1
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Viant MR, Amstalden E, Athersuch T, Bouhifd M, Camuzeaux S, Crizer DM, Driemert P, Ebbels T, Ekman D, Flick B, Giri V, Gómez-Romero M, Haake V, Herold M, Kende A, Lai F, Leonards PEG, Lim PP, Lloyd GR, Mosley J, Namini C, Rice JR, Romano S, Sands C, Smith MJ, Sobanski T, Southam AD, Swindale L, van Ravenzwaay B, Walk T, Weber RJM, Zickgraf FM, Kamp H. Demonstrating the reliability of in vivo metabolomics based chemical grouping: towards best practice. Arch Toxicol 2024; 98:1111-1123. [PMID: 38368582 PMCID: PMC10944399 DOI: 10.1007/s00204-024-03680-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/15/2024] [Indexed: 02/19/2024]
Abstract
While grouping/read-across is widely used to fill data gaps, chemical registration dossiers are often rejected due to weak category justifications based on structural similarity only. Metabolomics provides a route to robust chemical categories via evidence of shared molecular effects across source and target substances. To gain international acceptance, this approach must demonstrate high reliability, and best-practice guidance is required. The MetAbolomics ring Trial for CHemical groupING (MATCHING), comprising six industrial, government and academic ring-trial partners, evaluated inter-laboratory reproducibility and worked towards best-practice. An independent team selected eight substances (WY-14643, 4-chloro-3-nitroaniline, 17α-methyl-testosterone, trenbolone, aniline, dichlorprop-p, 2-chloroaniline, fenofibrate); ring-trial partners were blinded to their identities and modes-of-action. Plasma samples were derived from 28-day rat tests (two doses per substance), aliquoted, and distributed to partners. Each partner applied their preferred liquid chromatography-mass spectrometry (LC-MS) metabolomics workflows to acquire, process, quality assess, statistically analyze and report their grouping results to the European Chemicals Agency, to ensure the blinding conditions of the ring trial. Five of six partners, whose metabolomics datasets passed quality control, correctly identified the grouping of eight test substances into three categories, for both male and female rats. Strikingly, this was achieved even though a range of metabolomics approaches were used. Through assessing intrastudy quality-control samples, the sixth partner observed high technical variation and was unable to group the substances. By comparing workflows, we conclude that some heterogeneity in metabolomics methods is not detrimental to consistent grouping, and that assessing data quality prior to grouping is essential. We recommend development of international guidance for quality-control acceptance criteria. This study demonstrates the reliability of metabolomics for chemical grouping and works towards best-practice.
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Affiliation(s)
- Mark R Viant
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - E Amstalden
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - T Athersuch
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - M Bouhifd
- European Chemicals Agency, Telakkakatu 6, FI-00121, Helsinki, Finland
| | - S Camuzeaux
- Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK
| | - D M Crizer
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - P Driemert
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - T Ebbels
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - D Ekman
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - B Flick
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
- NUVISAN ICB GmbH, Toxicology, 13353, Berlin, Germany
| | - V Giri
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
| | - M Gómez-Romero
- Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK
| | - V Haake
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - M Herold
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - A Kende
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - F Lai
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - P E G Leonards
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - P P Lim
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - G R Lloyd
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - J Mosley
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - C Namini
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - J R Rice
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - S Romano
- Center for Environmental Measurement and Modeling, Environmental Protection Agency, Athens, GA, 30605, USA
| | - C Sands
- Department of Metabolism, Digestion and Reproduction, National Phenome Centre, Imperial College London, London, W12 0NN, UK
| | - M J Smith
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - T Sobanski
- European Chemicals Agency, Telakkakatu 6, FI-00121, Helsinki, Finland
| | - A D Southam
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - L Swindale
- Syngenta, Jealott's Hill International Research Centre, Bracknell, RG42 6EY, UK
| | - B van Ravenzwaay
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
- Environmental Sciences Consulting, 67122, Altrip, Germany
| | - T Walk
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
| | - R J M Weber
- Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - F M Zickgraf
- BASF SE, Carl-Bosch-Str 38, 67056, Ludwigshafen, Germany
| | - H Kamp
- BASF Metabolome Solutions GmbH, Tegeler Weg 33, 10589, Berlin, Germany
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2
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Arnot JA, Toose L, Armitage JM, Embry M, Sangion A, Hughes L. A weight of evidence approach for bioaccumulation assessment. Integr Environ Assess Manag 2023; 19:1235-1253. [PMID: 35049141 DOI: 10.1002/ieam.4583] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Bioaccumulation assessments conducted by regulatory agencies worldwide use a variety of methods, types of data, metrics, and categorization criteria. Lines of evidence (LoE) for bioaccumulation assessment can include bioaccumulation metrics such as in vivo bioconcentration factor (BCF) and biomagnification factor (BMF) data measured from standardized laboratory experiments, and field (monitoring) data such as BMFs, bioaccumulation factors (BAFs), and trophic magnification factors (TMFs). In silico predictions from mass-balance models and quantitative structure-activity relationships (QSARs) and a combination of in vitro biotransformation rates and in vitro-in vivo extrapolation (IVIVE) models can also be used. The myriad bioaccumulation metrics and categorization criteria and underlying uncertainty in measured or modeled data can make decision-making challenging. A weight of evidence (WoE) approach is recommended to address uncertainty. The Bioaccumulation Assessment Tool (BAT) guides a user through the process of collecting and generating various LoE required for assessing the bioaccumulation of neutral and ionizable organic chemicals in aquatic (water-respiring) and air-breathing organisms. The BAT includes data evaluation templates (DETs) to critically evaluate the reliability of the LoE used in the assessment. The DETs were developed from standardized testing guidance. The approach used in the BAT is consistent with OECD and SETAC WoE principles and facilitates the implementation of chemical policy objectives in chemical assessment and management. The recommended methods are also iterative and tiered, providing pragmatic methods to reduce unnecessary animal testing. General concepts of the BAT are presented and case study applications of the tool for hexachlorobenzene (HCB) and β-hexachlorocyclohexane (β-HCH) are demonstrated. The BAT provides a consistent and transparent WoE framework to address uncertainty in bioaccumulation assessment and is envisaged to evolve with scientific and regulatory developments. Integr Environ Assess Manag 2023;19:1235-1253. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
