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Najeeb HA, Sanusi T, Saldanha G, Brown K, Cooke MS, Jones GD. Redox modulation of oxidatively-induced DNA damage by ascorbate enhances both in vitro and ex-vivo DNA damage formation and cell death in melanoma cells. Free Radic Biol Med 2024; 213:309-321. [PMID: 38262545 DOI: 10.1016/j.freeradbiomed.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 01/25/2024]
Abstract
Elevated genomic instability in cancer cells suggests a possible model-scenario for their selective killing via the therapeutic delivery of well-defined levels of further DNA damage. To examine this scenario, this study investigated the potential for redox modulation of oxidatively-induced DNA damage by ascorbate in malignant melanoma (MM) cancer cells, to selectively enhance both DNA damage and MM cell killing. DNA damage was assessed by Comet and ɣH2AX assays, intracellular oxidising species by dichlorofluorescein fluorescence, a key antioxidant enzymatic defence by assessment of catalase activity and cell survival was determined by clonogenic assay. Comet revealed that MM cells had higher endogenous DNA damage levels than normal keratinocytes (HaCaT cells); this correlated MM cells having higher intracellular oxidising species and lower catalase activity, and ranked with MM cell melanin pigmentation. Comet also showed MM cells more sensitive towards the DNA damaging effects of exogenous H2O2, and that ascorbate further enhanced this H2O2-induced damage in MM cells; again, with MM cell sensitivity to induced damage ranking with degree of cell pigmentation. Furthermore, cell survival data indicated that ascorbate enhanced H2O2-induced clonogenic cell death selectively in MM cells whilst protecting HaCaT cells. Finally, we show that ascorbate serves to enhance the oxidising effects of the MM therapeutic drug Elesclomol in both established MM cells in vitro and primary cell cultures ex vivo. Together, these results suggest that ascorbate selectively enhances DNA damage and cell-killing in MM cells. This raises the option of incorporating ascorbate into clinical oxidative therapies to treat MM.
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Affiliation(s)
- Hishyar A Najeeb
- Leicester Cancer Research Centre, Department of Genetics & Genome Biology, University of Leicester, UK
| | - Timi Sanusi
- Leicester Medical School, University of Leicester, UK
| | - Gerald Saldanha
- University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, UK
| | - Karen Brown
- Leicester Cancer Research Centre, Department of Genetics & Genome Biology, University of Leicester, UK
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, USA.
| | - George Dd Jones
- Leicester Cancer Research Centre, Department of Genetics & Genome Biology, University of Leicester, UK.
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2
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Mentana A, Orsière T, Malard V, Lamartiniere Y, Grisolia C, Tassistro V, Iaria O, Guardamagna I, Lonati L, Baiocco G. Gaining insight into genotoxicity with the comet assay in inhomogenoeous exposure scenarios: The effects of tritiated steel and cement particles on human lung cells in an inhalation perspective. Toxicol In Vitro 2023; 92:105656. [PMID: 37532108 DOI: 10.1016/j.tiv.2023.105656] [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: 04/17/2023] [Revised: 06/28/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
The comet assay was recently applied for the first time to test the genotoxicity of micrometric stainless steel and cement particles, representative of those produced in the dismantling of nuclear power plants. A large dataset was obtained from in vitro exposure of BEAS-2B lung cells to different concentrations of hydrogenated (non-radiative control) and tritiated particles, to assess the impact of accidental inhalation. Starting from the distributions of the number of nuclei scored at different extent of DNA damage (% tail DNA values), we propose a new comet data treatment designed to consider the inhomogeneity of the action of such particles. Indeed, due to particle behavior in biological media and concentration, a large fraction of cells remains undamaged, and standard averaging of genotoxicity indicators leads to a misinterpretation of experimental results. The analysis we propose reaches the following goals: genotoxicity in human lung cells is assessed for stainless steel and cement microparticles; the role of radiative damage due to tritium is disentangled from particulate stress; the fraction of damaged cells and their average level of DNA damage are assessed separately, which is essential for carcinogenesis implications and sets the basis for a better-informed risk management for human exposure to radioactive particles.
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Affiliation(s)
- Alice Mentana
- Laboratory of Radiation Biophysics and Radiobiology, Department of Physics, University of Pavia, Via Bassi 6, 27100 Pavia, Italy
| | - Thierry Orsière
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, F-13005 Marseille, France
| | - Véronique Malard
- Aix Marseille Univ, CEA, CNRS, BIAM, IPM, F-13108 Saint Paul-Lez-Durance, France
| | | | | | - Virginie Tassistro
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, F-13005 Marseille, France
| | - Ombretta Iaria
- Laboratory of Radiation Biophysics and Radiobiology, Department of Physics, University of Pavia, Via Bassi 6, 27100 Pavia, Italy
| | - Isabella Guardamagna
- Laboratory of Radiation Biophysics and Radiobiology, Department of Physics, University of Pavia, Via Bassi 6, 27100 Pavia, Italy
| | - Leonardo Lonati
- Laboratory of Radiation Biophysics and Radiobiology, Department of Physics, University of Pavia, Via Bassi 6, 27100 Pavia, Italy
| | - Giorgio Baiocco
- Laboratory of Radiation Biophysics and Radiobiology, Department of Physics, University of Pavia, Via Bassi 6, 27100 Pavia, Italy.
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3
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Standards for Quantitative Measurement of DNA Damage in Mammalian Cells. Int J Mol Sci 2023; 24:ijms24065427. [PMID: 36982502 PMCID: PMC10051712 DOI: 10.3390/ijms24065427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023] Open
Abstract
As the potential applications of DNA diagnostics continue to expand, there is a need for improved methods and standards for DNA analysis. This report describes several methods that could be considered for the production of reference materials for the quantitative measurement of DNA damage in mammalian cells. With the focus on DNA strand breaks, potentially useful methods for assessing DNA damage in mammalian cells are reviewed. The advantages and limitations of each method, as well as additional concerns with respect to reference material development, are also discussed. In conclusion, we outline strategies for developing candidate DNA damage reference materials that could be adopted by research laboratories in a wide variety of applications.
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4
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Dirven Y, Eide DM, Henriksson EW, Hjorth R, Sharma AK, Graupner A, Brunborg G, Ballangby J, Boisen AMZ, Swedmark S, Gützkow KB, Olsen AK. Assessing testicular germ cell DNA damage in the comet assay; introduction of a proof-of-concept. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2023; 64:88-104. [PMID: 36629742 DOI: 10.1002/em.22527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 12/30/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
The in vivo comet assay is widely used to measure genotoxicity; however, the current OECD test guideline (TG 489) does not recommend using the assay to assess testicular germ cells, due to the presence of testicular somatic cells. An adapted approach to specifically assess testicular germ cells within the comet assay is certainly warranted, considering regulatory needs for germ cell-specific genotoxicity data in relation to the increasing global production of and exposure to potentially hazardous chemicals. Here, we provide a proof-of-concept to selectively analyze round spermatids and primary spermatocytes, distinguishing them from other cells of the testicle. Utilizing the comet assay recordings of DNA content (total fluorescence intensity) and DNA damage (% tail intensity) of individual comets, we developed a framework to distinguish testicular cell populations based on differences in DNA content/ploidy and appearance. Haploid round spermatid comets are identified through (1) visual inspection of DNA content distributions, (2) setting DNA content thresholds, and (3) modeling DNA content distributions using a normal mixture distribution function. We also describe an approach to distinguish primary spermatocytes during comet scoring, based on their high DNA content and large physical size. Our concept allows both somatic and germ cells to be analyzed in the same animal, adding a versatile, sensitive, rapid, and resource-efficient assay to the limited genotoxicity assessment toolbox for germ cells. An adaptation of TG 489 facilitates accumulation of valuable information regarding distribution of substances to germ cells and their potential for inducing germ cell gene mutations and structural chromosomal aberrations.
