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Yang Z, DeLoid GM, Baw J, Zarbl H, Demokritou P. Assessment of Ingested Micro- and Nanoplastic (MNP)-Mediated Genotoxicity in an In Vitro Model of the Small Intestinal Epithelium (SIE). NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:807. [PMID: 38727401 PMCID: PMC11085749 DOI: 10.3390/nano14090807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/12/2024]
Abstract
Micro- and nanoplastics (MNPs) have become ubiquitous contaminants of water and foods, resulting in high levels of human ingestion exposure. MNPs have been found in human blood and multiple tissues, suggesting that they are readily absorbed by the gastrointestinal tract (GIT) and widely distributed. Growing toxicological evidence suggests that ingested MNPs may pose a serious health threat. The potential genotoxicity of MNPs, however, remains largely unknown. In this study, genotoxicity of primary and environmentally relevant secondary MNPs was assessed in a triculture small intestinal epithelium (SIE) model using the CometChip assay. Aqueous suspensions of 25 and 1000 nm carboxylated polystyrene spheres (PS25C and PS1KC), and incinerated polyethylene (PEI PM0.1) were subjected to simulated GIT digestion to create physiologically relevant exposures (digestas), which were applied to the SIE model at final MNP concentrations of 1, 5, and 20 μg/mL for 24 or 48 h. PS25C and PS1KC induced DNA damage in a time- and concentration-dependent manner. To our knowledge, this is one of the first assessment of MNP genotoxicity in an integrated in vitro ingestion platform including simulated GIT digestion and a triculture SIE model. These findings suggest that ingestion of high concentrations of carboxylated PS MNPs could have serious genotoxic consequences in the SIE.
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Affiliation(s)
- Zhenning Yang
- Nanoscience and Advanced Materials Center, Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ 08854, USA; (Z.Y.); (G.M.D.)
- Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA;
| | - Glen M. DeLoid
- Nanoscience and Advanced Materials Center, Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ 08854, USA; (Z.Y.); (G.M.D.)
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ 08854, USA;
| | - Joshua Baw
- Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA;
| | - Helmut Zarbl
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ 08854, USA;
- School of Public Health, Rutgers University, Piscataway, NJ 08854, USA
| | - Philip Demokritou
- Nanoscience and Advanced Materials Center, Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ 08854, USA; (Z.Y.); (G.M.D.)
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ 08854, USA;
- School of Public Health, Rutgers University, Piscataway, NJ 08854, USA
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2
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Flórez González SJ, Stashenko EE, Ocazionez RE, Vinardell MP, Fuentes JL. In vitro Safety Assessment of Extracts and Compounds From Plants as Sunscreen Ingredients. Int J Toxicol 2024; 43:243-252. [PMID: 38183303 DOI: 10.1177/10915818231225661] [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] [Indexed: 01/08/2024]
Abstract
This work investigated the safety of extracts obtained from plants growing in Colombia, which have previously shown UV-filter/antigenotoxic properties. The compounds in plant extracts obtained by the supercritical fluid (CO2) extraction method were identified using gas chromatography coupled to mass spectrometry (GC/MS) analysis. Cytotoxicity measured as cytotoxic concentration 50% (CC50) and genotoxicity of the plant extracts and some compounds were studied in human fibroblasts using the trypan blue exclusion assay and the Comet assay, respectively. The extracts from Pipper eriopodon and Salvia aratocensis species and the compound trans-β-caryophyllene were clearly cytotoxic to human fibroblasts. Conversely, Achyrocline satureioides, Chromolaena pellia, and Lippia origanoides extracts were relatively less cytotoxic with CC50 values of 173, 184, and 89 μg/mL, respectively. The C. pellia and L. origanoides extracts produced some degree of DNA breaks at cytotoxic concentrations. The cytotoxicity of the studied compounds was as follows, with lower CC50 values representing the most cytotoxic compounds: resveratrol (91 μM) > pinocembrin (144 μM) > quercetin (222 μM) > titanium dioxide (704 μM). Quercetin was unique among the compounds assayed in being genotoxic to human fibroblasts. Our work indicates that phytochemicals can be cytotoxic and genotoxic, demonstrating the need to establish safe concentrations of these extracts for their potential use in cosmetics.
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Affiliation(s)
- Silvia Juliana Flórez González
- Laboratorio de Microbiología y Mutagénesis Ambiental (LMMA), Grupo de Investigación en Microbiología y Genética, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Elena E Stashenko
- Centro de Investigación en Biomoléculas (CIBIMOL), Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
- Centro de Cromatografía y Espectrometría de Masas (CROM-MASS), Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Raquel Elvira Ocazionez
- Centro de Cromatografía y Espectrometría de Masas (CROM-MASS), Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - María Pilar Vinardell
- Departamento de Bioquímica y Fisiología, Facultad de Farmacia y Ciencias de la Alimentación, Universitat de Barcelona, Barcelona 08028, Spain
| | - Jorge Luis Fuentes
- Laboratorio de Microbiología y Mutagénesis Ambiental (LMMA), Grupo de Investigación en Microbiología y Genética, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
- Centro de Investigación en Biomoléculas (CIBIMOL), Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
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3
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Guo X, Xu H, Seo JE. Application of HepaRG cells for genotoxicity assessment: a review. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, TOXICOLOGY AND CARCINOGENESIS 2024:1-24. [PMID: 38566478 DOI: 10.1080/26896583.2024.2331956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
There has been growing interest in the use of human-derived metabolically competent cells for genotoxicity testing. The HepaRG cell line is considered one of the most promising cell models because it is TP53-proficient and retains many characteristics of primary human hepatocytes. In recent years, HepaRG cells, cultured in both a traditional two-dimensional (2D) format and as more advanced in-vivo-like 3D spheroids, have been employed in assays that measure different types of genetic toxicity endpoints, including DNA damage, mutations, and chromosomal damage. This review summarizes published studies that have used HepaRG cells for genotoxicity assessment, including cell model evaluation studies and risk assessment for various compounds. Both 2D and 3D HepaRG models can be adapted to several high-throughput genotoxicity assays, generating a large number of data points that facilitate quantitative benchmark concentration modeling. With further validation, HepaRG cells could serve as a unique, human-based new alternative methodology for in vitro genotoxicity testing.
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Affiliation(s)
- Xiaoqing Guo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
| | - Hannah Xu
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
| | - Ji-Eun Seo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
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4
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Fernandes AS, de Melo Bisneto AV, Silva LS, Flávia Luiz Cardoso Bailão E, Cardoso CG, Carneiro CC, da Costa Santos S, Chen-Chen L. Tellimagrandin-I and camptothin a exhibit chemopreventive effects in Salmonella enterica serovar Typhimurium strains and human lymphocytes. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2024; 87:185-198. [PMID: 38073488 DOI: 10.1080/15287394.2023.2290641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Tellimagrandin-I (TL) and camptothin A (CA) are ellagitannins widely found in diverse plant species. Numerous studies demonstrated their significant biological activities, which include antitumor, antioxidant, and hepatoprotective properties. Despite this protective profile, the effects of TL and CA on DNA have not been comprehensively investigated. Thus, the aim of this study was to determine the mutagenic and antimutagenic effects attributed to TL and CA exposure on Salmonella enterica serovar Typhimurium strains using the Ames test. In addition, the cytotoxic and genotoxic effects were examined on human lymphocytes, employing both trypan blue exclusion and CometChip assay. The antigenotoxic effect was determined following TL and CA exposure in the presence of co-treatment with doxorubicin (DXR). Our results from the Ames test indicated that TL or CA did not display marked mutagenic activity. However, TL or CA demonstrated an ability to protect DNA against the damaging effects of the mutagens 4-nitroquinoline-1-oxide and sodium azide, thereby exhibiting antimutagenic properties. In relation to human lymphocytes, TL or CA did not induce significant cytotoxic or genotoxic actions on these cells. Further, these ellagitannins exhibited an ability to protect DNA from damage induced by DOX during co-treatment, indicating their potential beneficial usefulness as antigenotoxic agents. In conclusion, the protective effects of TL or CA against mutagens, coupled with their absence of genotoxic and cytotoxic effects on human lymphocytes, emphasize their potential therapeutic value in chemopreventive strategies.
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Affiliation(s)
- Amanda Silva Fernandes
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Abel Vieira de Melo Bisneto
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Luana Santos Silva
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | | | - Clever Gomes Cardoso
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Cristiene Costa Carneiro
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | | | - Lee Chen-Chen
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
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Collia M, Møller P, Langie SAS, Vettorazzi A, Azqueta A. Further development of CometChip technology to measure DNA damage in vitro and in vivo: Comparison with the 2 gels/slide format of the standard and enzyme-modified comet assay. Toxicology 2024; 501:153690. [PMID: 38040084 DOI: 10.1016/j.tox.2023.153690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
DNA damage plays a pivotal role in carcinogenesis and other diseases. The comet assay has been used for more than three decades to measure DNA damages. The 1-2 gels/slide format is the most used version of the assay. In 2010, a high throughput 96 macrowell format with a spatially encoded array of microwells patterned in agarose was developed, called the CometChip. The commercial version (CometChip®) has been used for the in vitro standard version of the comet assay (following the manufacturer's protocol), although it has not been compared directly with the 2 gels/slide format. The aim of this work is to developed new protocols to allow use of DNA repair enzymes as well as the analysis of in vivo frozen tissue samples in the CometChip®, to increase the throughput, and to compare its performance with the classic 2 gels/slide format. We adapted the manufacturer's protocol to allow the use of snap frozen tissue samples, using male Wistar rats orally dosed with methyl methanesulfonate (MMS, 200 mg/kg b.w.), and to detect altered nucleobases using DNA repair enzymes, with TK6 cells treated with potassium bromate (KBrO3, 0-4 mM, 3 h) and formamidopyrimidine DNA glycosylase (Fpg) as the enzyme. Regarding the standard version of the comet, we performed thee comparison of the 2 gel/slide and CometChip® format (using the the manufacturer's protocol), using TK6 cells with MMS (100-800 µM, 1 h) and hydrogen peroxide (H2O2, 7.7-122.5 µM, 5 min) as testing compounds. In all cases the CometChip® was performed along with the 2 gels/slide format. Results obtained were comparable and the CometChip® is a good alternative to the 2 gels/slide format when a higher throughput is required.