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Affiliation(s)
- Jon A Arnot
- ARC Arnot Research & Consulting, Toronto, Ontario, Canada
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Liisa Toose
- ARC Arnot Research & Consulting, Toronto, Ontario, Canada
| | - James M Armitage
- AES Armitage Environmental Sciences, Inc., Ottawa, Ontario, Canada
| | - Michelle Embry
- Health and Environmental Sciences Institute, Washington, DC, USA
| | - Alessandro Sangion
- ARC Arnot Research & Consulting, Toronto, Ontario, Canada
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Lauren Hughes
- ARC Arnot Research & Consulting, Toronto, Ontario, Canada
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3
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Wang Z, Haange SB, Haake V, Huisinga M, Kamp H, Buesen R, Schubert K, Canzler S, Hackermüller J, Rolle-Kampczyk U, Bergen MV. Assessing the Influence of Propylthiouracil and Phenytoin on the Metabolomes of the Thyroid, Liver, and Plasma in Rats. Metabolites 2023; 13:847. [PMID: 37512556 PMCID: PMC10383188 DOI: 10.3390/metabo13070847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/26/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The thyroid hormones (THs) regulate various physiological mechanisms in mammals, such as cellular metabolism, cell structure, and membrane transport. The therapeutic drugs propylthiouracil (PTU) and phenytoin are known to induce hypothyroidism and decrease blood thyroid hormone levels. To analyze the impact of these two drugs on systemic metabolism, we focused on metabolic changes after treatment. Therefore, in a rat model, the metabolome of thyroid and liver tissue as well as from the blood plasma, after 2-week and 4-week administration of the drugs and after a following 2-week recovery phase, was investigated using targeted LC-MS/MS and GC-MS. Both drugs were tested at a low dose and a high dose. We observed decreases in THs plasma levels, and higher doses of the drugs were associated with a high decrease in TH levels. PTU administration had a more pronounced effect on TH levels than phenytoin. Both drugs had little or no influence on the metabolomes at low doses. Only PTU exhibited apparent metabolome alterations at high doses, especially concerning lipids. In plasma, acylcarnitines and triglycerides were detected at decreased levels than in the controls after 2- and 4-week exposure to the drug, while sphingomyelins and phosphatidylcholines were observed at increased levels. Interestingly, in the thyroid tissue, triglycerides were observed at increased concentrations in the 2-week exposure group to PTU, which was not observed in the 4-week exposure group and in the 4-week exposure group followed by the 2-week recovery group, suggesting an adaptation by the thyroid tissue. In the liver, no metabolites were found to have significantly changed. After the recovery phase, the thyroid, liver, and plasma metabolomic profiles showed little or no differences from the controls. In conclusion, although there were significant changes observed in several plasma metabolites in PTU/Phenytoin exposure groups, this study found that only PTU exposure led to adaptation-dependent changes in thyroid metabolites but did not affect hepatic metabolites.
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Affiliation(s)
- Zhipeng Wang
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Volker Haake
- BASF Metabolome Solutions GmbH, 10589 Berlin, Germany
| | - Maike Huisinga
- Experimental Toxicology and Ecology, BASF SE, 67056 Ludwigshafen, Germany
| | - Hennicke Kamp
- BASF Metabolome Solutions GmbH, 10589 Berlin, Germany
| | - Roland Buesen
- Experimental Toxicology and Ecology, BASF SE, 67056 Ludwigshafen, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Sebastian Canzler
- Department of Computational Biology, Helmholtz-Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Jörg Hackermüller
- Department of Computational Biology, Helmholtz-Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
- Department of Computer Science, University of Leipzig, 04109 Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research-UFZ, 04318 Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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4
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Zhang N, Wang J, Bakker W, Zheng W, Baccaro M, Murali A, van Ravenzwaay B, Rietjens IMCM. In vitro models to detect in vivo bile acid changes induced by antibiotics. Arch Toxicol 2022; 96:3291-3303. [PMID: 36074177 PMCID: PMC9584874 DOI: 10.1007/s00204-022-03373-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/25/2022] [Indexed: 11/20/2022]
Abstract
Bile acid homeostasis plays an important role in many biological activities through the bile-liver-gut axis. In this study, two in vitro models were applied to further elucidate the mode of action underlying reported in vivo bile acid changes induced by antibiotics (colistin sulfate, tobramycin, meropenem trihydrate, and doripenem hydrate). 16S rRNA analysis of rat fecal samples anaerobically incubated with these antibiotics showed that especially tobramycin induced changes in the gut microbiota. Furthermore, tobramycin was shown to inhibit the microbial deconjugation of taurocholic acid (TCA) and the transport of TCA over an in vitro Caco-2 cell layer used as a model to mimic intestinal bile acid reuptake. The effects induced by the antibiotics in the in vitro model systems provide novel and complementary insight explaining the effects of the antibiotics on microbiota and fecal bile acid levels upon 28-day in vivo treatment of rats. In particular, our results provide insight in the mode(s) of action underlying the increased levels of TCA in the feces upon tobramycin exposure. Altogether, the results of the present study provide a proof-of-principle on how in vitro models can be used to elucidate in vivo effects on bile acid homeostasis, and to obtain insight in the mode(s) of action underlying the effect of an antibiotic, in this case tobramycin, on bile acid homeostasis via effects on intestinal bile acid metabolism and reuptake.