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Affiliation(s)
- Yvette Dirven
- Norwegian Institute of Public Health, Division of Climate and Environmental Health, Oslo, Norway
- Centre for Environmental Radioactivity (CERAD, Centre of Excellence of the Norwegian Research Council), Oslo, Norway
| | - Dag Markus Eide
- Norwegian Institute of Public Health, Division of Climate and Environmental Health, Oslo, Norway
- Centre for Environmental Radioactivity (CERAD, Centre of Excellence of the Norwegian Research Council), Oslo, Norway
| | - Erika Witasp Henriksson
- Swedish Chemicals Agency, Department of Development of Legislation and Other Instruments, Unit of Proposals for Classification and Restriction, Sundbyberg, Sweden
- Swedish Chemicals Agency, Department of Development of Legislation and Other Instruments, Unit of Evaluation of Substances, Sundbyberg, Sweden
| | - Rune Hjorth
- The Danish Environmental Protection Agency, Odense, Denmark
| | - Anoop Kumar Sharma
- Technical University of Denmark, National Food Institute, Lyngby, Denmark
| | - Anne Graupner
- Norwegian Institute of Public Health, Division of Climate and Environmental Health, Oslo, Norway
- Centre for Environmental Radioactivity (CERAD, Centre of Excellence of the Norwegian Research Council), Oslo, Norway
| | - Gunnar Brunborg
- Norwegian Institute of Public Health, Division of Climate and Environmental Health, Oslo, Norway
- Centre for Environmental Radioactivity (CERAD, Centre of Excellence of the Norwegian Research Council), Oslo, Norway
| | - Jarle Ballangby
- Norwegian Institute of Public Health, Division of Climate and Environmental Health, Oslo, Norway
- Centre for Environmental Radioactivity (CERAD, Centre of Excellence of the Norwegian Research Council), Oslo, Norway
| | | | - Stellan Swedmark
- Swedish Chemicals Agency, Department of Development of Legislation and Other Instruments, Unit of Evaluation of Substances, Sundbyberg, Sweden
| | - Kristine Bjerve Gützkow
- Norwegian Institute of Public Health, Division of Climate and Environmental Health, Oslo, Norway
- Centre for Environmental Radioactivity (CERAD, Centre of Excellence of the Norwegian Research Council), Oslo, Norway
| | - Ann-Karin Olsen
- Norwegian Institute of Public Health, Division of Climate and Environmental Health, Oslo, Norway
- Centre for Environmental Radioactivity (CERAD, Centre of Excellence of the Norwegian Research Council), Oslo, Norway
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5
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Brunborg G, Eide DM, Graupner A, Gutzkow K, Shaposhnikov S, Kruszewski M, Sirota N, Jones GDD, Koppen G, Vanhavere F, Møller P, Stetina R, Dahl H, Collins A. Calibration of the comet assay using ionising radiation. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 885:503560. [PMID: 36669811 DOI: 10.1016/j.mrgentox.2022.503560] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/25/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Several trials have attempted to identify sources of inter-laboratory variability in comet assay results, aiming at achieving more equal responses. Ionising radiation induces a defined level of DNA single-strand breaks (per dose/base pairs) and is used as a reference when comparing comet results but relies on accurately determined radiation doses. In this ring test we studied the significance of dose calibrations and comet assay protocol differences, with the object of identifying causes of variability and how to deal with them. Eight participating laboratories, using either x-ray or gamma radiation units, measured dose rates using alanine pellet dosimeters that were subsequently sent to a specialised laboratory for analysis. We found substantial deviations between calibrated and nominal (uncalibrated) dose rates, with up to 46% difference comparing highest and lowest values. Three additional dosimetry systems were employed in some laboratories: thermoluminescence detectors and two aqueous chemical dosimeters. Fricke's and Benzoic Acid dosimetry solutions gave reliable quantitative dose estimations using local equipment. Mononuclear cells from fresh human blood or mammalian cell lines were irradiated locally with calibrated (alanine) radiation doses and analysed for DNA damage using a standardised comet assay protocol and a lab-specific protocol. The dose response of eight laboratories, calculated against calibrated radiation doses, was linear with slope variance CV= 29% with the lab-specific protocol, reduced to CV= 16% with the standard protocol. Variation between laboratories indicate post-irradiation repair differences. Intra-laboratory variation was very low judging from the dose response of 8 donors (CV=4%). Electrophoresis conditions were different in the lab-specific protocols explaining some dose response variations which were reduced by systematic corrections for electrophoresis conditions. The study shows that comet assay data obtained in different laboratories can be compared quantitatively using calibrated radiation doses and that systematic corrections for electrophoresis conditions are useful.
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Affiliation(s)
- Gunnar Brunborg
- Division of Climate and Environmental Health, Norwegian Institute of Public Health, P.O. Box 222, N-0213 Oslo, Norway.
| | - Dag M Eide
- Division of Climate and Environmental Health, Norwegian Institute of Public Health, P.O. Box 222, N-0213 Oslo, Norway.
| | - Anne Graupner
- Division of Climate and Environmental Health, Norwegian Institute of Public Health, P.O. Box 222, N-0213 Oslo, Norway.
| | - Kristine Gutzkow
- Division of Climate and Environmental Health, Norwegian Institute of Public Health, P.O. Box 222, N-0213 Oslo, Norway.
| | | | - Marcin Kruszewski
- Faculty of Medicine, University of Information Technology and Management in Rzeszów, ul. Sucharskiego 2, 35-225 Rzeszów, Poland; Department of Molecular Biology and Translational Research, Institute of Rural Health, ul. Jaczewskiego 2, 20-090 Lublin, Poland.
| | - Nikolai Sirota
- Institute of Theoretical and Experimental Biophysics of Russian Academy of Sciences, Pushchino, Russia.
| | - George D D Jones
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK.
| | - Gudrun Koppen
- Flemish Institute for Technological Research (VITO), Environmental Risk and Health Unit, Boeretang 200, B-2400 Mol, Belgium.
| | - Filip Vanhavere
- Radiation Protection, Dosimetry and Calibration, Belgian Nuclear Research Centre SCK·CEN, Boeretang 200, Mol 2400, Belgium.
| | - Peter Møller
- Section of Environmental Health, Department of Public Health, University of Copenhagen, Øster Farimagsgade 5A, P.O. Box 2099, DK-1014 Copenhagen, Denmark.
| | - Rudolf Stetina
- University of Defence, Faculty of Military Health Sciences, Department of Toxicology, Trebesska 1575, 50001 Hradec Kralove, Czech Republic.
| | - Hildegunn Dahl
- Division of Climate and Environmental Health, Norwegian Institute of Public Health, P.O. Box 222, N-0213 Oslo, Norway.
| | - Andrew Collins
- Dept of Nutrition, Faculty of Medicine, University of Oslo, PB 1046 Blindern, 0316 Oslo, Norway.
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6
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Development of a Reference Method and Materials for Quantitative Measurement of UV-Induced DNA Damage in Mammalian Cells: Comparison of Comet Assay and Cell Viability. J Nucleic Acids 2022; 2022:9188636. [PMID: 36164440 PMCID: PMC9509282 DOI: 10.1155/2022/9188636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/06/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022] Open
Abstract
Application of DNA damage diagnostic tests is rapidly growing, in particular for ovarian, prostate, and skin cancers; environmental monitoring; chronic and degenerative diseases; and male infertility. Such tests suffer from significant variability among different laboratories due the lack of standardization, experimental validation, and differences in data interpretation. Reference methods and materials for quantitative measurement of UVA-induced DNA damage in mammalian cells are frequently needed. In this study, we examined the use of the single-cell gel electrophoresis (comet) assay to assess the UVA-induced DNA damage in surface-attached Chinese hamster ovary (CHO) cells treated with a photosensitizer as a candidate cellular oxidative damage reference material. We found that the comet images became diffused and the viability of the cells decreased substantially (>20%) as the UVA dose and benzo [a] pyrene (BaP) concentration exceeded 6.3 J/cm2 and 10−6 mol/L BaP. Maintaining the conditions of exposure within this range can improve DNA damage measurement fidelity, particularly if used as a quantitative reference method and to produce materials considered as an in vitro standard for the comet assay.
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7
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Li J, Beiser A, Dey NB, Takeda S, Saha L, Hirota K, Parker L, Carter M, Arrieta M, Sobol R. A high-throughput 384-well CometChip platform reveals a role for 3-methyladenine in the cellular response to etoposide-induced DNA damage. NAR Genom Bioinform 2022; 4:lqac065. [PMID: 36110898 PMCID: PMC9469923 DOI: 10.1093/nargab/lqac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/11/2022] [Accepted: 09/05/2022] [Indexed: 01/31/2023] Open
Abstract
The Comet or single-cell gel electrophoresis assay is a highly sensitive method to measure cellular, nuclear genome damage. However, low throughput can limit its application for large-scale studies. To overcome these limitations, a 96-well CometChip platform was recently developed that increases throughput and reduces variation due to simultaneous processing and automated analysis of 96 samples. To advance throughput further, we developed a 384-well CometChip platform that allows analysis of ∼100 cells per well. The 384-well CometChip extends the capacity by 4-fold as compared to the 96-well system, enhancing application for larger DNA damage analysis studies. The overall sensitivity of the 384-well CometChip is consistent with that of the 96-well system, sensitive to genotoxin exposure and to loss of DNA repair capacity. We then applied the 384-well platform to screen a library of protein kinase inhibitors to probe each as enhancers of etoposide induced DNA damage. Here, we found that 3-methyladenine significantly increased levels of etoposide-induced DNA damage. Our results suggest that a 384-well CometChip is useful for large-scale DNA damage analyses, which may have increased potential in the evaluation of chemotherapy efficacy, compound library screens, population-based analyses of genome damage and evaluating the impact of environmental genotoxins on genome integrity.