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Affiliation(s)
- Miguel Collia
- Department of Pharmaceutical Sciences, School of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - Peter Møller
- Department of Public Health, Section of Environmental Health, University of Copenhagen, Copenhagen, Denmark
| | - Sabine A S Langie
- Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, the Netherlands
| | - Ariane Vettorazzi
- Department of Pharmaceutical Sciences, School of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | - Amaya Azqueta
- Department of Pharmaceutical Sciences, School of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain.
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Karbaschi M, Ji Y, Mujawar MA, Mendoza M, Marquez JS, Sonawane A, Shah P, Ross C, Bhansali S, Cooke MS. Development of a Novel, Automated High-Throughput Device for Performing the Comet Assay. Int J Mol Sci 2023; 24:ijms24087187. [PMID: 37108351 PMCID: PMC10138556 DOI: 10.3390/ijms24087187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
A comet assay is a trusted and widely used method for assessing DNA damage in individual eukaryotic cells. However, it is time-consuming and requires extensive monitoring and sample manipulation by the user. This limits the throughput of the assay, increases the risk of errors, and contributes to intra- and inter-laboratory variability. Here, we describe the development of a device which automates high throughput sample processing for a comet assay. This device is based upon our patented, high throughput, vertical comet assay electrophoresis tank, and incorporates our novel, patented combination of assay fluidics, temperature control, and a sliding electrophoresis tank to facilitate sample loading and removal. Additionally, we demonstrated that the automated device performs at least as well as our "manual" high throughput system, but with all the advantages of a fully "walkaway" device, such as a decreased need for human involvement and a decreased assay run time. Our automated device represents a valuable, high throughput approach for reliably assessing DNA damage with the minimal operator involvement, particularly if combined with the automated analysis of comets.
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Affiliation(s)
| | - Yunhee Ji
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Mubarak A Mujawar
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA
| | - Mario Mendoza
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA
| | - Juan S Marquez
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA
| | - Apurva Sonawane
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA
| | - Pratikkumar Shah
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA
| | - Chris Ross
- Engineering Resources Group, Pembroke Pines, FL 33029, USA
| | - Shekhar Bhansali
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
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7
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Measuring DNA modifications with the comet assay: a compendium of protocols. Nat Protoc 2023; 18:929-989. [PMID: 36707722 DOI: 10.1038/s41596-022-00754-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/05/2022] [Indexed: 01/28/2023]
Abstract
The comet assay is a versatile method to detect nuclear DNA damage in individual eukaryotic cells, from yeast to human. The types of damage detected encompass DNA strand breaks and alkali-labile sites (e.g., apurinic/apyrimidinic sites), alkylated and oxidized nucleobases, DNA-DNA crosslinks, UV-induced cyclobutane pyrimidine dimers and some chemically induced DNA adducts. Depending on the specimen type, there are important modifications to the comet assay protocol to avoid the formation of additional DNA damage during the processing of samples and to ensure sufficient sensitivity to detect differences in damage levels between sample groups. Various applications of the comet assay have been validated by research groups in academia, industry and regulatory agencies, and its strengths are highlighted by the adoption of the comet assay as an in vivo test for genotoxicity in animal organs by the Organisation for Economic Co-operation and Development. The present document includes a series of consensus protocols that describe the application of the comet assay to a wide variety of cell types, species and types of DNA damage, thereby demonstrating its versatility.
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8
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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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Owiti NA, Kaushal S, Martin L, Sly J, Swartz CD, Fowler J, Corrigan JJ, Recio L, Engelward BP. Using the HepaCometChip Assay for Broad-Spectrum DNA Damage Analysis. Curr Protoc 2022; 2:e563. [PMID: 36165707 PMCID: PMC9522315 DOI: 10.1002/cpz1.563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Exposure to DNA damaging agents can lead to mutations that cause cancer. The liver is particularly vulnerable because it contains high levels of Cytochrome P450 enzymes that can convert xenobiotics into DNA reactive metabolites that form potentially carcinogenic bulky DNA adducts. As such, current requirements for preclinical testing include in vivo testing for DNA damage in the liver, which often requires many animals. Given that efforts are underway in many countries to reduce or eliminate the use of animals in research, there is a critical need for fast and robust in vitro tests to discern whether xenobiotics or potential pharmaceutical agents can damage the hepatocyte genome. One possible approach is to leverage the alkaline comet assay, which is used to assess genotoxicity based on the ability of damaged DNA to become free to migrate toward the anode during electrophoresis. The comet assay, however, has several limitations. The assay is (i) slow and (ii) vulnerable to experimental noise, (iii) it is difficult to detect bulky DNA adducts since they do not directly affect DNA migration, and (iv) cell types typically used do not have robust metabolic capacity. To address some of these concerns, we have developed the "HepaCometChip" (a.k.a. the HepaRG CometChip), wherein metabolically competent cells are incorporated into a higher throughput CometChip platform. Repair trapping is used to increase sensitivity for bulky lesions: undetectable bulky lesions are converted into repair intermediates (specifically, single-strand breaks) that can be detected with the assay. Here, we describe a protocol for performing the HepaCometChip assay that includes handling and dosing of HepaRG cells and performing the CometChip assay. With its higher throughput, ability to capture metabolic activation, and sensitivity to bulky lesions, the HepaCometChip offers a potential alternative to the use of animals for genotoxicity testing. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: HepaRG cell culturing and dosing Basic Protocol 2: CometChip assay.
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Affiliation(s)
- Norah A. Owiti
- Department of Biological EngineeringMassachusetts Institute of Technology (MIT)CambridgeMassachusetts
| | - Simran Kaushal
- Department of Biological EngineeringMassachusetts Institute of Technology (MIT)CambridgeMassachusetts
| | - Lincoln Martin
- Integrated Laboratory Systems, Inc. (ILS)Research Triangle ParkNorth Carolina
| | - Jamie Sly
- Integrated Laboratory Systems, Inc. (ILS)Research Triangle ParkNorth Carolina
| | - Carol D. Swartz
- Integrated Laboratory Systems, Inc. (ILS)Research Triangle ParkNorth Carolina
| | - Jasmine Fowler
- Integrated Laboratory Systems, Inc. (ILS)Research Triangle ParkNorth Carolina
| | - Joshua J. Corrigan
- Department of Biological EngineeringMassachusetts Institute of Technology (MIT)CambridgeMassachusetts
| | - Les Recio
- Integrated Laboratory Systems, Inc. (ILS)Research Triangle ParkNorth Carolina
| | - Bevin P. Engelward
- Department of Biological EngineeringMassachusetts Institute of Technology (MIT)CambridgeMassachusetts
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10
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Cheong A, Nagel ZD. Human Variation in DNA Repair, Immune Function, and Cancer Risk. Front Immunol 2022; 13:899574. [PMID: 35935942 PMCID: PMC9354717 DOI: 10.3389/fimmu.2022.899574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
DNA damage constantly threatens genome integrity, and DNA repair deficiency is associated with increased cancer risk. An intuitive and widely accepted explanation for this relationship is that unrepaired DNA damage leads to carcinogenesis due to the accumulation of mutations in somatic cells. But DNA repair also plays key roles in the function of immune cells, and immunodeficiency is an important risk factor for many cancers. Thus, it is possible that emerging links between inter-individual variation in DNA repair capacity and cancer risk are driven, at least in part, by variation in immune function, but this idea is underexplored. In this review we present an overview of the current understanding of the links between cancer risk and both inter-individual variation in DNA repair capacity and inter-individual variation in immune function. We discuss factors that play a role in both types of variability, including age, lifestyle, and environmental exposures. In conclusion, we propose a research paradigm that incorporates functional studies of both genome integrity and the immune system to predict cancer risk and lay the groundwork for personalized prevention.
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11
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Silva Fernandes A, Hollanda Véras J, Silva LS, Puga SC, Luiz Cardoso Bailão EF, de Oliveira MG, Cardoso CG, Carneiro CC, Costa Santos SD, Chen-Chen L. Pedunculagin isolated from Plinia cauliflora seeds exhibits genotoxic, antigenotoxic and cytotoxic effects in bacteria and human lymphocytes. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2022; 85:353-363. [PMID: 34875975 DOI: 10.1080/15287394.2021.2009947] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Pedunculagin (PD), an ellagitannin found in different plant species, possesses several pharmaceutical properties, including antitumor, antioxidant, gastroprotective, hepatoprotective, and anti-inflammatory properties. However, the effects of PD alone on DNA remain to be determined. The aim of this study was to investigate the potential cytotoxic, genotoxic, and antigenotoxic activities of PD isolated from Plinia cauliflora seeds using in silico and in vitro assays. To elucidate the biological activities of PD, in silico tools indicative of antioxidant, antineoplastic, and chemopreventive activities of PD were used. Subsequently, the mutagenic/antimutagenic effects of PD were later assessed using bacteria with the Ames test, and the cytotoxic, genotoxic, and antigenotoxic effects utilizing human lymphocytes as evidenced by trypan blue exclusion test and CometChip assay. In silico analysis indicated potential antioxidant, chemopreventive, free radical scavenger, and cytostatic activities of PD. In the Ames test, PD was found to be not mutagenic; however, this plant component protected DNA against damage-mediated by mutagens 4-nitroquinoline-1-oxide and sodium azide. Regarding human lymphocytes, PD alone was cytotoxic and genotoxic; however, it also reduced DNA damage induced by doxorubicin at co- and post-treatment. In conclusion, PD showed genotoxic, antigenotoxic and cytotoxic effects in human lymphocytes and antimutagenic effects in bacteria.
