1
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Huchthausen J, Braasch J, Escher BI, König M, Henneberger L. Effects of Chemicals in Reporter Gene Bioassays with Different Metabolic Activities Compared to Baseline Toxicity. Chem Res Toxicol 2024; 37:744-756. [PMID: 38652132 PMCID: PMC11110108 DOI: 10.1021/acs.chemrestox.4c00017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
High-throughput cell-based bioassays are used for chemical screening and risk assessment. Chemical transformation processes caused by abiotic degradation or metabolization can reduce the chemical concentration or, in some cases, lead to the formation of more toxic transformation products. Unaccounted loss processes may falsify the bioassay results. Capturing the formation and effects of transformation products is important for relating the in vitro effects to in vivo. Reporter gene cell lines are believed to have low metabolic activity, but inducibility of cytochrome P450 (CYP) enzymes has been reported. Baseline toxicity is the minimal toxicity a chemical can have and is caused by the incorporation of the chemical into cell membranes. In the present study, we improved an existing baseline toxicity model based on a newly defined critical membrane burden derived from freely dissolved effect concentrations, which are directly related to the membrane concentration. Experimental effect concentrations of 94 chemicals in three bioassays (AREc32, ARE-bla and GR-bla) were compared with baseline toxicity by calculating the toxic ratio (TR). CYP activities of all cell lines were determined by using fluorescence-based assays. Only ARE-bla showed a low basal CYP activity and inducibility and AREc32 showed a low inducibility. Overall cytotoxicity was similar in all three assays despite the different metabolic activities indicating that chemical metabolism is not relevant for the cytotoxicity of the tested chemicals in these assays. Up to 28 chemicals showed specific cytotoxicity with TR > 10 in the bioassays, but baseline toxicity could explain the effects of the majority of the remaining chemicals. Seven chemicals showed TR < 0.1 indicating inaccurate physicochemical properties or experimental artifacts like chemical precipitation, volatilization, degradation, or other loss processes during the in vitro bioassay. The new baseline model can be used not only to identify specific cytotoxicity mechanisms but also to identify potential problems in the experimental performance or evaluation of the bioassay and thus improve the quality of the bioassay data.
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Affiliation(s)
- Julia Huchthausen
- Department
of Cell Toxicology, Helmholtz Centre for
Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Jenny Braasch
- Department
of Cell Toxicology, Helmholtz Centre for
Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Beate I. Escher
- Department
of Cell Toxicology, Helmholtz Centre for
Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Environmental
Toxicology, Department of Geosciences, Eberhard
Karls University Tübingen, 72076 Tübingen, Germany
| | - Maria König
- Department
of Cell Toxicology, Helmholtz Centre for
Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Luise Henneberger
- Department
of Cell Toxicology, Helmholtz Centre for
Environmental Research − UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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2
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Ye L, Ngan DK, Xu T, Liu Z, Zhao J, Sakamuru S, Zhang L, Zhao T, Xia M, Simeonov A, Huang R. Prediction of drug-induced liver injury and cardiotoxicity using chemical structure and in vitro assay data. Toxicol Appl Pharmacol 2022; 454:116250. [PMID: 36150479 PMCID: PMC9561045 DOI: 10.1016/j.taap.2022.116250] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/24/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022]
Abstract
Drug-induced liver injury (DILI) and cardiotoxicity (DICT) are major adverse effects triggered by many clinically important drugs. To provide an alternative to in vivo toxicity testing, the U.S. Tox21 consortium has screened a collection of ∼10K compounds, including drugs in clinical use, against >70 cell-based assays in a quantitative high-throughput screening (qHTS) format. In this study, we compiled reference compound lists for DILI and DICT and compared the potential of Tox21 assay data with chemical structure information in building prediction models for human in vivo hepatotoxicity and cardiotoxicity. Models were built with four different machine learning algorithms (e.g., Random Forest, Naïve Bayes, eXtreme Gradient Boosting, and Support Vector Machine) and model performance was evaluated by calculating the area under the receiver operating characteristic curve (AUC-ROC). Chemical structure-based models showed reasonable predictive power for DILI (best AUC-ROC = 0.75 ± 0.03) and DICT (best AUC-ROC = 0.83 ± 0.03), while Tox21 assay data alone only showed better than random performance. DILI and DICT prediction models built using a combination of assay data and chemical structure information did not have a positive impact on model performance. The suboptimal predictive performance of the assay data is likely due to insufficient coverage of an adequately predictive number of toxicity mechanisms. The Tox21 consortium is currently expanding coverage of biological response space with additional assays that probe toxicologically important targets and under-represented pathways that may improve the prediction of in vivo toxicity such as DILI and DICT.
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Affiliation(s)
- Lin Ye
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Deborah K Ngan
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Tuan Xu
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Zhichao Liu
- National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, AR 72079, USA
| | - Jinghua Zhao
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Srilatha Sakamuru
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Li Zhang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Tongan Zhao
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Menghang Xia
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Anton Simeonov
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA
| | - Ruili Huang
- Division of Pre-clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD 20850, USA.
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3
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Deng T, Xu X, Fu J, Xu Y, Qu W, Pi J, Wang H. Application of ARE-reporter systems in drug discovery and safety assessment. Toxicol Appl Pharmacol 2022; 454:116243. [PMID: 36115658 DOI: 10.1016/j.taap.2022.116243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/16/2022] [Accepted: 09/09/2022] [Indexed: 11/28/2022]
Abstract
The human body is continuously exposed to xenobiotics and internal or external oxidants. The health risk assessment of exogenous chemicals remains a complex and challenging issue. Alternative toxicological test methods have become an essential strategy for health risk assessment. As a core regulator of constitutive and inducible expression of antioxidant response element (ARE)-dependent genes, nuclear factor erythroid 2-related factor 2 (Nrf2) plays a critical role in maintaining cellular redox homeostasis. Consistent with the properties of Nrf2-mediated antioxidant response, Nrf2-ARE activity is a direct indicator of oxidative stress and thus has been used to identify and characterize oxidative stressors and redox modulators. To screen and distinguish chemicals or environmental insults that affect the cellular antioxidant activity and/or induce oxidative stress, various in vitro cell models expressing distinct ARE reporters with high-throughput and high-content properties have been developed. These ARE-reporter systems are currently widely applied in drug discovery and safety assessment. In the present review, we provide an overview of the basic structures and applications of various ARE-reporter systems employed for discovering Nrf2-ARE modulators and characterizing oxidative stressors.
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Affiliation(s)
- Tianqi Deng
- Laboratory of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, Shenyang 110122, China
| | - Xiaoge Xu
- Laboratory of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, Shenyang 110122, China
| | - Jingqi Fu
- Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang 110122, China
| | - Yuanyuan Xu
- Laboratory of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, Shenyang 110122, China
| | - Weidong Qu
- Key Laboratory of Public Health Safety, Ministry of Education, Department of Environmental Health, School of Public Health, Fudan University, Shanghai 200032, China
| | - Jingbo Pi
- Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang 110122, China.
| | - Huihui Wang
- Laboratory of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, Shenyang 110122, China.
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4
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Jia X, Wen X, Russo DP, Aleksunes LM, Zhu H. Mechanism-driven modeling of chemical hepatotoxicity using structural alerts and an in vitro screening assay. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129193. [PMID: 35739723 PMCID: PMC9262097 DOI: 10.1016/j.jhazmat.2022.129193] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 05/20/2023]
Abstract
Traditional experimental approaches to evaluate hepatotoxicity are expensive and time-consuming. As an advanced framework of risk assessment, adverse outcome pathways (AOPs) describe the sequence of molecular and cellular events underlying chemical toxicities. We aimed to develop an AOP that can be used to predict hepatotoxicity by leveraging computational modeling and in vitro assays. We curated 869 compounds with known hepatotoxicity classifications as a modeling set and extracted assay data from PubChem. The antioxidant response element (ARE) assay, which quantifies transcriptional responses to oxidative stress, showed a high correlation to hepatotoxicity (PPV=0.82). Next, we developed quantitative structure-activity relationship (QSAR) models to predict ARE activation for compounds lacking testing results. Potential toxicity alerts were identified and used to construct a mechanistic hepatotoxicity model. For experimental validation, 16 compounds in the modeling set and 12 new compounds were selected and tested using an in-house ARE-luciferase assay in HepG2-C8 cells. The mechanistic model showed good hepatotoxicity predictivity (accuracy = 0.82) for these compounds. Potential false positive hepatotoxicity predictions by only using ARE results can be corrected by incorporating structural alerts and vice versa. This mechanistic model illustrates a potential toxicity pathway for hepatotoxicity, and this strategy can be expanded to develop predictive models for other complex toxicities.
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Affiliation(s)
- Xuelian Jia
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ 08102, USA
| | - Xia Wen
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
| | - Daniel P Russo
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ 08102, USA
| | - Lauren M Aleksunes
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
| | - Hao Zhu
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ 08102, USA; Department of Chemistry, Rutgers University, Camden, NJ 08102, USA.