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Affiliation(s)
- Nina Zhang
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Jingxuan Wang
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Wouter Bakker
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Weijia Zheng
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Marta Baccaro
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | | | | | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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5
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Li L, Zhang Z, Men Y, Baskaran S, Sangion A, Wang S, Arnot JA, Wania F. Retrieval, Selection, and Evaluation of Chemical Property Data for Assessments of Chemical Emissions, Fate, Hazard, Exposure, and Risks. ACS Environ Au 2022; 2:376-395. [PMID: 37101455 PMCID: PMC10125307 DOI: 10.1021/acsenvironau.2c00010] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 04/28/2023]
Abstract
Reliable chemical property data are the key to defensible and unbiased assessments of chemical emissions, fate, hazard, exposure, and risks. However, the retrieval, evaluation, and use of reliable chemical property data can often be a formidable challenge for chemical assessors and model users. This comprehensive review provides practical guidance for use of chemical property data in chemical assessments. We assemble available sources for obtaining experimentally derived and in silico predicted property data; we also elaborate strategies for evaluating and curating the obtained property data. We demonstrate that both experimentally derived and in silico predicted property data can be subject to considerable uncertainty and variability. Chemical assessors are encouraged to use property data derived through the harmonization of multiple carefully selected experimental data if a sufficient number of reliable laboratory measurements is available or through the consensus consolidation of predictions from multiple in silico tools if the data pool from laboratory measurements is not adequate.
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Affiliation(s)
- Li Li
- School
of Public Health, University of Nevada Reno, Reno, Nevada 89557, United States
- . Phone: +1 (775) 682 7077
| | - Zhizhen Zhang
- School
of Public Health, University of Nevada Reno, Reno, Nevada 89557, United States
| | - Yujie Men
- Department
of Chemical & Environmental Engineering, University of California Riverside, Riverside, California 92521, United States
| | - Sivani Baskaran
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
| | - Alessandro Sangion
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
- ARC
Arnot Research & Consulting, Toronto, Ontario M4M 1W4, Canada
| | - Shenghong Wang
- School
of Public Health, University of Nevada Reno, Reno, Nevada 89557, United States
| | - Jon A. Arnot
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
- ARC
Arnot Research & Consulting, Toronto, Ontario M4M 1W4, Canada
- Department
of Pharmacology and Toxicology, University
of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Frank Wania
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
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6
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Breivik K, McLachlan MS, Wania F. The Emissions Fractions Approach to Assessing the Long-Range Transport Potential of Organic Chemicals. Environ Sci Technol 2022; 56:11983-11990. [PMID: 35951418 PMCID: PMC9454247 DOI: 10.1021/acs.est.2c03047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
The assessment of long-range transport potential (LRTP) is enshrined in several frameworks for chemical regulation such as the Stockholm Convention. Screening for LRTP is commonly done with the OECD Pov and LRTP Screening Tool employing two metrics, characteristic travel distance (CTD) and transfer efficiency (TE). Here we introduce a set of three alternative metrics and implement them in the Tool's model. Each metric is expressed as a fraction of the emissions in a source region. The three metrics quantify the extent to which the chemical (i) reaches a remote region (dispersion, ϕ1), (ii) is transferred to surface media in the remote region (transfer, ϕ2), and (iii) accumulates in these surface media (accumulation, ϕ3). In contrast to CTD and TE, the emissions fractions metrics can integrate transport via water and air, enabling comprehensive LRTP assessment. Furthermore, since there is a coherent relationship between the three metrics, the new approach provides quantitative mechanistic insight into different phenomena determining LRTP. Finally, the accumulation metric, ϕ3, allows assessment of LRTP in the context of the Stockholm Convention, where the ability of a chemical to elicit adverse effects in surface media is decisive. We conclude that the emission fractions approach has the potential to reduce the risk of false positives/negatives in LRTP assessments.
