1
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Achar J, Cronin MTD, Firman JW, Öberg G. A problem formulation framework for the application of in silico toxicology methods in chemical risk assessment. Arch Toxicol 2024; 98:1727-1740. [PMID: 38555325 PMCID: PMC11106140 DOI: 10.1007/s00204-024-03721-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/29/2024] [Indexed: 04/02/2024]
Abstract
The first step in the hazard or risk assessment of chemicals should be to formulate the problem through a systematic and iterative process aimed at identifying and defining factors critical to the assessment. However, no general agreement exists on what components an in silico toxicology problem formulation (PF) should include. The present work aims to develop a PF framework relevant to the application of in silico models for chemical toxicity prediction. We modified and applied a PF framework from the general risk assessment literature to peer reviewed papers describing PFs associated with in silico toxicology models. Important gaps between the general risk assessment literature and the analyzed PF literature associated with in silico toxicology methods were identified. While the former emphasizes the need for PFs to address higher-level conceptual questions, the latter does not. There is also little consistency in the latter regarding the PF components addressed, reinforcing the need for a PF framework that enable users of in silico toxicology models to answer the central conceptual questions aimed at defining components critical to the model application. Using the developed framework, we highlight potential areas of uncertainty manifestation in in silico toxicology PF in instances where particular components are missing or implicitly described. The framework represents the next step in standardizing in silico toxicology PF component. The framework can also be used to improve the understanding of how uncertainty is apparent in an in silico toxicology PF, thus facilitating ways to address uncertainty.
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Affiliation(s)
- Jerry Achar
- Institute for Resources Environment, and Sustainability, The University of British Columbia, 2202 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Mark T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK.
| | - James W Firman
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Gunilla Öberg
- Institute for Resources Environment, and Sustainability, The University of British Columbia, 2202 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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2
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Wang K, Kim N, Bagherian M, Li K, Chou E, Colacino JA, Dolinoy DC, Sartor MA. Gene Target Prediction of Environmental Chemicals Using Coupled Matrix-Matrix Completion. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:5889-5898. [PMID: 38501580 PMCID: PMC11131040 DOI: 10.1021/acs.est.4c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Human exposure to toxic chemicals presents a huge health burden. Key to understanding chemical toxicity is knowledge of the molecular target(s) of the chemicals. Because a comprehensive safety assessment for all chemicals is infeasible due to limited resources, a robust computational method for discovering targets of environmental exposures is a promising direction for public health research. In this study, we implemented a novel matrix completion algorithm named coupled matrix-matrix completion (CMMC) for predicting direct and indirect exposome-target interactions, which exploits the vast amount of accumulated data regarding chemical exposures and their molecular targets. Our approach achieved an AUC of 0.89 on a benchmark data set generated using data from the Comparative Toxicogenomics Database. Our case studies with bisphenol A and its analogues, PFAS, dioxins, PCBs, and VOCs show that CMMC can be used to accurately predict molecular targets of novel chemicals without any prior bioactivity knowledge. Our results demonstrate the feasibility and promise of computationally predicting environmental chemical-target interactions to efficiently prioritize chemicals in hazard identification and risk assessment.
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Affiliation(s)
- Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicole Kim
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maryam Bagherian
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Institute for Data Science (MIDAS), University of Michigan, Ann Arbor, MI 48109, USA
| | - Kai Li
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elysia Chou
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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3
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Dawson DE, Lau C, Pradeep P, Sayre RR, Judson RS, Tornero-Velez R, Wambaugh JF. A Machine Learning Model to Estimate Toxicokinetic Half-Lives of Per- and Polyfluoro-Alkyl Substances (PFAS) in Multiple Species. TOXICS 2023; 11:98. [PMID: 36850973 PMCID: PMC9962572 DOI: 10.3390/toxics11020098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are a diverse group of man-made chemicals that are commonly found in body tissues. The toxicokinetics of most PFAS are currently uncharacterized, but long half-lives (t½) have been observed in some cases. Knowledge of chemical-specific t½ is necessary for exposure reconstruction and extrapolation from toxicological studies. We used an ensemble machine learning method, random forest, to model the existing in vivo measured t½ across four species (human, monkey, rat, mouse) and eleven PFAS. Mechanistically motivated descriptors were examined, including two types of surrogates for renal transporters: (1) physiological descriptors, including kidney geometry, for renal transporter expression and (2) structural similarity of defluorinated PFAS to endogenous chemicals for transporter affinity. We developed a classification model for t½ (Bin 1: <12 h; Bin 2: <1 week; Bin 3: <2 months; Bin 4: >2 months). The model had an accuracy of 86.1% in contrast to 32.2% for a y-randomized null model. A total of 3890 compounds were within domain of the model, and t½ was predicted using the bin medians: 4.9 h, 2.2 days, 33 days, and 3.3 years. For human t½, 56% of PFAS were classified in Bin 4, 7% were classified in Bin 3, and 37% were classified in Bin 2. This model synthesizes the limited available data to allow tentative extrapolation and prioritization.
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Affiliation(s)
- Daniel E. Dawson
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA
| | - Christopher Lau
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Public Health and Environmental Assessment, 109 T.W. Alexander Drive, Research Triangle Park, NC 277011, USA
| | - Prachi Pradeep
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA
- Oak Ridge Institutes for Science and Education, Oak Ridge, TN 37830, USA
| | - Risa R. Sayre
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA
| | - Richard S. Judson
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA
| | - Rogelio Tornero-Velez
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA
| | - John F. Wambaugh
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, 109 T.W. Alexander Drive, Research Triangle Park, NC 27711, USA
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4
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Boyce M, Favela KA, Bonzo JA, Chao A, Lizarraga LE, Moody LR, Owens EO, Patlewicz G, Shah I, Sobus JR, Thomas RS, Williams AJ, Yau A, Wambaugh JF. Identifying xenobiotic metabolites with in silico prediction tools and LCMS suspect screening analysis. FRONTIERS IN TOXICOLOGY 2023; 5:1051483. [PMID: 36742129 PMCID: PMC9889941 DOI: 10.3389/ftox.2023.1051483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Understanding the metabolic fate of a xenobiotic substance can help inform its potential health risks and allow for the identification of signature metabolites associated with exposure. The need to characterize metabolites of poorly studied or novel substances has shifted exposure studies towards non-targeted analysis (NTA), which often aims to profile many compounds within a sample using high-resolution liquid-chromatography mass-spectrometry (LCMS). Here we evaluate the suitability of suspect screening analysis (SSA) liquid-chromatography mass-spectrometry to inform xenobiotic chemical metabolism. Given a lack of knowledge of true metabolites for most chemicals, predictive tools were used to generate potential metabolites as suspect screening lists to guide the identification of selected xenobiotic substances and their associated metabolites. Thirty-three substances were selected to represent a diverse array of pharmaceutical, agrochemical, and industrial chemicals from Environmental Protection Agency's ToxCast chemical library. The compounds were incubated in a metabolically-active in vitro assay using primary hepatocytes and the resulting supernatant and lysate fractions were analyzed with high-resolution LCMS. Metabolites were simulated for each compound structure using software and then combined to serve as the suspect screening list. The exact masses of the predicted metabolites were then used to select LCMS features for fragmentation via tandem mass spectrometry (MS/MS). Of the starting chemicals, 12 were measured in at least one sample in either positive or negative ion mode and a subset of these were used to develop the analysis workflow. We implemented a screening level workflow for background subtraction and the incorporation of time-varying kinetics into the identification of likely metabolites. We used haloperidol as a case study to perform an in-depth analysis, which resulted in identifying five known metabolites and five molecular features that represent potential novel metabolites, two of which were assigned discrete structures based on in silico predictions. This workflow was applied to five additional test chemicals, and 15 molecular features were selected as either reported metabolites, predicted metabolites, or potential metabolites without a structural assignment. This study demonstrates that in some-but not all-cases, suspect screening analysis methods provide a means to rapidly identify and characterize metabolites of xenobiotic chemicals.