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Affiliation(s)
- Amanda Silva Fernandes
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Jefferson Hollanda Véras
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Luana Santos Silva
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Sara Cristina Puga
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | | | | | - Clever Gomes Cardoso
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Cristiene Costa Carneiro
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | | | - Lee Chen-Chen
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
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12
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Cicutto L, Roche J, Arurault L. Local Anodizing of a Newly Prepared Aluminum Micrometric Disk. NANOMATERIALS 2022; 12:nano12050845. [PMID: 35269332 PMCID: PMC8912718 DOI: 10.3390/nano12050845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 11/16/2022]
Abstract
A search through the literature reveals that the vast majority of studies about aluminum anodizing were conducted at the macroscale (i.e., from cm2 up to m2), while those focused on local anodizing (i.e., on surfaces of less than 1 mm2) are rare. The last ones either used insulating masks or were conducted in an electrolyte droplet. The present study describes on the one hand a new way to prepare aluminum microelectrodes of conventional disk-shaped geometry, and on the other hand the local anodizing of their respective aluminum micrometric top-disks. The influence of the anodizing voltage on anodic film characteristics (i.e., thickness, growth rate and expansion factor) was studied during local anodizing. Compared with the values reported for macroscopic anodizing, the pore diameter appears to be significantly low and the film growth rate can reach atypically high values, both specificities probably resulting from a very limited increase in the temperature on the aluminum surface during anodizing.
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13
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Véras JH, Cardoso CG, Puga SC, de Melo Bisneto AV, Roma RR, Santos Silva RR, Teixeira CS, Chen-Chen L. Lactose-binding lectin from Vatairea macrocarpa seeds induces in vivo angiogenesis via VEGF and TNF-ɑ expression and modulates in vitro doxorubicin-induced genotoxicity. Biochimie 2021; 194:55-66. [PMID: 34973362 DOI: 10.1016/j.biochi.2021.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/04/2021] [Accepted: 12/27/2021] [Indexed: 11/26/2022]
Abstract
Lactose-binding lectin from Vatairea macrocarpa seeds (VML) has attracted great attention due to its interesting biological activities, such as pro-inflammatory effects and macrophage activation. This study evaluated the cytotoxicity and genotoxicity/antigenotoxicity of VML in human lymphocytes using the CometChip assay, and angiogenic activity by the chick embryo chorioallantoic membrane (CAM) assay. In genotoxicity, lymphocytes were treated with different concentrations of VML (0.5, 2 and 8 μM). In antigenotoxicity, lymphocytes were treated with the same concentrations of VML concomitant doxorubicin (90 μM DXR). To evaluate angiogenesis, all CAM were treated with different concentrations of VML (0.5, 2 and 8 μM) alone or co-treated with lactose (0.1 M). Furthermore, the levels of vascular endothelial growth factor (VEGF) and tumor necrosis factor-alpha (TNF-α) in CAM were assessed by immunohistochemistry. The results showed that VML was cytotoxic to lymphocytes, genotoxic at the highest concentration (8 μM) and antigenotoxic at low concentrations (0.5, and 2 μM). Regarding the CAM assay and immunohistochemistry, VML was angiogenic and significantly increased VEGF and TNF-α levels. In contrast, co-treatment with lactose significantly reduced the angiogenic effect and VEGF levels. We propose that protein-carbohydrate interactions between VML and glycans in the cell membrane are probably the major events involved in these activities. It seems likely that VML elicits a pro-inflammatory response through VEGF and TNF-α expression, resulting in increased vascularization at the site of inflammation. Therefore, our results show novel information on the effects of VML on DNA, as well as provide data regarded the neovascularization process involving this lectin.
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Affiliation(s)
- Jefferson Hollanda Véras
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | - Clever Gomes Cardoso
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | - Sara Cristina Puga
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | - Abel Vieira de Melo Bisneto
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | - Renato Rodrigues Roma
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | | | - Lee Chen-Chen
- Laboratory of Radiobiology and Mutagenesis, Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil.
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14
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Ge J, Ngo LP, Kaushal S, Tay IJ, Thadhani E, Kay JE, Mazzucato P, Chow DN, Fessler JL, Weingeist DM, Sobol RW, Samson LD, Floyd SR, Engelward BP. CometChip enables parallel analysis of multiple DNA repair activities. DNA Repair (Amst) 2021; 106:103176. [PMID: 34365116 PMCID: PMC8439179 DOI: 10.1016/j.dnarep.2021.103176] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/09/2021] [Accepted: 07/08/2021] [Indexed: 12/28/2022]
Abstract
DNA damage can be cytotoxic and mutagenic, and it is directly linked to aging, cancer, and other diseases. To counteract the deleterious effects of DNA damage, cells have evolved highly conserved DNA repair pathways. Many commonly used DNA repair assays are relatively low throughput and are limited to analysis of one protein or one pathway. Here, we have explored the capacity of the CometChip platform for parallel analysis of multiple DNA repair activities. Taking advantage of the versatility of the traditional comet assay and leveraging micropatterning techniques, the CometChip platform offers increased throughput and sensitivity compared to the traditional comet assay. By exposing cells to DNA damaging agents that create substrates of Base Excision Repair, Nucleotide Excision Repair, and Non-Homologous End Joining, we show that the CometChip is an effective method for assessing repair deficiencies in all three pathways. With these applications of the CometChip platform, we expand the utility of the comet assay for precise, high-throughput, parallel analysis of multiple DNA repair activities.
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Affiliation(s)
- Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Simran Kaushal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, United States
| | - Ian J Tay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Elina Thadhani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jennifer E Kay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Patrizia Mazzucato
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Danielle N Chow
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Jessica L Fessler
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - David M Weingeist
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Robert W Sobol
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232, United States; University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, United States
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Scott R Floyd
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27514, United States
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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15
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Ngo LP, Kaushal S, Chaim IA, Mazzucato P, Ricciardi C, Samson LD, Nagel ZD, Engelward BP. CometChip analysis of human primary lymphocytes enables quantification of inter-individual differences in the kinetics of repair of oxidative DNA damage. Free Radic Biol Med 2021; 174:89-99. [PMID: 34324980 PMCID: PMC8477454 DOI: 10.1016/j.freeradbiomed.2021.07.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 01/15/2023]
Abstract
Although DNA repair is known to impact susceptibility to cancer and other diseases, relatively few population studies have been performed to evaluate DNA repair kinetics in people due to the difficulty of assessing DNA repair in a high-throughput manner. Here we use the CometChip, a high-throughput comet assay, to explore inter-individual variation in repair of oxidative damage to DNA, a known risk factor for aging, cancer and other diseases. DNA repair capacity after H2O2-induced DNA oxidation damage was quantified in peripheral blood mononuclear cells (PBMCs). For 10 individuals, blood was drawn at several times over the course of 4-6 weeks. In addition, blood was drawn once from each of 56 individuals. DNA damage levels were quantified prior to exposure to H2O2 and at 0, 15, 30, 60, and 120-min post exposure. We found that there is significant variability in DNA repair efficiency among individuals. When subdivided into quartiles by DNA repair efficiency, we found that the average t1/2 is 81 min for the slowest group and 24 min for the fastest group. This work shows that the CometChip can be used to uncover significant differences in repair kinetics among people, pointing to its utility in future epidemiological and clinical studies.
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Affiliation(s)
- Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Simran Kaushal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Patrizia Mazzucato
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Catherine Ricciardi
- MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Clinical Research Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Zachary D Nagel
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; MIT Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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16
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Xiong A, Kaushal S, Tay IJ, Engelward BP, Han J, Preiser PR. MalariaCometChip for high-throughput quantification of DNA damage in Plasmodium falciparum. STAR Protoc 2021; 2:100797. [PMID: 34527954 PMCID: PMC8430384 DOI: 10.1016/j.xpro.2021.100797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Comet assay is a standard approach for studying DNA damage in malaria, but high-throughput options are not available. The CometChip was previously developed using mammalian cells as a high-throughput version of the comet assay. It is based on the same principle as the comet assay but provides greater efficacy, automated data processing, and improved consistency between experiments. In this protocol, we present MalariaCometChip to quantitatively assess drug-induced DNA damage in Plasmodium falciparum. For complete details on the use and execution of this protocol, please refer to Xiong et al. (2020).