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Affiliation(s)
- Knut Breivik
- Norwegian
Institute for Air Research, P.O. Box
100, NO-2027 Kjeller, Norway
- Department
of Chemistry, University of Oslo, P.O. Box 1033, NO-0315 Oslo, Norway
| | - Michael S. McLachlan
- Department
of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Frank Wania
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
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7
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Ribbenstedt A, Armitage JM, Günther F, Arnot JA, Droge STJ, McLachlan MS. In Vivo Bioconcentration of 10 Anionic Surfactants in Rainbow Trout Explained by In Vitro Data on Partitioning and S9 Clearance. Environ Sci Technol 2022; 56:6305-6314. [PMID: 35467837 PMCID: PMC9118553 DOI: 10.1021/acs.est.1c05543] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Bioconcentration factors (BCFs) in rainbow trout were measured for 10 anionic surfactants with a range of alkyl chain lengths and different polar head groups. The BCFs ranged from 0.04 L kg-1 ww (for C10SO3) to 1370 L kg-1 ww (C16SO3). There was a strong correlation between the log BCF and log membrane lipid-water distribution ratio (DMLW, r2 = 0.96), and biotransformation was identified as the dominant elimination mechanism. The strong positive influence of DMLW on BCF was attributed to two phenomena: (i) increased partitioning from water into the epithelial membrane of the gill, leading to more rapid diffusion across this barrier and more rapid uptake, and (ii) increased sequestration of the surfactant body burden into membranes and other body tissues, resulting in lower freely dissolved concentrations available for biotransformation. Estimated whole-body in vivo biotransformation rate constants kB-BCF are within a factor three of rate constants estimated from S9 in vitro assays for six of the eight test chemicals for which kB-BCF could be determined. A model-based assessment indicated that the hepatic clearance rate of freely dissolved chemicals was similar for the studied surfactants. The dataset will be useful for evaluation of in silico and in vitro methods to assess bioaccumulation.
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Affiliation(s)
- Anton Ribbenstedt
- Department
of Environmental Science, Stockholm University, 106 91 Stockholm, Sweden
| | - James M. Armitage
- AES
Armitage Environmental Sciences, Inc., Ottawa, Ontario K1L 8C3, Canada
| | - Felix Günther
- Department
of Mathematics, Stockholm University, 106 91 Stockholm, Sweden
| | - Jon A. Arnot
- ARC
Arnot Research and Consulting Inc., Toronto, Ontario M4M 1W4, Canada
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada
| | - Steven T. J. Droge
- Institute
for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Michael S. McLachlan
- Department
of Environmental Science, Stockholm University, 106 91 Stockholm, Sweden
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8
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Coffin S, Bouwmeester H, Brander S, Damdimopoulou P, Gouin T, Hermabessiere L, Khan E, Koelmans AA, Lemieux CL, Teerds K, Wagner M, Weisberg SB, Wright S. Development and application of a health-based framework for informing regulatory action in relation to exposure of microplastic particles in California drinking water. Microplast nanoplast 2022; 2:12. [PMID: 35634037 PMCID: PMC9132802 DOI: 10.1186/s43591-022-00030-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/11/2022] [Indexed: 05/06/2023]
Abstract
UNLABELLED Microplastics have been documented in drinking water, but their effects on human health from ingestion, or the concentrations at which those effects begin to manifest, are not established. Here, we report on the outcome of a virtual expert workshop conducted between October 2020 and October 2021 in which a comprehensive review of mammalian hazard studies was conducted. A key objective of this assessment was to evaluate the feasibility and confidence in deriving a human health-based threshold value to inform development of the State of California's monitoring and management strategy for microplastics in drinking water. A tiered approach was adopted to evaluate the quality and reliability of studies identified from a review of the peer-reviewed scientific literature. A total of 41 in vitro and 31 in vivo studies using mammals were identified and subjected to a Tier 1 screening and prioritization exercise, which was based on an evaluation of how each of the studies addressed various quality criteria. Prioritized studies were identified largely based on their application and reporting of dose-response relationships. Given that methods for extrapolating between in vitro and in vivo systems are currently lacking, only oral exposure in vivo studies were identified as fit-for-purpose within the context of this workshop. Twelve mammalian toxicity studies were prioritized and subjected to a Tier 2 qualitative evaluation by external experts. Of the 12 studies, 7 report adverse effects on male and female reproductive systems, while 5 reported effects on various other physiological endpoints. It is notable that the majority of studies (83%) subjected to Tier 2 evaluation report results from exposure to a single polymer type (polystyrene spheres), representing a size range of 0.040 to 20 µm. No single study met all desired quality criteria, but collectively toxicological effects with respect to biomarkers of inflammation and oxidative stress represented a consistent trend. While it was possible to derive a conservative screening level to inform monitoring activities, it was not possible to extrapolate a human-health-based threshold value for microplastics, which is largely due to concerns regarding the relative quality and reliability of current data, but also due to the inability to extrapolate data from studies using monodisperse plastic particles, such as polystyrene spheres to an environmentally relevant exposure of microplastics. Nevertheless, a conservative screening level value was used to estimate a volume of drinking water (1000 L) that could be used to support monitoring activities and improve our overall understanding of exposure in California's drinking water. In order to increase confidence in our ability to derive a human-health-based threshold value in the future, several research recommendations are provided, with an emphasis towards strengthening how toxicity studies should be conducted in the future and an improved understanding of human exposure to microplastics, insights critically important to better inform future risk assessments. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s43591-022-00030-6.