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5
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Gui B, Wang C, Xu X, Li C, Zhao Y, Su L. Identification of active or inactive agonists of tumor suppressor protein based on Tox21 library. Toxicology 2022; 474:153224. [PMID: 35659517 DOI: 10.1016/j.tox.2022.153224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/15/2022] [Accepted: 05/25/2022] [Indexed: 11/18/2022]
Abstract
Exposure of cells to xenobiotic human-made products can lead to genotoxicity and cause DNA damage. It is an urgent need to quickly identify the chemicals that cause DNA damage, and their toxicity should be predicted. In this study, recursive partitioning (RP), binary logistic regression, and one machine learning approach, namely, random forest (RF) classifier, were used to predict the active and inactive compounds of a total 5036 data based on the assay conducted by a β-lactamase reporter gene under control of the p53 response element (p53RE) from Tox21 library. Results show that the binary logistic regression model with a threshold of 0.5 has a high accuracy rate (83%) to distinguish active and inactive compounds. The RF classifier method has satisfactory results, with an accuracy rate (84.38%) approximately higher than that of binary logistic regression. The models established can identify compounds that induce DNA damage and activate p53, and provide a scientific basis for the risk assessment of organic chemicals in the environment.
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Affiliation(s)
- Bingxin Gui
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, 2555 Jingyue Street, Changchun 130117 Jilin, PR China
| | - Chen Wang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, 2555 Jingyue Street, Changchun 130117 Jilin, PR China
| | - Xiaotian Xu
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, 2555 Jingyue Street, Changchun 130117 Jilin, PR China
| | - Chao Li
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, 2555 Jingyue Street, Changchun 130117 Jilin, PR China
| | - Yuanhui Zhao
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, 2555 Jingyue Street, Changchun 130117 Jilin, PR China
| | - Limin Su
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, School of Environment, Northeast Normal University, 2555 Jingyue Street, Changchun 130117 Jilin, PR China.
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6
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Wei Z, Zhao J, Zhang L, Xia M. Cell-Based Assays to Identify Modulators of Nrf2/ARE Pathway. Methods Mol Biol 2022; 2474:59-69. [PMID: 35294756 PMCID: PMC9438791 DOI: 10.1007/978-1-0716-2213-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The nuclear factor erythroid 2-related factor (Nrf2) and antioxidant response element (ARE) signaling pathway play an important role in the amelioration of cellular oxidative stress. Thus, assays that detect this pathway can be useful for identifying chemicals that induce or inhibit oxidative stress signaling. This chapter is to describe two cell-based Nrf2/ARE assays in a quantitative high-throughput screening (HTS) format to test a large collection of chemicals for oxidative stress induction ability. The assay descriptions involve cell handling, assay preparation, instrument usage, and assay procedure.
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Affiliation(s)
- Zhengxi Wei
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Jinghua Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Li Zhang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA.
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7
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Tice RR, Bassan A, Amberg A, Anger LT, Beal MA, Bellion P, Benigni R, Birmingham J, Brigo A, Bringezu F, Ceriani L, Crooks I, Cross K, Elespuru R, Faulkner DM, Fortin MC, Fowler P, Frericks M, Gerets HHJ, Jahnke GD, Jones DR, Kruhlak NL, Lo Piparo E, Lopez-Belmonte J, Luniwal A, Luu A, Madia F, Manganelli S, Manickam B, Mestres J, Mihalchik-Burhans AL, Neilson L, Pandiri A, Pavan M, Rider CV, Rooney JP, Trejo-Martin A, Watanabe-Sailor KH, White AT, Woolley D, Myatt GJ. In Silico Approaches In Carcinogenicity Hazard Assessment: Current Status and Future Needs. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 20. [PMID: 35368437 DOI: 10.1016/j.comtox.2021.100191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Historically, identifying carcinogens has relied primarily on tumor studies in rodents, which require enormous resources in both money and time. In silico models have been developed for predicting rodent carcinogens but have not yet found general regulatory acceptance, in part due to the lack of a generally accepted protocol for performing such an assessment as well as limitations in predictive performance and scope. There remains a need for additional, improved in silico carcinogenicity models, especially ones that are more human-relevant, for use in research and regulatory decision-making. As part of an international effort to develop in silico toxicological protocols, a consortium of toxicologists, computational scientists, and regulatory scientists across several industries and governmental agencies evaluated the extent to which in silico models exist for each of the recently defined 10 key characteristics (KCs) of carcinogens. This position paper summarizes the current status of in silico tools for the assessment of each KC and identifies the data gaps that need to be addressed before a comprehensive in silico carcinogenicity protocol can be developed for regulatory use.
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Affiliation(s)
- Raymond R Tice
- RTice Consulting, Hillsborough, North Carolina, 27278, USA
| | | | - Alexander Amberg
- Sanofi Preclinical Safety, Industriepark Höchst, 65926 Frankfurt, Germany
| | - Lennart T Anger
- Genentech, Inc., South San Francisco, California, 94080, USA
| | - Marc A Beal
- Healthy Environments and Consumer Safety Branch, Health Canada, Government of Canada, Ottawa, Ontario, Canada K1A 0K9
| | | | | | - Jeffrey Birmingham
- GlaxoSmithKline, David Jack Centre for R&D, Ware, Hertfordshire, SG12 0DP, United Kingdom
| | - Alessandro Brigo
- Roche Pharmaceutical Research & Early Development, Pharmaceutical Sciences, Roche Innovation, Center Basel, F. Hoffmann-La Roche Ltd, CH-4070, Basel, Switzerland
| | | | - Lidia Ceriani
- Humane Society International, 1000 Brussels, Belgium
| | - Ian Crooks
- British American Tobacco (Investments) Ltd, GR&D Centre, Southampton, SO15 8TL, United Kingdom
| | | | - Rosalie Elespuru
- Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, Maryland, 20993, USA
| | - David M Faulkner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marie C Fortin
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey, 08855, USA
| | - Paul Fowler
- FSTox Consulting (Genetic Toxicology), Northamptonshire, United Kingdom
| | | | | | - Gloria D Jahnke
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | | | - Naomi L Kruhlak
- Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, Maryland, 20993, USA
| | - Elena Lo Piparo
- Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | - Juan Lopez-Belmonte
- Cuts Ice Ltd Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | - Amarjit Luniwal
- North American Science Associates (NAMSA) Inc., Minneapolis, Minnesota, 55426, USA
| | - Alice Luu
- Healthy Environments and Consumer Safety Branch, Health Canada, Government of Canada, Ottawa, Ontario, Canada K1A 0K9
| | - Federica Madia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Serena Manganelli
- Chemical Food Safety Group, Nestlé Research, CH-1000 Lausanne 26, Switzerland
| | | | - Jordi Mestres
- IMIM Institut Hospital Del Mar d'Investigacions Mèdiques and Universitat Pompeu Fabra, Doctor Aiguader 88, Parc de Recerca Biomèdica, 08003 Barcelona, Spain; and Chemotargets SL, Baldiri Reixac 4, Parc Científic de Barcelona, 08028, Barcelona, Spain
| | | | - Louise Neilson
- Broughton Nicotine Services, Oak Tree House, Earby, Lancashire, BB18 6JZ United Kingdom
| | - Arun Pandiri
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | | | - Cynthia V Rider
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA
| | - John P Rooney
- Integrated Laboratory Systems, LLC., Morrisville, North Carolina, 27560, USA
| | | | - Karen H Watanabe-Sailor
- School of Mathematical and Natural Sciences, Arizona State University, West Campus, Glendale, Arizona, 85306, USA
| | - Angela T White
- GlaxoSmithKline, David Jack Centre for R&D, Ware, Hertfordshire, SG12 0DP, United Kingdom
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Ooka M, Lynch C, Xia M. Application of In Vitro Metabolism Activation in High-Throughput Screening. Int J Mol Sci 2020; 21:ijms21218182. [PMID: 33142951 PMCID: PMC7663506 DOI: 10.3390/ijms21218182] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023] Open
Abstract
In vitro methods which incorporate metabolic capability into the assays allow us to assess the activity of metabolites from their parent compounds. These methods can be applied into high-throughput screening (HTS) platforms, thereby increasing the speed to identify compounds that become active via the metabolism process. HTS was originally used in the pharmaceutical industry and now is also used in academic settings to evaluate biological activity and/or toxicity of chemicals. Although most chemicals are metabolized in our body, many HTS assays lack the capability to determine compound activity via metabolism. To overcome this problem, several in vitro metabolic methods have been applied to an HTS format. In this review, we describe in vitro metabolism methods and their application in HTS assays, as well as discuss the future perspectives of HTS with metabolic activity. Each in vitro metabolism method has advantages and disadvantages. For instance, the S9 mix has a full set of liver metabolic enzymes, but it displays high cytotoxicity in cell-based assays. In vitro metabolism requires liver fractions or the use of other metabolically capable systems, including primary hepatocytes or recombinant enzymes. Several newly developed in vitro metabolic methods, including HepaRG cells, three-dimensional (3D) cell models, and organ-on-a-chip technology, will also be discussed. These newly developed in vitro metabolism approaches offer significant progress in dissecting biological processes, developing drugs, and making toxicology studies quicker and more efficient.