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Affiliation(s)
- Aoli Xiong
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore.,BioSystems and Micromechanics (BioSyM) interdisciplinary research group (IRG), Singapore-MIT Alliance for Research and Technology (SMART), Singapore 138602, Singapore.,Anti-Microbial Resistance (AMR) IRG, Singapore-MIT Alliance for Research and Technology (SMART), Singapore 138602, Singapore
| | - Simran Kaushal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Ian Junjie Tay
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jongyoon Han
- BioSystems and Micromechanics (BioSyM) interdisciplinary research group (IRG), Singapore-MIT Alliance for Research and Technology (SMART), Singapore 138602, Singapore.,Anti-Microbial Resistance (AMR) IRG, Singapore-MIT Alliance for Research and Technology (SMART), Singapore 138602, Singapore.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter R Preiser
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore.,Anti-Microbial Resistance (AMR) IRG, Singapore-MIT Alliance for Research and Technology (SMART), Singapore 138602, Singapore
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17
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Buick JK, Williams A, Meier MJ, Swartz CD, Recio L, Gagné R, Ferguson SS, Engelward BP, Yauk CL. A Modern Genotoxicity Testing Paradigm: Integration of the High-Throughput CometChip® and the TGx-DDI Transcriptomic Biomarker in Human HepaRG™ Cell Cultures. Front Public Health 2021; 9:694834. [PMID: 34485225 PMCID: PMC8416458 DOI: 10.3389/fpubh.2021.694834] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/14/2021] [Indexed: 12/14/2022] Open
Abstract
Higher-throughput, mode-of-action-based assays provide a valuable approach to expedite chemical evaluation for human health risk assessment. In this study, we combined the high-throughput alkaline DNA damage-sensing CometChip® assay with the TGx-DDI transcriptomic biomarker (DDI = DNA damage-inducing) using high-throughput TempO-Seq®, as an integrated genotoxicity testing approach. We used metabolically competent differentiated human HepaRG™ cell cultures to enable the identification of chemicals that require bioactivation to cause genotoxicity. We studied 12 chemicals (nine DDI, three non-DDI) in increasing concentrations to measure and classify chemicals based on their ability to damage DNA. The CometChip® classified 10/12 test chemicals correctly, missing a positive DDI call for aflatoxin B1 and propyl gallate. The poor detection of aflatoxin B1 adducts is consistent with the insensitivity of the standard alkaline comet assay to bulky lesions (a shortcoming that can be overcome by trapping repair intermediates). The TGx-DDI biomarker accurately classified 10/12 agents. TGx-DDI correctly identified aflatoxin B1 as DDI, demonstrating efficacy for combined used of these complementary methodologies. Zidovudine, a known DDI chemical, was misclassified as it inhibits transcription, which prevents measurable changes in gene expression. Eugenol, a non-DDI chemical known to render misleading positive results at high concentrations, was classified as DDI at the highest concentration tested. When combined, the CometChip® assay and the TGx-DDI biomarker were 100% accurate in identifying chemicals that induce DNA damage. Quantitative benchmark concentration (BMC) modeling was applied to evaluate chemical potencies for both assays. The BMCs for the CometChip® assay and the TGx-DDI biomarker were highly concordant (within 4-fold) and resulted in identical potency rankings. These results demonstrate that these two assays can be integrated for efficient identification and potency ranking of DNA damaging agents in HepaRG™ cell cultures.
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Affiliation(s)
- Julie K Buick
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Carol D Swartz
- Integrated Laboratory Systems Inc. (ILS), Research Triangle Park, Durham, NC, United States
| | - Leslie Recio
- Integrated Laboratory Systems Inc. (ILS), Research Triangle Park, Durham, NC, United States
| | - Rémi Gagné
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Stephen S Ferguson
- National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, United States
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.,Department of Biology, University of Ottawa, Ottawa, ON, Canada
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18
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K13-Mediated Reduced Susceptibility to Artemisinin in Plasmodium falciparum Is Overlaid on a Trait of Enhanced DNA Damage Repair. Cell Rep 2021; 32:107996. [PMID: 32755588 PMCID: PMC7408483 DOI: 10.1016/j.celrep.2020.107996] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 05/21/2020] [Accepted: 07/14/2020] [Indexed: 11/23/2022] Open
Abstract
Southeast Asia has been the hotbed for the development of drug-resistant malaria parasites, including those with resistance to artemisinin combination therapy. While mutations in the kelch propeller domain (K13 mutations) are associated with artemisinin resistance, a range of evidence suggests that other factors are critical for the establishment and subsequent transmission of resistance in the field. Here, we perform a quantitative analysis of DNA damage and repair in the malaria parasite Plasmodium falciparum and find a strong link between enhanced DNA damage repair and artemisinin resistance. This experimental observation is further supported when variations in seven known DNA repair genes are found in resistant parasites, with six of these mutations being associated with K13 mutations. Our data provide important insights on confounding factors that are important for the establishment and spread of artemisinin resistance and may explain why resistance has not yet arisen in Africa. High-throughput MalariaCometChip to measure DNA damage level in P. falciparum Subpopulation of Cambodian isolates possess enhanced DNA damage repair Important link between enhanced DNA damage repair and artemisinin resistance
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19
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Owiti NA, Nagel ZD, Engelward BP. Fluorescence Sheds Light on DNA Damage, DNA Repair, and Mutations. Trends Cancer 2020; 7:240-248. [PMID: 33203608 DOI: 10.1016/j.trecan.2020.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/09/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
DNA damage can lead to carcinogenic mutations and toxicity that promotes diseases. Therefore, having rapid assays to quantify DNA damage, DNA repair, mutations, and cytotoxicity is broadly relevant to health. For example, DNA damage assays can be used to screen chemicals for genotoxicity, and knowledge about DNA repair capacity has applications in precision prevention and in personalized medicine. Furthermore, knowledge of mutation frequency has predictive power for downstream cancer, and assays for cytotoxicity can predict deleterious health effects. Tests for all of these purposes have been rendered faster and more effective via adoption of fluorescent readouts. Here, we provide an overview of established and emerging cell-based assays that exploit fluorescence for studies of DNA damage and its consequences.
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Affiliation(s)
- Norah A Owiti
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zachary D Nagel
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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20
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Abstract
Environmental exposures have long been known to impact public health and safety. For example, exposures to airborne particulates, heavy metals in water, or certain industrial chemicals can contribute to aging and to risk of developing cancer and other diseases. Environmental factors can impact health in a variety of ways, but a key concern is DNA damage, which can lead to mutations that cause cancer. Cancer can take years to develop following chemical exposure; however, one way to predict carcinogenicity in a more practical time frame is by studying the chemical's ability to induce DNA damage. The comet assay (or single-cell gel electrophoresis assay) has been used successfully for genotoxicity testing. The comet assay allows for the detection of DNA strand breaks via analysis of DNA migration during electrophoresis. Previously, the Engelward laboratory, in collaboration with the Bhatia laboratory, developed the CometChip for measurements of DNA damage and repair. The CometChip is a high-throughput comet assay that improves user reproducibility and significantly shortens total assay time. Here, we describe how the high-throughput CometChip platform can be used to measure DNA damage in established cell lines, animal models, and human samples. We also discuss technical challenges associated with these studies and provide recommendations on how to achieve optimal results for researchers interested in adopting this assay.
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Affiliation(s)
- Christy Chao
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, Massachusetts, United States
| | - Bevin P. Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, Massachusetts, United States
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21
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Repurposing Drugs for Cancer Radiotherapy: Early Successes and Emerging Opportunities. ACTA ACUST UNITED AC 2020; 25:106-115. [PMID: 30896532 DOI: 10.1097/ppo.0000000000000369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It has long been recognized that combining radiotherapy with cytotoxic drugs such as cisplatin can improve efficacy. However, while concurrent chemoradiotherapy improves patient outcomes, it comes at costs of increased toxicity. A tremendous opportunity remains to investigate drug combinations in the clinical setting that might increase the benefits of radiation without additional toxicity. This chapter highlights opportunities to apply repurposing of drugs along with a mechanistic understanding of radiation effects on cancer and normal tissue to discover new therapy-modifying drugs and help rapidly translate them to the clinic. We survey candidate radiosensitizers that alter DNA repair, decrease hypoxia, block tumor survival signaling, modify tumor metabolism, block growth factor signaling, slow tumor invasiveness, impair angiogenesis, or stimulate antitumor immunity. Promising agents include widely used drugs such as aspirin, metformin, and statins, offering the potential to improve outcomes, decrease radiation doses, and lower costs. Many other candidate drugs are also discussed.
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22
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Tian S, Cyr A, Zeise K, Bryce SM, Hall N, Bemis JC, Dertinger SD. 3Rs-friendly approach to exogenous metabolic activation that supports high-throughput genetic toxicology testing. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:408-432. [PMID: 32039521 DOI: 10.1002/em.22361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 06/10/2023]
Abstract
MultiFlow® DNA Damage-p53, γH2AX, Phospho-Histone H3 is a miniaturized, flow cytometry-based assay that provides genotoxic mode of action information by distinguishing clastogens, aneugens, and nongenotoxicants. Work to date has focused on the p53-competent human cell line TK6. While mammalian cell genotoxicity assays typically supply exogenous metabolic activation in the form of concentrated rat liver S9, this is a less-than-ideal approach for several reasons, including 3Rs considerations. Here, we describe our experiences with low concentration S9 and saturating co-factors which were allowed to remain in contact with cells and test chemicals for 24 continuous hours. We exposed TK6 cells in 96-well plates to each of 15 reference chemicals over a range of concentrations, both in the presence and absence of 0.25% v/v phenobarbital/β-naphthoflavone-induced rat liver S9. After 4 and 24 hr of treatment cell aliquots were added to wells of a microtiter plate containing the working detergent/stain/antibody cocktail. After a brief incubation robotic sampling was employed for walk-away flow cytometric data acquisition. PROAST benchmark dose (BMD) modeling was used to characterize the resulting dose-response curves. For each of the 8 reference pro-genotoxicants studied, relative nuclei count, γH2AX, and/or p53 biomarker BMD values were order(s) of magnitude lower for 0.25% S9 conditions compared to 0% S9. Conversely, several of the direct-acting reference chemicals exhibited appreciably lower cytotoxicity and/or genotoxicity BMD values in the presence of S9 (eg, resorcinol). These results prove the efficacy of the low concentration S9 system, and indicate that an efficient and highly scalable multiplexed assay can effectively identify chemicals that require bioactivation to exert their genotoxic effects.