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Affiliation(s)
- Scott Coffin
- California State Water Resources Control Board, Sacramento, CA USA
| | - Hans Bouwmeester
- Division of Toxicology, Wageningen University & Research, Wageningen, Netherlands
| | - Susanne Brander
- Fisheries, Wildlife, and Conservation Sciences Dept, Coastal Oregon Marine Experiment Station, Oregon State University, Newport, OR USA
| | - Pauliina Damdimopoulou
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital Huddinge, 14186 Stockholm, Sweden
| | - Todd Gouin
- TG Environmental Research, Sharnbrook, MK44 1PL UK
| | - Ludovic Hermabessiere
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON Canada
| | - Elaine Khan
- California Office of Environmental Health and Hazard Assessment, Sacramento, CA USA
| | - Albert A. Koelmans
- Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, Wageningen, Netherlands
| | - Christine L. Lemieux
- Safe Environments Directorate, Health Canada, Water and Air Quality Bureau, Ottawa, ON Canada
| | - Katja Teerds
- Department of Animal Sciences, Human and Animal Physiology, Wageningen University & Research, Wageningen, Netherlands
| | - Martin Wagner
- Norwegian University of Science & Technology, Trondheim, Norway
| | | | - Stephanie Wright
- Environmental Research Group, School of Public Health, Imperial College London, Sir Michael Uren Hub, 86 Wood Lane, London, W12 0BZ UK
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9
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Kierkegaard A, Sundbom M, Yuan B, Armitage JM, Arnot JA, Droge STJ, McLachlan MS. Bioconcentration of Several Series of Cationic Surfactants in Rainbow Trout. Environ Sci Technol 2021; 55:8888-8897. [PMID: 34133133 PMCID: PMC8277129 DOI: 10.1021/acs.est.1c02063] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/22/2021] [Accepted: 06/07/2021] [Indexed: 05/03/2023]
Abstract
Cationic surfactants have a strong affinity to sorb to phospholipid membranes and thus possess an inherent potential to bioaccumulate, but there are few measurements of bioconcentration in fish. We measured the bioconcentration of 10 alkylamines plus two quaternary ammonium compounds in juvenile rainbow trout at pH 7.6, and repeated the measurements at pH 6.2 for 6 of these surfactants. The BCF of the amines with chain lengths ≤ C14 was positively correlated with chain length, increasing ∼0.5 log units per carbon. Their BCF was also pH dependent and approximately proportional to the neutral fraction of the amine in the water. The BCFs of the quaternary ammonium compounds showed no pH dependence and were >2 orders of magnitude less than for amines of the same chain length at pH 7.6. This indicates that systemic uptake of permanently charged cationic surfactants is limited. The behavior of the quaternary ammonium compounds and the two C16 amines studied was consistent with previous observations that these surfactants accumulate primarily to the gills and external surfaces of the fish. At pH 7.6 the BCF exceeded 2000 L kg-1 for 4 amines with chains ≥ C13, showing that bioconcentration can be considerable for some longer chained cationic surfactants.
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Affiliation(s)
- Amelie Kierkegaard
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - Marcus Sundbom
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - Bo Yuan
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - James M. Armitage
- AES
Armitage Environmental Sciences, Incorporated, Ottawa, Ontario K1L 8C3, Canada
| | - Jon A. Arnot
- ARC
Arnot Research and Consulting, Incorporated, Toronto, Ontario M4M 1W4, Canada
- Department
of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario MM1C 1A4, Canada
| | - Steven T. J. Droge
- Institute
for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam 1090 GE, The Netherlands
- Dutch
Board
for the Authorisation of Plant Protection Products and Biocides (Ctgb), Ede 6717 LL, The Netherlands
| | - Michael S. McLachlan
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
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10
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Batke M, Afrapoli FM, Kellner R, Rathman JF, Yang C, Cronin MTD, Escher SE. Threshold of Toxicological Concern—An Update for Non-Genotoxic Carcinogens. Front Toxicol 2021; 3:688321. [PMID: 35295144 PMCID: PMC8915827 DOI: 10.3389/ftox.2021.688321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/25/2021] [Indexed: 11/22/2022] Open
Abstract
The Threshold of Toxicological Concern (TTC) concept can be applied to organic compounds with the known chemical structure to derive a threshold for exposure, below which a toxic effect on human health by the compound is not expected. The TTC concept distinguishes between carcinogens that may act as genotoxic and non-genotoxic compounds. A positive prediction of a genotoxic mode of action, either by structural alerts or experimental data, leads to the application of the threshold value for genotoxic compounds. Non-genotoxic substances are assigned to the TTC value of their respective Cramer class, even though it is recognized that they could test positive in a rodent cancer bioassay. This study investigated the applicability of the Cramer classes specifically to provide adequate protection for non-genotoxic carcinogens. For this purpose, benchmark dose levels based on tumor incidence were compared with no observed effect levels (NOELs) derived from non-, pre- or neoplastic lesions. One key aspect was the categorization of compounds as non-genotoxic carcinogens. The recently finished CEFIC LRI project B18 classified the carcinogens of the Carcinogenicity Potency DataBase (CPDB) as either non-genotoxic or genotoxic compounds based on experimental or in silico data. A detailed consistency check resulted in a dataset of 137 non-genotoxic organic compounds. For these 137 compounds, NOEL values were derived from high quality animal studies with oral exposure and chronic duration using well-known repositories, such as RepDose, ToxRef, and COSMOS DB. Further, an effective tumor dose (ETD10) was calculated and compared with the lower confidence limit on benchmark dose levels (BMDL10) derived by model averaging. Comparative analysis of NOEL/EDT10/BMDL10 values showed that potentially bioaccumulative compounds in humans, as well as steroids, which both belong to the exclusion categories, occur predominantly in the region of the fifth percentiles of the distributions. Excluding these 25 compounds resulted in significantly higher but comparable fifth percentile chronic NOEL and BMDL10 values, while the fifth percentile EDT10 value was slightly higher but not statistically significant. The comparison of the obtained distributions of NOELs with the existing Cramer classes and their derived TTC values supports the application of Cramer class thresholds to all non-genotoxic compounds, such as non-genotoxic carcinogens.
