029] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 04/30/2013] [Accepted: 05/05/2013] [Indexed: 06/02/2023]
Abstract
Bisphenol A (BPA) has been found in plastic food containers, paper currencies and toys. BPA has been reported for various adverse health concerns including reproduction, development and carcinogenesis. These potential health implications have led to increasing use of alternative bisphenols such as bisphenol F and bisphenol S among many. However, little is known about the toxicity of alternative bisphenols and most of the toxicological information is limited to endocrine disrupting potentials. In this study, we evaluated cytotoxicity and the genotoxic potentials of several bisphenol compounds, and identified the mechanism of genotoxicity using a panel of mutant chicken DT40 cell lines deficient in DNA repair pathways. Several bisphenols including bisphenol AP, bisphenol M, or bisphenol P exerted genotoxic potentials that are greater than that of BPA. Generally RAD54(-/-) mutant cells were the most sensitive to all bisphenols except for bisphenol F, suggesting the induction of DNA double-strand breaks that could be rescued by homologous recombination. Genotoxic potential of bisphenols was confirmed by chromosomal aberration assay and γ-H2AX foci forming assay between wild-type and RAD54(-/-) mutant. Among the tested bisphenols, BPP at 12.5μM showed the greatest genotoxic potency, inducing chromosomal aberration and γ-H2AX foci in RAD54(-/-) mutant by 2.6 and 4.8 folds greater than those in wild-type, respectively. Our results clearly show several alternative bisphenols can cause genotoxicity that could be rescued by homologous recombination pathway, and some bisphenols induced even greater genotoxic potentials than that of BPA.
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Affiliation(s)
- Sangwoo Lee
- School of Public Health, Seoul National University, Seoul 151-742, Republic of Korea
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20
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Mohiuddin, Keka IS, Evans TJ, Hirota K, Shimizu H, Kono K, Takeda S, Hirano S. A novel genotoxicity assay of carbon nanotubes using functional macrophage receptor with collagenous structure (MARCO)-expressing chicken B lymphocytes. Arch Toxicol 2013; 88:145-60. [PMID: 23963510 DOI: 10.1007/s00204-013-1084-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 06/20/2013] [Indexed: 01/09/2023]
Abstract
Although carbon nanotubes (CNTs) are promising nanomaterials, their potential carcinogenicity is a major concern. We previously established a genetic method of analyzing genotoxicity of chemical compounds, where we evaluated their cytotoxic effect on the DT40 lymphoid cell line comparing DNA-repair-deficient isogenic clones with parental wild-type cells. However, application of our DT40 system for the cytotoxic and genotoxic evaluation of nanomaterials seemed to be difficult, because DT40 cells only poorly internalized nanoparticles. To solve this problem, we have constructed a chimeric gene encoding a trans-membrane receptor consisting of the 5' region of the transferrin receptor (TR) gene (to facilitate internalization of nanoparticles) and the 3' region of the macrophage receptor with collagenous structure (MARCO) gene (which is a receptor for environmental particles). We expressed the resulting MARCO-TR chimeric receptor on DNA-repair-proficient wild-type cells and mutants deficient in base excision repair (FEN1 (-/-)) and translesion DNA synthesis (REV3 (-/-)). We demonstrated that the chimera mediates uptake of particles such as fluorescence-tagged polystyrene particles and multi-walled carbon nanotubes (MWCNTs), with very poor uptake of those particles by DT40 cells not expressing the chimera. MWCNTs were cytotoxic and this effect was greater in FEN1 (-/-)and REV3 (-/-) cells than in wild-type cells. Furthermore, MWCNTs induced greater oxidative damage (measured as 8-OH-dG formation) and a larger number of mitotic chromosomal aberrations in repair-deficient cells compared to repair-proficient cells. Taken together, our novel assay system using the chimeric receptor-expressing DT40 cells provides a sensitive method to screen for genotoxicity of CNTs and possibly other nanomaterials.