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Affiliation(s)
| | - Aiyana Cyr
- Litron Laboratories, Rochester, New York
| | | | | | - Nikki Hall
- Litron Laboratories, Rochester, New York
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23
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Chao C, Ngo Le P, Engelward BP. SpheroidChip: Patterned Agarose Microwell Compartments Harboring HepG2 Spheroids are Compatible with Genotoxicity Testing. ACS Biomater Sci Eng 2020; 6:2427-2439. [PMID: 33145399 DOI: 10.1021/acsbiomaterials.9b01951] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Three-dimensional tissue culture models are emerging as effective alternatives to animal testing. They are especially beneficial for liver toxicity studies, enabling hepatocytes to display improved levels of liver-specific functions. One common model is hepatocyte spheroids, which are spontaneously formed cell aggregates. Techniques for spheroid formation include the use of ultralow attachment plates and the hanging drop method, both of which are technically challenging and relatively low throughput. Here, we describe a simple-to-use platform that improves spheroid production and is compatible with genotoxicity testing by the comet assay. To achieve this, we created a chip containing a microwell array where dozens of spheroids are contained within a single well of a 96-well plate. The microwells are made from agarose, a nontoxic material suitable for cell growth and spheroid formation. HepG2 cells loaded into customizable microwells formed spheroids through agarose-assisted aggregation within one to two days. In addition, the agarose matrix allows the same platform to be used in DNA damage analysis. Specifically, the comet assay enables quantification of DNA breaks based on the increased migration of damaged DNA through agarose during electrophoresis. Here, we developed a modified comet assay and show that intact HepG2 spheroids cultured in microwells can be electrophoresed to reveal the extent of DNA damage following exposure to inflammatory chemicals (H2O2 and SIN-1). With this SpheroidChip analysis method, we detected a dose-dependent increase in DNA damage and observed rapid repair of H2O2-induced DNA damage. In summary, we utilized an agarose microarray to condense what had required an entire 96-well plate into a single well, enabling analysis techniques that were cumbersome or impossible under conditions of a single spheroid per well of a 96-well plate.
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Affiliation(s)
- Christy Chao
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - P Ngo Le
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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24
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Ngo LP, Owiti NA, Swartz C, Winters J, Su Y, Ge J, Xiong A, Han J, Recio L, Samson LD, Engelward B. Sensitive CometChip assay for screening potentially carcinogenic DNA adducts by trapping DNA repair intermediates. Nucleic Acids Res 2020; 48:e13. [PMID: 31822921 PMCID: PMC7026589 DOI: 10.1093/nar/gkz1077] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 10/08/2019] [Accepted: 11/19/2019] [Indexed: 12/27/2022] Open
Abstract
Genotoxicity testing is critical for predicting adverse effects of pharmaceutical, industrial, and environmental chemicals. The alkaline comet assay is an established method for detecting DNA strand breaks, however, the assay does not detect potentially carcinogenic bulky adducts that can arise when metabolic enzymes convert pro-carcinogens into a highly DNA reactive products. To overcome this, we use DNA synthesis inhibitors (hydroxyurea and 1-β-d-arabinofuranosyl cytosine) to trap single strand breaks that are formed during nucleotide excision repair, which primarily removes bulky lesions. In this way, comet-undetectable bulky lesions are converted into comet-detectable single strand breaks. Moreover, we use HepaRG™ cells to recapitulate in vivo metabolic capacity, and leverage the CometChip platform (a higher throughput more sensitive comet assay) to create the 'HepaCometChip', enabling the detection of bulky genotoxic lesions that are missed by current genotoxicity screens. The HepaCometChip thus provides a broadly effective approach for detection of bulky DNA adducts.
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Affiliation(s)
- Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Norah A Owiti
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carol Swartz
- Toxicology Program, Integrated Laboratory Systems, Inc., Research Triangle Park, NC 27560, USA
| | - John Winters
- Toxicology Program, Integrated Laboratory Systems, Inc., Research Triangle Park, NC 27560, USA
| | - Yang Su
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Aoli Xiong
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
| | - Jongyoon Han
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology, 138602 Singapore
- Department of Electrical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leslie Recio
- Toxicology Program, Integrated Laboratory Systems, Inc., Research Triangle Park, NC 27560, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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25
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Guo X, Seo JE, Li X, Mei N. Genetic toxicity assessment using liver cell models: past, present, and future. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2019; 23:27-50. [PMID: 31746269 DOI: 10.1080/10937404.2019.1692744] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Genotoxic compounds may be detoxified to non-genotoxic metabolites while many pro-carcinogens require metabolic activation to exert their genotoxicity in vivo. Standard genotoxicity assays were developed and utilized for risk assessment for over 40 years. Most of these assays are conducted in metabolically incompetent rodent or human cell lines. Deficient in normal metabolism and relying on exogenous metabolic activation systems, the current in vitro genotoxicity assays often have yielded high false positive rates, which trigger unnecessary and costly in vivo studies. Metabolically active cells such as hepatocytes have been recognized as a promising cell model in predicting genotoxicity of carcinogens in vivo. In recent years, significant advances in tissue culture and biological technologies provided new opportunities for using hepatocytes in genetic toxicology. This review encompasses published studies (both in vitro and in vivo) using hepatocytes for genotoxicity assessment. Findings from both standard and newly developed genotoxicity assays are summarized. Various liver cell models used for genotoxicity assessment are described, including the potential application of advanced liver cell models such as 3D spheroids, organoids, and engineered hepatocytes. An integrated strategy, that includes the use of human-based cells with enhanced biological relevance and throughput, and applying the quantitative analysis of data, may provide an approach for future genotoxicity risk assessment.
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Affiliation(s)
- Xiaoqing Guo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
| | - Ji-Eun Seo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
| | - Xilin Li
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
| | - Nan Mei
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
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26
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Wilson MR, Jiang Y, Villalta PW, Stornetta A, Boudreau PD, Carrá A, Brennan CA, Chun E, Ngo L, Samson LD, Engelward BP, Garrett WS, Balbo S, Balskus EP. The human gut bacterial genotoxin colibactin alkylates DNA. Science 2019; 363:363/6428/eaar7785. [PMID: 30765538 DOI: 10.1126/science.aar7785] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 10/16/2018] [Accepted: 12/21/2018] [Indexed: 12/13/2022]
Abstract
Certain Escherichia coli strains residing in the human gut produce colibactin, a small-molecule genotoxin implicated in colorectal cancer pathogenesis. However, colibactin's chemical structure and the molecular mechanism underlying its genotoxic effects have remained unknown for more than a decade. Here we combine an untargeted DNA adductomics approach with chemical synthesis to identify and characterize a covalent DNA modification from human cell lines treated with colibactin-producing E. coli Our data establish that colibactin alkylates DNA with an unusual electrophilic cyclopropane. We show that this metabolite is formed in mice colonized by colibactin-producing E. coli and is likely derived from an initially formed, unstable colibactin-DNA adduct. Our findings reveal a potential biomarker for colibactin exposure and provide mechanistic insights into how a gut microbe may contribute to colorectal carcinogenesis.
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Affiliation(s)
- Matthew R Wilson
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Yindi Jiang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Peter W Villalta
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA
| | - Alessia Stornetta
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA
| | - Paul D Boudreau
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Andrea Carrá
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA
| | - Caitlin A Brennan
- Department of Immunology and Infectious Diseases and Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Eunyoung Chun
- Department of Immunology and Infectious Diseases and Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lizzie Ngo
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | | | - Wendy S Garrett
- Department of Immunology and Infectious Diseases and Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Department of Medical Oncology, Dana-Farber Institute, Boston, MA 02115, USA
| | - Silvia Balbo
- Masonic Cancer Center, University of Minnesota, 2231 Sixth Street Southeast, Minneapolis, MN 55455, USA.
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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27
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Burja B, Kuret T, Janko T, Topalović D, Živković L, Mrak-Poljšak K, Spremo-Potparević B, Žigon P, Distler O, Čučnik S, Sodin-Semrl S, Lakota K, Frank-Bertoncelj M. Olive Leaf Extract Attenuates Inflammatory Activation and DNA Damage in Human Arterial Endothelial Cells. Front Cardiovasc Med 2019; 6:56. [PMID: 31157238 PMCID: PMC6531989 DOI: 10.3389/fcvm.2019.00056] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/16/2019] [Indexed: 12/27/2022] Open
Abstract
Olive leaf extract (OLE) is used in traditional medicine as a food supplement and as an over-the-counter drug for a variety of its effects, including anti-inflammatory and anti-atherosclerotic ones. Mechanisms through which OLE could modulate these pathways in human vasculature remain largely unknown. Serum amyloid A (SAA) plays a causal role in atherosclerosis and cardiovascular diseases and induces pro-inflammatory and pro-adhesive responses in human coronary artery endothelial cells (HCAEC). Within this study we explored whether OLE can attenuate SAA-driven responses in HCAEC. HCAEC were treated with SAA (1,000 nM) and/or OLE (0.5 and 1 mg/ml). The expression of adhesion molecules VCAM-1 and E-selectin, matrix metalloproteinases (MMP2 and MMP9) and microRNA 146a, let-7e, and let-7g (involved in the regulation of inflammation) was determined by qPCR. The amount of secreted IL-6, IL-8, MIF, and GRO-α in cell culture supernatants was quantified by ELISA. Phosphorylation of NF-κB was assessed by Western blot and DNA damage was measured using the COMET assay. OLE decreased significantly released protein levels of IL-6 and IL-8, as well as mRNA expression of E-selectin in SAA-stimulated HCAEC and reduced MMP2 levels in unstimulated cells. Phosphorylation of NF-κB (p65) was upregulated in the presence of SAA, with OLE significantly attenuating this SAA-induced effect. OLE stabilized SAA-induced upregulation of microRNA-146a and let-7e in HCAEC, suggesting that OLE could fine-tune the SAA-driven activity of NF-κB by changing the microRNA networks in HCAEC. SAA induced DNA damage and worsened the oxidative DNA damage in HCAEC, whereas OLE protected HCAEC from SAA- and H2O2-driven DNA damage. OLE significantly attenuated certain pro-inflammatory and pro-adhesive responses and decreased DNA damage in HCAEC upon stimulation with SAA. The reversal of SAA-driven endothelial activation by OLE might contribute to its anti-inflammatory and anti-atherogenic effects in HCAEC.