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Affiliation(s)
- Matthew Boyce
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | | | - Jessica A. Bonzo
- Thermo Fisher Scientific, South San Francisco, CA, United States
| | - Alex Chao
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Lucina E. Lizarraga
- Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, United States
| | - Laura R. Moody
- Thermo Fisher Scientific, South San Francisco, CA, United States
| | - Elizabeth O. Owens
- Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, United States
| | - Grace Patlewicz
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Imran Shah
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Jon R. Sobus
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Russell S. Thomas
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Antony J. Williams
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Alice Yau
- Southwest Research Institute, San Antonio, TX, United States
| | - John F. Wambaugh
- Center for Computational Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States,*Correspondence: John F. Wambaugh,
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5
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Lambert JC. Adverse Outcome Pathway 'Footprinting': A Novel Approach to the Integration of 21st Century Toxicology Information into Chemical Mixtures Risk Assessment. TOXICS 2022; 11:37. [PMID: 36668763 PMCID: PMC9860797 DOI: 10.3390/toxics11010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
For over a decade, New Approach Methodologies (NAMs) such as structure-activity/read-across, -omics technologies, and Adverse Outcome Pathway (AOP), have been considered within regulatory communities as alternative sources of chemical and biological information potentially relevant to human health risk assessment. Integration of NAMs into applications such as chemical mixtures risk assessment has been limited due to the lack of validation of qualitative and quantitative application to adverse health outcomes in vivo, and acceptance by risk assessors. However, leveraging existent hazard and dose-response information, including NAM-based data, for mixture component chemicals across one or more levels of biological organization using novel approaches such as AOP 'footprinting' proposed herein, may significantly advance mixtures risk assessment. AOP footprinting entails the systematic stepwise profiling and comparison of all known or suspected AOPs involved in a toxicological effect at the level of key event (KE). The goal is to identify key event(s) most proximal to an adverse outcome within each AOP suspected of contributing to a given health outcome at which similarity between mixture chemicals can be confidently determined. These key events are identified as the 'footprint' for a given AOP. This work presents the general concept, and a hypothetical example application, of AOP footprinting as a key methodology for the integration of NAM data into mixtures risk assessment.
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Affiliation(s)
- Jason C Lambert
- United States Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Cincinnati, OH 45268, USA
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6
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Lizarraga LE, Suter GW, Lambert JC, Patlewicz G, Zhao JQ, Dean JL, Kaiser P. Advancing the science of a read-across framework for evaluation of data-poor chemicals incorporating systematic and new approach methods. Regul Toxicol Pharmacol 2022; 137:105293. [PMID: 36414101 DOI: 10.1016/j.yrtph.2022.105293] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/18/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022]
Abstract
The assessment of human health hazards posed by chemicals traditionally relies on toxicity studies in experimental animals. However, most chemicals currently in commerce do not meet the minimum data requirements for hazard identification and dose-response analysis in human health risk assessment. Previously, we introduced a read-across framework designed to address data gaps for screening-level assessment of chemicals with insufficient in vivo toxicity information (Wang et al., 2012). It relies on inference by analogy from suitably tested source analogues to a target chemical, based on structural, toxicokinetic, and toxicodynamic similarity. This approach has been used for dose-response assessment of data-poor chemicals relevant to the U.S. EPA's Superfund program. We present herein, case studies of the application of this framework, highlighting specific examples of the use of biological similarity for chemical grouping and quantitative read-across. Based on practical knowledge and technological advances in the fields of read-across and predictive toxicology, we propose a revised framework. It includes important considerations for problem formulation, systematic review, target chemical analysis, analogue identification, analogue evaluation, and incorporation of new approach methods. This work emphasizes the integration of systematic methods and alternative toxicity testing data and tools in chemical risk assessment to inform regulatory decision-making.
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Affiliation(s)
- Lucina E Lizarraga
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, 26 W. Martin L. King Drive, Cincinnati, OH, 45268, USA.
| | - Glenn W Suter
- Office of Research and Development, Emeritus, U.S. Environmental Protection Agency, 26 W. Martin L. King Drive, Cincinnati, OH, 45268, USA
| | - Jason C Lambert
- Center for Computational Toxicology & Exposure (CCTE), U.S. Environmental Protection Agency, Research Triangle Park, NC, 27709, USA
| | - Grace Patlewicz
- Center for Computational Toxicology & Exposure (CCTE), U.S. Environmental Protection Agency, Research Triangle Park, NC, 27709, USA
| | - Jay Q Zhao
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, 26 W. Martin L. King Drive, Cincinnati, OH, 45268, USA
| | - Jeffry L Dean
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, 26 W. Martin L. King Drive, Cincinnati, OH, 45268, USA
| | - Phillip Kaiser
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, 26 W. Martin L. King Drive, Cincinnati, OH, 45268, USA
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7
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Boyce M, Meyer B, Grulke C, Lizarraga L, Patlewicz G. Comparing the performance and coverage of selected in silico (liver) metabolism tools relative to reported studies in the literature to inform analogue selection in read-across: A case study. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 21:1-15. [PMID: 35386221 PMCID: PMC8979226 DOI: 10.1016/j.comtox.2021.100208] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Changes in the regulatory landscape of chemical safety assessment call for the use of New Approach Methodologies (NAMs) including read-across to fill data gaps. One critical aspect of analogue evaluation is the extent to which target and source analogues are metabolically similar. In this study, a set of 37 structurally diverse chemicals were compiled from the EPA ToxCast inventory to compare and contrast a selection of metabolism in silico tools, in terms of their coverage and performance relative to metabolism information reported in the literature. The aim was to build understanding of the scope and capabilities of these tools and how they could be utilised in a read-across assessment. The tools were Systematic Generation of Metabolites (SyGMa), Meteor Nexus, BioTransformer, Tissue Metabolism Simulator (TIMES), OECD Toolbox, and Chemical Transformation Simulator (CTS). Performance was characterised by sensitivity and precision determined by comparing predictions against literature reported metabolites (from 44 publications). A coverage score was derived to provide a relative quantitative comparison between the tools. Meteor, TIMES, Toolbox, and CTS predictions were run in batch mode, using default settings. SyGMa and BioTransformer were run with user-defined settings, (two passes of phase I and one pass of phase II). Hierarchical clustering revealed high similarity between TIMES and Toolbox. SyGMa had the highest coverage, matching an average of 38.63% of predictions generated by the other tools though was prone to significant overprediction. It generated 5,125 metabolites, which represented 54.67% of all predictions. Precision and sensitivity values ranged from 1.1-29% and 14.7-28.3% respectively. The Toolbox had the highest performance overall. A case study was presented for 3,4-Toluenediamine (3,4-TDA), assessed for the derivation of screening-level Provisional Peer Reviewed Toxicity Values (PPRTVs), was used to demonstrate the practical role in silico metabolism information can play in analogue evaluation as part of a read-across approach.