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Zhang S, Khan WA, Su L, Zhang X, Li C, Qin W, Zhao Y. Predicting oxidative stress induced by organic chemicals by using quantitative Structure-Activity relationship methods. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 201:110817. [PMID: 32512417 DOI: 10.1016/j.ecoenv.2020.110817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
Cellular exposure to xenobiotic human-made products will lead to oxidative stress that gives rise to DNA damage, as well as chemical or mechanical damage. Distinguishing the chemicals that will induce oxidative stress and predicting their toxicity is necessary. In the present study, 4270 compounds in the ARE-bla assay were investigated to predict active and inactive compounds by using simple algorithms, namely, recursive partitioning (RP) and binomial logistic regression, and to develop the quantitative structure-activity relationship (QSAR) models of chemicals that activate the ARE pathway to induce oxidative stress and exert toxic effects on cells. A decision tree based on scaffold-based fragments obtained through RP analysis showed the best identification accuracy. However, the overall identification accuracy of this model for active compounds was unsatisfactory due to limited fragments. Furthermore, a binomial logistic regression model was developed from 638 active compounds and 3632 inactive chemicals. The model with a cutoff of 0.15 could predict chemicals that were active or inactive with the prediction accuracy of 69.1%. Its area under the receiver operating characteristic (ROC) curve metric (AUROC) was 0.762, which indicated the acceptable predictive ability of this model. The parameters nBM (number of multiple bonds) and H% (percentage of H atom) played dominant roles in the prediction of the activity (inactive or active) of chemicals. A global QSAR model was developed to predict the toxicity of active chemicals. However, the model displayed an unsatisfactory result with R2 = 0.316 and R2ext = 0.090. Active chemicals were then classified on the basis of structure. A total of 79 compounds with carbon chains could be predicted with acceptable performance by using a QSAR model with six descriptors (R2 = 0.722, R2ext = 0.798, Q2Loo = 0.654, Q2Boot = 0.755, Q2ext = 0.721). The simple models established here contribute to efforts on identification compounds inducing oxidative stress and provide the scientific basis for risk assessment to organisms in the environment.
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Affiliation(s)
- Shengnan Zhang
- School of Environment, And State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, Jilin, PR China
| | - Waqas Amin Khan
- School of Environment, And State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, Jilin, PR China
| | - Limin Su
- School of Environment, And State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, Jilin, PR China.
| | - Xuehua Zhang
- School of Water Conservancy and Environment Engineering, Changchun Institute of Technology, Changchun, 130012, Jilin, PR China
| | - Chao Li
- School of Environment, And State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, Jilin, PR China
| | - Weichao Qin
- School of Environment, And State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, Jilin, PR China
| | - Yuanhui Zhao
- School of Environment, And State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, Jilin, PR China
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10
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Taguchi K, Kensler TW. Nrf2 in liver toxicology. Arch Pharm Res 2019; 43:337-349. [PMID: 31782059 DOI: 10.1007/s12272-019-01192-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 11/19/2019] [Indexed: 12/14/2022]
Abstract
Liver plays essential roles in the metabolism of many endogenous chemicals and exogenous toxicants. Mechanistic studies in liver have been at the forefront of efforts to probe the roles of bioactivation and detoxication of environmental toxins and toxicants in hepatotoxicity. Moreover, idiosyncratic hepatoxicity remains a key barrier in the clinical development of drugs. The now vast Nrf2 field emerged in part from biochemical and molecular studies on chemical inducers of hepatic detoxication enzymes and subsequent characterization of the modulation of drug/toxicant induced hepatotoxicities in mice through disruption of either Nrf2 or Keap1 genes. In general, loss of Nrf2 increases the sensitivity to such toxic chemicals, highlighting a central role of this transcription factor and its downstream target genes as a modifier to chemical stress. In this review, we summarize the impact of Nrf2 on the toxicology of multiple hepatotoxicants, and discuss efforts to utilize the Nrf2 response in predictive toxicology.
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Affiliation(s)
- Keiko Taguchi
- Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba, Sendai, 980-8575, Japan.
| | - Thomas W Kensler
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA, 98109, USA
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11
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Escher BI, Glauch L, König M, Mayer P, Schlichting R. Baseline Toxicity and Volatility Cutoff in Reporter Gene Assays Used for High-Throughput Screening. Chem Res Toxicol 2019; 32:1646-1655. [PMID: 31313575 DOI: 10.1021/acs.chemrestox.9b00182] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Most studies using high-throughput in vitro cell-based bioassays tested chemicals up to a certain fixed concentration. It would be more appropriate to test up to concentrations predicted to elicit baseline toxicity because this is the minimal toxicity of every chemical. Baseline toxicity is also called narcosis and refers to nonspecific intercalation of chemicals in biological membranes, leading to loss of membrane structure and impaired functioning of membrane-related processes such as mitochondrial respiration. In cells, baseline toxicity manifests as cytotoxicity, which was quantified by a robust live-cell imaging method. Inhibitory concentrations for baseline toxicity varied by orders of magnitude between chemicals and were described by a simple quantitative structure activity relationship (QSAR) with the liposome-water partition constant as a sole descriptor. The QSAR equations were remarkably similar for eight reporter gene cell lines of different cellular origin, six of which were used in Tox21. Mass-balance models indicated constant critical membrane concentrations for all cells and all chemicals with a mean of 69 mmol·kglip-1(95% CI: 49-89), which is in the same range as for bacteria and aquatic organisms and consistent with the theory of critical membrane burden of narcosis. The challenge of developing baseline QSARs for cell lines is that many confirmed baseline toxicants are rather volatile. We deduced from cytotoxicity experiments with semi-volatile chemicals that only chemicals with medium-air partition constants >10,000 L/L can be tested in standard robotic setups without appreciable loss of effect. Chemicals just below that cutoff showed crossover effects in neighboring wells, whereas the effects of chemicals with lower medium-air partition constants were plainly lost. Applying the "volatility cut-off" to >8000 chemicals tested in Tox21 indicated that approximately 20% of Tox21 chemicals could have partially been lost during the experiments. We recommend applying the baseline QSARs together with volatility cut-offs for experimental planning of reporter gene assays, that is, to dose only chemicals with medium-air partition constants >10,000 at concentrations up to the baseline toxicity level.
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Affiliation(s)
- Beate I Escher
- Department of Cell Toxicology , Helmholtz Centre for Environmental Research - UFZ , Permoserstr. 15 , DE-04318 Leipzig , Germany.,Environmental Toxicology, Center for Applied Geoscience , Eberhard Karls University Tübingen , Hölderlinstr. 12 , DE-72074 Tübingen , Germany
| | - Lisa Glauch
- Department of Cell Toxicology , Helmholtz Centre for Environmental Research - UFZ , Permoserstr. 15 , DE-04318 Leipzig , Germany
| | - Maria König
- Department of Cell Toxicology , Helmholtz Centre for Environmental Research - UFZ , Permoserstr. 15 , DE-04318 Leipzig , Germany
| | - Philipp Mayer
- Department of Environmental Engineering , Technical University of Denmark , Bygningstorvet 115 , DK-2800 Kongens Lyngby , Denmark
| | - Rita Schlichting
- Department of Cell Toxicology , Helmholtz Centre for Environmental Research - UFZ , Permoserstr. 15 , DE-04318 Leipzig , Germany
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12
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Fischer FC, Henneberger L, Schlichting R, Escher BI. How To Improve the Dosing of Chemicals in High-Throughput in Vitro Mammalian Cell Assays. Chem Res Toxicol 2019; 32:1462-1468. [DOI: 10.1021/acs.chemrestox.9b00167] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Fabian C. Fischer
- Department Cell Toxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Luise Henneberger
- Department Cell Toxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Rita Schlichting
- Department Cell Toxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Beate I. Escher
- Department Cell Toxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Centre for Applied Geoscience, Eberhard Karls University Tübingen, 72074 Tübingen, Germany
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13
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Raghunath A, Sundarraj K, Nagarajan R, Arfuso F, Bian J, Kumar AP, Sethi G, Perumal E. Antioxidant response elements: Discovery, classes, regulation and potential applications. Redox Biol 2018; 17:297-314. [PMID: 29775961 PMCID: PMC6007815 DOI: 10.1016/j.redox.2018.05.002] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/25/2018] [Accepted: 05/05/2018] [Indexed: 12/20/2022] Open
Abstract
Exposure to antioxidants and xenobiotics triggers the expression of a myriad of genes encoding antioxidant proteins, detoxifying enzymes, and xenobiotic transporters to offer protection against oxidative stress. This articulated universal mechanism is regulated through the cis-acting elements in an array of Nrf2 target genes called antioxidant response elements (AREs), which play a critical role in redox homeostasis. Though the Keap1/Nrf2/ARE system involves many players, AREs hold the key in transcriptional regulation of cytoprotective genes. ARE-mediated reporter constructs have been widely used, including xenobiotics profiling and Nrf2 activator screening. The complexity of AREs is brought by the presence of other regulatory elements within the AREs. The diversity in the ARE sequences not only bring regulatory selectivity of diverse transcription factors, but also confer functional complexity in the Keap1/Nrf2/ARE pathway. The different transcription factors either homodimerize or heterodimerize to bind the AREs. Depending on the nature of partners, they may activate or suppress the transcription. Attention is required for deeper mechanistic understanding of ARE-mediated gene regulation. The computational methods of identification and analysis of AREs are still in their infancy. Investigations are required to know whether epigenetics mechanism plays a role in the regulation of genes mediated through AREs. The polymorphisms in the AREs leading to oxidative stress related diseases are warranted. A thorough understanding of AREs will pave the way for the development of therapeutic agents against cancer, neurodegenerative, cardiovascular, metabolic and other diseases with oxidative stress.