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Affiliation(s)
- Blaž Burja
- Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia.,Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Tadeja Kuret
- Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia.,Chair of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Tea Janko
- Faculty of Mathematics, Natural Science and Information Technology, University of Primorska, Koper, Slovenia
| | - Dijana Topalović
- Department of Pathobiology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Lada Živković
- Department of Pathobiology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | | | | | - Polona Žigon
- Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia
| | - Oliver Distler
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Saša Čučnik
- Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia.,Chair of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Snezna Sodin-Semrl
- Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia.,Faculty of Mathematics, Natural Science and Information Technology, University of Primorska, Koper, Slovenia
| | - Katja Lakota
- Department of Rheumatology, University Medical Centre, Ljubljana, Slovenia.,Faculty of Mathematics, Natural Science and Information Technology, University of Primorska, Koper, Slovenia
| | - Mojca Frank-Bertoncelj
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zurich, Zurich, Switzerland
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28
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Seo JE, Tryndyak V, Wu Q, Dreval K, Pogribny I, Bryant M, Zhou T, Robison TW, Mei N, Guo X. Quantitative comparison of in vitro genotoxicity between metabolically competent HepaRG cells and HepG2 cells using the high-throughput high-content CometChip assay. Arch Toxicol 2019; 93:1433-1448. [PMID: 30788552 DOI: 10.1007/s00204-019-02406-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/31/2019] [Indexed: 12/18/2022]
Abstract
In vitro genotoxicity testing that employs metabolically active human cells may be better suited for evaluating human in vivo genotoxicity than current bacterial or non-metabolically active mammalian cell systems. In the current study, 28 compounds, known to have different genotoxicity and carcinogenicity modes of action (MoAs), were evaluated over a wide range of concentrations for the ability to induce DNA damage in human HepG2 and HepaRG cells. DNA damage dose-responses in both cell lines were quantified using a combination of high-throughput high-content (HTHC) CometChip technology and benchmark dose (BMD) quantitative approaches. Assays of metabolic activity indicated that differentiated HepaRG cells had much higher levels of cytochromes P450 activity than did HepG2 cells. DNA damage was observed for four and two out of five indirect-acting genotoxic carcinogens in HepaRG and HepG2 cells, respectively. Four out of seven direct-acting carcinogens were positive in both cell lines, with two of the three negatives being genotoxic mainly through aneugenicity. The four chemicals positive in both cell lines generated HTHC Comet data in HepaRG and HepG2 cells with comparable BMD values. All the non-genotoxic compounds, including six non-genotoxic carcinogens, were negative in HepaRG cells; five genotoxic non-carcinogens also were negative. Our results indicate that the HTHC CometChip assay detects a greater proportion of genotoxic carcinogens requiring metabolic activation (i.e., indirect carcinogens) when conducted with HepaRG cells than with HepG2 cells. In addition, BMD genotoxicity potency estimate is useful for quantitatively evaluating CometChip assay data in a scientifically rigorous manner.
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Affiliation(s)
- Ji-Eun Seo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, 72079, USA
| | - Volodymyr Tryndyak
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR, 72079, USA
| | - Qiangen Wu
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR, 72079, USA
| | - Kostiantyn Dreval
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR, 72079, USA.,Department of Internal Medicine, Division of Molecular Medicine, Program in Cancer Genetics, Epigenetics and Genomics, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87131, USA
| | - Igor Pogribny
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR, 72079, USA
| | - Matthew Bryant
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR, 72079, USA
| | - Tong Zhou
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Rockville, MD, 20855, USA
| | - Timothy W Robison
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Nan Mei
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, 72079, USA
| | - Xiaoqing Guo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, 72079, USA.
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29
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Ngo LP, Chan TK, Ge J, Samson LD, Engelward BP. Microcolony Size Distribution Assay Enables High-Throughput Cell Survival Quantitation. Cell Rep 2019; 26:1668-1678.e4. [PMID: 30726746 PMCID: PMC6431241 DOI: 10.1016/j.celrep.2019.01.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/02/2018] [Accepted: 01/14/2019] [Indexed: 01/14/2023] Open
Abstract
Cell survival is a critical and ubiquitous endpoint in biology. The broadly accepted colony formation assay (CFA) directly measures a cell's ability to divide; however, it takes weeks to perform and is incompatible with high-throughput screening (HTS) technologies. Here, we describe the MicroColonyChip, which exploits microwell array technology to create an array of colonies. Unlike the CFA, where visible colonies are counted by eye, using fluorescence microscopy, microcolonies can be analyzed in days rather than weeks. Using automated analysis of microcolony size distributions, the MicroColonyChip achieves comparable sensitivity to the CFA (and greater sensitivity than the 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide [XTT] assay). Compared to CellTiter-Glo, the MicroColonyChip is as sensitive and also robust to artifacts caused by differences in initial cell seeding density. We demonstrate efficacy via studies of radiosensitivity and chemosensitivity and show that the approach is amenable to multiplexing. We conclude that the MicroColonyChip is a rapid and automated alternative for cell survival quantitation.
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Affiliation(s)
- Le P Ngo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tze Khee Chan
- Singapore-MIT Alliance for Research and Technology, Infectious Diseases IRG, Singapore 117600, Singapore
| | - Jing Ge
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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30
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Parrish MC, Chaim IA, Nagel ZD, Tannenbaum SR, Samson LD, Engelward BP. Nitric oxide induced S-nitrosation causes base excision repair imbalance. DNA Repair (Amst) 2018; 68:25-33. [PMID: 29929044 DOI: 10.1016/j.dnarep.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 03/20/2018] [Accepted: 04/30/2018] [Indexed: 02/05/2023]
Abstract
It is well established that inflammation leads to the creation of potent DNA damaging chemicals, including reactive oxygen and nitrogen species. Nitric oxide can react with glutathione to create S-nitrosoglutathione (GSNO), which can in turn lead to S-nitrosated proteins. Of particular interest is the impact of GSNO on the function of DNA repair enzymes. The base excision repair (BER) pathway can be initiated by the alkyl-adenine DNA glycosylase (AAG), a monofunctional glycosylase that removes methylated bases. After base removal, an abasic site is formed, which then gets cleaved by AP endonuclease and processed by downstream BER enzymes. Interestingly, using the Fluorescence-based Multiplexed Host Cell Reactivation Assay (FM-HCR), we show that GSNO actually enhances AAG activity, which is consistent with the literature. This raised the possibility that there might be imbalanced BER when cells are challenged with a methylating agent. To further explore this possibility, we confirmed that GSNO can cause AP endonuclease to translocate from the nucleus to the cytoplasm, which might further exacerbate imbalanced BER by increasing the levels of AP sites. Analysis of abasic sites indeed shows GSNO induces an increase in the level of AP sites. Furthermore, analysis of DNA damage using the CometChip (a higher throughput version of the comet assay) shows an increase in the levels of BER intermediates. Finally, we found that GSNO exposure is associated with an increase in methylation-induced cytotoxicity. Taken together, these studies support a model wherein GSNO increases BER initiation while processing of AP sites is decreased, leading to a toxic increase in BER intermediates. This model is also supported by additional studies performed in our laboratory showing that inflammation in vivo leads to increased large-scale sequence rearrangements. Taken together, this work provides new evidence that inflammatory chemicals can drive cytotoxicity and mutagenesis via BER imbalance.
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Affiliation(s)
- Marcus C Parrish
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Zachary D Nagel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Steven R Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bevin P Engelward
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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31
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Bryce SM, Bernacki DT, Smith-Roe SL, Witt KL, Bemis JC, Dertinger SD. Investigating the Generalizability of the MultiFlow ® DNA Damage Assay and Several Companion Machine Learning Models With a Set of 103 Diverse Test Chemicals. Toxicol Sci 2018; 162:146-166. [PMID: 29106658 PMCID: PMC6059150 DOI: 10.1093/toxsci/kfx235] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The in vitro MultiFlow DNA Damage assay multiplexes p53, γH2AX, phospho-histone H3, and polyploidization biomarkers into 1 flow cytometric analysis (Bryce, S. M., Bernacki, D. T., Bemis, J. C., and Dertinger, S. D. (2016). Genotoxic mode of action predictions from a multiplexed flow cytometric assay and a machine learning approach. Environ. Mol. Mutagen. 57, 171-189). The work reported herein evaluated the generalizability of the method, as well as several data analytics strategies, to a range of chemical classes not studied previously. TK6 cells were exposed to each of 103 diverse chemicals, 86 of which were supplied by the National Toxicology Program (NTP) and selected based upon responses in genetic damage assays conducted under the Tox21 program. Exposures occurred for 24 h over a range of concentrations, and cell aliquots were removed at 4 and 24 h for analysis. Multiplexed response data were evaluated using 3 machine learning models designed to predict genotoxic mode of action based on data from a training set of 85 previously studied chemicals. Of 54 chemicals with sufficient information to make an a priori call on genotoxic potential, the prediction models' accuracies were 79.6% (random forest), 88.9% (logistic regression), and 90.7% (artificial neural network). A majority vote ensemble of the 3 models provided 92.6% accuracy. Forty-nine NTP chemicals were not adequately tested (maximum concentration did not approach assay's cytotoxicity limit) and/or had insufficient conventional genotoxicity data to allow their genotoxic potential to be defined. For these chemicals MultiFlow data will be useful in future research and hypothesis testing. Collectively, the results suggest the MultiFlow assay and associated data analysis strategies are broadly generalizable, demonstrating high predictability when applied to new chemicals and classes of compounds.