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Affiliation(s)
- Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Alison Beiser
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Nupur B Dey
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Liton Kumar Saha
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University Minamiosawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - L Lynette Parker
- Center for Healthy Communities, College of Medicine, University of South Alabama Mobile, AL 36604, USA
| | - Mariah Carter
- Center for Healthy Communities, College of Medicine, University of South Alabama Mobile, AL 36604, USA
| | - Martha I Arrieta
- Department of Internal Medicine, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
- Center for Healthy Communities, College of Medicine, University of South Alabama Mobile, AL 36604, USA
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
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8
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Barghouth PG, Rojas S, O'Dell LR, Betancourt AM, Oviedo NJ. Analysis of DNA Double-Stranded Breaks Using the Comet Assay in Planarians. Methods Mol Biol 2022; 2450:479-491. [PMID: 35359324 PMCID: PMC9761910 DOI: 10.1007/978-1-0716-2172-1_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Comet assay provides the opportunity to detect and characterize DNA strand breaks. Cellular lysing followed by embedding in agarose slide is used to visualize under an electrical current migration patterns corresponding to DNA fragments of different sizes. Here we describe the process of detecting and characterizing DNA damage by Comet assay on planarians, which is a model organism commonly used to understand the process of whole-body regeneration, stem cell regulation, and adult tissue maintenance.
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Affiliation(s)
- Paul G Barghouth
- Department of Molecular & Cell Biology, University of California, Merced, CA, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA, USA
| | - Salvador Rojas
- Department of Molecular & Cell Biology, University of California, Merced, CA, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA, USA
| | - Lacey R O'Dell
- Department of Molecular & Cell Biology, University of California, Merced, CA, USA
| | - Andrew M Betancourt
- Department of Molecular & Cell Biology, University of California, Merced, CA, USA
| | - Néstor J Oviedo
- Department of Molecular & Cell Biology, University of California, Merced, CA, USA.
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA, USA.
- Health Sciences Research Institute, University of California, Merced, CA, USA.
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9
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Genotoxicity Assessment of Metal-Based Nanocomposites Applied in Drug Delivery. MATERIALS 2021; 14:ma14216551. [PMID: 34772074 PMCID: PMC8585152 DOI: 10.3390/ma14216551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/13/2021] [Accepted: 10/27/2021] [Indexed: 12/24/2022]
Abstract
Nanocomposites as drug delivery systems (e.g., metal nanoparticles) are being exploited for several applications in the biomedical field, from therapeutics to diagnostics. Green nanocomposites stand for nanoparticles of biocompatible, biodegradable and non-toxic profiles. When using metal nanoparticles for drug delivery, the question of how hazardous these "virus-sized particles" can be is posed, due to their nanometer size range with enhanced reactivity compared to their respective bulk counterparts. These structures exhibit a high risk of being internalized by cells and interacting with the genetic material, with the possibility of inducing DNA damage. The Comet Assay, or Single-Cell Gel Electrophoresis (SCGE), stands out for its capacity to detect DNA strand breaks in eukaryotic cells. It has huge potential in the genotoxicity assessment of nanoparticles and respective cells' interactions. In this review, the Comet assay is described, discussing several examples of its application in the genotoxicity evaluation of nanoparticles commonly administered in a set of routes (oral, skin, inhaled, ocular and parenteral administration). In the nanoparticles boom era, where guidelines for their evaluation are still very limited, it is urgent to ensure their safety, alongside their quality and efficacy. Comet assay or SCGE can be considered an essential tool and a reliable source to achieve a better nanotoxicology assessment of metal nanoparticles used in drug delivery.
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10
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Milić M, Ceppi M, Bruzzone M, Azqueta A, Brunborg G, Godschalk R, Koppen G, Langie S, Møller P, Teixeira JP, Alija A, Anderson D, Andrade V, Andreoli C, Asllani F, Bangkoglu EE, Barančoková M, Basaran N, Boutet-Robinet E, Buschini A, Cavallo D, Costa Pereira C, Costa C, Costa S, Da Silva J, Del Boˊ C, Dimitrijević Srećković V, Djelić N, Dobrzyńska M, Duračková Z, Dvořáková M, Gajski G, Galati S, García Lima O, Giovannelli L, Goroshinskaya IA, Grindel A, Gutzkow KB, Hernández A, Hernández C, Holven KB, Ibero-Baraibar I, Ottestad I, Kadioglu E, Kažimirová A, Kuznetsova E, Ladeira C, Laffon B, Lamonaca P, Lebailly P, Louro H, Mandina Cardoso T, Marcon F, Marcos R, Moretti M, Moretti S, Najafzadeh M, Nemeth Z, Neri M, Novotna B, Orlow I, Paduchova Z, Pastor S, Perdry H, Spremo-Potparević B, Ramadhani D, Riso P, Rohr P, Rojas E, Rossner P, Safar A, Sardas S, Silva MJ, Sirota N, Smolkova B, Staruchova M, Stetina R, Stopper H, Surikova EI, Ulven SM, Ursini CL, Valdiglesias V, Valverde M, Vodicka P, Volkovova K, Wagner KH, Živković L, Dušinská M, Collins AR, Bonassi S. The hCOMET project: International database comparison of results with the comet assay in human biomonitoring. Baseline frequency of DNA damage and effect of main confounders. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2021; 787:108371. [PMID: 34083035 PMCID: PMC8525632 DOI: 10.1016/j.mrrev.2021.108371] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 01/11/2023]
Abstract
The alkaline comet assay, or single cell gel electrophoresis, is one of the most popular methods for assessing DNA damage in human population. One of the open issues concerning this assay is the identification of those factors that can explain the large inter-individual and inter-laboratory variation. International collaborative initiatives such as the hCOMET project - a COST Action launched in 2016 - represent a valuable tool to meet this challenge. The aims of hCOMET were to establish reference values for the level of DNA damage in humans, to investigate the effect of host factors, lifestyle and exposure to genotoxic agents, and to compare different sources of assay variability. A database of 19,320 subjects was generated, pooling data from 105 studies run by 44 laboratories in 26 countries between 1999 and 2019. A mixed random effect log-linear model, in parallel with a classic meta-analysis, was applied to take into account the extensive heterogeneity of data, due to descriptor, specimen and protocol variability. As a result of this analysis interquartile intervals of DNA strand breaks (which includes alkali-labile sites) were reported for tail intensity, tail length, and tail moment (comet assay descriptors). A small variation by age was reported in some datasets, suggesting higher DNA damage in oldest age-classes, while no effect could be shown for sex or smoking habit, although the lack of data on heavy smokers has still to be considered. Finally, highly significant differences in DNA damage were found for most exposures investigated in specific studies. In conclusion, these data, which confirm that DNA damage measured by the comet assay is an excellent biomarker of exposure in several conditions, may contribute to improving the quality of study design and to the standardization of results of the comet assay in human populations.
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Affiliation(s)
- Mirta Milić
- Mutagenesis Unit, Institute for Medical Research and Occupational Health, Ksaverska cesta 2, 10000, Zagreb, Croatia
| | - Marcello Ceppi
- Biostatistics Unit, San Martino Policlinic Hospital, Genoa, Italy
| | - Marco Bruzzone
- Biostatistics Unit, San Martino Policlinic Hospital, Genoa, Italy
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, University of Navarra, C/Irunlarrea 1, 31008, Pamplona, Spain; IdiSNA, Navarra Institute for Health Research, C/Irunlarrea 3, 31008, Pamplona, Spain
| | - Gunnar Brunborg
- Department of Environmental Health, Section of Molecular Toxicology, Norwegian Institute of Public Health (NIPH), Lovisenberggt 6, 0456, Oslo, Norway
| | - Roger Godschalk
- School of Nutrition and Translational Research in Metabolism, Department of Pharmacology and Toxicology, University of Maastricht, Universiteitssingel 50, 6200 MD, Maastricht, the Netherlands
| | - Gudrun Koppen
- Flemish Institute of Technological Research, Environmental Risk and Health unit VITO - BIOMo, Belgium
| | - Sabine Langie
- School of Nutrition and Translational Research in Metabolism, Department of Pharmacology and Toxicology, University of Maastricht, Universiteitssingel 50, 6200 MD, Maastricht, the Netherlands
| | - Peter Møller
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Oster Farimagsgade 5A, DK-1014, Copenhagen, Denmark
| | - João Paulo Teixeira
- Environmental Health Department, National Institute of Health Dr. Ricardo Jorge, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Rua das Taipas, no 135, 4050-600, Porto, Portugal
| | - Avdulla Alija
- Department of Biology, University of Prishtina, George Bush, N.N., 10000, Prishtina, Kosovo
| | - Diana Anderson
- Biomedical Sciences Department, University of Bradford, Richmond Road Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Vanessa Andrade
- Laboratory of Translational Biomedicine, University of Southern Santa Catarina, UNESC, Criciúma, SC, Brazil
| | - Cristina Andreoli
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - Fisnik Asllani
- Department of Biology, University of Prishtina, George Bush, N.N., 10000, Prishtina, Kosovo
| | - Ezgi Eyluel Bangkoglu
- Institute of Pharmacology and Toxicology, University of Wuerzburg, VersbacherStrasse 9, 97078, Wuerzburg, Germany
| | - Magdalena Barančoková
- Institute of Biology, Medical Faculty, Slovak Medical University, Limbova 12, 83303, Bratislava, Slovakia
| | - Nursen Basaran