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Affiliation(s)
- Monika Batke
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | | | - Rupert Kellner
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | - James F. Rathman
- Altamira, LLC, Columbus, OH, United States
- Molecular Networks GmbH, Nuremberg, Germany
| | - Chihae Yang
- Altamira, LLC, Columbus, OH, United States
- Molecular Networks GmbH, Nuremberg, Germany
| | - Mark T. D. Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Sylvia E. Escher
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover, Germany
- *Correspondence: Sylvia E. Escher
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11
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Urlings MJE, Duyx B, Swaen GMH, Bouter LM, Zeegers MPA. Determinants of Citation in Epidemiological Studies on Phthalates: A Citation Analysis. Sci Eng Ethics 2020; 26:3053-3067. [PMID: 32789752 PMCID: PMC7755632 DOI: 10.1007/s11948-020-00260-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/06/2020] [Indexed: 05/04/2023]
Abstract
Citing of previous publications is an important factor in knowledge development. Because of the great amount of publications available, only a selection of studies gets cited, for varying reasons. If the selection of citations is associated with study outcome this is called citation bias. We will study determinants of citation in a broader sense, including e.g. study design, journal impact factor or the funding source of the publication. As a case study we assess which factors drive citation in the human literature on phthalates, specifically the metabolite mono(2-ethylhexyl) phthalate (MEHP). A systematic literature search identified all relevant publications on human health effect of MEHP. Data on potential determinants of citation were extracted in duplo. Specialized software was used to create a citation network, including all potential citation pathways. Random effect logistic regression was used to assess whether these determinants influence the likelihood of citation. 112 Publications on MEHP were identified, with 5684 potential citation pathways of which 551 were actual citations. Reporting of a harmful point estimate, journal impact factor, authority of the author, a male corresponding author, research performed in North America and self-citation were positively associated with the likelihood of being cited. In the literature on MEHP, citation is mostly driven by a number of factors that are not related to study outcome. Although the identified determinants do not necessarily give strong indications of bias, it shows selective use of published literature for a variety of reasons.
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Affiliation(s)
- Miriam J E Urlings
- Nutrition and Translational Research in Metabolism, School NUTRIM, Maastricht University, Maastricht, The Netherlands.
| | - Bram Duyx
- Nutrition and Translational Research in Metabolism, School NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Gerard M H Swaen
- Nutrition and Translational Research in Metabolism, School NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Lex M Bouter
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Philosophy, Faculty of Humanities, Vrije Universiteit, Amsterdam, The Netherlands
| | - Maurice P A Zeegers
- Nutrition and Translational Research in Metabolism, School NUTRIM, Maastricht University, Maastricht, The Netherlands
- Care and Public Health Research Institute, School CAPHRI, Maastricht University, Maastricht, The Netherlands
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12
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Kosfeld V, Fu Q, Ebersbach I, Esser D, Schauerte A, Bischof I, Hollender J, Schlechtriem C. Comparison of Alternative Methods for Bioaccumulation Assessment: Scope and Limitations of In Vitro Depletion Assays with Rainbow Trout and Bioconcentration Tests in the Freshwater Amphipod Hyalella azteca. Environ Toxicol Chem 2020; 39:1813-1825. [PMID: 32495970 DOI: 10.1002/etc.4791] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/14/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Bioaccumulation assessment predominantly relies on the bioconcentration factor (BCF) as the sole decisive metric. The test guideline 305 by the Organisation for Economic Co-operation and Development (OECD) provides the standard procedure for deriving this in vivo fish BCF, which is not only expensive and labor-intensive, but also requires many animals. Accordingly, there is a great need for and interest in alternative methods that can help to reduce, replace, and refine vertebrate tests, as described in the 3R principles. Two alternative approaches have been developed: the bioconcentration test with the freshwater amphipod Hyalella azteca and the OECD test guideline 319 which provides a method to determine experimentally derived in vitro metabolism rates that can then be incorporated into in silico prediction models for rainbow trout BCF calculation. In the present study both alternative methods were applied to 5 substances of different physicochemical characteristics. The results were compared with literature values of fish in vivo BCFs and additional BCFs obtained with the alternative methods, if available. Potential differences between the results of the test methods are discussed utilizing information such as in vivo metabolism rates. The currently available data set suggests that these 2 alternative methods pose promising alternatives to predict bioaccumulation in fish, although defined applicability domains have yet to be determined. Environ Toxicol Chem 2020;39:1813-1825. © 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Verena Kosfeld
- Department Bioaccumulation and Animal Metabolism, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany
- Institute for Environmental Research (Biology V), RWTH Aachen University, Aachen, Germany
| | - Qiuguo Fu
- Department Environmental Chemistry, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Ina Ebersbach
- Department Bioaccumulation and Animal Metabolism, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany
| | - Dana Esser
- Department Bioaccumulation and Animal Metabolism, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany
| | - Anna Schauerte