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Affiliation(s)
- Matthew Boyce
- Oak Ridge Associated University, Oak Ridge, TN, 37830, USA
- Center for Computational Toxicology & Exposure (CCTE), U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, 27709, USA
| | - Brian Meyer
- Center for Computational Toxicology & Exposure (CCTE), U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, 27709, USA
| | - Chris Grulke
- Center for Computational Toxicology & Exposure (CCTE), U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, 27709, USA
| | - Lucina Lizarraga
- Center for Public Human Health and Environmental Assessment (CPHEA), U.S. Environmental Protection Agency, Cincinnati, OH, USA
| | - Grace Patlewicz
- Center for Computational Toxicology & Exposure (CCTE), U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, 27709, USA
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8
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Suter GW, Lizarraga LE. Clearly weighing the evidence in read-across can improve assessments of data-poor chemicals. Regul Toxicol Pharmacol 2021; 129:105111. [PMID: 34973387 DOI: 10.1016/j.yrtph.2021.105111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 02/07/2023]
Abstract
This paper provides a systematic weight-of-evidence method for read-across analyses of data-poor chemicals. The read-across technique extrapolates toxicity from analogous chemicals for which suitable test data are available to a target chemical. To determine that a candidate analogue is the 'best' and is sufficiently similar, the evidence for similarity of each candidate analogue to the target is weighed. We present a systematic weight of evidence method that provides transparency and imposes a consistent and rigorous inferential process. The method assembles relevant information concerning structure, physicochemical attributes, toxicokinetics, and toxicodynamics of the target and analogues. The information is then organized by evidence types and subtypes and weighted in terms of properties: relevance, strength, and reliability into weight levels, expressed as symbols. After evidence types are weighted, the bodies of evidence are weighted for collective properties: number, diversity, and coherence. Finally, the weights for the types and bodies of evidence are weighed for each analogue, and, if the overall weight of evidence is sufficient for one or more analogues, the analogue with the greatest weight is used to estimate the endpoint effect. We illustrate this WoE approach with a read-across analysis for screening the organochlorine contaminant, p,p'-dichlorodiphenyldichloroethane (DDD), for noncancer oral toxicity.
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Affiliation(s)
- Glenn W Suter
- Office of Research and Development, Emeritus, U.S. Environmental Protection Agency, 26 W. Martin L. King Drive, Cincinnati, OH, 45268, USA.
| | - Lucina E Lizarraga
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, 26 W. Martin L. King Drive, Cincinnati, OH, 45268, USA.
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9
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Zhong S, Zhang K, Bagheri M, Burken JG, Gu A, Li B, Ma X, Marrone BL, Ren ZJ, Schrier J, Shi W, Tan H, Wang T, Wang X, Wong BM, Xiao X, Yu X, Zhu JJ, Zhang H. Machine Learning: New Ideas and Tools in Environmental Science and Engineering. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:12741-12754. [PMID: 34403250 DOI: 10.1021/acs.est.1c01339] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The rapid increase in both the quantity and complexity of data that are being generated daily in the field of environmental science and engineering (ESE) demands accompanied advancement in data analytics. Advanced data analysis approaches, such as machine learning (ML), have become indispensable tools for revealing hidden patterns or deducing correlations for which conventional analytical methods face limitations or challenges. However, ML concepts and practices have not been widely utilized by researchers in ESE. This feature explores the potential of ML to revolutionize data analysis and modeling in the ESE field, and covers the essential knowledge needed for such applications. First, we use five examples to illustrate how ML addresses complex ESE problems. We then summarize four major types of applications of ML in ESE: making predictions; extracting feature importance; detecting anomalies; and discovering new materials or chemicals. Next, we introduce the essential knowledge required and current shortcomings in ML applications in ESE, with a focus on three important but often overlooked components when applying ML: correct model development, proper model interpretation, and sound applicability analysis. Finally, we discuss challenges and future opportunities in the application of ML tools in ESE to highlight the potential of ML in this field.
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Affiliation(s)
- Shifa Zhong
- Department of Civil and Environmental Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Kai Zhang
- Department of Civil and Environmental Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Majid Bagheri
- Department of Civil, Architectural, and Environmental Engineering, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Joel G Burken
- Department of Civil, Architectural, and Environmental Engineering, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - April Gu
- Department of Civil and Environmental Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Baikun Li
- Department of Civil and Environmental Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Xingmao Ma
- Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, 77843, United States
| | - Babetta L Marrone
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Zhiyong Jason Ren
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Joshua Schrier
- Department of Chemistry, Fordham University, The Bronx, New York 10458 United States
| | - Wei Shi
- School of Environment, Nanjing University, Nanjing, 210093 China
| | - Haoyue Tan
- School of Environment, Nanjing University, Nanjing, 210093 China
| | - Tianbao Wang
- Department of Civil and Environmental Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Xu Wang
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Bryan M Wong
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, University of California-Riverside, Riverside, California 92521 United States
| | - Xusheng Xiao
- Department of Computer and Data Sciences, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Xiong Yu
- Department of Civil and Environmental Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Jun-Jie Zhu
- Department of Civil and Environmental Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Huichun Zhang
- Department of Civil and Environmental Engineering, Case Western Reserve University, Cleveland, Ohio 44106, United States
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10
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Hisaki T, Kaneko MAN, Hirota M, Matsuoka M, Kouzuki H. Integration of read-across and artificial neural network-based QSAR models for predicting systemic toxicity: A case study for valproic acid. J Toxicol Sci 2020; 45:95-108. [PMID: 32062621 DOI: 10.2131/jts.45.95] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We present a systematic, comprehensive and reproducible weight-of-evidence approach for predicting the no-observed-adverse-effect level (NOAEL) for systemic toxicity by using read-across and quantitative structure-activity relationship (QSAR) models to fill gaps in rat repeated-dose and developmental toxicity data. As a case study, we chose valproic acid, a developmental toxicant in humans and animals. High-quality in vivo oral rat repeated-dose and developmental toxicity data were available for five and nine analogues, respectively, and showed qualitative consistency, especially for developmental toxicity. Similarity between the target and analogues is readily defined computationally, and data uncertainties associated with the similarities in structural, physico-chemical and toxicological properties, including toxicophores, were low. Uncertainty associated with metabolic similarity is low-to-moderate, largely because the approach was limited to in silico prediction to enable systematic and objective data collection. Uncertainty associated with completeness of read-across was reduced by including in vitro and in silico metabolic data and expanding the experimental animal database. Taking the "worst-case" approach, the smallest NOAEL values among the analogs (i.e., 200 and 100 mg/kg/day for repeated-dose and developmental toxicity, respectively) were read-across to valproic acid. Our previous QSAR models predict repeated-dose NOAEL of 148 (males) and 228 (females) mg/kg/day, and developmental toxicity NOAEL of 390 mg/kg/day for valproic acid. Based on read-across and QSAR, the conservatively predicted NOAEL is 148 mg/kg/day for repeated-dose toxicity, and 100 mg/kg/day for developmental toxicity. Experimental values are 341 mg/kg/day and 100 mg/kg/day, respectively. The present approach appears promising for quantitative and qualitative in silico systemic toxicity prediction of untested chemicals.