- Department of Pharmaceutical Toxicology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Elisa Boutet-Robinet
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Annamaria Buschini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11A, 43124, Parma, Italy
| | - Delia Cavallo
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene (DiMEILA), Italian Workers' Compensation Authority (INAIL), Via Fontana Candida 1, 00078, Monte Porzio Catone(Rome), Italy
| | - Cristiana Costa Pereira
- Environmental Health Department, National Institute of Health Dr. Ricardo Jorge, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Rua das Taipas, no 135, 4050-600, Porto, Portugal
| | - Carla Costa
- Environmental Health Department, National Institute of Health Dr. Ricardo Jorge, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Rua das Taipas, no 135, 4050-600, Porto, Portugal
| | - Solange Costa
- Environmental Health Department, National Institute of Health Dr. Ricardo Jorge, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Rua das Taipas, no 135, 4050-600, Porto, Portugal
| | - Juliana Da Silva
- Laboratory of Genetic Toxicology, Lutheran University of Brazil (ULBRA), Av. Farroupilha 8001, Prédio 22/Sala 22, 92425-900, Canoas, RS, Brazil
| | - Cristian Del Boˊ
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Vesna Dimitrijević Srećković
- Faculty of Medicine, Clinic for Endocrinology, Diabetes and Metabolic Disease, University of Belgrade, Dr Subotića 13, Belgrade, Serbia
| | - Ninoslav Djelić
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Oslobodjenja Blvd 18, 11000, Belgrade, Serbia
| | - Malgorzata Dobrzyńska
- Department of Radiation Hygiene and Radiobiology, National Institute of Public Health - National Institute of Hygiene, 24 Chocimska Street, 00-791, Warsaw, Poland
| | - Zdenka Duračková
- Institute for Medical Chemistry, Biochemistry and Clinical Biochemistry, Faculty of Medicine, Comenius University, Sasinkova 2, Bratislava, Slovakia
| | - Monika Dvořáková
- Institute for Medical Chemistry, Biochemistry and Clinical Biochemistry, Faculty of Medicine, Comenius University, Sasinkova 2, Bratislava, Slovakia
| | - Goran Gajski
- Mutagenesis Unit, Institute for Medical Research and Occupational Health, Ksaverska cesta 2, 10000, Zagreb, Croatia
| | - Serena Galati
- Centre for Molecular and Translational Oncology, University of Parma, Parco Area delle Scienze 11A, 43124, Parma, Italy
| | - Omar García Lima
- Center for RadiationProtection and Hygiene, Calle 20, No 4113, e/41 y 47. Playa. C.P. 11300, La Habana, A.P. 6195, C.P. 10600, Habana, Cuba
| | - Lisa Giovannelli
- Department NEUROFARBA, University of Florence, Viale G. Pieraccini 6, 50139, Florence, Italy
| | - Irina A Goroshinskaya
- Laboratory for the Study of the Pathogenesis of Malignant Tumors, National Medical Research Center for Oncology, 14 line 63, 344037, Rostov-on-Don, Russia
| | - Annemarie Grindel
- Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Kristine B Gutzkow
- Department of Environmental Health, Section of Molecular Toxicology, Norwegian Institute of Public Health (NIPH), Lovisenberggt 6, 0456, Oslo, Norway
| | - Alba Hernández
- Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Barcelona), Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Carlos III Institute of Health, 28029, Madrid, Spain
| | - Carlos Hernández
- Department of Biochemistry, Instituto de Ciencias Básicas y Preclínicas "Victoria de Giron", 146 St. and 31 Ave, No 3102, Playa, Habana, Cuba
| | - Kirsten B Holven
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Sognsvannsveien 9, 0372, Oslo, Norway
| | - Idoia Ibero-Baraibar
- Department of Nutrition, Food Science and Physiology, Centre for Nutrition Research, University of Navarra, Irunlarrea 1, 31008, Pamplona, Navarra, Spain
| | - Inger Ottestad
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Sognsvannsveien 9, 0372, Oslo, Norway
| | - Ela Kadioglu
- Toxicology Department, Faculty of Pharmacy, Gazi University, Ankara, Turkey
| | - Alena Kažimirová
- Institute of Biology, Medical Faculty, Slovak Medical University, Limbova 12, 83303, Bratislava, Slovakia
| | - Elena Kuznetsova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290, Institutskaya 3, Pushchino, Moscow Region, Russia
| | - Carina Ladeira
- H&TRC-Health & Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, 1990-096, Lisbon, Portugal; NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Blanca Laffon
- Grupo DICOMOSA, Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Psicología, Facultad de Ciencias de la Educación, Universidade da Coruña, Campus Elviña s/n, 15071, A Coruña, Spain
| | - Palma Lamonaca
- IRCCS San Raffaele Pisana, Unit of Clinical and Molecular Epidemiology, Department of Human Sciences and Quality of Life Promotion, San Raffaele University, Via di Val Cannuta, 247., 00161, Rome, Italy
| | - Pierre Lebailly
- ANTICIPE Unit, INSERM &University of Caen-Normandie Centre François Baclesse, Avenue du Général Harris 14076, Caen Cedex 05, France
| | - Henriqueta Louro
- Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal; ToxOmics, NMS, NOVA University of Lisbon, Lisbon, Portugal
| | - Tania Mandina Cardoso
- Center for RadiationProtection and Hygiene, Calle 20, No 4113, e/41 y 47. Playa. C.P. 11300, La Habana, A.P. 6195, C.P. 10600, Habana, Cuba
| | - Francesca Marcon
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - Ricard Marcos
- Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Barcelona), Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Carlos III Institute of Health, 28029, Madrid, Spain
| | - Massimo Moretti
- Department of Pharmaceutical Sciences (Unit of Public Health), University of Perugia, Via del Giochetto, 06122, Perugia, Italy
| | - Silvia Moretti
- Department of Health Sciences, University of Florence, Division of Dermatology, Palagi Hospital, Viale Michelangelo 41, Florence, Italy
| | - Mojgan Najafzadeh
- Biomedical Sciences Department, University of Bradford, Richmond Road Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Zsuzsanna Nemeth
- Department of Non-ionizing Radiation, National Public Health Center, Anna Street 5, 1221, Budapest, Hungary
| | - Monica Neri
- IRCCS San Raffaele Pisana, Unit of Clinical and Molecular Epidemiology, Department of Human Sciences and Quality of Life Promotion, San Raffaele University, Via di Val Cannuta, 247., 00161, Rome, Italy
| | - Bozena Novotna
- Department of Nanotoxicolgy and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, Prague, Czech Republic
| | - Irene Orlow
- Memorial Sloan Kettering Cancer Center, Epidemiology and Biostatistics, New York, New York, 10065, USA
| | - Zuzana Paduchova
- Institute for Medical Chemistry, Biochemistry and Clinical Biochemistry, Faculty of Medicine, Comenius University, Sasinkova 2, Bratislava, Slovakia
| | - Susana Pastor
- Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Barcelona), Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), Carlos III Institute of Health, 28029, Madrid, Spain
| | | | - Biljana Spremo-Potparević
- Center of Biological Research, Faculty of Pharmacy, University of Belgrade, VojvodeStepe, 450, Belgrade, Serbia
| | - Dwi Ramadhani
- Center for Radiation Safety Technology and Metrology, National Nuclear Energy Agency of Indonesia, Jl. LebakBulus Raya No. 49, Kotak Pos 7043 JKSKL JakartaSelatan, 12440, Jakarta, Indonesia
| | - Patrizia Riso
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Paula Rohr
- Laboratory of Translational Biomedicine, University of Southern Santa Catarina, UNESC, Criciúma, SC, Brazil
| | - Emilio Rojas
- Genomic Medicine and EnvironmentalToxicology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CU, Mexico
| | - Pavel Rossner
- Department of Nanotoxicolgy and Molecular Epidemiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, Prague, Czech Republic
| | - Anna Safar
- Department of Non-ionizing Radiation, National Public Health Center, Anna Street 5, 1221, Budapest, Hungary
| | - Semra Sardas
- Toxicology Department, Faculty of Pharmacy, Istinye University, Istanbul, Turkey
| | - Maria João Silva
- Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal; ToxOmics, NMS, NOVA University of Lisbon, Lisbon, Portugal
| | - Nikolay Sirota
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290, Institutskaya 3, Pushchino, Moscow Region, Russia
| | - Bozena Smolkova
- Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Marta Staruchova
- Institute of Biology, Medical Faculty, Slovak Medical University, Limbova 12, 83303, Bratislava, Slovakia
| | - Rudolf Stetina
- Department of Toxicology and Military Pharmacy, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 500 01, Hradec Kralove, Czech Republic
| | - Helga Stopper
- Institute of Pharmacology and Toxicology, University of Wuerzburg, VersbacherStrasse 9, 97078, Wuerzburg, Germany
| | - Ekaterina I Surikova
- Laboratory for the Study of the Pathogenesis of Malignant Tumors, National Medical Research Center for Oncology, 14 line 63, 344037, Rostov-on-Don, Russia
| | - Stine M Ulven
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Sognsvannsveien 9, 0372, Oslo, Norway
| | - Cinzia Lucia Ursini
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene (DiMEILA), Italian Workers' Compensation Authority (INAIL), Via Fontana Candida 1, 00078, Monte Porzio Catone(Rome), Italy
| | - Vanessa Valdiglesias
- Grupo DICOMOSA, Centro de Investigaciones Científicas Avanzadas (CICA), Departamento de Biología, Facultad de Ciencias, Universidade da Coruña, Campus A Zapateira s/n, 15071, A Coruña, Spain
| | - Mahara Valverde
- Genomic Medicine and EnvironmentalToxicology, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CU, Mexico
| | - Pavel Vodicka
- Experimental Medicine, Molecular Biology of Cancer, IEM AVCR, Videnska 1083, Prague 4, Prague, Czech Republic
| | - Katarina Volkovova
- Institute of Biology, Medical Faculty, Slovak Medical University, Limbova 12, 83303, Bratislava, Slovakia
| | - Karl-Heinz Wagner
- Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Lada Živković
- Center of Biological Research, Faculty of Pharmacy, University of Belgrade, VojvodeStepe, 450, Belgrade, Serbia
| | | | - Andrew R Collins
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Sognsvannsveien 9, 0372, Oslo, Norway
| | - Stefano Bonassi
- IRCCS San Raffaele Pisana, Unit of Clinical and Molecular Epidemiology, Department of Human Sciences and Quality of Life Promotion, San Raffaele University, Via di Val Cannuta, 247., 00161, Rome, Italy.