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Affiliation(s)
- Mohiuddin
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
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Fujita M, Sasanuma H, Yamamoto KN, Harada H, Kurosawa A, Adachi N, Omura M, Hiraoka M, Takeda S, Hirota K. Interference in DNA replication can cause mitotic chromosomal breakage unassociated with double-strand breaks. PLoS One 2013; 8:e60043. [PMID: 23573231 PMCID: PMC3616066 DOI: 10.1371/journal.pone.0060043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/20/2013] [Indexed: 12/24/2022] Open
Abstract
Morphological analysis of mitotic chromosomes is used to detect mutagenic chemical compounds and to estimate the dose of ionizing radiation to be administered. It has long been believed that chromosomal breaks are always associated with double-strand breaks (DSBs). We here provide compelling evidence against this canonical theory. We employed a genetic approach using two cell lines, chicken DT40 and human Nalm-6. We measured the number of chromosomal breaks induced by three replication-blocking agents (aphidicolin, 5-fluorouracil, and hydroxyurea) in DSB-repair-proficient wild-type cells and cells deficient in both homologous recombination and nonhomologous end-joining (the two major DSB-repair pathways). Exposure of cells to the three replication-blocking agents for at least two cell cycles resulted in comparable numbers of chromosomal breaks for RAD54−/−/KU70−/− DT40 clones and wild-type cells. Likewise, the numbers of chromosomal breaks induced in RAD54−/−/LIG4−/− Nalm-6 clones and wild-type cells were also comparable. These data indicate that the replication-blocking agents can cause chromosomal breaks unassociated with DSBs. In contrast with DSB-repair-deficient cells, chicken DT40 cells deficient in PIF1 or ATRIP, which molecules contribute to the completion of DNA replication, displayed higher numbers of mitotic chromosomal breaks induced by aphidicolin than did wild-type cells, suggesting that single-strand gaps left unreplicated may result in mitotic chromosomal breaks.
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Affiliation(s)
- Mari Fujita
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Kimiyo N. Yamamoto
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Hiroshi Harada
- Group of Radiation and Tumor Biology, Career-Path Promotion Unit for Young Life Scientists, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Aya Kurosawa
- International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Japan
| | - Noritaka Adachi
- International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Japan
| | - Masato Omura
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Masahiro Hiraoka
- Radiation Oncology and Image-Applied Therapy, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Kouji Hirota
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
- * E-mail:
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Fox JT, Myung K. Cell-based high-throughput screens for the discovery of chemotherapeutic agents. Oncotarget 2012; 3:581-5. [PMID: 22653910 PMCID: PMC3388188 DOI: 10.18632/oncotarget.513] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
With modern advances in robotics and data processing, high-throughput screening (HTS) is playing an increasingly growing role in the drug discovery process. The ultimate success of HTS depends upon the development of assays that are robust and reproducible in miniaturized formats, have low false-positive rates, and can identify drugs that offer improvements over those currently on the market. One example of such an assay is the ATAD5-luciferase HTS assay, which identified three antioxidants that could kill cancer cells without inducing mutagenesis. Here we discuss the ATAD5-luciferase assay and expand upon the value of HTS in identifying other potential cancer drugs, focusing on cell-based assays that involve DNA damage or repair pathways.
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Affiliation(s)
- Jennifer T Fox
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Geno-Tox: Cell Array Biochip for Genotoxicity Monitoring and Classification. Appl Biochem Biotechnol 2012; 168:752-60. [DOI: 10.1007/s12010-012-9815-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/25/2012] [Indexed: 10/28/2022]
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Liu X, Lee J, Ji K, Takeda S, Choi K. Potentials and mechanisms of genotoxicity of six pharmaceuticals frequently detected in freshwater environment. Toxicol Lett 2012; 211:70-6. [DOI: 10.1016/j.toxlet.2012.03.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 03/07/2012] [Accepted: 03/07/2012] [Indexed: 01/22/2023]
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Hu J, Nakamura J, Richardson SD, Aitken MD. Evaluating the effects of bioremediation on genotoxicity of polycyclic aromatic hydrocarbon-contaminated soil using genetically engineered, higher eukaryotic cell lines. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:4607-13. [PMID: 22443351 PMCID: PMC3348858 DOI: 10.1021/es300020e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Bioremediation is one of the commonly applied remediation strategies at sites contaminated with polycyclic aromatic hydrocarbons (PAHs). However, remediation goals are typically based on removal of the target contaminants rather than on broader measures related to health risks. We investigated changes in the toxicity and genotoxicity of PAH-contaminated soil from a former manufactured-gas plant site before and after two simulated bioremediation processes: a sequencing batch bioreactor system and a continuous-flow column system. Toxicity and genotoxicity of the residues from solvent extracts of the soil were determined by the chicken DT40 B-lymphocyte isogenic cell line and its DNA-repair-deficient mutants. Although both bioremediation processes significantly removed PAHs from the contaminated soil (bioreactor 69% removal, column 84% removal), bioreactor treatment resulted in an increase in toxicity and genotoxicity over the course of a treatment cycle, whereas long-term column treatment resulted in a decrease in toxicity and genotoxicity. However, when screening with a battery of DT40 mutants for genotoxicity profiling, we found that column treatment induced DNA damage types that were not observed in untreated soil. Toxicity and genotoxicity bioassays can supplement chemical analysis-based risk assessment for contaminated soil when evaluating the efficacy of bioremediation.