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Affiliation(s)
- Azhwar Raghunath
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641046, Tamilnadu, India
| | - Kiruthika Sundarraj
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641046, Tamilnadu, India
| | - Raju Nagarajan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India
| | - Frank Arfuso
- Stem Cell and Cancer Biology Laboratory, School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6009, Australia
| | - Jinsong Bian
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600 Singapore, Singapore
| | - Alan P Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600 Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Medical Science Cluster, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, WA, Australia.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600 Singapore, Singapore.
| | - Ekambaram Perumal
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641046, Tamilnadu, India.
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14
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Satoh D, Abe S, Kobayashi K, Nakajima Y, Oshimura M, Kazuki Y. Human and mouse artificial chromosome technologies for studies of pharmacokinetics and toxicokinetics. Drug Metab Pharmacokinet 2018; 33:17-30. [DOI: 10.1016/j.dmpk.2018.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/29/2017] [Accepted: 12/21/2017] [Indexed: 12/27/2022]
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15
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Melnikov F, Hsieh JH, Sipes NS, Anastas PT. Channel Interactions and Robust Inference for Ratiometric β-lactamase Assay Data: a Tox21 Library Analysis. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2018; 6:3233-3241. [PMID: 32461840 PMCID: PMC7252516 DOI: 10.1021/acssuschemeng.7b03394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ratiometric β-lactamase (BLA) reporters are widely used to study transcriptional responses in a high-throughput screening (HTS) format. Typically, a ratio readout (background/target fluorescence) is used for toxicity assessment and structure-activity modeling efforts from BLA HTS data. This ratio readout may be confounded by channel-specific artifacts. To maximize the utility of BLA HTS data, we analyzed the relationship between individual channels and ratio readouts after fitting 10,000 chemical titration series screened in seven BLA stress-response assays from the Tox21 initiative. Similar to previous observations, we found that activity classifications based on BLA ratio readout alone are confounded by interference patterns for up to 85% (50 % on average) of active chemicals. Most Tox21 analyses adjust for this issue by evaluating target and ratio readout direction. In addition, we found that the potency and efficacy estimates derived from the ratio readouts may not represent the target channel effects and thus complicates chemical activity comparison. From these analyses we recommend a simpler approach using a direct evaluation of the target and background channels as well as the respective noise levels when using BLA data for toxicity assessment. This approach eliminates the channel interference issues and allows for straightforward chemical assessment and comparisons.
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Affiliation(s)
- Fjodor Melnikov
- School of Forestry and Environmental Studies, Yale University, New Haven, CT 06520, United States
| | - Jui-Hua Hsieh
- Kelly Government Solutions, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - Nisha S Sipes
- National Toxicology Program / National Institute of Environmental Health Sciences (NIEHS), 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - Paul T Anastas
- School of Forestry and Environmental Studies, Yale University, New Haven, CT 06520, United States
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06520, United States
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16
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Abstract
The new strategy for chemical toxicity testing and modeling is to use in vitro human cell-based assays in conjunction with quantitative high-throughput screening (qHTS) technology, to identify molecular mechanisms and predict in vivo responses. Stem cells are more physiologically relevant than immortalized cell lines because of their unique proliferation and differentiation potentials. We established a robust two stem cells-two lineages assay system, encompassing human mesenchymal stem cells (hMSCs) along osteogenesis and human induced pluripotent stem cells (hiPSCs) along hepatogenesis. We performed qHTS phenotypic screening of LOPAC1280 and identified 38 preliminary hits for hMSCs. This was followed by validation of a selected number of hits and determination of their IC50 values and mechanistic studies of idarubicin and cantharidin treatments using proteomics and bioinformatics. In general, hiPSCs were more sensitive than hMSCs to chemicals, and differentiated progenies were less sensitive than their progenitors. We showed that chemical toxicity depends on both stem cell types and their differentiation stages. Proteomics identified and quantified over 3000 proteins for both stem cells. Bioinformatics identified apoptosis and G2/M as the top pathways conferring idarubicin toxicity. Our Omics-based assays of stem cells provide mechanistic insights into chemical toxicity and may help prioritize chemicals for in-depth toxicological evaluations.
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Affiliation(s)
- Yan Han
- Newomics Inc., Emeryville, California, USA
| | - Jinghua Zhao
- National Center for Advancing Translational Sciences, Bethesda, Maryland, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, Bethesda, Maryland, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, Bethesda, Maryland, USA
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17
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Bogen KT. Linear-No-Threshold Default Assumptions are Unwarranted for Cytotoxic Endpoints Independently Triggered by Ultrasensitive Molecular Switches. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2017; 37:1808-1816. [PMID: 28437864 DOI: 10.1111/risa.12813] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 03/03/2017] [Indexed: 06/07/2023]
Abstract
Crump's response in this issue to my critique of linear-no-threshold (LNT) default assumptions for noncancer and nongenotoxic cancer risks (Risk Analysis 2016; 36(3):589-604) is rebutted herein. Crump maintains that distinguishing between a low-dose linear dose response and a threshold dose response on the basis of dose-response data is impossible even for endpoints involving increased cytotoxicity. My rebuttal relies on descriptions and specific illustrations of two well-characterized ultrasensitive molecular switches that govern two key cytoprotective responses to cellular stress-heat shock response and antioxidant response element activation, respectively-each of which serve to suppress stress-induced apoptotic cell death unless overwhelmed. Because detailed dose-response data for each endpoint is shown to be J- or inverted-J-shaped with high confidence, and because independent pathways can explain background rates of apoptosis, LNT assumptions for this cytotoxic endpoint are unwarranted, at least in some cases and perhaps generally.
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18
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Neale PA, Achard MES, Escher BI, Leusch FDL. Exploring the oxidative stress response mechanism triggered by environmental water samples. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:1126-1133. [PMID: 28009908 DOI: 10.1039/c6em00541a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Environmental waters can contain a wide range of micropollutants. Bioanalytical test batteries using assays indicative of different stages of cellular toxicity pathways, such as adaptive stress responses, have been applied to a range of water samples. Oxidative stress response assays have proven to be sensitive tools, but the mechanism by which water samples are inducing the oxidative stress response remains unclear because both electrophiles and reactive oxygen species (ROS) may activate the Nrf2-antioxidant response element (ARE) pathway. The current study aimed to explore the underlying mechanisms of the oxidative stress response triggered by exposure to surface water extracts previously shown to be active in the ARE GeneBLAzer oxidative stress response assay. ROS formation and changes in glutathione (GSH) concentration were assessed in human liver cells exposed to water extracts from a large river in addition to individual chemicals that were detected in these water extracts and reported to be active in the ARE GeneBLAzer assay in a previous study. Many of the surface water samples induced ROS formation and decreased the GSH to glutathione disulfide (GSSG) ratio, suggesting that the formation of ROS is an important mechanism. However, some of the most responsive samples in the ARE GeneBLAzer assay, as well as the individual chemicals, did not have a significant effect on either ROS formation or the GSH/GSSG ratio, suggesting a different mechanism. Antioxidants can also induce the Nrf2-ARE pathway and the ARE GeneBLAzer assay may also detect compounds that activate ARE by Nrf2-independent mechanisms, thus further research is required to characterise active chemicals in oxidative stress response assays. However, these tests are still useful for quantifying the integrated cellular response to multiple molecular initiating events and can be used complementary to assays indicative of specific effects, such as receptor-mediated assays.
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Affiliation(s)
- Peta A Neale
- Australian Rivers Institute, Griffith School of Environment, Griffith University, Southport, QLD 4222, Australia.
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19
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Pals JA, Wagner ED, Plewa MJ, Xia M, Attene-Ramos MS. Monohalogenated acetamide-induced cellular stress and genotoxicity are related to electrophilic softness and thiol/thiolate reactivity. J Environ Sci (China) 2017; 58:224-230. [PMID: 28774613 PMCID: PMC6239421 DOI: 10.1016/j.jes.2017.04.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 05/08/2023]
Abstract
Haloacetamides (HAMs) are cytotoxic, genotoxic, and mutagenic byproducts of drinking water disinfection. They are soft electrophilic compounds that form covalent bonds with the free thiol/thiolate in cysteine residues through an SN2 reaction mechanism. Toxicity of the monohalogenated HAMs (iodoacetamide, IAM; bromoacetamide, BAM; or chloroacetamide, CAM) varied depending on the halogen substituent. The aim of this research was to investigate how the halogen atom affects the reactivity and toxicological properties of HAMs, measured as induction of oxidative/electrophilic stress response and genotoxicity. Additionally, we wanted to determine how well in silico estimates of electrophilic softness matched thiol/thiolate reactivity and in vitro toxicological endpoints. Each of the HAMs significantly induced nuclear Rad51 accumulation and ARE signaling activity compared to a negative control. The rank order of effect was IAM>BAM>CAM for Rad51, and BAM≈IAM>CAM for ARE. In general, electrophilic softness and in chemico thiol/thiolate reactivity provided a qualitative indicator of toxicity, as the softer electrophiles IAM and BAM were more thiol/thiolate reactive and were more toxic than CAM.
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Affiliation(s)
- Justin A Pals
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Elizabeth D Wagner
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Safe Global Water Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Michael J Plewa
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Safe Global Water Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, MD, United States
| | - Matias S Attene-Ramos
- Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, United States.