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11
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Cordelli E, Bignami M, Pacchierotti F. Comet assay: a versatile but complex tool in genotoxicity testing. Toxicol Res (Camb) 2021; 10:68-78. [PMID: 33613974 DOI: 10.1093/toxres/tfaa093] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/26/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
The comet assay is a versatile method for measuring DNA strand breaks in individual cells. It can also be applied to cells isolated from treated animals. In this review, we highlight advantages and limitations of this in vivo comet assay in a regulatory context. Modified versions of the standard protocol detect oxidized DNA bases and may be used to reveal sites of DNA base loss, DNA interstrand crosslinks, and the extent of DNA damage induced indirectly by reactive oxygen species elicited by chemical-induced oxidative stress. The assay is, however, at best semi-quantitative, and we discuss possible approaches to improving DNA damage quantitation and highlight the necessity of optimizing protocol standardization to enhance the comparability of results between laboratories. As a genotoxicity test in vivo, the in vivo comet assay has the advantage over the better established micronucleus erythrocyte test that it can be applied to any organ, including those that are specific targets of chemical carcinogens or those that are the first sites of contact of ingested or inhaled mutagens. We illustrate this by examples of its use in risk assessment for the food contaminants ochratoxin and furan. We suggest that improved quantitation is required to reveal the full potential of the comet assay and enhance its role in the battery of in vivo approaches to characterize the mechanisms of toxicity and carcinogenicity of chemicals and to aid the determination of safe human exposure limits.
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Affiliation(s)
- Eugenia Cordelli
- Territorial and Production Systems Sustainability Department, Health Protection Technology Division, ENEA, CR Casaccia, Via Anguillarese 301, Rome 00123, Italy
| | - Margherita Bignami
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome 00161, Italy
| | - Francesca Pacchierotti
- Territorial and Production Systems Sustainability Department, Health Protection Technology Division, ENEA, CR Casaccia, Via Anguillarese 301, Rome 00123, Italy
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12
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The impact of comet assay data normalization in human biomonitoring studies outcomes. Toxicol Lett 2020; 332:56-64. [DOI: 10.1016/j.toxlet.2020.06.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/12/2020] [Accepted: 06/30/2020] [Indexed: 01/21/2023]
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13
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Geldert A, Huang H, Herr AE. Probe-target hybridization depends on spatial uniformity of initial concentration condition across large-format chips. Sci Rep 2020; 10:8768. [PMID: 32472029 PMCID: PMC7260366 DOI: 10.1038/s41598-020-65563-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/23/2020] [Indexed: 12/30/2022] Open
Abstract
Diverse assays spanning from immunohistochemistry (IHC), to microarrays (protein, DNA), to high-throughput screens rely on probe-target hybridization to detect analytes. These large-format 'chips' array numerous hybridization sites across centimeter-scale areas. However, the reactions are prone to intra-assay spatial variation in hybridization efficiency. The mechanism of spatial bias in hybridization efficiency is poorly understood, particularly in IHC and in-gel immunoassays, where immobilized targets are heterogeneously distributed throughout a tissue or hydrogel network. In these systems, antibody probe hybridization to a target protein antigen depends on the interplay of dilution, thermodynamic partitioning, diffusion, and reaction. Here, we investigate parameters governing antibody probe transport and reaction (i.e., immunoprobing) in a large-format hydrogel immunoassay. Using transport and bimolecular binding theory, we identify a regime in which immunoprobing efficiency (η) is sensitive to the local concentration of applied antibody probe solution, despite the antibody probe being in excess compared to antigen. Sandwiching antibody probe solution against the hydrogel surface yields spatially nonuniform dilution. Using photopatterned fluorescent protein targets and a single-cell immunoassay, we identify regimes in which nonuniformly distributed antibody probe solution causes intra-assay variation in background and η. Understanding the physicochemical factors affecting probe-target hybridization reduces technical variation in large-format chips, improving measurement precision.
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Affiliation(s)
- Alisha Geldert
- UC Berkeley - UCSF Graduate Program in Bioengineering, Berkeley, United States
| | - Haiyan Huang
- Department of Statistics, University of California Berkeley, Berkeley, California, 94720, United States
- Center for Computational Biology, University of California Berkeley, Berkeley, California, 94720, United States
| | - Amy E Herr
- UC Berkeley - UCSF Graduate Program in Bioengineering, Berkeley, United States.
- Department of Bioengineering, University of California Berkeley, Berkeley, California, 94720, United States.
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14
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Cellular Reference Materials for DNA Damage Using Electrochemical Oxidation. J Nucleic Acids 2020; 2020:2928104. [PMID: 32411438 PMCID: PMC7212329 DOI: 10.1155/2020/2928104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/25/2019] [Indexed: 11/18/2022] Open
Abstract
Reference materials are needed to quantify the level of DNA damage in cells, to assess sources of measurement variability and to compare results from different laboratories. The comet assay (single cell gel electrophoresis) is a widely used method to determine DNA damage in the form of strand breaks. Here we examine the use of electrochemical oxidation to produce DNA damage in cultured mammalian cells and quantify its percentage using the comet assay. Chinese hamster ovary (CHO) cells were grown on an indium tin oxide electrode surface and exposed 12 h to electrochemical potentials ranging from 0.5 V to 1.5 V (vs Ag/AgCl). The resulting cells were harvested and analyzed by comet and a cell viability assay. We observed a linear increase in the percentage (DNA in tail) of strand breaks along with a loss of cell viability with increasing oxidation potential value. The results indicate that electrochemically induced DNA damage can be produced in mammalian cells under well-controlled conditions and could be considered in making a cellular reference material for the comet assay.
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15
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Brunborg G. Reference cells in the comet assay. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2019; 845:403064. [DOI: 10.1016/j.mrgentox.2019.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 10/26/2022]
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16
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Kayumov AR, Solovyev DA, Bobrov DE, Rizvanov AA. Current Approaches to the Evaluation of Soil Genotoxicity. BIONANOSCIENCE 2019. [DOI: 10.1007/s12668-019-00652-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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17
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Lee T, Lee S, Sim WY, Jung YM, Han S, Won JH, Min H, Yoon S. HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment. BMC Bioinformatics 2018; 19:44. [PMID: 29504903 PMCID: PMC5836828 DOI: 10.1186/s12859-018-2015-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background DNA damage causes aging, cancer, and other serious diseases. The comet assay can detect multiple types of DNA lesions with high sensitivity, and it has been widely applied. Although comet assay platforms have improved the limited throughput and reproducibility of traditional assays in recent times, analyzing large quantities of comet data often requires a tremendous human effort. To overcome this challenge, we proposed HiComet, a computational tool that can rapidly recognize and characterize a large number of comets, using little user intervention. Results We tested HiComet with real data from 35 high-throughput comet assay experiments, with over 700 comets in total. The proposed method provided unprecedented levels of performance as an automated comet recognition tool in terms of robustness (measured by precision and recall) and throughput. Conclusions HiComet is an automated tool for high-throughput comet-assay analysis and could significantly facilitate characterization of individual comets by accelerating its most rate-limiting step. An online implementation of HiComet is freely available at https://github.com/taehoonlee/HiComet/.
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Affiliation(s)
- Taehoon Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Sungmin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Woo Young Sim
- R&D Center, Wearable Healthcare, Gyeonggi-do, 16954, Korea
| | - Yu Mi Jung
- Research Division, NanoEnTek, Seoul, 08389, Korea
| | - Sunmi Han
- Research Division, NanoEnTek, Seoul, 08389, Korea
| | - Joong-Ho Won
- Department of Statistics, Seoul National University, Seoul, 08826, Korea
| | - Hyeyoung Min
- College of Pharmachy, Chung-Ang University, Seoul, 06974, Korea
| | - Sungroh Yoon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea. .,Bioinformatics Institute, Seoul National University, Seoul, 08826, Korea.