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Affiliation(s)
- Tomoka Hisaki
- Shiseido Global Innovation Center.,Department of Hygiene and Public Health, Tokyo Women's Medical University
| | | | | | - Masato Matsuoka
- Department of Hygiene and Public Health, Tokyo Women's Medical University
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11
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Karmaus AL, Bialk H, Fitzpatrick S, Krishan M. State of the science on alternatives to animal testing and integration of testing strategies for food safety assessments: Workshop proceedings. Regul Toxicol Pharmacol 2020; 110:104515. [DOI: 10.1016/j.yrtph.2019.104515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/24/2019] [Accepted: 11/03/2019] [Indexed: 12/31/2022]
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12
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Krewski D, Andersen ME, Tyshenko MG, Krishnan K, Hartung T, Boekelheide K, Wambaugh JF, Jones D, Whelan M, Thomas R, Yauk C, Barton-Maclaren T, Cote I. Toxicity testing in the 21st century: progress in the past decade and future perspectives. Arch Toxicol 2019; 94:1-58. [DOI: 10.1007/s00204-019-02613-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022]
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13
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Patlewicz G, Lizarraga LE, Rua D, Allen DG, Daniel AB, Fitzpatrick SC, Garcia-Reyero N, Gordon J, Hakkinen P, Howard AS, Karmaus A, Matheson J, Mumtaz M, Richarz AN, Ruiz P, Scarano L, Yamada T, Kleinstreuer N. Exploring current read-across applications and needs among selected U.S. Federal Agencies. Regul Toxicol Pharmacol 2019; 106:197-209. [PMID: 31078681 PMCID: PMC6814248 DOI: 10.1016/j.yrtph.2019.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/27/2019] [Accepted: 05/08/2019] [Indexed: 10/26/2022]
Abstract
Read-across is a well-established data gap-filling technique applied for regulatory purposes. In US Environmental Protection Agency's New Chemicals Program under TSCA, read-across has been used extensively for decades, however the extent of application and acceptance of read-across among U.S. federal agencies is less clear. In an effort to build read-across capacity, raise awareness of the state of the science, and work towards a harmonization of read-across approaches across U.S. agencies, a new read-across workgroup was established under the Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM). This is one of several ad hoc groups ICCVAM has convened to implement the ICCVAM Strategic Roadmap. In this article, we outline the charge and scope of the workgroup and summarize the current applications, tools used, and needs of the agencies represented on the workgroup for read-across. Of the agencies surveyed, the Environmental Protection Agency had the greatest experience in using read-across whereas other agencies indicated that they would benefit from gaining a perspective of the landscape of the tools and available guidance. Two practical case studies are also described to illustrate how the read-across approaches applied by two agencies vary on account of decision context.
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Affiliation(s)
- Grace Patlewicz
- (a)National Center for Computational Toxicology, U.S. Environmental Protection Agency, 109 TW Alexander Dr, Research Triangle Park, NC, 27709, USA.
| | - Lucina E Lizarraga
- (b)National Center for Environmental Assessment, U.S. Environmental Protection Agency, 26 West Martin Luther King Drive, Cincinnati, OH, 45268, USA
| | - Diego Rua
- Center for Devices and Radiological Health, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - David G Allen
- ILS, P.O. Box 13501, Research Triangle Park, NC, 27709, USA
| | - Amber B Daniel
- ILS, P.O. Box 13501, Research Triangle Park, NC, 27709, USA
| | - Suzanne C Fitzpatrick
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD, 20740, USA
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, U.S. Army Engineer Research and Developmental Center, 3909 Halls Ferry Rd., Vicksburg, MS, 39180, USA
| | - John Gordon
- U.S. Consumer Product Safety Commission, 5 Research Place, Rockville, MD, 20850, USA
| | - Pertti Hakkinen
- National Library of Medicine, 6707 Democracy Blvd., Bethesda, MD, 20892, USA
| | | | - Agnes Karmaus
- ILS, P.O. Box 13501, Research Triangle Park, NC, 27709, USA
| | - Joanna Matheson
- U.S. Consumer Product Safety Commission, 5 Research Place, Rockville, MD, 20850, USA
| | - Moiz Mumtaz
- Agency for Toxic Substances and Disease Registry, 1600 Clifton Rd., Chamblee, GA, 30341, USA
| | | | - Patricia Ruiz
- Agency for Toxic Substances and Disease Registry, 1600 Clifton Rd., Chamblee, GA, 30341, USA
| | - Louis Scarano
- Office of Pollution Prevention and Toxics, U.S. Environmental Protection Agency, 1200 Pennsylvania Ave. NW, Washington, DC, 20460, USA
| | - Takashi Yamada
- Division of Risk Assessment, Biological Safety Research Center, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Nicole Kleinstreuer
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, P.O. Box 12233, Research Triangle Park, NC, 27709, USA
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14
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Kim HY, Lee JD, Kim JY, Lee JY, Bae ON, Choi YK, Baek E, Kang S, Min C, Seo K, Choi K, Lee BM, Kim KB. Risk assessment of volatile organic compounds (VOCs) detected in sanitary pads. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2019; 82:678-695. [PMID: 31328663 DOI: 10.1080/15287394.2019.1642607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Disposable sanitary pads are a necessity for women's health, but safety concerns regarding the use of these products have created anxiety. The aim of this study was to conduct a risk assessment of 74 volatile organic compounds (VOCs), which were expected to be contained within sanitary pads. Of the 74 VOCs, 50 were found in sanitary pads retailed in Korea at concentrations ranging from 0.025 to 3548.09 µg/pad. In order to undertake a risk assessment of the VOCs, the toxicological database of these compounds in the United States Environmental Protection Agency (USEPA), Agency for Toxic Substances and Disease Registry (ATSDR), National Toxicology Program (NTP) and World Health Organization (WHO) was searched. Ethanol was found to exhibit the highest reference dose (RfD) while 1,2-dibromo-3-chloro-propane displayed the lowest RfD. Consequently, a worst-case exposure scenario was applied in this study. It was assumed that there was the use of 7.5 sanitary napkins/day for 7 days/month. In the case of panty liners or overnight sanitary napkins, the utilization of 90 panty liners/month or 21 overnight sanitary napkins/month was assumed, respectively. In addition, 43 kg, the body weight of 12 to 13-year-old young women, and 100% VOCs skin absorption were employed for risk assessment. The systemic exposure dose (SED) values were calculated ranging from 1.74 (1,1,2-trichloroethane) ng/kg/day to 144.4 (ethanol, absolute) µg/kg/day. Uncertainty factors (UFs) were applied ranging from 10 to 100,000 in accordance with the robustness of animal or human experiments. The margin of exposure (MOE) of 34 VOCs was more than 1 (acceptable MOE > 1). Applicable carcinogenic references reported that the cancer risk of five VOCs was below 10-6. Based on our findings, evidence indicates that the non-cancer and cancer risks associated with VOCs detected in sanitary pads currently used in South Korea do not pose an adverse health risk in women.