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20
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Belanova AA, Smirnov DS, Makarenko MS, Belousova MM, Mashkina EV, Aleksandrova AA, Soldatov AV, Zolotukhin PV. Individual expression features of GPX2, NQO1 and SQSTM1 transcript variants induced by hydrogen peroxide treatment in HeLa cells. Genet Mol Biol 2017; 40:515-524. [PMID: 28558074 PMCID: PMC5488449 DOI: 10.1590/1678-4685-gmb-2016-0005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 11/22/2016] [Indexed: 12/24/2022] Open
Abstract
Pathway activity assessment-based approaches are becoming highly influential in various fields of biology and medicine. However, these approaches mostly rely on analysis of mRNA expression, and total mRNA from a given locus is measured in the majority of cases. Notably, a significant portion of protein-coding genes produces more than one transcript. This biological fact is responsible for significant noise when changes in total mRNA transcription of a single gene are analyzed. The NFE2L2/AP-1 pathway is an attractive target for biomedical applications. To date, there is a lack of data regarding the agreement in expression of even classical target genes of this pathway. In the present paper we analyzed whether transcript variants of GPX2, NQO1 and SQSTM1 were characterized by individual features of expression when HeLa cells were exposed to pro-oxidative stimulation with hydrogen peroxide. We found that all the transcripts (10 in total) appeared to be significantly individually regulated under the conditions tested. We conclude that individual transcripts, rather than total mRNA, are best markers of pathway activation. We also discuss here some biological roles of individual transcript regulation.
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Affiliation(s)
- Anna A Belanova
- Evolution Corporate Group, Cell Physiology Laboratory, Southern Federal University, Rostov-on-Don, Russia
| | - Dmitry S Smirnov
- Evolution Corporate Group, Cell Physiology Laboratory, Southern Federal University, Rostov-on-Don, Russia
| | - Maxim S Makarenko
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Mariya M Belousova
- Department of English Language for Natural Sciences Faculties, Southern Federal University, Rostov-on-Don, Russia
| | - Elena V Mashkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Anzhela A Aleksandrova
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia
| | - Alexander V Soldatov
- Department of Nanosystems Physics and Spectroscopy, Southern Federal University, Rostov-on-Don, Russia
| | - Peter V Zolotukhin
- Evolution Corporate Group, Cell Physiology Laboratory, Southern Federal University, Rostov-on-Don, Russia
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21
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Abstract
Kelch-like ECH-associated protein 1 (Keap1), nuclear factor erythroid 2-like factor 2-related factor 2 (Nrf2), and the antioxidant response element (ARE) are interacting components of a master regulatory signaling pathway that coordinates redox homeostasis, cytoprotective responses, and shifts in stem cell state. This study reexamined detailed dose–response (DR) data reported for in vitro Nrf2-ARE activation in human hepatoblastoma HepG2 cell lines containing either a ARE-bla or ARE-luc reporter at 12 different concentrations of each of 15 chemicals. The normalized study data were combined among chemicals exhibiting a positive response, yielding n = 531 (179) DR data for 9 (7) chemicals using the ARE-bla (ARE-luc) assay. Three-parameter linear/kth-power regression fits obtained to each combined set of ARE-bla- or ARE-luc-assay response data provided good fits (R2 = .99 or .91, respectively, Pfit > .99) that each incorporate a highly significant negative initial linear slope (P = 4 × 10−5 or .00025) and an overall J-shaped DR pattern. Results from this reanalysis of high-resolution ARE response data support the hypothesis that nonlinear ARE-mediated adaptive cellular responses to oxidative stress are governed by an ultrasensitive molecular switch.
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22
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Fischer FC, Henneberger L, König M, Bittermann K, Linden L, Goss KU, Escher BI. Modeling Exposure in the Tox21 in Vitro Bioassays. Chem Res Toxicol 2017; 30:1197-1208. [DOI: 10.1021/acs.chemrestox.7b00023] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fabian C. Fischer
- Department
Cell Toxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Luise Henneberger
- Department
Cell Toxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Maria König
- Department
Cell Toxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Kai Bittermann
- Department
Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Lukas Linden
- Department
Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Kai-Uwe Goss
- Department
Analytical Environmental Chemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
| | - Beate I. Escher
- Department
Cell Toxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
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23
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Wakuri S, Yamakage K, Kazuki Y, Kazuki K, Oshimura M, Aburatani S, Yasunaga M, Nakajima Y. Correlation between luminescence intensity and cytotoxicity in cell-based cytotoxicity assay using luciferase. Anal Biochem 2017; 522:18-29. [PMID: 28111305 DOI: 10.1016/j.ab.2017.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
The luciferase reporter assay has become one of the conventional methods for cytotoxicity evaluation. Typically, the decrease of luminescence expressed by a constitutive promoter is used as an index of cytotoxicity. However, to our knowledge, there have been no reports of the correlation between cytotoxicity and luminescence intensity. In this study, to accurately verify the correlation between them, beetle luciferase was stably expressed in human hepatoma HepG2 cells harboring the multi-integrase mouse artificial chromosome vector. We showed that the cytotoxicity assay using luciferase does not depend on the stability of luciferase protein and the kind of constitutive promoter. Next, HepG2 cells in which green-emitting beetle luciferase was expressed under the control of CAG promoter were exposed to 58 compounds. The luminescence intensity and cytotoxicity curves of cells exposed to 48 compounds showed similar tendencies, whereas those of cells exposed to 10 compounds did not do so, although the curves gradually approached each other with increasing exposure time. Finally, we demonstrated that luciferase expressed under the control of a constitutive promoter can be utilized both as an internal control reporter for normalizing a test reporter and for monitoring cytotoxicity when two kinds of luciferases are simultaneously used in the cytotoxicity assay.
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Affiliation(s)
- S Wakuri
- Hatano Research Institute, Food and Drug Safety Center, Hadano, Kanagawa 257-8523, Japan
| | - K Yamakage
- Hatano Research Institute, Food and Drug Safety Center, Hadano, Kanagawa 257-8523, Japan
| | - Y Kazuki
- Chromosome Engineering Research Center, Tottori University, Yonago, Tottori 683-8503, Japan; Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Tottori 683-8503, Japan
| | - K Kazuki
- Chromosome Engineering Research Center, Tottori University, Yonago, Tottori 683-8503, Japan
| | - M Oshimura
- Chromosome Engineering Research Center, Tottori University, Yonago, Tottori 683-8503, Japan
| | - S Aburatani
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Tokyo 135-0064, Japan
| | - M Yasunaga
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395, Japan
| | - Y Nakajima
- Chromosome Engineering Research Center, Tottori University, Yonago, Tottori 683-8503, Japan; Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395, Japan.
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24
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Bogen KT, Arnold LL, Chowdhury A, Pennington KL, Cohen SM. Low-dose dose-response for reduced cell viability after exposure of human keratinocyte (HEK001) cells to arsenite. Toxicol Rep 2016; 4:32-38. [PMID: 28959622 PMCID: PMC5615095 DOI: 10.1016/j.toxrep.2016.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 11/01/2016] [Accepted: 12/08/2016] [Indexed: 12/21/2022] Open
Abstract
The in vitro arsenite (AsIII) cytotoxicity dose-response (DR) of human keratinocytes (HEK001) was examined at greater statistical resolution than ever previously reported using the MTT assay to determine cell viability. Fifty-four 96-well plates were treated with AsIII concentrations of 0.25, 0.5, 1, 2, 3, 4, 5, 7, 10, 15, 20, 25, or 30 μM. Because of unexpected variation in viability response patterns, a two-stage DR analysis was used in which data on plate-specific viability (%), estimated as 100% times the ratio of measured viability in exposed to unexposed cells, were fit initially to a generalized lognormal response function positing that HEK001 cells studied consisted of: a proportion P of relatively highly sensitive (HS) cells, a proportion Po of relatively resistant cells, and a remaining (1-P-Po) fraction of typical-sensitivity (TS) cells exhibiting the intermediate level of AsIII sensitivity characteristic of most cells in each assay. The estimated fractions P and Po were used to adjust data from all 54 plates (and from the 28 plates yielding the best fits) to reflect the condition that P = Po = 0 to provide detailed DR analysis specifically for TS cells. Four DR models fit to the combined adjusted data were each very predictive (R2 > 0.97) overall but were inconsistent with at least one of the data set examined (p < 10-5). Adjusted mean responses at ≤3 μM were approximately equal (p > 0.30) and exceeded 100% significance (p ≤ 10-6). A low-dose hormetic model provided the best fit to the combined adjusted data for TS cells (R2 = 0.995). Marked variability in estimates of P (the proportion of apparent HS cells) was unexpected, not readily explained, and warrants further study using additional cell lines and assay methods, and in vivo.