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18
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Koppen G, Azqueta A, Pourrut B, Brunborg G, Collins AR, Langie SAS. The next three decades of the comet assay: a report of the 11th International Comet Assay Workshop. Mutagenesis 2017; 32:397-408. [DOI: 10.1093/mutage/gex002] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Gudrun Koppen
- Environmental Risk and Health unit, Flemish Institute of Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium,
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, University of Navarra, and IdiSNA, Navarra Institute for Health Research, C/Irunlarrea 1, 31009 Pamplona, Spain,
| | - Bertrand Pourrut
- ISA Lille – LGCgE, University of Lille Nord de France, 48 boulevard Vauban, 59046 Lille, France,
| | - Gunnar Brunborg
- Department of Molecular Biology, Norwegian Institute of Public Health, PO Box 4404 Nydalen, Oslo, Norway and
| | - Andrew R. Collins
- Department of Nutrition, University of Oslo, PB 1046 Blindern, Oslo, Norway
| | - Sabine A. S. Langie
- Environmental Risk and Health unit, Flemish Institute of Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium,
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19
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Afshari V, Elahian F, Ayari Y, Yazdinezhad A, Mirzaei SA. Diversity and ecotypic variation in the antioxidant and antigenotoxic effects ofThymus kotschyanusBoiss & Hohen. FLAVOUR FRAG J 2016. [DOI: 10.1002/ffj.3333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Vahid Afshari
- Department of Pharmaceutical Biotechnology, School of Pharmacy; Zanjan University of Medical Sciences; Iran
| | - Fatemeh Elahian
- Cellular and Molecular Research Center; Shahrekord University of Medical Sciences; Shahrekord Iran
| | - Yasaman Ayari
- Department of Pharmaceutical Biotechnology, School of Pharmacy; Zanjan University of Medical Sciences; Iran
| | - Alireza Yazdinezhad
- Department of Pharmaceutical Biotechnology, School of Pharmacy; Zanjan University of Medical Sciences; Iran
| | - Seyed Abbas Mirzaei
- Clinical Biochemistry Research Center; Shahrekord University of Medical Sciences; Shahrekord Iran
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20
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Ge J, Chow DN, Fessler JL, Weingeist DM, Wood DK, Engelward BP. Micropatterned comet assay enables high throughput and sensitive DNA damage quantification. Mutagenesis 2015; 30:11-9. [PMID: 25527723 DOI: 10.1093/mutage/geu063] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The single cell gel electrophoresis assay, also known as the comet assay, is a versatile method for measuring many classes of DNA damage, including base damage, abasic sites, single strand breaks and double strand breaks. However, limited throughput and difficulties with reproducibility have limited its utility, particularly for clinical and epidemiological studies. To address these limitations, we created a microarray comet assay. The use of a micrometer scale array of cells increases the number of analysable comets per square centimetre and enables automated imaging and analysis. In addition, the platform is compatible with standard 24- and 96-well plate formats. Here, we have assessed the consistency and sensitivity of the microarray comet assay. We showed that the linear detection range for H2O2-induced DNA damage in human lymphoblastoid cells is between 30 and 100 μM, and that within this range, inter-sample coefficient of variance was between 5 and 10%. Importantly, only 20 comets were required to detect a statistically significant induction of DNA damage for doses within the linear range. We also evaluated sample-to-sample and experiment-to-experiment variation and found that for both conditions, the coefficient of variation was lower than what has been reported for the traditional comet assay. Finally, we also show that the assay can be performed using a 4× objective (rather than the standard 10× objective for the traditional assay). This adjustment combined with the microarray format makes it possible to capture more than 50 analysable comets in a single image, which can then be automatically analysed using in-house software. Overall, throughput is increased more than 100-fold compared to the traditional assay. Together, the results presented here demonstrate key advances in comet assay technology that improve the throughput, sensitivity, and robustness, thus enabling larger scale clinical and epidemiological studies.
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Affiliation(s)
- Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Danielle N Chow
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jessica L Fessler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - David M Weingeist
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - David K Wood
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bevin P Engelward
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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Brunborg G, Collins A, Graupner A, Gutzkow KB, Olsen AK. Reference cells and ploidy in the comet assay. Front Genet 2015; 6:61. [PMID: 25774164 PMCID: PMC4343028 DOI: 10.3389/fgene.2015.00061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 02/08/2015] [Indexed: 11/13/2022] Open
Abstract
In the comet assay single cells are analyzed with respect to their level of DNA damage. Discrimination of the individual cell or cell type based on DNA content, with concomitant scoring of the DNA damage, is useful since this may allow analysis of mixtures of cells. Different cells can then be characterized based on their ploidy, cell cycle stage, or genome size. We here describe two applications of such a cell type-specific comet assay: (i) Testicular cell suspensions, analyzed on the basis of their ploidy during spermatogenesis; and (ii) reference cells in the form of fish erythrocytes which can be included as internal standards to correct for inter-assay variations. With standard fluorochromes used in the comet assay, the total staining signal from each cell - whether damaged or undamaged - was found to be associated with the cell's DNA content. Analysis of the fluorescence intensity of single cells is straightforward since these data are available in scoring systems based on image analysis. The analysis of testicular cell suspensions provides information on cell type specific composition, susceptibility to genotoxicants, and DNA repair. Internal reference cells, either untreated or carrying defined numbers of lesions induced by ionizing radiation, are useful for investigation of experimental factors that can cause variation in comet assay results, and for routine inclusion in experiments to facilitate standardization of methods, and comparison of comet assay data obtained in different experiments or in different laboratories. They can also be used - in combination with a reference curve - to quantify the DNA lesions induced by a certain treatment. Fish cells of a range of genome sizes, both greater and smaller than human, are suitable for this purpose, and they are inexpensive.
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Affiliation(s)
- Gunnar Brunborg
- Department of Chemicals and Radiation, Division of Environmental Medicine, Norwegian Institute of Public Health, Oslo Norway
| | - Andrew Collins
- Department of Nutrition, University of Oslo, Oslo Norway
| | - Anne Graupner
- Department of Chemicals and Radiation, Division of Environmental Medicine, Norwegian Institute of Public Health, Oslo Norway
| | - Kristine B Gutzkow
- Department of Chemicals and Radiation, Division of Environmental Medicine, Norwegian Institute of Public Health, Oslo Norway
| | - Ann-Karin Olsen
- Department of Chemicals and Radiation, Division of Environmental Medicine, Norwegian Institute of Public Health, Oslo Norway
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22
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Does the duration of lysis affect the sensitivity of the in vitro alkaline comet assay? Mutagenesis 2014; 30:21-8. [DOI: 10.1093/mutage/geu047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Dasgupta S, Cao A, Mauer B, Yan B, Uno S, McElroy A. Genotoxicity of oxy-PAHs to Japanese medaka (Oryzias latipes) embryos assessed using the comet assay. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:13867-13876. [PMID: 24510601 DOI: 10.1007/s11356-014-2586-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 01/21/2014] [Indexed: 06/03/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) have long been recognized as important environmental toxicants. Despite a plethora of information on the fate and effects of parent PAHs, relatively little is known about the environmental fate and toxicity of ketone- and quinone-substituted PAH oxidation products (termed oxy-PAHs), particularly in the aquatic environment. This study begins to fill that gap using embryos of the Japanese medaka (Oryzias latipes) as a model species. The genotoxic potential of two environmentally relevant oxy-PAHs, acenaphthenequinone and 7,12-benz[a]anthracenquinone, was assessed using the comet assay. We found that both oxy-PAHs could cause significant increases in DNA damage after only 48 h of exposure at the lowest concentrations tested (5 μg/L). Comparisons of the genotoxic potential between these oxy-PAHs and their corresponding parent PAHs (acenaphthene and benz[a]anthracene) and a well-known mutagenic PAH, benzo[a]pyrene, indicated similar potencies among all five of these compounds, particularly after longer (7 day) exposures. This study demonstrates the mutagenic potential of oxy-PAHs to an in vivo fish embryo model and points out the need for further study of their environmental occurrence and biologic effects.
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Affiliation(s)
- Subham Dasgupta
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA
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24
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Collins AR, El Yamani N, Lorenzo Y, Shaposhnikov S, Brunborg G, Azqueta A. Controlling variation in the comet assay. Front Genet 2014; 5:359. [PMID: 25368630 PMCID: PMC4202776 DOI: 10.3389/fgene.2014.00359] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/26/2014] [Indexed: 11/13/2022] Open
Abstract
Variability of the comet assay is a serious issue, whether it occurs from experiment to experiment in the same laboratory, or between different laboratories analysing identical samples. Do we have to live with high variability, just because the comet assay is a biological assay rather than analytical chemistry? Numerous attempts have been made to limit variability by standardizing the assay protocol, and the critical steps in the assay have been identified; agarose concentration, duration of alkaline incubation, and electrophoresis conditions (time, temperature, and voltage gradient) are particularly important. Even when these are controlled, variation seems to be inevitable. It is helpful to include in experiments reference standards, i.e., cells with a known amount of specific damage to the DNA. They can be aliquots frozen from a single large batch of cells, either untreated (negative controls) or treated with, for example, H2O2 or X-rays to induce strand breaks (positive control for the basic assay), or photosensitiser plus light to oxidize guanine (positive control for Fpg- or OGG1-sensitive sites). Reference standards are especially valuable when performing a series of experiments over a long period-for example, analysing samples of white blood cells from a large human biomonitoring trial-to check that the assay is performing consistently, and to identify anomalous results necessitating a repeat experiment. The reference values of tail intensity can also be used to iron out small variations occurring from day to day. We present examples of the use of reference standards in human trials, both within one laboratory and between different laboratories, and describe procedures that can be used to control variation.
