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Atkinson J, Bezak E, Le H, Kempson I. DNA Double Strand Break and Response Fluorescent Assays: Choices and Interpretation. Int J Mol Sci 2024; 25:2227. [PMID: 38396904 PMCID: PMC10889524 DOI: 10.3390/ijms25042227] [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] [Received: 12/22/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Accurately characterizing DNA double-stranded breaks (DSBs) and understanding the DNA damage response (DDR) is crucial for assessing cellular genotoxicity, maintaining genomic integrity, and advancing gene editing technologies. Immunofluorescence-based techniques have proven to be invaluable for quantifying and visualizing DSB repair, providing valuable insights into cellular repair processes. However, the selection of appropriate markers for analysis can be challenging due to the intricate nature of DSB repair mechanisms, often leading to ambiguous interpretations. This comprehensively summarizes the significance of immunofluorescence-based techniques, with their capacity for spatiotemporal visualization, in elucidating complex DDR processes. By evaluating the strengths and limitations of different markers, we identify where they are most relevant chronologically from DSB detection to repair, better contextualizing what each assay represents at a molecular level. This is valuable for identifying biases associated with each assay and facilitates accurate data interpretation. This review aims to improve the precision of DSB quantification, deepen the understanding of DDR processes, assay biases, and pathway choices, and provide practical guidance on marker selection. Each assay offers a unique perspective of the underlying processes, underscoring the need to select markers that are best suited to specific research objectives.
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Affiliation(s)
- Jake Atkinson
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia;
| | - Eva Bezak
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA 5095, Australia; (E.B.)
- Department of Physics, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Hien Le
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA 5095, Australia; (E.B.)
- Department of Radiation Oncology, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Ivan Kempson
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia;
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Misaki K, Matsuda S, Matsuda T, Kusakabe T, Shimizu Y. Detection of DNA damage formation by natural organic matter using EGFP-fused MDC1-expressing cells. CHEMOSPHERE 2019; 235:169-174. [PMID: 31255757 DOI: 10.1016/j.chemosphere.2019.06.126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 06/09/2023]
Abstract
Studies have been conducted on the genotoxicity and carcinogenicity of disinfection by-products formed from natural organic matter (NOM) and mitigation effect for mutagens and clastogens by NOM. Whereas, reportedly, synthetic humic acid in high concentration has induced genotoxicity in human cells, and NOM samples have provoked mild oxidative and other physiological responses in aquatic organisms. Our group developed a novel detection method for DNA damage formation, namely enhanced green fluorescent protein (EGFP)-fused mediator of DNA damage checkpoint 1 (MDC1)-expressing human cells as simple and high-sensitive system. By using this method, a significant increase in the foci area was observed after 3 h, but not 24 h for 130 mgC L-1 Suwannee River fulvic acid (SRFA), 38 mgC L-1 humic acid (SRHA), and 19 mgC L-1 NOM (SRNOM). The SRNOM concentration is the original environmental one; therefore, it was suggested that the formation and repair of DNA damage associated with γ-H2AX, a biomarker for DNA double-strand breaks by mild oxidative stress, in Suwannee River (SR) were detected for the first time. The increase in the foci area was not observed for 18 mgC L-1 Lake Biwa fulvic acid (LBFA) and 50 mg L-1 catechin after both 3 h and 24 h. The difference between the SR and Lake Biwa (LB) samples may result from the differences in their electron-accepting capacity. The application of this methodology is expected to elucidate oxidative stress and toxicological effects shortly and in detail for many water samples.
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Affiliation(s)
- Kentaro Misaki
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan; School of Nursing, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Japan.