- Department Bioaccumulation and Animal Metabolism, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany
| | - Ina Bischof
- Department Bioaccumulation and Animal Metabolism, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany
| | - Juliane Hollender
- Department Environmental Chemistry, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - Christian Schlechtriem
- Department Bioaccumulation and Animal Metabolism, Fraunhofer Institute for Molecular Biology and Applied Ecology, Schmallenberg, Germany
- Institute for Environmental Research (Biology V), RWTH Aachen University, Aachen, Germany
- Department Chemistry and Biology, "Ecotoxicology" Work Group, University of Siegen, Siegen, Germany
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13
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Gobas FAPC, Lee YS, Lo JC, Parkerton TF, Letinski DJ. A Toxicokinetic Framework and Analysis Tool for Interpreting Organisation for Economic Co-operation and Development Guideline 305 Dietary Bioaccumulation Tests. Environ Toxicol Chem 2020; 39:171-188. [PMID: 31546284 DOI: 10.1002/etc.4599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/12/2019] [Accepted: 09/16/2019] [Indexed: 05/15/2023]
Abstract
The Organisation for Economic Co-operation and Development guideline 305 for bioaccumulation testing in fish includes the option to conduct a dietary test for assessing a chemical's bioaccumulation behavior. However, the one-compartment toxicokinetic model that is used in the guidelines to analyze the results from dietary bioaccumulation tests is not consistent with the current state of the science, experimental practices, and information needs for bioaccumulation and risk assessment. The present study presents 1) a 2-compartment toxicokinetic modeling framework for describing the bioaccumulation of neutral hydrophobic organic chemicals in fish and 2) an associated toxicokinetic analysis tool (absorption, distribution, metabolism, and excretion [ADME] B calculator) for the analysis and interpretation of dietary bioaccumulation test data from OECD-305 dietary tests. The model framework and ADME-B calculator are illustrated by analysis of fish dietary bioaccumulation test data for 238 substances representing different structural classes and susceptibilities to biotransformation. The ADME of the chemicals is determined from dietary bioaccumulation tests and bioconcentration factors, biomagnification factors, and somatic and intestinal biotransformation rates. The 2-compartment fish toxicokinetic model can account for the effect of the exposure pathway on bioaccumulation, which the one-compartment model cannot. This insight is important for applying a weight-of-evidence approach to bioaccumulation assessment where information from aqueous and dietary test endpoints can be integrated to improve the evaluation of a chemical's bioaccumulation potential. Environ Toxicol Chem 2019;39:171-188. © 2019 SETAC.
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Affiliation(s)
- Frank A P C Gobas
- Resource and Environmental Management, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Yung-Shan Lee
- Resource and Environmental Management, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Justin C Lo
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Thomas F Parkerton
- Toxicology & Environmental Science Division, ExxonMobil Biomedical Sciences, Spring, Texas, USA
| | - Daniel J Letinski
- Toxicology & Environmental Science Division, ExxonMobil Biomedical Sciences, Annandale, New Jersey, USA
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14
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Perkins EJ, Ashauer R, Burgoon L, Conolly R, Landesmann B, Mackay C, Murphy CA, Pollesch N, Wheeler JR, Zupanic A, Scholz S. Building and Applying Quantitative Adverse Outcome Pathway Models for Chemical Hazard and Risk Assessment. Environ Toxicol Chem 2019; 38:1850-1865. [PMID: 31127958 PMCID: PMC6771761 DOI: 10.1002/etc.4505] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/26/2019] [Accepted: 05/21/2019] [Indexed: 05/20/2023]
Abstract
An important goal in toxicology is the development of new ways to increase the speed, accuracy, and applicability of chemical hazard and risk assessment approaches. A promising route is the integration of in vitro assays with biological pathway information. We examined how the adverse outcome pathway (AOP) framework can be used to develop pathway-based quantitative models useful for regulatory chemical safety assessment. By using AOPs as initial conceptual models and the AOP knowledge base as a source of data on key event relationships, different methods can be applied to develop computational quantitative AOP models (qAOPs) relevant for decision making. A qAOP model may not necessarily have the same structure as the AOP it is based on. Useful AOP modeling methods range from statistical, Bayesian networks, regression, and ordinary differential equations to individual-based models and should be chosen according to the questions being asked and the data available. We discuss the need for toxicokinetic models to provide linkages between exposure and qAOPs, to extrapolate from in vitro to in vivo, and to extrapolate across species. Finally, we identify best practices for modeling and model building and the necessity for transparent and comprehensive documentation to gain confidence in the use of qAOP models and ultimately their use in regulatory applications. Environ Toxicol Chem 2019;38:1850-1865. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
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Affiliation(s)
- Edward J. Perkins
- US Army Engineer Research and Development CenterVicksburgMississippiUSA
| | - Roman Ashauer
- Environment DepartmentUniversity of York, HeslingtonYorkUK
- ToxicodynamicsYorkUK
| | - Lyle Burgoon
- US Army Engineer Research and Development CenterVicksburgMississippiUSA
| | - Rory Conolly
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and DevelopmentUS Environmental Protection Agency, Research Triangle ParkNorth CarolinaUSA
| | | | - Cameron Mackay
- Unilever Safety and Environmental Assurance Centre, SharnbrookBedfordUK
| | - Cheryl A. Murphy
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
| | - Nathan Pollesch