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Affiliation(s)
- Andrew R Collins
- Department of Nutrition, Faculty of Medicine, University of Oslo Oslo, Norway
| | - Naouale El Yamani
- Department of Nutrition, Faculty of Medicine, University of Oslo Oslo, Norway
| | - Yolanda Lorenzo
- Department of Nutrition, Faculty of Medicine, University of Oslo Oslo, Norway
| | - Sergey Shaposhnikov
- Department of Nutrition, Faculty of Medicine, University of Oslo Oslo, Norway
| | - Gunnar Brunborg
- Department of Chemicals and Radiation, Norwegian Institute of Public Health Oslo, Norway
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, University of Navarra Pamplona, Spain
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25
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Katarkar A, Mukherjee S, Khan MH, Ray JG, Chaudhuri K. Comparative evaluation of genotoxicity by micronucleus assay in the buccal mucosa over comet assay in peripheral blood in oral precancer and cancer patients. Mutagenesis 2014; 29:325-334. [DOI: 10.1093/mutage/geu023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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26
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Christian WV, Oliver LD, Paustenbach DJ, Kreider ML, Finley BL. Toxicology-based cancer causation analysis of CoCr-containing hip implants: a quantitative assessment of genotoxicity and tumorigenicity studies. J Appl Toxicol 2014; 34:939-67. [DOI: 10.1002/jat.3039] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/23/2014] [Accepted: 05/24/2014] [Indexed: 12/12/2022]
Affiliation(s)
| | - Lindsay D. Oliver
- Cardno ChemRisk; LLC, 4840 Pearl East Circle, Suite 300 West Boulder CO 80301 USA
| | | | - Marisa L. Kreider
- Cardno ChemRisk, LLC; 20 Stanwix St., Suite 505 Pittsburgh PA 15222 USA
| | - Brent L. Finley
- Cardno ChemRisk; LLC, 231 Front St., Suite 201 Brooklyn NY 11201 USA
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27
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Garcia-Canton C, Errington G, Anadon A, Meredith C. Characterisation of an aerosol exposure system to evaluate the genotoxicity of whole mainstream cigarette smoke using the in vitro γH2AX assay by high content screening. BMC Pharmacol Toxicol 2014; 15:41. [PMID: 25056295 PMCID: PMC4122049 DOI: 10.1186/2050-6511-15-41] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 07/16/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The genotoxic effect of cigarette smoke is routinely measured by treating cells with cigarette Particulate Matter (PM) at different dose levels in submerged cell cultures. However, PM exposure cannot be considered as a complete exposure as it does not contain the gas phase component of the cigarette smoke. The in vitro γH2AX assay by High Content Screening (HCS) has been suggested as a complementary tool to the standard battery of genotoxicity assays as it detects DNA double strand breaks in a high-throughput fashion. The aim of this study was to further optimise the in vitro γH2AX assay by HCS to enable aerosol exposure of human bronchial epithelial BEAS-2B cells at the air-liquid interface (ALI). METHODS Whole mainstream cigarette smoke (WMCS) from two reference cigarettes (3R4F and M4A) were assessed for their genotoxic potential. During the study, a further characterisation of the Borgwaldt RM20S® aerosol exposure system to include single dilution assessment with a reference gas was also carried out. RESULTS The results of the optimisation showed that both reference cigarettes produced a positive genotoxic response at all dilutions tested. However, the correlation between dose and response was low for both 3R4F and M4A (Pearson coefficient, r = -0.53 and -0.44 respectively). During the additional characterisation of the exposure system, it was observed that several pre-programmed dilutions did not perform as expected. CONCLUSIONS Overall, the in vitro γH2AX assay by HCS could be used to evaluate WMCS in cell cultures at the ALI. Additionally, the extended characterisation of the exposure system indicates that assessing the performance of the dilutions could improve the existing routine QC checks.
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Affiliation(s)
- Carolina Garcia-Canton
- British American Tobacco, Group Research and Development, Regents Park Road, Southampton, Hampshire SO15 8TL, UK
- Department of Toxicology and Pharmacology, Universidad Complutense de Madrid, Madrid, Spain
| | - Graham Errington
- British American Tobacco, Group Research and Development, Regents Park Road, Southampton, Hampshire SO15 8TL, UK
| | - Arturo Anadon
- Department of Toxicology and Pharmacology, Universidad Complutense de Madrid, Madrid, Spain
| | - Clive Meredith
- British American Tobacco, Group Research and Development, Regents Park Road, Southampton, Hampshire SO15 8TL, UK
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28
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The comet assay as a tool for human biomonitoring studies: The ComNet Project. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 759:27-39. [DOI: 10.1016/j.mrrev.2013.10.001] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 10/17/2013] [Accepted: 10/23/2013] [Indexed: 02/07/2023]
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29
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Ersson C, Møller P, Forchhammer L, Loft S, Azqueta A, Godschalk RWL, van Schooten FJ, Jones GDD, Higgins JA, Cooke MS, Mistry V, Karbaschi M, Phillips DH, Sozeri O, Routledge MN, Nelson-Smith K, Riso P, Porrini M, Matullo G, Allione A, Stepnik M, Ferlińska M, Teixeira JP, Costa S, Corcuera LA, López de Cerain A, Laffon B, Valdiglesias V, Collins AR, Möller L. An ECVAG inter-laboratory validation study of the comet assay: inter-laboratory and intra-laboratory variations of DNA strand breaks and FPG-sensitive sites in human mononuclear cells. Mutagenesis 2013; 28:279-86. [PMID: 23446176 DOI: 10.1093/mutage/get001] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024] Open
Abstract
The alkaline comet assay is an established, sensitive method extensively used in biomonitoring studies. This method can be modified to measure a range of different types of DNA damage. However, considerable differences in the protocols used by different research groups affect the inter-laboratory comparisons of results. The aim of this study was to assess the inter-laboratory, intra-laboratory, sample and residual (unexplained) variations in DNA strand breaks and formamidopyrimidine DNA glycosylase (FPG)-sensitive sites measured by the comet assay by using a balanced Latin square design. Fourteen participating laboratories used their own comet assay protocols to measure the level of DNA strand breaks and FPG-sensitive sites in coded samples containing peripheral blood mononuclear cells (PBMC) and the level of DNA strand breaks in coded calibration curve samples (cells exposed to different doses of ionising radiation) on three different days of analysis. Eleven laboratories found dose-response relationships in the coded calibration curve samples on two or three days of analysis, whereas three laboratories had technical problems in their assay. In the coded calibration curve samples, the dose of ionising radiation, inter-laboratory variation, intra-laboratory variation and residual variation contributed to 60.9, 19.4, 0.1 and 19.5%, respectively, of the total variation. In the coded PBMC samples, the inter-laboratory variation explained the largest fraction of the overall variation of DNA strand breaks (79.2%) and the residual variation (19.9%) was much larger than the intra-laboratory (0.3%) and inter-subject (0.5%) variation. The same partitioning of the overall variation of FPG-sensitive sites in the PBMC samples indicated that the inter-laboratory variation was the strongest contributor (56.7%), whereas the residual (42.9%), intra-laboratory (0.2%) and inter-subject (0.3%) variations again contributed less to the overall variation. The results suggest that the variation in DNA damage, measured by comet assay, in PBMC from healthy subjects is assay variation rather than variation between subjects.