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Affiliation(s)
| | | | - Stephanie L Smith-Roe
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Kristine L Witt
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
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32
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Sykora P, Witt KL, Revanna P, Smith-Roe SL, Dismukes J, Lloyd DG, Engelward BP, Sobol RW. Next generation high throughput DNA damage detection platform for genotoxic compound screening. Sci Rep 2018; 8:2771. [PMID: 29426857 PMCID: PMC5807538 DOI: 10.1038/s41598-018-20995-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/29/2018] [Indexed: 11/23/2022] Open
Abstract
Methods for quantifying DNA damage, as well as repair of that damage, in a high-throughput format are lacking. Single cell gel electrophoresis (SCGE; comet assay) is a widely-used method due to its technical simplicity and sensitivity, but the standard comet assay has limitations in reproducibility and throughput. We have advanced the SCGE assay by creating a 96-well hardware platform coupled with dedicated data processing software (CometChip Platform). Based on the original cometchip approach, the CometChip Platform increases capacity ~200 times over the traditional slide-based SCGE protocol, with excellent reproducibility. We tested this platform in several applications, demonstrating a broad range of potential uses including the routine identification of DNA damaging agents, using a 74-compound library provided by the National Toxicology Program. Additionally, we demonstrated how this tool can be used to evaluate human populations by analysis of peripheral blood mononuclear cells to characterize susceptibility to genotoxic exposures, with implications for epidemiological studies. In summary, we demonstrated a high level of reproducibility and quantitative capacity for the CometChip Platform, making it suitable for high-throughput screening to identify and characterize genotoxic agents in large compound libraries, as well as for human epidemiological studies of genetic diversity relating to DNA damage and repair.
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Affiliation(s)
- Peter Sykora
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA
| | - Kristine L Witt
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Pooja Revanna
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA
| | - Stephanie L Smith-Roe
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Jonathan Dismukes
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA
| | | | - Bevin P Engelward
- Department of Biological Engineering, MIT, Cambridge, MA, 02139, USA
| | - Robert W Sobol
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL, 36604, USA.
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33
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Townsend TA, Parrish MC, Engelward BP, Manjanatha MG. The development and validation of EpiComet-Chip, a modified high-throughput comet assay for the assessment of DNA methylation status. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:508-521. [PMID: 28755435 PMCID: PMC5839338 DOI: 10.1002/em.22101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/25/2017] [Accepted: 04/28/2017] [Indexed: 05/10/2023]
Abstract
DNA damage and alterations in global DNA methylation status are associated with multiple human diseases and are frequently correlated with clinically relevant information. Therefore, assessing DNA damage and epigenetic modifications, including DNA methylation, is critical for predicting human exposure risk of pharmacological and biological agents. We previously developed a higher-throughput platform for the single cell gel electrophoresis (comet) assay, CometChip, to assess DNA damage and genotoxic potential. Here, we utilized the methylation-dependent endonuclease, McrBC, to develop a modified alkaline comet assay, "EpiComet," which allows single platform evaluation of genotoxicity and global DNA methylation [5-methylcytosine (5-mC)] status of single-cell populations under user-defined conditions. Further, we leveraged the CometChip platform to create an EpiComet-Chip system capable of performing quantification across simultaneous exposure protocols to enable unprecedented speed and simplicity. This system detected global methylation alterations in response to exposures which included chemotherapeutic and environmental agents. Using EpiComet-Chip on 63 matched samples, we correctly identified single-sample hypermethylation (≥1.5-fold) at 87% (20/23), hypomethylation (≥1.25-fold) at 100% (9/9), with a 4% (2/54) false-negative rate (FNR), and 10% (4/40) false-positive rate (FPR). Using a more stringent threshold to define hypermethylation (≥1.75-fold) allowed us to correctly identify 94% of hypermethylation (17/18), but increased our FPR to 16% (7/45). The successful application of this novel technology will aid hazard identification and risk characterization of FDA-regulated products, while providing utility for investigating epigenetic modes of action of agents in target organs, as the assay is amenable to cultured cells or nucleated cells from any tissue. Environ. Mol. Mutagen. 58:508-521, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Todd A. Townsend
- United States Food & Drug Administration, National Center for Toxicological Research, Division of Genetic and Molecular Toxicology, Jefferson, AR, USA
- Correspondence to: Todd Townsend, United States Food & Drug Administration, National Center for Toxicological Research, Division of Genetic and Molecular Toxicology, 3900 NCTR Road, Jefferson, AR, USA, ; Phone: +1 (870) 543-7155
| | - Marcus C. Parrish
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, MA, USA
| | - Bevin P. Engelward
- Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, MA, USA
| | - Mugimane G. Manjanatha
- United States Food & Drug Administration, National Center for Toxicological Research, Division of Genetic and Molecular Toxicology, Jefferson, AR, USA
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Chan TK, Tan WSD, Peh HY, Wong WSF. Aeroallergens Induce Reactive Oxygen Species Production and DNA Damage and Dampen Antioxidant Responses in Bronchial Epithelial Cells. THE JOURNAL OF IMMUNOLOGY 2017; 199:39-47. [PMID: 28526682 DOI: 10.4049/jimmunol.1600657] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 04/21/2017] [Indexed: 12/31/2022]
Abstract
Exposure to environmental allergens is a major risk factor for asthma development. Allergens possess proteolytic activity that is capable of disrupting the airway epithelium. Although there is increasing evidence pointing to asthma as an epithelial disease, the underlying mechanism that drives asthma has not been fully elucidated. In this study, we investigated the direct DNA damage potential of aeroallergens on human bronchial epithelial cells and elucidated the mechanisms mediating the damage. Human bronchial epithelial cells, BEAS-2B, directly exposed to house dust mites (HDM) resulted in enhanced DNA damage, as measured by the CometChip and the staining of DNA double-strand break marker, γH2AX. HDM stimulated cellular reactive oxygen species production, increased mitochondrial oxidative stress, and promoted nitrosative stress. Notably, expression of nuclear factor erythroid 2-related factor 2-dependent antioxidant genes was reduced immediately after HDM exposure, suggesting that HDM altered antioxidant responses. HDM exposure also reduced cell proliferation and induced cell death. Importantly, HDM-induced DNA damage can be prevented by the antioxidants glutathione and catalase, suggesting that HDM-induced reactive oxygen and nitrogen species can be neutralized by antioxidants. Mechanistic studies revealed that HDM-induced cellular injury is NADPH oxidase (NOX)-dependent, and apocynin, a NOX inhibitor, protected cells from double-strand breaks induced by HDM. Our results show that direct exposure of bronchial epithelial cells to HDM leads to the production of reactive oxygen and nitrogen species that damage DNA and induce cytotoxicity. Antioxidants and NOX inhibitors can prevent HDM-induced DNA damage, revealing a novel role for antioxidants and NOX inhibitors in mitigating allergic airway disease.
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Affiliation(s)
- Tze Khee Chan
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University Health System, Singapore 117600, Singapore.,Immunology Program, Life Science Institute, National University of Singapore, Singapore 117456, Singapore.,Infectious Diseases Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore; and
| | - W S Daniel Tan
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University Health System, Singapore 117600, Singapore.,Immunology Program, Life Science Institute, National University of Singapore, Singapore 117456, Singapore
| | - Hong Yong Peh
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University Health System, Singapore 117600, Singapore.,Immunology Program, Life Science Institute, National University of Singapore, Singapore 117456, Singapore
| | - W S Fred Wong
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University Health System, Singapore 117600, Singapore; .,Immunology Program, Life Science Institute, National University of Singapore, Singapore 117456, Singapore.,Molecular Mechanisms of Inflammatory Diseases Interdisciplinary Research Group, Singapore-HUJ Alliance for Research and Enterprise, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore
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Hall J, Jeggo PA, West C, Gomolka M, Quintens R, Badie C, Laurent O, Aerts A, Anastasov N, Azimzadeh O, Azizova T, Baatout S, Baselet B, Benotmane MA, Blanchardon E, Guéguen Y, Haghdoost S, Harms-Ringhdahl M, Hess J, Kreuzer M, Laurier D, Macaeva E, Manning G, Pernot E, Ravanat JL, Sabatier L, Tack K, Tapio S, Zitzelsberger H, Cardis E. Ionizing radiation biomarkers in epidemiological studies - An update. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2017; 771:59-84. [PMID: 28342453 DOI: 10.1016/j.mrrev.2017.01.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/09/2017] [Indexed: 01/13/2023]
Abstract
Recent epidemiology studies highlighted the detrimental health effects of exposure to low dose and low dose rate ionizing radiation (IR): nuclear industry workers studies have shown increased leukaemia and solid tumour risks following cumulative doses of <100mSv and dose rates of <10mGy per year; paediatric patients studies have reported increased leukaemia and brain tumours risks after doses of 30-60mGy from computed tomography scans. Questions arise, however, about the impact of even lower doses and dose rates where classical epidemiological studies have limited power but where subsets within the large cohorts are expected to have an increased risk. Further progress requires integration of biomarkers or bioassays of individual exposure, effects and susceptibility to IR. The European DoReMi (Low Dose Research towards Multidisciplinary Integration) consortium previously reviewed biomarkers for potential use in IR epidemiological studies. Given the increased mechanistic understanding of responses to low dose radiation the current review provides an update covering technical advances and recent studies. A key issue identified is deciding which biomarkers to progress. A roadmap is provided for biomarker development from discovery to implementation and used to summarise the current status of proposed biomarkers for epidemiological studies. Most potential biomarkers remain at the discovery stage and for some there is sufficient evidence that further development is not warranted. One biomarker identified in the final stages of development and as a priority for further research is radiation specific mRNA transcript profiles.