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Affiliation(s)
- Hyang Yeon Kim
- a College of Pharmacy, Dankook University , Cheonan , Republic of Korea
| | - Jung Dae Lee
- b Division of Toxicology, College of Pharmacy, Sungkyunkwan University , Suwon , Republic of Korea
| | - Ji-Young Kim
- a College of Pharmacy, Dankook University , Cheonan , Republic of Korea
| | - Joo Young Lee
- c BK21plus team, College of Pharmacy, The Catholic University of Korea , Bucheon , Republic of Korea
| | - Ok-Nam Bae
- d College of Pharmacy, Hanyang University , Ansan , South Korea
| | - Yong-Kyu Choi
- e Cosmetics Research Team, Pharmaceuticals and Medical Devices Research Department, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety , Osong , Republic of Korea
| | - Eunji Baek
- e Cosmetics Research Team, Pharmaceuticals and Medical Devices Research Department, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety , Osong , Republic of Korea
| | - Sejin Kang
- e Cosmetics Research Team, Pharmaceuticals and Medical Devices Research Department, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety , Osong , Republic of Korea
| | - Chungsik Min
- e Cosmetics Research Team, Pharmaceuticals and Medical Devices Research Department, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety , Osong , Republic of Korea
| | - Kyungwon Seo
- e Cosmetics Research Team, Pharmaceuticals and Medical Devices Research Department, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety , Osong , Republic of Korea
| | - Kihwan Choi
- e Cosmetics Research Team, Pharmaceuticals and Medical Devices Research Department, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety , Osong , Republic of Korea
| | - Byung-Mu Lee
- b Division of Toxicology, College of Pharmacy, Sungkyunkwan University , Suwon , Republic of Korea
| | - Kyu-Bong Kim
- a College of Pharmacy, Dankook University , Cheonan , Republic of Korea
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15
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Thomas RS, Bahadori T, Buckley TJ, Cowden J, Deisenroth C, Dionisio KL, Frithsen JB, Grulke CM, Gwinn MR, Harrill JA, Higuchi M, Houck KA, Hughes MF, Hunter ES, Isaacs KK, Judson RS, Knudsen TB, Lambert JC, Linnenbrink M, Martin TM, Newton SR, Padilla S, Patlewicz G, Paul-Friedman K, Phillips KA, Richard AM, Sams R, Shafer TJ, Setzer RW, Shah I, Simmons JE, Simmons SO, Singh A, Sobus JR, Strynar M, Swank A, Tornero-Valez R, Ulrich EM, Villeneuve DL, Wambaugh JF, Wetmore BA, Williams AJ. The Next Generation Blueprint of Computational Toxicology at the U.S. Environmental Protection Agency. Toxicol Sci 2019; 169:317-332. [PMID: 30835285 PMCID: PMC6542711 DOI: 10.1093/toxsci/kfz058] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The U.S. Environmental Protection Agency (EPA) is faced with the challenge of efficiently and credibly evaluating chemical safety often with limited or no available toxicity data. The expanding number of chemicals found in commerce and the environment, coupled with time and resource requirements for traditional toxicity testing and exposure characterization, continue to underscore the need for new approaches. In 2005, EPA charted a new course to address this challenge by embracing computational toxicology (CompTox) and investing in the technologies and capabilities to push the field forward. The return on this investment has been demonstrated through results and applications across a range of human and environmental health problems, as well as initial application to regulatory decision-making within programs such as the EPA's Endocrine Disruptor Screening Program. The CompTox initiative at EPA is more than a decade old. This manuscript presents a blueprint to guide the strategic and operational direction over the next 5 years. The primary goal is to obtain broader acceptance of the CompTox approaches for application to higher tier regulatory decisions, such as chemical assessments. To achieve this goal, the blueprint expands and refines the use of high-throughput and computational modeling approaches to transform the components in chemical risk assessment, while systematically addressing key challenges that have hindered progress. In addition, the blueprint outlines additional investments in cross-cutting efforts to characterize uncertainty and variability, develop software and information technology tools, provide outreach and training, and establish scientific confidence for application to different public health and environmental regulatory decisions.
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Affiliation(s)
- Russell S. Thomas
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Tina Bahadori
- National Center for Environmental Assessment, Office of Research and Development, US Environmental Protection Agency
| | - Timothy J. Buckley
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - John Cowden
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Chad Deisenroth
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Kathie L. Dionisio
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Jeffrey B. Frithsen
- Chemical Safety for Sustainability National Research Program, Office of Research and Development, US Environmental Protection Agency
| | - Christopher M. Grulke
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Maureen R. Gwinn
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Joshua A. Harrill
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Mark Higuchi
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Keith A. Houck
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Michael F. Hughes
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - E. Sidney Hunter
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Kristin K. Isaacs
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Richard S. Judson
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Thomas B. Knudsen
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Jason C. Lambert
- National Center for Environmental Assessment, Office of Research and Development, US Environmental Protection Agency
| | - Monica Linnenbrink
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Todd M. Martin
- National Risk Management Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Seth R. Newton
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Stephanie Padilla
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Grace Patlewicz
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Katie Paul-Friedman
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Katherine A. Phillips
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Ann M. Richard
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Reeder Sams
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Timothy J. Shafer
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - R. Woodrow Setzer
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Imran Shah
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Jane E. Simmons
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Steven O. Simmons
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Amar Singh
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Jon R. Sobus
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Mark Strynar
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Adam Swank
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Rogelio Tornero-Valez
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Elin M. Ulrich
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Daniel L Villeneuve
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - John F. Wambaugh
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Barbara A. Wetmore
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Antony J. Williams
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
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16
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Russo DP, Strickland J, Karmaus AL, Wang W, Shende S, Hartung T, Aleksunes LM, Zhu H. Nonanimal Models for Acute Toxicity Evaluations: Applying Data-Driven Profiling and Read-Across. ENVIRONMENTAL HEALTH PERSPECTIVES 2019; 127:47001. [PMID: 30933541 PMCID: PMC6785238 DOI: 10.1289/ehp3614] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND Low-cost, high-throughput in vitro bioassays have potential as alternatives to animal models for toxicity testing. However, incorporating in vitro bioassays into chemical toxicity evaluations such as read-across requires significant data curation and analysis based on knowledge of relevant toxicity mechanisms, lowering the enthusiasm of using the massive amount of unstructured public data. OBJECTIVE We aimed to develop a computational method to automatically extract useful bioassay data from a public repository (i.e., PubChem) and assess its ability to predict animal toxicity using a novel bioprofile-based read-across approach. METHODS A training database containing 7,385 compounds with diverse rat acute oral toxicity data was searched against PubChem to establish in vitro bioprofiles. Using a novel subspace clustering algorithm, bioassay groups that may inform on relevant toxicity mechanisms underlying acute oral toxicity were identified. These bioassays groups were used to predict animal acute oral toxicity using read-across through a cross-validation process. Finally, an external test set of over 600 new compounds was used to validate the resulting model predictivity. RESULTS Several bioassay clusters showed high predictivity for acute oral toxicity (positive prediction rates range from 62-100%) through cross-validation. After incorporating individual clusters into an ensemble model, chemical toxicants in the external test set were evaluated for putative acute toxicity (positive prediction rate equal to 76%). Additionally, chemical fragment -in vitro-in vivo relationships were identified to illustrate new animal toxicity mechanisms. CONCLUSIONS The in vitro bioassay data-driven profiling strategy developed in this study meets the urgent needs of computational toxicology in the current big data era and can be extended to develop predictive models for other complex toxicity end points. https://doi.org/10.1289/EHP3614.