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Affiliation(s)
- Clara Ersson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge SE-141 83, Sweden
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30
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Li Y, Feng X, Du W, Li Y, Liu BF. Ultrahigh-Throughput Approach for Analyzing Single-Cell Genomic Damage with an Agarose-Based Microfluidic Comet Array. Anal Chem 2013; 85:4066-73. [DOI: 10.1021/ac4000893] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yiwei Li
- Britton Chance Center for Biomedical
Photonics at Wuhan
National Laboratory for Optoelectronics−Hubei Bioinformatics
and Molecular Imaging Key Laboratory, Systems Biology Theme, Department
of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan
430074, China
| | - Xiaojun Feng
- Britton Chance Center for Biomedical
Photonics at Wuhan
National Laboratory for Optoelectronics−Hubei Bioinformatics
and Molecular Imaging Key Laboratory, Systems Biology Theme, Department
of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan
430074, China
| | - Wei Du
- Britton Chance Center for Biomedical
Photonics at Wuhan
National Laboratory for Optoelectronics−Hubei Bioinformatics
and Molecular Imaging Key Laboratory, Systems Biology Theme, Department
of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan
430074, China
| | - Ying Li
- Britton Chance Center for Biomedical
Photonics at Wuhan
National Laboratory for Optoelectronics−Hubei Bioinformatics
and Molecular Imaging Key Laboratory, Systems Biology Theme, Department
of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan
430074, China
| | - Bi-Feng Liu
- Britton Chance Center for Biomedical
Photonics at Wuhan
National Laboratory for Optoelectronics−Hubei Bioinformatics
and Molecular Imaging Key Laboratory, Systems Biology Theme, Department
of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan
430074, China
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31
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Forchhammer L, Ersson C, Loft S, Möller L, Godschalk RWL, van Schooten FJ, Jones GDD, Higgins JA, Cooke M, Mistry V, Karbaschi M, Collins AR, Azqueta A, Phillips DH, Sozeri O, Routledge MN, Nelson-Smith K, Riso P, Porrini M, Matullo G, Allione A, Stępnik M, Steepnik M, Komorowska M, Teixeira JP, Costa S, Corcuera LA, López de Cerain A, Laffon B, Valdiglesias V, Møller P. Inter-laboratory variation in DNA damage using a standard comet assay protocol. Mutagenesis 2012; 27:665-72. [PMID: 22844078 DOI: 10.1093/mutage/ges032] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024] Open
Abstract
There are substantial inter-laboratory variations in the levels of DNA damage measured by the comet assay. The aim of this study was to investigate whether adherence to a standard comet assay protocol would reduce inter-laboratory variation in reported values of DNA damage. Fourteen laboratories determined the baseline level of DNA strand breaks (SBs)/alkaline labile sites and formamidopyrimidine DNA glycosylase (FPG)-sensitive sites in coded samples of mononuclear blood cells (MNBCs) from healthy volunteers. There were technical problems in seven laboratories in adopting the standard protocol, which were not related to the level of experience. Therefore, the inter-laboratory variation in DNA damage was only analysed using the results from laboratories that had obtained complete data with the standard comet assay protocol. This analysis showed that the differences between reported levels of DNA SBs/alkaline labile sites in MNBCs were not reduced by applying the standard assay protocol as compared with the laboratory's own protocol. There was large inter-laboratory variation in FPG-sensitive sites by the laboratory-specific protocol and the variation was reduced when the samples were analysed by the standard protocol. The SBs and FPG-sensitive sites were measured in the same experiment, indicating that the large spread in the latter lesions was the main reason for the reduced inter-laboratory variation. However, it remains worrying that half of the participating laboratories obtained poor results using the standard procedure. This study indicates that future comet assay validation trials should take steps to evaluate the implementation of standard procedures in participating laboratories.
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Affiliation(s)
- Lykke Forchhammer
- Section of Environmental Health, Department of Public Health, University of Copenhagen, Copenhagen K, Denmark
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Garcia-Canton C, Anadón A, Meredith C. γH2AX as a novel endpoint to detect DNA damage: applications for the assessment of the in vitro genotoxicity of cigarette smoke. Toxicol In Vitro 2012; 26:1075-86. [PMID: 22735693 DOI: 10.1016/j.tiv.2012.06.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/17/2012] [Accepted: 06/14/2012] [Indexed: 01/02/2023]
Abstract
Histone H2AX is rapidly phosphorylated to become γH2AX after exposure to DNA-damaging agents that cause double-strand DNA breaks (DSBs). γH2AX can be detected and quantified by numerous methods, giving a direct correlation with the number of DSBs. This relationship has made γH2AX an increasingly utilised endpoint in multiple scientific fields since its discovery in 1998. Applications include its use in pre-clinical drug assessment, as a biomarker of DNA damage and in in vitro mechanistic studies. Here, we review current in vitro regulatory and non-regulatory genotoxicity assays proposing the γH2AX assay as a potential complement to the current test battery. Additionally, we evaluate the use of the γH2AX assay to measure DSBs in vitro in tobacco product testing.
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Affiliation(s)
- Carolina Garcia-Canton
- British American Tobacco, Group Research and Development, Regents Park Road, Southampton, Hampshire SO15 8TL, UK.
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Møller P, Cooke MS, Collins A, Olinski R, Rozalski R, Loft S. Harmonising measurements of 8-oxo-7,8-dihydro-2′-deoxyguanosine in cellular DNA and urine. Free Radic Res 2012; 46:541-53. [DOI: 10.3109/10715762.2011.644241] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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34
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Liu H, Zhang H, Jiang X, Ma Y, Xu Y, Feng S, Liu F. Knockdown of Secreted Protein Acidic and Rich in Cysteine (SPARC) Expression Diminishes Radiosensitivity of Glioma Cells. Cancer Biother Radiopharm 2011; 26:705-15. [DOI: 10.1089/cbr.2011.0987] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Haiyan Liu
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
- Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, Jiangsu Province, China
| | - Haowen Zhang
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Xin Jiang
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Yan Ma
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Yuanyuan Xu
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Shuang Feng
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
| | - Fenju Liu
- School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou, Jiangsu Province, China
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Rosenberger A, Rössler U, Hornhardt S, Sauter W, Bickeböller H, Wichmann HE, Gomolka M. Validation of a fully automated COMET assay: 1.75 million single cells measured over a 5 year period. DNA Repair (Amst) 2011; 10:322-37. [DOI: 10.1016/j.dnarep.2010.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 12/02/2010] [Accepted: 12/10/2010] [Indexed: 11/16/2022]
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36
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Halliwell B. Free radicals and antioxidants – quo vadis? Trends Pharmacol Sci 2011; 32:125-30. [DOI: 10.1016/j.tips.2010.12.002] [Citation(s) in RCA: 383] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/02/2010] [Accepted: 12/02/2010] [Indexed: 10/25/2022]
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37
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Single cell trapping and DNA damage analysis using microwell arrays. Proc Natl Acad Sci U S A 2010; 107:10008-13. [PMID: 20534572 DOI: 10.1073/pnas.1004056107] [Citation(s) in RCA: 180] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
With a direct link to cancer, aging, and heritable diseases as well as a critical role in cancer treatment, the importance of DNA damage is well-established. The intense interest in DNA damage in applications ranging from epidemiology to drug development drives an urgent need for robust, high throughput, and inexpensive tools for objective, quantitative DNA damage analysis. We have developed a simple method for high throughput DNA damage measurements that provides information on multiple lesions and pathways. Our method utilizes single cells captured by gravity into a microwell array with DNA damage revealed morphologically by gel electrophoresis. Spatial encoding enables simultaneous assays of multiple experimental conditions performed in parallel with fully automated analysis. This method also enables novel functionalities, including multiplexed labeling for parallel single cell assays, as well as DNA damage measurement in cell aggregates. We have also developed 24- and 96-well versions, which are applicable to high throughput screening. Using this platform, we have quantified DNA repair capacities of individuals with different genetic backgrounds, and compared the efficacy of potential cancer chemotherapeutics as inhibitors of a critical DNA repair enzyme, human AP endonuclease. This platform enables high throughput assessment of multiple DNA repair pathways and subpathways in parallel, thus enabling new strategies for drug discovery, genotoxicity testing, and environmental health.
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38
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Johansson C, Møller P, Forchhammer L, Loft S, Godschalk RWL, Langie SAS, Lumeij S, Jones GDD, Kwok RWL, Azqueta A, Phillips DH, Sozeri O, Routledge MN, Charlton AJ, Riso P, Porrini M, Allione A, Matullo G, Palus J, Stepnik M, Collins AR, Möller L. An ECVAG trial on assessment of oxidative damage to DNA measured by the comet assay. Mutagenesis 2009; 25:125-32. [PMID: 19948595 PMCID: PMC2825342 DOI: 10.1093/mutage/gep055] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The increasing use of single cell gel electrophoresis (the comet assay) highlights its popularity as a method for detecting DNA damage, including the use of enzymes for assessment of oxidatively damaged DNA. However, comparison of DNA damage levels between laboratories can be difficult due to differences in assay protocols (e.g. lysis conditions, enzyme treatment, the duration of the alkaline treatment and electrophoresis) and in the end points used for reporting results (e.g. %DNA in tail, arbitrary units, tail moment and tail length). One way to facilitate comparisons is to convert primary comet assay end points to number of lesions/106 bp by calibration with ionizing radiation. The aim of this study was to investigate the inter-laboratory variation in assessment of oxidatively damaged DNA by the comet assay in terms of oxidized purines converted to strand breaks with formamidopyrimidine DNA glycosylase (FPG). Coded samples with DNA oxidation damage induced by treatment with different concentrations of photosensitizer (Ro 19-8022) plus light and calibration samples irradiated with ionizing radiation were distributed to the 10 participating laboratories to measure DNA damage using their own comet assay protocols. Nine of 10 laboratories reported the same ranking of the level of damage in the coded samples. The variation in assessment of oxidatively damaged DNA was largely due to differences in protocols. After conversion of the data to lesions/106 bp using laboratory-specific calibration curves, the variation between the laboratories was reduced. The contribution of the concentration of photosensitizer to the variation in net FPG-sensitive sites increased from 49 to 73%, whereas the inter-laboratory variation decreased. The participating laboratories were successful in finding a dose–response of oxidatively damaged DNA in coded samples, but there remains a need to standardize the protocols to enable direct comparisons between laboratories.
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Affiliation(s)
- Clara Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 57 Huddinge, Sweden
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