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Affiliation(s)
| | - Lora L. Arnold
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Karen L. Pennington
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Samuel M. Cohen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
- Havlik-Wall Professor of Oncology
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Muthusamy S, Peng C, Ng JC. Effects of multi-component mixtures of polyaromatic hydrocarbons and heavy metal/loid(s) on Nrf2-antioxidant response element (ARE) pathway in ARE reporter-HepG2 cells. Toxicol Res (Camb) 2016; 5:1160-1171. [PMID: 30090422 PMCID: PMC6072108 DOI: 10.1039/c6tx00024j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/05/2016] [Indexed: 12/28/2022] Open
Abstract
Exposure to polyaromatic hydrocarbons (PAHs) and heavy metal/loid(s) has been demonstrated to induce an oxidative stress response in mammalian cells. The combined effect of PAHs and heavy metal/loid(s) on the oxidative stress response has not been reported extensively. The Nrf2 antioxidant response pathway plays an important role in cellular antioxidant defense against oxidative stress-induced cell damage. In this study, we have determined the combined effect of four PAHs (benzo[a]pyrene (B[a]P), naphthalene (Nap), phenanthrene (Phe) and pyrene (Pyr)) and three heavy metal/loid(s) (arsenic (As), cadmium (Cd) and lead (Pb)) on the Nrf2 antioxidant pathway using the ARE reporter-HepG2 cell line. The mixture study was carried out for binary, ternary, quaternary and seven-component combinations of PAHs and heavy metal/loid(s). Initially, individual dose responses for the PAHs (B[a]P, Nap, Phe and Pyr) and heavy metal/loid(s) (As, Cd and Pb), as well as their respective concentrations that induced an induction ratio of 1.5 (ECIR1.5), were determined. The luciferase assay system was used to quantify the induction of the Nrf2 antioxidant pathway. The individual dose response study showed that both PAHs and heavy metal/loid(s) activated the Nrf2 antioxidant pathway in ARE reporter-HepG2 cells. Among these chemicals, Cd was the most potent inducer, followed by B[a]P and As. Based on the individual dose response findings, PAHs and heavy metal/loid(s) were mixed at equipotent ratios using a fixed concentration ratio, and the effects of the mixtures of PAHs and heavy metal/loid(s) (binary to seven-component) on the Nrf2 antioxidant pathway were determined. The mixture effects were predicted by using the concentration addition (CA) model. Overall, the results showed that the multi-component mixtures of PAHs and heavy metal/loid(s) induced an oxidative stress response in ARE reporter-HepG2 cells, and that the CA model is an appropriate model to predict the interaction effect of these selected mixtures. A human cell line-based reporter gene assay system was successfully used to determine the mixture effects of two groups of common contaminants on oxidative stress response pathway.
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Affiliation(s)
- Sasikumar Muthusamy
- The University of Queensland , National Research Centre for Environmental Toxicology (Entox) , Member of Queensland Alliance for Environmental Health Science (QAEHS) , Coopers Plains , Brisbane , QLD 4108 , Australia
- CRC CARE , The University of Newcastle , University Drive , Callaghan , NSW 2308 , Australia . ; ; Tel: +61 414 747 147
| | - Cheng Peng
- The University of Queensland , National Research Centre for Environmental Toxicology (Entox) , Member of Queensland Alliance for Environmental Health Science (QAEHS) , Coopers Plains , Brisbane , QLD 4108 , Australia
- CRC CARE , The University of Newcastle , University Drive , Callaghan , NSW 2308 , Australia . ; ; Tel: +61 414 747 147
| | - Jack C Ng
- The University of Queensland , National Research Centre for Environmental Toxicology (Entox) , Member of Queensland Alliance for Environmental Health Science (QAEHS) , Coopers Plains , Brisbane , QLD 4108 , Australia
- CRC CARE , The University of Newcastle , University Drive , Callaghan , NSW 2308 , Australia . ; ; Tel: +61 414 747 147
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Kim MT, Huang R, Sedykh A, Wang W, Xia M, Zhu H. Mechanism Profiling of Hepatotoxicity Caused by Oxidative Stress Using Antioxidant Response Element Reporter Gene Assay Models and Big Data. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:634-41. [PMID: 26383846 PMCID: PMC4858396 DOI: 10.1289/ehp.1509763] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 09/16/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Hepatotoxicity accounts for a substantial number of drugs being withdrawn from the market. Using traditional animal models to detect hepatotoxicity is expensive and time-consuming. Alternative in vitro methods, in particular cell-based high-throughput screening (HTS) studies, have provided the research community with a large amount of data from toxicity assays. Among the various assays used to screen potential toxicants is the antioxidant response element beta lactamase reporter gene assay (ARE-bla), which identifies chemicals that have the potential to induce oxidative stress and was used to test > 10,000 compounds from the Tox21 program. OBJECTIVE The ARE-bla computational model and HTS data from a big data source (PubChem) were used to profile environmental and pharmaceutical compounds with hepatotoxicity data. METHODS Quantitative structure-activity relationship (QSAR) models were developed based on ARE-bla data. The models predicted the potential oxidative stress response for known liver toxicants when no ARE-bla data were available. Liver toxicants were used as probe compounds to search PubChem Bioassay and generate a response profile, which contained thousands of bioassays (> 10 million data points). By ranking the in vitro-in vivo correlations (IVIVCs), the most relevant bioassay(s) related to hepatotoxicity were identified. RESULTS The liver toxicants profile contained the ARE-bla and relevant PubChem assays. Potential toxicophores for well-known toxicants were created by identifying chemical features that existed only in compounds with high IVIVCs. CONCLUSION Profiling chemical IVIVCs created an opportunity to fully explore the source-to-outcome continuum of modern experimental toxicology using cheminformatics approaches and big data sources. CITATION Kim MT, Huang R, Sedykh A, Wang W, Xia M, Zhu H. 2016. Mechanism profiling of hepatotoxicity caused by oxidative stress using antioxidant response element reporter gene assay models and big data. Environ Health Perspect 124:634-641; http://dx.doi.org/10.1289/ehp.1509763.
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Affiliation(s)
- Marlene Thai Kim
- Department of Chemistry, Rutgers University, Camden, New Jersey, USA
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Alexander Sedykh
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
- Multicase Inc., Beachwood, Ohio, USA
| | - Wenyi Wang
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Hao Zhu
- Department of Chemistry, Rutgers University, Camden, New Jersey, USA
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
- Address correspondence to H. Zhu, 315 Penn St., Rutgers University, Camden, NJ 08102 USA. Telephone: (856) 225-6781. E-mail:
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27
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Thorne N, Malik N, Shah S, Zhao J, Class B, Aguisanda F, Southall N, Xia M, McKew JC, Rao M, Zheng W. High-Throughput Phenotypic Screening of Human Astrocytes to Identify Compounds That Protect Against Oxidative Stress. Stem Cells Transl Med 2016; 5:613-27. [PMID: 27034412 PMCID: PMC4835244 DOI: 10.5966/sctm.2015-0170] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 01/14/2016] [Indexed: 01/17/2023] Open
Abstract
UNLABELLED Astrocytes are the predominant cell type in the nervous system and play a significant role in maintaining neuronal health and homeostasis. Recently, astrocyte dysfunction has been implicated in the pathogenesis of many neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. Astrocytes are thus an attractive new target for drug discovery for neurological disorders. Using astrocytes differentiated from human embryonic stem cells, we have developed an assay to identify compounds that protect against oxidative stress, a condition associated with many neurodegenerative diseases. This phenotypic oxidative stress assay has been optimized for high-throughput screening in a 1,536-well plate format. From a screen of approximately 4,100 bioactive tool compounds and approved drugs, we identified a set of 22 that acutely protect human astrocytes from the consequences of hydrogen peroxide-induced oxidative stress. Nine of these compounds were also found to be protective of induced pluripotent stem cell-differentiated astrocytes in a related assay. These compounds are thought to confer protection through hormesis, activating stress-response pathways and preconditioning astrocytes to handle subsequent exposure to hydrogen peroxide. In fact, four of these compounds were found to activate the antioxidant response element/nuclear factor-E2-related factor 2 pathway, a protective pathway induced by toxic insults. Our results demonstrate the relevancy and utility of using astrocytes differentiated from human stem cells as a disease model for drug discovery and development. SIGNIFICANCE Astrocytes play a key role in neurological diseases. Drug discovery efforts that target astrocytes can identify novel therapeutics. Human astrocytes are difficult to obtain and thus are challenging to use for high-throughput screening, which requires large numbers of cells. Using human embryonic stem cell-derived astrocytes and an optimized astrocyte differentiation protocol, it was possible to screen approximately 4,100 compounds in titration to identify 22 that are cytoprotective of astrocytes. This study is the largest-scale high-throughput screen conducted using human astrocytes, with a total of 17,536 data points collected in the primary screen. The results demonstrate the relevancy and utility of using astrocytes differentiated from human stem cells as a disease model for drug discovery and development.