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Affiliation(s)
- Janet Hall
- Centre de Recherche en Cancérologie de Lyon, INSERM 1052, CNRS 5286, Univ Lyon, Université Claude Bernard, Lyon 1, Lyon, F-69424, France.
| | - Penny A Jeggo
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, United Kingdom
| | - Catharine West
- Translational Radiobiology Group, Institute of Cancer Sciences, The University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, M20 4BX, United Kingdom
| | - Maria Gomolka
- Federal Office for Radiation Protection, Department of Radiation Protection and Health, D-85764 Neuherberg, Germany
| | - Roel Quintens
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium
| | - Christophe Badie
- Cancer Mechanisms and Biomarkers group, Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, United Kingdom
| | - Olivier Laurent
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - An Aerts
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium
| | - Nataša Anastasov
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Omid Azimzadeh
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Tamara Azizova
- Southern Urals Biophysics Institute, Clinical Department, Ozyorsk, Russia
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium; Cell Systems and Imaging Research Group, Department of Molecular Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - Bjorn Baselet
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium; Pole of Pharmacology, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, B-1200 Brussels, Belgium
| | - Mohammed A Benotmane
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium
| | - Eric Blanchardon
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Yann Guéguen
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Siamak Haghdoost
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Mats Harms-Ringhdahl
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Julia Hess
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Michaela Kreuzer
- Federal Office for Radiation Protection, Department of Radiation Protection and Health, D-85764 Neuherberg, Germany
| | - Dominique Laurier
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Ellina Macaeva
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium; Cell Systems and Imaging Research Group, Department of Molecular Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - Grainne Manning
- Cancer Mechanisms and Biomarkers group, Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, United Kingdom
| | - Eileen Pernot
- INSERM U897, Université de Bordeaux, F-33076 Bordeaux cedex, France
| | - Jean-Luc Ravanat
- Laboratoire des Lésions des Acides Nucléiques, Univ. Grenoble Alpes, INAC-SCIB, F-38000 Grenoble, France; Commissariat à l'Énergie Atomique, INAC-SyMMES, F-38000 Grenoble, France
| | - Laure Sabatier
- Commissariat à l'Énergie Atomique, BP6, F-92265 Fontenay-aux-Roses, France
| | - Karine Tack
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Soile Tapio
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Horst Zitzelsberger
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Elisabeth Cardis
- Barcelona Institute of Global Health (ISGlobal), Centre for Research in Environmental Epidemiology, Radiation Programme, Barcelona Biomedical Research Park, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF) (MTD formerly), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
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36
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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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37
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Li L, Wang W, Ding M, Luo G, Liang Q. Single-Cell-Arrayed Agarose Chip for in Situ Analysis of Cytotoxicity and Genotoxicity of DNA Cross-Linking Agents. Anal Chem 2016; 88:6734-42. [PMID: 27269449 DOI: 10.1021/acs.analchem.6b01008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Development of approach or device to allow continuous multiple measurements, such as integrating cytotoxic and genotoxic analysis, is quite appealing for study of the drug's activity and mechanism of action or resistance. In this study, a single-cell-arrayed agarose chip system was developed to combine cell cultivation with subsequent in situ analysis of cytotoxicity and genotoxicity of the chemotherapeutic agent. The modified alkaline comet assay coupled with the Live/Dead assay was used to monitor the interstrand cross-links (ICLs) formation and the cytotoxic effects in different glioma cell lines. In addition, the ICL-induced double strand breaks (DSBs) was measured on the chip to reflect the level of ICLs indirectly. Compared with the traditional methods, the microarray agarose device offers higher throughput, reproducibility, and robustness, exhibiting good potential for high-content drug screening.
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Affiliation(s)
- Lili Li
- Beijing Key Lab of Microanalytical Methods & Instrumentation, Key Lab of Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, P. R. China
| | - Weixing Wang
- Beijing Key Lab of Microanalytical Methods & Instrumentation, Key Lab of Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, P. R. China
| | - Mingyu Ding
- Beijing Key Lab of Microanalytical Methods & Instrumentation, Key Lab of Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, P. R. China
| | - Guoan Luo
- Beijing Key Lab of Microanalytical Methods & Instrumentation, Key Lab of Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, P. R. China
| | - Qionglin Liang
- Beijing Key Lab of Microanalytical Methods & Instrumentation, Key Lab of Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University , Beijing 100084, P. R. China
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38
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Albert O, Reintsch WE, Chan P, Robaire B. HT-COMET: a novel automated approach for high throughput assessment of human sperm chromatin quality. Hum Reprod 2016; 31:938-46. [PMID: 26975326 DOI: 10.1093/humrep/dew030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/04/2016] [Indexed: 11/12/2022] Open
Abstract
STUDY QUESTION Can we make the comet assay (single-cell gel electrophoresis) for human sperm a more accurate and informative high throughput assay? SUMMARY ANSWER We developed a standardized automated high throughput comet (HT-COMET) assay for human sperm that improves its accuracy and efficiency, and could be of prognostic value to patients in the fertility clinic. WHAT IS KNOWN ALREADY The comet assay involves the collection of data on sperm DNA damage at the level of the single cell, allowing the use of samples from severe oligozoospermic patients. However, this makes comet scoring a low throughput procedure that renders large cohort analyses tedious. Furthermore, the comet assay comes with an inherent vulnerability to variability. Our objective is to develop an automated high throughput comet assay for human sperm that will increase both its accuracy and efficiency. STUDY DESIGN, SIZE, DURATION The study comprised two distinct components: a HT-COMET technical optimization section based on control versus DNAse treatment analyses ( ITALIC! n = 3-5), and a cross-sectional study on 123 men presenting to a reproductive center with sperm concentrations categorized as severe oligozoospermia, oligozoospermia or normozoospermia. PARTICIPANTS/MATERIALS, SETTING, METHODS Sperm chromatin quality was measured using the comet assay: on classic 2-well slides for software comparison; on 96-well slides for HT-COMET optimization; after exposure to various concentrations of a damage-inducing agent, DNAse, using HT-COMET; on 123 subjects with different sperm concentrations using HT-COMET. Data from the 123 subjects were correlated to classic semen quality parameters and plotted as single-cell data in individual DNA damage profiles. MAIN RESULTS AND THE ROLE OF CHANCE We have developed a standard automated HT-COMET procedure for human sperm. It includes automated scoring of comets by a fully integrated high content screening setup that compares well with the most commonly used semi-manual analysis software. Using this method, a cross-sectional study on 123 men showed no significant correlation between sperm concentration and sperm DNA damage, confirming the existence of hidden chromatin damage in men with apparently normal semen characteristics, and a significant correlation between percentage DNA in the tail and percentage of progressively motile spermatozoa. Finally, the use of DNA damage profiles helped to distinguish subjects between and within sperm concentration categories, and allowed a determination of the proportion of highly damaged cells. LIMITATIONS, REASONS FOR CAUTION The main limitations of the HT-COMET are the high, yet indispensable, investment in an automated liquid handling system and heating block to ensure accuracy, and the availability of an automated plate reading microscope and analysis software. WIDER IMPLICATIONS OF THE FINDINGS This standardized HT-COMET assay offers many advantages, including higher accuracy and evenness due to automation of sensitive steps, a 14.4-fold increase in sample analysis capacity, and an imaging and scoring time of 1 min/well. Overall, HT-COMET offers a decrease in total experimental time of more than 90%. Hence, this assay constitutes a more efficient option to assess sperm chromatin quality, paves the way to using this assay to screen large cohorts, and holds prognostic value for infertile patients. STUDY FUNDING/COMPETING INTERESTS Funded by the CIHR Institute of Human Development, Child and Youth Health (IHDCYH; RHF 100625). O.A. is a fellow supported by the Fonds de la Recherche du Québec - Santé (FRQS) and the CIHR Training Program in Reproduction, Early Development, and the Impact on Health (REDIH). B.R. is a James McGill Professor. The authors declare no conflicts of interest.
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Affiliation(s)
- Océane Albert
- Department of Pharmacology &Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Wolfgang E Reintsch
- Department of Pharmacology & Therapeutics, McGill University, Green Chemistry CFI Platform, Montreal, QC, H3G 1Y6, Canada
| | - Peter Chan
- Department of Urology, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Bernard Robaire
- Department of Pharmacology &Therapeutics, McGill University, Montreal, QC, H3G 1Y6, Canada Department of Obstetrics & Gynecology, McGill University, Montreal, QC, H4A 3J1, Canada
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