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Affiliation(s)
- Daniel P. Russo
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | - Judy Strickland
- Integrated Laboratory Systems (ILS), Research Triangle Park, North Carolina, USA
| | - Agnes L. Karmaus
- Integrated Laboratory Systems (ILS), Research Triangle Park, North Carolina, USA
| | - Wenyi Wang
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
| | - Sunil Shende
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
- Department of Computer Science, Rutgers University, Camden, New Jersey, USA
| | - Thomas Hartung
- Johns Hopkins Bloomberg School of Public Health, Center for Alternatives to Animal Testing (CAAT), Baltimore, Maryland, USA
- University of Konstanz, CAAT-Europe, Konstanz, Germany
| | - Lauren M. Aleksunes
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey, USA
| | - Hao Zhu
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, USA
- Department of Chemistry, Rutgers University, Camden, New Jersey, USA
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17
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Lizarraga LE, Dean JL, Kaiser JP, Wesselkamper SC, Lambert JC, Zhao QJ. A case study on the application of an expert-driven read-across approach in support of quantitative risk assessment of p,p'-dichlorodiphenyldichloroethane. Regul Toxicol Pharmacol 2019; 103:301-313. [PMID: 30794837 DOI: 10.1016/j.yrtph.2019.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/14/2019] [Accepted: 02/16/2019] [Indexed: 11/19/2022]
Abstract
Deriving human health risk estimates for environmental chemicals has traditionally relied on in vivo toxicity databases to characterize potential adverse health effects and associated dose-response relationships. In the absence of in vivo toxicity information, new approach methods (NAMs) such as read-across have the potential to fill the required data gaps. This case study applied an expert-driven read-across approach to identify and evaluate analogues to fill non-cancer oral toxicity data gaps for p,p'-dichlorodiphenyldichloroethane (p,p'-DDD), an organochlorine contaminant known to occur at contaminated sites in the U.S. The source analogue p,p'-dichlorodiphenyltrichloroethane (DDT) and its no-observed-adverse-effect level of 0.05 mg/kg-day were proposed for the derivation of screening-level health reference values for the target chemical, p,p'-DDD. Among the primary similarity contexts (structure, toxicokinetics, and toxicodynamics), toxicokinetic considerations were instrumental in separating p,p'-DDT as the best source analogue from other potential candidates (p,p'-DDE and methoxychlor). In vitro high-throughput screening (HTS) assays from ToxCast were used to evaluate similarity in bioactivity profiles and make inferences toward plausible mechanisms of toxicity to build confidence in the read-across approach. This work demonstrated the value of NAMs such as read-across and in vitro HTS in human health risk assessment of environmental contaminants with the potential to inform regulatory decision-making.
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Affiliation(s)
- Lucina E Lizarraga
- National Center for Environmental Assessment (NCEA), U.S. Environmental Protection Agency, Cincinnati, OH, 45268, USA.
| | - Jeffry L Dean
- National Center for Environmental Assessment (NCEA), U.S. Environmental Protection Agency, Cincinnati, OH, 45268, USA
| | - J Phillip Kaiser
- National Center for Environmental Assessment (NCEA), U.S. Environmental Protection Agency, Cincinnati, OH, 45268, USA
| | - Scott C Wesselkamper
- National Center for Environmental Assessment (NCEA), U.S. Environmental Protection Agency, Cincinnati, OH, 45268, USA
| | - Jason C Lambert
- National Center for Environmental Assessment (NCEA), U.S. Environmental Protection Agency, Cincinnati, OH, 45268, USA
| | - Q Jay Zhao
- National Center for Environmental Assessment (NCEA), U.S. Environmental Protection Agency, Cincinnati, OH, 45268, USA
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18
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Schultz TW, Richarz AN, Cronin MT. Assessing uncertainty in read-across: Questions to evaluate toxicity predictions based on knowledge gained from case studies. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.comtox.2018.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Helman G, Shah I, Patlewicz G. Extending the Generalised Read-Across approach (GenRA): A systematic analysis of the impact of physicochemical property information on read-across performance. ACTA ACUST UNITED AC 2018; 8:34-50. [PMID: 31667446 DOI: 10.1016/j.comtox.2018.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Read-across is a useful data gap filling technique used within category and analogue approaches in regulatory hazard and risk assessment. Recently we developed an algorithmic, approach called Generalised Read-Across (GenRA) (Shah et al., 2016) which makes read-across predictions of toxicity effects using a similarity weighted average of source analogues characterised by their chemical and/or bioactivity descriptors. A default GenRA approach (termed baseline GenRA) relies on identifying 10 source analogues relative to a target substance that are structurally similar based on Morgan chemical fingerprints and computing an activity score to estimate presence or absence of in vivo toxicity. This current study investigated the impact that similarity in bioavailability plays in altering the local neighbourhood of source analogues as well as read-across performance relative to baseline GenRA using physicochemical property information as a surrogate for bioavailability. Two approaches were evaluated: 1) a filtering approach which restricted structurally related analogues based on their physicochemical properties; and 2) a search expansion approach which included additional analogues based on a combined structural and physicochemical similarity index. Filtering minimally improved performance, and was very dependent on the similarity threshold selected. The search expansion approach performed at least as well as the baseline GenRA, and showed up to a 9% improvement in read-across performance for at least 10 of the 50 organs considered. We summarise the overall impact that physicochemical information plays on GenRA performance, illustrate the improvement for a specific case study substance and describe how to select the most appropriate physicochemical similarity threshold to achieve optimal read-across performance depending on the toxicity effect and chemical of interest. The analyses show that physicochemical property information does result in a modest (up to 9% increase) improvement in structural based read-across predictions.
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Affiliation(s)
- George Helman
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, USA.,National Center for Computational Toxicology (NCCT), Office of Research and Development, US Environmental Protection Agency, 109 TW Alexander Dr, Research Triangle Park (RTP), NC 27711, USA
| | - Imran Shah
- National Center for Computational Toxicology (NCCT), Office of Research and Development, US Environmental Protection Agency, 109 TW Alexander Dr, Research Triangle Park (RTP), NC 27711, USA
| | - Grace Patlewicz
- National Center for Computational Toxicology (NCCT), Office of Research and Development, US Environmental Protection Agency, 109 TW Alexander Dr, Research Triangle Park (RTP), NC 27711, USA
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20
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Dean JL, Zhao QJ, Lambert JC, Hawkins BS, Thomas RS, Wesselkamper SC. Editor's Highlight: Application of Gene Set Enrichment Analysis for Identification of Chemically Induced, Biologically Relevant Transcriptomic Networks and Potential Utilization in Human Health Risk Assessment. Toxicol Sci 2018; 157:85-99. [PMID: 28123101 DOI: 10.1093/toxsci/kfx021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The rate of new chemical development in commerce combined with a paucity of toxicity data for legacy chemicals presents a unique challenge for human health risk assessment. There is a clear need to develop new technologies and incorporate novel data streams to more efficiently inform derivation of toxicity values. One avenue of exploitation lies in the field of transcriptomics and the application of gene expression analysis to characterize biological responses to chemical exposures. In this context, gene set enrichment analysis (GSEA) was employed to evaluate tissue-specific, dose-response gene expression data generated following exposure to multiple chemicals for various durations. Patterns of transcriptional enrichment were evident across time and with increasing dose, and coordinated enrichment plausibly linked to the etiology of the biological responses was observed. GSEA was able to capture both transient and sustained transcriptional enrichment events facilitating differentiation between adaptive versus longer term molecular responses. When combined with benchmark dose (BMD) modeling of gene expression data from key drivers of biological enrichment, GSEA facilitated characterization of dose ranges required for enrichment of biologically relevant molecular signaling pathways, and promoted comparison of the activation dose ranges required for individual pathways. Median transcriptional BMD values were calculated for the most sensitive enriched pathway as well as the overall median BMD value for key gene members of significantly enriched pathways, and both were observed to be good estimates of the most sensitive apical endpoint BMD value. Together, these efforts support the application of GSEA to qualitative and quantitative human health risk assessment.