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Affiliation(s)
- Natasha Thorne
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Nasir Malik
- Laboratory of Stem Cell Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sonia Shah
- Laboratory of Stem Cell Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jean Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Bradley Class
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Francis Aguisanda
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - John C McKew
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Mahendra Rao
- NIH Center for Regenerative Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
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28
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Stalter D, O'Malley E, von Gunten U, Escher BI. Fingerprinting the reactive toxicity pathways of 50 drinking water disinfection by-products. WATER RESEARCH 2016; 91:19-30. [PMID: 26773486 DOI: 10.1016/j.watres.2015.12.047] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 12/02/2015] [Accepted: 12/28/2015] [Indexed: 05/08/2023]
Abstract
A set of nine in vitro cellular bioassays indicative of different stages of the cellular toxicity pathway was applied to 50 disinfection by-products (DBPs) to obtain a better understanding of the commonalities and differences in the molecular mechanisms of reactive toxicity of DBPs. An Eschericia coli test battery revealed reactivity towards proteins/peptides for 64% of the compounds. 98% activated the NRf2-mediated oxidative stress response and 68% induced an adaptive stress response to genotoxic effects as indicated by the activation of the tumor suppressor protein p53. All DBPs reactive towards DNA in the E. coli assay and activating p53 also induced oxidative stress, confirming earlier studies that the latter could trigger DBP's carcinogenicity. The energy of the lowest unoccupied molecular orbital ELUMO as reactivity descriptor was linearly correlated with oxidative stress induction for trihalomethanes (r(2)=0.98) and haloacetamides (r(2)=0.58), indicating that potency of these DBPs is connected to electrophilicity. However, the descriptive power was poor for haloacetic acids (HAAs) and haloacetonitriles (r(2) (<) 0.06). For HAAs, we additionally accounted for speciation by including the acidity constant with ELUMO in a two-parameter multiple linear regression model. This increased r(2) to >0.80, indicating that HAAs' potency is connected to both, electrophilicity and speciation. Based on the activation of oxidative stress response and the soft electrophilic character of most tested DBPs we hypothesize that indirect genotoxicity-e.g., through oxidative stress induction and/or enzyme inhibition-is more plausible than direct DNA damage for most investigated DBPs. The results provide not only a mechanistic understanding of the cellular effects of DBPs but the effect concentrations may also serve to evaluate mixture effects of DBPs in water samples.
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Affiliation(s)
- Daniel Stalter
- National Research Centre for Environmental Toxicology, Entox, The University of Queensland, Brisbane, Australia; Eawag, Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland.
| | - Elissa O'Malley
- National Research Centre for Environmental Toxicology, Entox, The University of Queensland, Brisbane, Australia
| | - Urs von Gunten
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland; School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Beate I Escher
- National Research Centre for Environmental Toxicology, Entox, The University of Queensland, Brisbane, Australia; Department of Cell Toxicology, UFZ - Helmholtz Centre for Environmental Research, Leipzig, Germany; Department of Environmental Toxicology, Center for Applied Geosciences, Eberhard Karls University, Tübingen, Germany
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29
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Huang R, Xia M, Sakamuru S, Zhao J, Shahane SA, Attene-Ramos M, Zhao T, Austin CP, Simeonov A. Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization. Nat Commun 2016; 7:10425. [PMID: 26811972 PMCID: PMC4777217 DOI: 10.1038/ncomms10425] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/10/2015] [Indexed: 02/06/2023] Open
Abstract
Target-specific, mechanism-oriented in vitro assays post a promising alternative to traditional animal toxicology studies. Here we report the first comprehensive analysis of the Tox21 effort, a large-scale in vitro toxicity screening of chemicals. We test ∼ 10,000 chemicals in triplicates at 15 concentrations against a panel of nuclear receptor and stress response pathway assays, producing more than 50 million data points. Compound clustering by structure similarity and activity profile similarity across the assays reveals structure-activity relationships that are useful for the generation of mechanistic hypotheses. We apply structural information and activity data to build predictive models for 72 in vivo toxicity end points using a cluster-based approach. Models based on in vitro assay data perform better in predicting human toxicity end points than animal toxicity, while a combination of structural and activity data results in better models than using structure or activity data alone. Our results suggest that in vitro activity profiles can be applied as signatures of compound mechanism of toxicity and used in prioritization for more in-depth toxicological testing.
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Affiliation(s)
- Ruili Huang
- Division of Pre-clinical Innovation, National Center for
Advancing Translational Sciences, National Institutes of Health, 9800 Medical
Center Drive, Rockville, Maryland
20850, USA
| | - Menghang Xia
- Division of Pre-clinical Innovation, National Center for
Advancing Translational Sciences, National Institutes of Health, 9800 Medical
Center Drive, Rockville, Maryland
20850, USA
| | - Srilatha Sakamuru
- Division of Pre-clinical Innovation, National Center for
Advancing Translational Sciences, National Institutes of Health, 9800 Medical
Center Drive, Rockville, Maryland
20850, USA
| | - Jinghua Zhao
- Division of Pre-clinical Innovation, National Center for
Advancing Translational Sciences, National Institutes of Health, 9800 Medical
Center Drive, Rockville, Maryland
20850, USA
| | - Sampada A. Shahane
- Division of Pre-clinical Innovation, National Center for
Advancing Translational Sciences, National Institutes of Health, 9800 Medical
Center Drive, Rockville, Maryland
20850, USA
| | - Matias Attene-Ramos
- Division of Pre-clinical Innovation, National Center for
Advancing Translational Sciences, National Institutes of Health, 9800 Medical
Center Drive, Rockville, Maryland
20850, USA
| | - Tongan Zhao
- Division of Pre-clinical Innovation, National Center for
Advancing Translational Sciences, National Institutes of Health, 9800 Medical
Center Drive, Rockville, Maryland
20850, USA
| | - Christopher P. Austin
- Division of Pre-clinical Innovation, National Center for
Advancing Translational Sciences, National Institutes of Health, 9800 Medical
Center Drive, Rockville, Maryland
20850, USA
| | - Anton Simeonov
- Division of Pre-clinical Innovation, National Center for
Advancing Translational Sciences, National Institutes of Health, 9800 Medical
Center Drive, Rockville, Maryland
20850, USA
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30
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Zhao J, Shukla SJ, Xia M. Cell-Based Assay for Identifying the Modulators of Antioxidant Response Element Signaling Pathway. Methods Mol Biol 2016; 1473:55-62. [PMID: 27518623 PMCID: PMC9922478 DOI: 10.1007/978-1-4939-6346-1_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The antioxidant response element (ARE) signaling pathway plays an important role in the amelioration of cellular oxidative stress. Thus, assays that detect this pathway can be useful for identifying chemicals that induce or inhibit oxidative stress signaling. The focus of this chapter is to describe a cell-based ARE assay in a quantitative high-throughput screening (qHTS) format to test a large collection of compounds that induce nuclear factor erythroid 2-related factor (Nrf2)/ARE signaling. The assay is described through cell handling, assay preparation, and instrument usage.
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Affiliation(s)
| | | | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Building C, MSC: 3375, 9800 Medical Center Drive, Bethesda, MD, 20892, USA.
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31
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Jin L, Gaus C, Escher BI. Adaptive stress response pathways induced by environmental mixtures of bioaccumulative chemicals in dugongs. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:6963-6973. [PMID: 25923886 DOI: 10.1021/acs.est.5b00947] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
To address the poorly understood mixture effects of chemicals in the marine mammal dugong, we coupled equilibrium-based passive sampling in blubber to a range of in vitro bioassays for screening mixtures of bioaccumulative chemicals. The modes of action included early effect indicators along important toxicity pathways, such as induction of xenobiotic metabolism, and some integrative indicators downstream of the molecular initiating event, such as adaptive stress responses. Activation of aryl hydrocarbon receptor (AhR) and Nrf2-mediated oxidative stress response were found to be the most prominent effects, while the p53-mediated DNA damage response and NF-κB-mediated response to inflammation were not significantly affected. Although polychlorinated dibenzo-p-dioxins (PCDDs) quantified in the samples accounted for the majority of AhR-mediated activity, PCDDs explained less than 5% of the total oxidative stress response, despite their known ability to activate this pathway. Altered oxidative stress response was observed with both individual chemicals and blubber extracts subject to metabolic activation by rat liver S9 fraction. Metabolic activation resulted in both enhanced and reduced toxicity, suggesting the relevance and utility of incorporating metabolic enzymes into in vitro bioassays. Our approach provides a first insight into the burden of toxicologically relevant bioaccumulative chemical mixtures in dugongs and can be applied to lipid tissue of other wildlife species.
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Affiliation(s)
- Ling Jin
- †The University of Queensland, National Research Centre for Environmental Toxicology (Entox), Brisbane, QLD 4018, Australia
| | - Caroline Gaus
- †The University of Queensland, National Research Centre for Environmental Toxicology (Entox), Brisbane, QLD 4018, Australia
| | - Beate I Escher
- †The University of Queensland, National Research Centre for Environmental Toxicology (Entox), Brisbane, QLD 4018, Australia
- ‡UFZ - Helmholtz Centre for Environmental Research, Cell Toxicology, 04318 Leipzig, Germany
- ∥Eberhard Karls University Tübingen, Environmental Toxicology, Center for Applied Geosciences, 72074 Tübingen, Germany
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32
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Harrison R. 2013 Lush Science Prize. Altern Lab Anim 2015; 42:395-402. [PMID: 25635648 DOI: 10.1177/026119291404200609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The annual Lush Science Prize is designed to reward outstanding contributions to 21st Century Toxicology Research. A Background Paper is prepared each year prior to the judging process, in order to provide the judging panel with a brief overview of current developments in the field of Replacement alternatives, particularly those relevant to the concept of toxicity pathways. The Background Paper includes information on some key institutional developments in the area--such as the OECD's Adverse Outcome Pathway Project, the Hamner Institute's work, and the Human Toxome Project, and on the phenomenon of collaborative computer systems relevant to the field. From the literature review that was also performed as part of the background research, the two papers receiving the highest score were recommended for consideration by the judges for the 2013 Science Prize.