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Affiliation(s)
| | - Jun Nakamura
- Corresponding authors: Jun Nakamura (T: 1-919-966-6140; F: 1-919-966-6123; ); Michael D. Aitken (T: 1-919-966-1024; F: 1-919-966-7911; ). Address: Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, U.S.A
| | | | - Michael D. Aitken
- Corresponding authors: Jun Nakamura (T: 1-919-966-6140; F: 1-919-966-6123; ); Michael D. Aitken (T: 1-919-966-1024; F: 1-919-966-7911; ). Address: Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599-7431, U.S.A
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Szymański P, Markowicz M, Mikiciuk-Olasik E. Adaptation of high-throughput screening in drug discovery-toxicological screening tests. Int J Mol Sci 2011; 13:427-52. [PMID: 22312262 PMCID: PMC3269696 DOI: 10.3390/ijms13010427] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 12/11/2011] [Accepted: 12/19/2011] [Indexed: 11/23/2022] Open
Abstract
High-throughput screening (HTS) is one of the newest techniques used in drug design and may be applied in biological and chemical sciences. This method, due to utilization of robots, detectors and software that regulate the whole process, enables a series of analyses of chemical compounds to be conducted in a short time and the affinity of biological structures which is often related to toxicity to be defined. Since 2008 we have implemented the automation of this technique and as a consequence, the possibility to examine 100,000 compounds per day. The HTS method is more frequently utilized in conjunction with analytical techniques such as NMR or coupled methods e.g., LC-MS/MS. Series of studies enable the establishment of the rate of affinity for targets or the level of toxicity. Moreover, researches are conducted concerning conjugation of nanoparticles with drugs and the determination of the toxicity of such structures. For these purposes there are frequently used cell lines. Due to the miniaturization of all systems, it is possible to examine the compound's toxicity having only 1-3 mg of this compound. Determination of cytotoxicity in this way leads to a significant decrease in the expenditure and to a reduction in the length of the study.
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Affiliation(s)
- Paweł Szymański
- Department of Pharmaceutical Chemistry and Drug Analysis, Medical University of Lodz, Muszyńskiego 1, Lodz 90-151, Poland; E-Mails: (P.S.); (E.M.-O.)
| | - Magdalena Markowicz
- Department of Pharmaceutical Chemistry and Drug Analysis, Medical University of Lodz, Muszyńskiego 1, Lodz 90-151, Poland; E-Mails: (P.S.); (E.M.-O.)
| | - Elżbieta Mikiciuk-Olasik
- Department of Pharmaceutical Chemistry and Drug Analysis, Medical University of Lodz, Muszyńskiego 1, Lodz 90-151, Poland; E-Mails: (P.S.); (E.M.-O.)
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Yamamoto KN, Hirota K, Kono K, Takeda S, Sakamuru S, Xia M, Huang R, Austin CP, Witt KL, Tice RR. Characterization of environmental chemicals with potential for DNA damage using isogenic DNA repair-deficient chicken DT40 cell lines. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2011; 52:547-61. [PMID: 21538559 PMCID: PMC3278799 DOI: 10.1002/em.20656] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 03/02/2011] [Indexed: 05/23/2023]
Abstract
Included among the quantitative high throughput screens (qHTS) conducted in support of the US Tox21 program are those being evaluated for the detection of genotoxic compounds. One such screen is based on the induction of increased cytotoxicity in seven isogenic chicken DT40 cell lines deficient in DNA repair pathways compared to the parental DNA repair-proficient cell line. To characterize the utility of this approach for detecting genotoxic compounds and identifying the type(s) of DNA damage induced, we evaluated nine of 42 compounds identified as positive for differential cytotoxicity in qHTS (actinomycin D, adriamycin, alachlor, benzotrichloride, diglycidyl resorcinol ether, lovastatin, melphalan, trans-1,4-dichloro-2-butene, tris(2,3-epoxypropyl)isocyanurate) and one non-cytotoxic genotoxic compound (2-aminothiamine) for (1) clastogenicity in mutant and wild-type cells; (2) the comparative induction of γH2AX positive foci by melphalan; (3) the extent to which a 72-hr exposure duration increased assay sensitivity or specificity; (4) the use of 10 additional DT40 DNA repair-deficient cell lines to better analyze the type(s) of DNA damage induced; and (5) the involvement of reactive oxygen species in the induction of DNA damage. All compounds but lovastatin and 2-aminothiamine were more clastogenic in at least one DNA repair-deficient cell line than the wild-type cells. The differential responses across the various DNA repair-deficient cell lines provided information on the type(s) of DNA damage induced. The results demonstrate the utility of this DT40 screen for detecting genotoxic compounds, for characterizing the nature of the DNA damage, and potentially for analyzing mechanisms of mutagenesis.
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Affiliation(s)
- Kimiyo N Yamamoto
- Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo, Japan.
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Magkoufopoulou C, Claessen S, Jennen D, Kleinjans J, van Delft J. Comparison of phenotypic and transcriptomic effects of false-positive genotoxins, true genotoxins and non-genotoxins using HepG2 cells. Mutagenesis 2011; 26:593-604. [DOI: 10.1093/mutage/ger021] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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