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Affiliation(s)
- Jeffry L Dean
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Q Jay Zhao
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Jason C Lambert
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Belinda S Hawkins
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Russell S Thomas
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Scott C Wesselkamper
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
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21
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Patlewicz G, Cronin MT, Helman G, Lambert JC, Lizarraga LE, Shah I. Navigating through the minefield of read-across frameworks: A commentary perspective. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.comtox.2018.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Wang Y, Wu F, Liu Y, Mu Y, Giesy JP, Meng W, Hu Q, Liu J, Dang Z. Effect doses for protection of human health predicted from physicochemical properties of metals/metalloids. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 232:458-466. [PMID: 28987569 DOI: 10.1016/j.envpol.2017.09.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
Effect doses (EDs) of metals/metalloids, usually obtained from toxicological experiments are required for developing environmental quality criteria/standards for use in assessment of hazard or risks. However, because in vivo tests are time-consuming, costly and sometimes impossible to conduct, among more than 60 metals/metalloids, there are sufficient data for development of EDs for only approximately 25 metals/metalloids. Hence, it was deemed a challenge to derive EDs for additional metals by use of alternative methods. This study found significant relationships between EDs and physicochemical parameters for twenty-five metals/metalloids. Elements were divided into three classes and then three individual empirical models were developed based on the most relevant parameters for each class. These parameters included log-βn, ΔE0 and Xm2r, respectively (R2 = 0.988, 0.839, 0.871, P < 0.01). Those models can satisfactorily predict EDs for another 25 metals/metalloids. Here, these alternative models for deriving thresholds of toxicity that could be used to perform preliminarily, screen-level health assessments for metals are presented.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Yuedan Liu
- The Key Laboratory of Water and Air Pollution Control of Guangdong Province, South China Institute of Environmental Sciences, MEP, Guangzhou 510065, China
| | - Yunsong Mu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - John P Giesy
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan, Saskatoon S7N 5B3, Canada
| | - Wei Meng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Qing Hu
- Engineering Technology Innovation Center (Beijing), South University of Science and Technology, Shenzhen 518055, China
| | - Jing Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Environmental Science Department, Baylor University, 76798, USA
| | - Zhi Dang
- School of Environmental Science and Engineering, South China University of Technology, University Town, Guangzhou 510640, China
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23
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Cote I, Andersen ME, Ankley GT, Barone S, Birnbaum LS, Boekelheide K, Bois FY, Burgoon LD, Chiu WA, Crawford-Brown D, Crofton KM, DeVito M, Devlin RB, Edwards SW, Guyton KZ, Hattis D, Judson RS, Knight D, Krewski D, Lambert J, Maull EA, Mendrick D, Paoli GM, Patel CJ, Perkins EJ, Poje G, Portier CJ, Rusyn I, Schulte PA, Simeonov A, Smith MT, Thayer KA, Thomas RS, Thomas R, Tice RR, Vandenberg JJ, Villeneuve DL, Wesselkamper S, Whelan M, Whittaker C, White R, Xia M, Yauk C, Zeise L, Zhao J, DeWoskin RS. The Next Generation of Risk Assessment Multi-Year Study-Highlights of Findings, Applications to Risk Assessment, and Future Directions. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:1671-1682. [PMID: 27091369 PMCID: PMC5089888 DOI: 10.1289/ehp233] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/30/2015] [Accepted: 03/29/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Next Generation (NexGen) of Risk Assessment effort is a multi-year collaboration among several organizations evaluating new, potentially more efficient molecular, computational, and systems biology approaches to risk assessment. This article summarizes our findings, suggests applications to risk assessment, and identifies strategic research directions. OBJECTIVE Our specific objectives were to test whether advanced biological data and methods could better inform our understanding of public health risks posed by environmental exposures. METHODS New data and methods were applied and evaluated for use in hazard identification and dose-response assessment. Biomarkers of exposure and effect, and risk characterization were also examined. Consideration was given to various decision contexts with increasing regulatory and public health impacts. Data types included transcriptomics, genomics, and proteomics. Methods included molecular epidemiology and clinical studies, bioinformatic knowledge mining, pathway and network analyses, short-duration in vivo and in vitro bioassays, and quantitative structure activity relationship modeling. DISCUSSION NexGen has advanced our ability to apply new science by more rapidly identifying chemicals and exposures of potential concern, helping characterize mechanisms of action that influence conclusions about causality, exposure-response relationships, susceptibility and cumulative risk, and by elucidating new biomarkers of exposure and effects. Additionally, NexGen has fostered extensive discussion among risk scientists and managers and improved confidence in interpreting and applying new data streams. CONCLUSIONS While considerable uncertainties remain, thoughtful application of new knowledge to risk assessment appears reasonable for augmenting major scope assessments, forming the basis for or augmenting limited scope assessments, and for prioritization and screening of very data limited chemicals. Citation: Cote I, Andersen ME, Ankley GT, Barone S, Birnbaum LS, Boekelheide K, Bois FY, Burgoon LD, Chiu WA, Crawford-Brown D, Crofton KM, DeVito M, Devlin RB, Edwards SW, Guyton KZ, Hattis D, Judson RS, Knight D, Krewski D, Lambert J, Maull EA, Mendrick D, Paoli GM, Patel CJ, Perkins EJ, Poje G, Portier CJ, Rusyn I, Schulte PA, Simeonov A, Smith MT, Thayer KA, Thomas RS, Thomas R, Tice RR, Vandenberg JJ, Villeneuve DL, Wesselkamper S, Whelan M, Whittaker C, White R, Xia M, Yauk C, Zeise L, Zhao J, DeWoskin RS. 2016. The Next Generation of Risk Assessment multiyear study-highlights of findings, applications to risk assessment, and future directions. Environ Health Perspect 124:1671-1682; http://dx.doi.org/10.1289/EHP233.