| | - Shun Matsuda
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan
| | - Tomonari Matsuda
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan
| | - Taketoshi Kusakabe
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan
| | - Yoshihisa Shimizu
- Research Center for Environmental Quality Management (RCEQM), Graduate School of Engineering, Kyoto University, 1-2 Yumihama, Otsu, Shiga, Japan
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Nelson BC, Wright CW, Ibuki Y, Moreno-Villanueva M, Karlsson HL, Hendriks G, Sims CM, Singh N, Doak SH. Emerging metrology for high-throughput nanomaterial genotoxicology. Mutagenesis 2016; 32:215-232. [PMID: 27565834 DOI: 10.1093/mutage/gew037] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The rapid development of the engineered nanomaterial (ENM) manufacturing industry has accelerated the incorporation of ENMs into a wide variety of consumer products across the globe. Unintentionally or not, some of these ENMs may be introduced into the environment or come into contact with humans or other organisms resulting in unexpected biological effects. It is thus prudent to have rapid and robust analytical metrology in place that can be used to critically assess and/or predict the cytotoxicity, as well as the potential genotoxicity of these ENMs. Many of the traditional genotoxicity test methods [e.g. unscheduled DNA synthesis assay, bacterial reverse mutation (Ames) test, etc.,] for determining the DNA damaging potential of chemical and biological compounds are not suitable for the evaluation of ENMs, due to a variety of methodological issues ranging from potential assay interferences to problems centered on low sample throughput. Recently, a number of sensitive, high-throughput genotoxicity assays/platforms (CometChip assay, flow cytometry/micronucleus assay, flow cytometry/γ-H2AX assay, automated 'Fluorimetric Detection of Alkaline DNA Unwinding' (FADU) assay, ToxTracker reporter assay) have been developed, based on substantial modifications and enhancements of traditional genotoxicity assays. These new assays have been used for the rapid measurement of DNA damage (strand breaks), chromosomal damage (micronuclei) and for detecting upregulated DNA damage signalling pathways resulting from ENM exposures. In this critical review, we describe and discuss the fundamental measurement principles and measurement endpoints of these new assays, as well as the modes of operation, analytical metrics and potential interferences, as applicable to ENM exposures. An unbiased discussion of the major technical advantages and limitations of each assay for evaluating and predicting the genotoxic potential of ENMs is also provided.
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Affiliation(s)
- Bryant C Nelson
- National Institute of Standards and Technology, Material Measurement Laboratory - Biosystems and Biomaterials Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA,
| | - Christa W Wright
- Department of Environmental Health, Center for Nanotechnology and Nanotoxicology, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue Building 1/Room 1309, Boston, MA 02115, USA
| | - Yuko Ibuki
- Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Shizuoka 422-8526, Japan
| | - Maria Moreno-Villanueva
- Department of Biology, University of Konstanz, Molecular Toxicology Group, D-78457 Konstanz, Germany
| | - Hanna L Karlsson
- Unit of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Giel Hendriks
- Toxys, Robert Boyleweg 4, 2333 CG Leiden, The Netherlands
| | - Christopher M Sims
- National Institute of Standards and Technology, Material Measurement Laboratory - Biosystems and Biomaterials Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Neenu Singh
- Faculty of Health and Life Sciences, School of Allied Health Sciences, De Montfort University, The Gateway, Leicester LE1 9BH, UK and
| | - Shareen H Doak
- Swansea University Medical School, Institute of Life Science, Centre for NanoHealth, Swansea University Medical School, Wales SA2 8PP, UK
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Matsuda S, Matsuda Y, Yanagisawa SY, Ikura M, Ikura T, Matsuda T. Disruption of DNA Damage-Response by Propyl Gallate and 9-Aminoacridine. Toxicol Sci 2016; 151:224-35. [PMID: 26928355 DOI: 10.1093/toxsci/kfw039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The DNA-damage response (DDR) protects the genome from various types of endogenous and exogenous DNA damage, and can itself be a target of certain chemicals that give rise to chromosomal aberrations. Here, we developed a screening method to detect inhibition of Mediator of DNA damage Checkpoint 1 (MDC1) foci formation (the Enhanced Green Fluorescent Protein (EGFP)-MDC1 foci formation-inhibition assay) using EGFP-MDC1-expressing human cells. The assay identified propyl gallate (PG) and 9-aminoacridine (9-AA) as inhibitors of camptothecin (CPT)-induced MDC1 foci formation. We demonstrated that the inhibition of CPT-induced MDC1 foci formation by PG was caused by the direct suppression of histone H2AX phosphorylation at Ser139 (γH2AX), which is required for MDC1 foci formation, by quantifying γH2AX in cells and in vitro 9-AA also directly suppressed H2AX Ser139-phosphorylation in vitro but the concentration was much higher than that required to suppress CPT-induced MDC1 foci formation in cells. Consistent with these findings, PG and 9-AA both suppressed CPT-induced G2/M cell-cycle arrest and increased the number of abnormal nuclei. Our results suggest that early DDR-inhibitory effects of PG and 9-AA contribute to their chromosome-damaging potential, and that the EGFP-MDC1 foci formation-inhibition assay is useful for detection of and screening for H2AX Ser139-phosphorylation-inhibitory effects of chemicals.
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Affiliation(s)
- Shun Matsuda
- *Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan; and
| | - Yoko Matsuda
- *Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan; and
| | - Shin-Ya Yanagisawa
- *Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan; and
| | - Masae Ikura
- Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Tsuyoshi Ikura
- Department of Mutagenesis, Laboratory of Chromatin Dynamics, Radiation Biology Center, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
| | - Tomonari Matsuda
- *Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan; and *Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan; and
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Absolute quantification of γH2AX using liquid chromatography–triple quadrupole tandem mass spectrometry. Anal Bioanal Chem 2015; 407:5521-7. [DOI: 10.1007/s00216-015-8725-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 01/13/2023]
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