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Horinouchi Y, Summers FA, Ehrenshaft M, Mason RP. Free radical generation from an aniline derivative in HepG2 cells: a possible captodative effect. Free Radic Biol Med 2015; 78:111-7. [PMID: 25450331 DOI: 10.1016/j.freeradbiomed.2014.10.577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 10/17/2014] [Accepted: 10/27/2014] [Indexed: 11/23/2022]
Abstract
Xenobiotic metabolism can induce the generation of protein radicals, which are believed to play an important role in the toxicity of chemicals and drugs. It is therefore important to identify chemical structures capable of inducing macromolecular free radical formation in living cells. In this study, we evaluated the ability of four structurally related environmental chemicals, aniline, nitrosobenzene, N,N-dimethylaniline, and N,N-dimethyl-4-nitrosoaniline (DMNA), to induce free radicals and cellular damage in the hepatoma cell line HepG2. Cytotoxicity was assessed using lactate dehydrogenase assays, and morphological changes were observed using phase contrast microscopy. Protein free radicals were detected by immuno-spin trapping using in-cell western experiments and confocal microscopy to determine the subcellular locale of free radical generation. DMNA induced free radical generation, lactate dehydrogenase release, and morphological changes in HepG2 cells, whereas aniline, nitrosobenzene, N,N-dimethylaniline did not. Confocal microscopy showed that DMNA induced free radical generation mainly in the cytosol. Preincubation of HepG2 cells with N-acetylcysteine and 2,2'-dipyridyl significantly prevented free radical generation on subsequent incubation with DMNA, whereas preincubation with apocynin and dimethyl sulfoxide had no effect. These results suggest that DMNA is metabolized to reactive free radicals capable of generating protein radicals which may play a critical role in DMNA toxicity. We propose that the captodative effect, the combined action of the electron-releasing dimethylamine substituent, and the electron-withdrawing nitroso substituent, leads to a thermodynamically stabilized radical, facilitating enhanced protein radical formation by DMNA.
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Affiliation(s)
- Yuya Horinouchi
- Free Radical Metabolism Group, Laboratory of Toxicology and Pharmacology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| | - Fiona A Summers
- Free Radical Metabolism Group, Laboratory of Toxicology and Pharmacology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| | - Marilyn Ehrenshaft
- Free Radical Metabolism Group, Laboratory of Toxicology and Pharmacology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| | - Ronald P Mason
- Free Radical Metabolism Group, Laboratory of Toxicology and Pharmacology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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Tice RR, Austin CP, Kavlock RJ, Bucher JR. Improving the human hazard characterization of chemicals: a Tox21 update. ENVIRONMENTAL HEALTH PERSPECTIVES 2013; 121:756-65. [PMID: 23603828 PMCID: PMC3701992 DOI: 10.1289/ehp.1205784] [Citation(s) in RCA: 414] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 04/18/2013] [Indexed: 05/17/2023]
Abstract
BACKGROUND In 2008, the National Institute of Environmental Health Sciences/National Toxicology Program, the U.S. Environmental Protection Agency's National Center for Computational Toxicology, and the National Human Genome Research Institute/National Institutes of Health Chemical Genomics Center entered into an agreement on "high throughput screening, toxicity pathway profiling, and biological interpretation of findings." In 2010, the U.S. Food and Drug Administration (FDA) joined the collaboration, known informally as Tox21. OBJECTIVES The Tox21 partners agreed to develop a vision and devise an implementation strategy to shift the assessment of chemical hazards away from traditional experimental animal toxicology studies to one based on target-specific, mechanism-based, biological observations largely obtained using in vitro assays. DISCUSSION Here we outline the efforts of the Tox21 partners up to the time the FDA joined the collaboration, describe the approaches taken to develop the science and technologies that are currently being used, assess the current status, and identify problems that could impede further progress as well as suggest approaches to address those problems. CONCLUSION Tox21 faces some very difficult issues. However, we are making progress in integrating data from diverse technologies and end points into what is effectively a systems-biology approach to toxicology. This can be accomplished only when comprehensive knowledge is obtained with broad coverage of chemical and biological/toxicological space. The efforts thus far reflect the initial stage of an exceedingly complicated program, one that will likely take decades to fully achieve its goals. However, even at this stage, the information obtained has attracted the attention of the international scientific community, and we believe these efforts foretell the future of toxicology.
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Affiliation(s)
- Raymond R Tice
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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35
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Pals J, Attene-Ramos MS, Xia M, Wagner ED, Plewa MJ. Human cell toxicogenomic analysis linking reactive oxygen species to the toxicity of monohaloacetic acid drinking water disinfection byproducts. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:12514-23. [PMID: 24050308 PMCID: PMC4014314 DOI: 10.1021/es403171b] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Chronic exposure to drinking water disinfection byproducts has been linked to adverse health risks. The monohaloacetic acids (monoHAAs) are generated as byproducts during the disinfection of drinking water and are cytotoxic, genotoxic, mutagenic, and teratogenic. Iodoacetic acid toxicity was mitigated by antioxidants, suggesting the involvement of oxidative stress. Other monoHAAs may share a similar mode of action. Each monoHAA generated a significant concentration-response increase in the expression of a β-lactamase reporter under the control of the antioxidant response element (ARE). The monoHAAs generated oxidative stress with a rank order of iodoacetic acid (IAA) > bromoacetic acid (BAA) ≫ chloroacetic acid (CAA); this rank order was observed with other toxicological end points. Toxicogenomic analysis was conducted with a nontransformed human intestinal epithelial cell line (FHs 74 Int). Exposure to the monoHAAs altered the transcription levels of multiple oxidative stress responsive genes, indicating that each exposure generated oxidative stress. The transcriptome profiles showed an increase in thioredoxin reductase 1 (TXNRD1) and sulfiredoxin (SRXN1), suggesting peroxiredoxin proteins had been oxidized during monoHAA exposures. Three possible sources of reactive oxygen species were identified, the hypohalous acid generating peroxidase enzymes lactoperoxidase (LPO) and myeloperoxidase (MPO), nicotinamide adenine dinucleotide phosphate (NADPH)-dependent oxidase 5 (NOX5), and PTGS2 (COX-2) mediated arachidonic acid metabolism. Each monoHAA exposure caused an increase in COX-2 mRNA levels. These data provide a functional association between monoHAA exposure and adverse health outcomes such as oxidative stress, inflammation, and cancer.
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Affiliation(s)
- Justin Pals
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, U.S.A
| | - Matias S. Attene-Ramos
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, U.S.A
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, U.S.A
| | - Elizabeth D. Wagner
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, U.S.A
- Safe Global Water Institute and NSF Science and Technology, Center of Advanced Materials for the Purification of Water with Systems, University of Illinois at Urbana-Champaign, Urbana, IL, U.S.A
| | - Michael J. Plewa
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, U.S.A
- Safe Global Water Institute and NSF Science and Technology, Center of Advanced Materials for the Purification of Water with Systems, University of Illinois at Urbana-Champaign, Urbana, IL, U.S.A
- Corresponding Author, Phone: 217-333-3614;
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Escher BI, Dutt M, Maylin E, Tang JYM, Toze S, Wolf CR, Lang M. Water quality assessment using the AREc32 reporter gene assay indicative of the oxidative stress response pathway. ACTA ACUST UNITED AC 2012; 14:2877-85. [PMID: 23032559 DOI: 10.1039/c2em30506b] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The reporter gene assay AREc32 is based on the induction of the Nrf2 mediated oxidative stress response pathway in the human breast cancer cell line MCF7, where eight copies of the antioxidant response element (ARE) are linked to a reporter gene encoding for luciferase. The Nrf2-ARE pathway is responsive to many chemicals that cause oxidative stress, among them a large number of pesticides and skin irritants. We adopted and validated the AREc32 bioassay for water quality testing. tert-Butylhydroquinone served as the positive control, phenol as the negative control and other reactive chemicals were assessed for their specificity. An environmentally relevant reference chemical, benzo(a)pyrene was the most potent inducer of all tested chemicals. The concentration causing an induction ratio (IR) of 1.5 (EC(IR1.5)) was chosen as the effect benchmark value. The assay was applied to 21 water samples ranging from sewage to drinking water, including secondary treatment and various tertiary treatment options (ozonation, biologically activated carbon filtration, membrane filtration, reverse osmosis, advanced oxidation, chlorination, chloramination). The samples were enriched by solid phase extraction. In most samples the oxidative stress response was far more sensitive than cytotoxicity. The primary and secondary treated effluent exceeded the effect threshold IR 1.5 at a relative enrichment factor (REF) of 1, i.e., the native samples were active. All tertiary treated samples were less potent and their EC(IR1.5) lay between REF 1 and 10. The Nrf2 pathway was induced at a REF of approximately 10 for surface waters and drinking water, and above this enrichment cytotoxicity took over in most samples and quenched the induction. The blank (ultrapure water run through the sample enrichment process) was cytotoxic at an REF of 100, which is the limit of concentrations range that can be evaluated. Treatment typically decreased both the cytotoxicity and oxidative stress response apart from drinking water treatment where chlorination caused an increase in oxidative stress response, presumably due to the formation of disinfection by-products. This study demonstrates the relevance and applicability of the oxidative stress response pathway for water quality monitoring.
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Affiliation(s)
- Beate I Escher
- National Research Centre for Environmental Toxicology (Entox), The University of Queensland, Brisbane, QLD 4108, Australia.
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