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Affiliation(s)
- Ila Cote
- National Center for Environmental Assessment, U.S. Environmental Protection Agency (EPA), Washington, District of Columbia, USA
- Address correspondence to I. Cote, U.S. Environmental Protection Agency, Region 8, Room 8152, 1595 Wynkoop St., Denver, CO 80202-1129 USA. Telephone: (202) 288-9539. E-mail:
| | | | - Gerald T. Ankley
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Duluth, Minnesota, USA
| | - Stanley Barone
- Office of Chemical Safety and Pollution Prevention, U.S. EPA, Washington, District of Columbia, USA
| | - Linda S. Birnbaum
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Kim Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Frederic Y. Bois
- Unité Modèles pour l’Écotoxicologie et la Toxicologie, Institut National de l’Environnement Industriel et des Risques, Verneuil en Halatte, France
| | - Lyle D. Burgoon
- U.S. Army Engineer Research and Development Center, Research Triangle Park, North Carolina, USA
| | - Weihsueh A. Chiu
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | | | | | - Michael DeVito
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Robert B. Devlin
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Stephen W. Edwards
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Research Triangle Park, North Carolina, USA
| | | | - Dale Hattis
- George Perkins Marsh Institute, Clark University, Worcester, Massachusetts, USA
| | | | - Derek Knight
- European Chemicals Agency, Annankatu, Helsinki, Finland
| | - Daniel Krewski
- McLaughlin Centre for Population Health Risk Assessment, University of Ottawa, Ottawa, Ontario, Canada
| | - Jason Lambert
- National Center for Environmental Assessment, U.S. EPA, Cincinnati, Ohio, USA
| | - Elizabeth Anne Maull
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Donna Mendrick
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Chirag Jagdish Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Edward J. Perkins
- U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi, USA
| | - Gerald Poje
- Grant Consulting Group, Washington, District of Columbia, USA
| | | | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Paul A. Schulte
- Education and Information Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, NIH, DHHS, Bethesda, Maryland, USA
| | - Martyn T. Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Kristina A. Thayer
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | | | - Reuben Thomas
- Gladstone Institutes, University of California, San Francisco, San Francisco, California, USA
| | - Raymond R. Tice
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - John J. Vandenberg
- National Center for Environmental Assessment, U.S. Environmental Protection Agency (EPA), Washington, District of Columbia, USA
| | - Daniel L. Villeneuve
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Duluth, Minnesota, USA
| | - Scott Wesselkamper
- National Center for Environmental Assessment, U.S. EPA, Cincinnati, Ohio, USA
| | - Maurice Whelan
- Systems Toxicology Unit, European Commission Joint Research Centre, Ispra, Italy
| | - Christine Whittaker
- Education and Information Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio, USA
| | - Ronald White
- Center for Effective Government, Washington, District of Columbia, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, NIH, DHHS, Bethesda, Maryland, USA
| | - Carole Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Lauren Zeise
- Office of Environmental Health Hazard Assessment, California EPA, Oakland, California, USA
| | - Jay Zhao
- National Center for Environmental Assessment, U.S. EPA, Cincinnati, Ohio, USA
| | - Robert S. DeWoskin
- National Center for Environmental Assessment, U.S. Environmental Protection Agency (EPA), Washington, District of Columbia, USA
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24
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Krewski D, Westphal M, Andersen ME, Paoli GM, Chiu WA, Al-Zoughool M, Croteau MC, Burgoon LD, Cote I. A framework for the next generation of risk science. ENVIRONMENTAL HEALTH PERSPECTIVES 2014; 122:796-805. [PMID: 24727499 PMCID: PMC4123023 DOI: 10.1289/ehp.1307260] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 04/09/2014] [Indexed: 05/19/2023]
Abstract
OBJECTIVES In 2011, the U.S. Environmental Protection Agency initiated the NexGen project to develop a new paradigm for the next generation of risk science. METHODS The NexGen framework was built on three cornerstones: the availability of new data on toxicity pathways made possible by fundamental advances in basic biology and toxicological science, the incorporation of a population health perspective that recognizes that most adverse health outcomes involve multiple determinants, and a renewed focus on new risk assessment methodologies designed to better inform risk management decision making. RESULTS The NexGen framework has three phases. Phase I (objectives) focuses on problem formulation and scoping, taking into account the risk context and the range of available risk management decision-making options. Phase II (risk assessment) seeks to identify critical toxicity pathway perturbations using new toxicity testing tools and technologies, and to better characterize risks and uncertainties using advanced risk assessment methodologies. Phase III (risk management) involves the development of evidence-based population health risk management strategies of a regulatory, economic, advisory, community-based, or technological nature, using sound principles of risk management decision making. CONCLUSIONS Analysis of a series of case study prototypes indicated that many aspects of the NexGen framework are already beginning to be adopted in practice.
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Affiliation(s)
- Daniel Krewski
- McLaughlin Centre for Population Health Risk Assessment, University of Ottawa, Ottawa, Ontario, Canada
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25
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Low YS, Sedykh AY, Rusyn I, Tropsha A. Integrative approaches for predicting in vivo effects of chemicals from their structural descriptors and the results of short-term biological assays. Curr Top Med Chem 2014; 14:1356-64. [PMID: 24805064 PMCID: PMC5344042 DOI: 10.2174/1568026614666140506121116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 12/22/2022]
Abstract
Cheminformatics approaches such as Quantitative Structure Activity Relationship (QSAR) modeling have been used traditionally for predicting chemical toxicity. In recent years, high throughput biological assays have been increasingly employed to elucidate mechanisms of chemical toxicity and predict toxic effects of chemicals in vivo. The data generated in such assays can be considered as biological descriptors of chemicals that can be combined with molecular descriptors and employed in QSAR modeling to improve the accuracy of toxicity prediction. In this review, we discuss several approaches for integrating chemical and biological data for predicting biological effects of chemicals in vivo and compare their performance across several data sets. We conclude that while no method consistently shows superior performance, the integrative approaches rank consistently among the best yet offer enriched interpretation of models over those built with either chemical or biological data alone. We discuss the outlook for such interdisciplinary methods and offer recommendations to further improve the accuracy and interpretability of computational models that predict chemical toxicity.
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Affiliation(s)
| | | | | | - Alexander Tropsha
- 100K Beard Hall, Campus Box 7568, University of North Carolina, Chapel Hill, NC 27599-7568, USA.
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26
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Craig EA, Wang NC, Zhao QJ. Using quantitative structure-activity relationship modeling to quantitatively predict the developmental toxicity of halogenated azole compounds. J Appl Toxicol 2013; 34:787-94. [PMID: 24122872 DOI: 10.1002/jat.2940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/05/2013] [Accepted: 09/06/2013] [Indexed: 11/10/2022]
Abstract
Developmental toxicity is a relevant endpoint for the comprehensive assessment of human health risk from chemical exposure. However, animal developmental toxicity data remain unavailable for many environmental contaminants due to the complexity and cost of these types of analyses. Here we describe an approach that uses quantitative structure-activity relationship modeling as an alternative methodology to fill data gaps in the developmental toxicity profile of certain halogenated compounds. Chemical information was obtained and curated using the OECD Quantitative Structure-Activity Relationship Toolbox, version 3.0. Data from 35 curated compounds were analyzed via linear regression to build the predictive model, which has an R(2) of 0.79 and a Q(2) of 0.77. The applicability domain (AD) was defined by chemical category and structural similarity. Seven halogenated chemicals that fit the AD but are not part of the training set were employed for external validation purposes. Our model predicted lowest observed adverse effect level values with a maximal threefold deviation from the observed experimental values for all chemicals that fit the AD. The good predictability of our model suggests that this method may be applicable to the analysis of qualifying compounds whenever developmental toxicity information is lacking or incomplete for risk assessment considerations.
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Affiliation(s)
- Evisabel A Craig
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA; National Center for Environmental Assessment, Office of Research Development, U.S. Environmental Protection Agency, Cincinnati, OH, USA
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27
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Pressor mechanism evaluation for phytochemical compounds using in silico compound–protein interaction prediction. Regul Toxicol Pharmacol 2013; 67:115-24. [DOI: 10.1016/j.yrtph.2013.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 07/20/2013] [Accepted: 07/22/2013] [Indexed: 01/30/2023]
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28
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Low Y, Sedykh A, Fourches D, Golbraikh A, Whelan M, Rusyn I, Tropsha A. Integrative chemical-biological read-across approach for chemical hazard classification. Chem Res Toxicol 2013; 26:1199-208. [PMID: 23848138 DOI: 10.1021/tx400110f] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Traditional read-across approaches typically rely on the chemical similarity principle to predict chemical toxicity; however, the accuracy of such predictions is often inadequate due to the underlying complex mechanisms of toxicity. Here, we report on the development of a hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays ("biological" similarity). The Chemical-Biological Read-Across (CBRA) approach infers each compound's toxicity from both chemical and biological analogues whose similarities are determined by the Tanimoto coefficient. Classification accuracy of CBRA was compared to that of classical RA and other methods using chemical descriptors alone or in combination with biological data. Different types of adverse effects (hepatotoxicity, hepatocarcinogenicity, mutagenicity, and acute lethality) were classified using several biological data types (gene expression profiling and cytotoxicity screening). CBRA-based hazard classification exhibited consistently high external classification accuracy and applicability to diverse chemicals. Transparency of the CBRA approach is aided by the use of radial plots that show the relative contribution of analogous chemical and biological neighbors. Identification of both chemical and biological features that give rise to the high accuracy of CBRA-based toxicity prediction facilitates mechanistic interpretation of the models.
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Affiliation(s)
- Yen Low
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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