- Mid‐Continent Ecology Division, National Health and Environmental Effects Laboratory, Office of Research and DevelopmentUS Environmental Protection AgencyDuluthMinnesotaUSA
| | | | - Anze Zupanic
- Department of Environmental ToxicologySwiss Federal Institute for Aquatic Science and TechnologyDübendorfSwitzerland
| | - Stefan Scholz
- Department of Bioanalytical EcotoxicologyHelmholtz Centre for Environmental Research‐UFZLeipzigGermany
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15
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Duyx B, Swaen GMH, Urlings MJE, Bouter LM, Zeegers MP. The strong focus on positive results in abstracts may cause bias in systematic reviews: a case study on abstract reporting bias. Syst Rev 2019; 8:174. [PMID: 31315665 PMCID: PMC6637611 DOI: 10.1186/s13643-019-1082-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/28/2019] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Research articles tend to focus on positive findings in their abstract, especially if multiple outcomes have been studied. At the same time, search queries in databases are generally limited to the abstract, title and keywords fields of an article. Negative findings are therefore less likely to be detected by systematic searches and to appear in systematic reviews. We aim to assess the occurrence of this 'abstract reporting bias' and quantify its impact in the literature on the association between diesel exhaust exposure (DEE) and bladder cancer. METHODS We set up a broad search query related to DEE and cancer in general. Full-texts of the articles identified in the search output were manually scanned. Articles were included if they reported, anywhere in the full-text, the association between DEE and bladder cancer. We assume that the use of a broad search query and manual full-text scanning allowed us to catch all the relevant articles, including those in which bladder cancer was not mentioned in the abstract, title or keywords. RESULTS We identified 28 articles. Only 12 of these (43%) had mentioned bladder in their abstract, title or keywords. A meta-analysis based on these 12 detectable articles yielded a pooled risk estimate of 1.10 (95% confidence interval [CI] 0.97-1.25), whereas the meta-analysis based on all 28 articles yielded a pooled estimate of 1.03 (95% CI 0.96-1.11). CONCLUSIONS This case study on abstract reporting bias shows that (a) more than half of all relevant articles were missed by a conventional search query and (b) this led to an overestimation of the pooled effect. Detection of articles will be improved if all studied exposure and outcome variables are reported in the keywords. The restriction on the maximum number of keywords should be lifted.
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Affiliation(s)
- Bram Duyx
- Nutrition and Translational Research in Metabolism (School NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Gerard M. H. Swaen
- Nutrition and Translational Research in Metabolism (School NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Miriam J. E. Urlings
- Nutrition and Translational Research in Metabolism (School NUTRIM), Maastricht University, Maastricht, The Netherlands
| | - Lex M. Bouter
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Philosophy, Faculty of Humanities, Vrije Universiteit, Amsterdam, The Netherlands
| | - Maurice P. Zeegers
- Nutrition and Translational Research in Metabolism (School NUTRIM), Maastricht University, Maastricht, The Netherlands
- Care and Public Health Research Institute (School CAPHRI), Maastricht University, Maastricht, The Netherlands
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16
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Duyx B, Urlings MJE, Swaen GMH, Bouter LM, Zeegers MP. Selective citation in the literature on the hygiene hypothesis: a citation analysis on the association between infections and rhinitis. BMJ Open 2019; 9:e026518. [PMID: 30782945 PMCID: PMC6377569 DOI: 10.1136/bmjopen-2018-026518] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVE Our objective was to assess the occurrence and determinants of selective citation in scientific publications on Strachan's original hygiene hypothesis. His hypothesis states that lack of exposure to infections in early childhood increases the risk of rhinitis. SETTING Web of Science Core Collection. PARTICIPANTS We identified 110 publications in this network, consisting of 5551 potential citations. PRIMARY AND SECONDARY OUTCOME MEASURES Whether a citation occurs or not, measured and analysed according to the preregistered protocol. RESULTS We found evidence for citation bias in this field: publications supportive of the hypothesis were cited more often than non-supportive publications (OR adjusted for study design [adjOR] 2.2, 95% CI 1.6 to 3.1), and the same was the case for publications with mixed findings (adjOR 3.1, 95% CI 2.2 to 4.5). Other relevant determinants for citation were type of exposure, specificity, journal impact factor, authority and self-citation. Surprisingly, prospective cohort studies were cited less often than other empirical studies. CONCLUSIONS There is clear evidence for selective citation in this research field, and particularly for citation bias.
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Affiliation(s)
- Bram Duyx
- Nutrition and Translational Research in Metabolism (School NUTRIM), Maastricht University, Maastricht, Limburg, The Netherlands
| | - Miriam J E Urlings
- Nutrition and Translational Research in Metabolism (School NUTRIM), Maastricht University, Maastricht, Limburg, The Netherlands
| | - Gerard M H Swaen
- Nutrition and Translational Research in Metabolism (School NUTRIM), Maastricht University, Maastricht, Limburg, The Netherlands
| | - Lex M Bouter
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, Amsterdam, The Netherlands
- Department of Philosophy, Faculty of Humanities, Vrije Universiteit, Amsterdam, Noord-Holland, The Netherlands
| | - Maurice P Zeegers
- Nutrition and Translational Research in Metabolism (School NUTRIM), Maastricht University, Maastricht, Limburg, The Netherlands
- Care and Public Health Research Institute (School CAPHRI), Maastricht University, Maastricht, Limburg, The Netherlands
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17
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Kochev N, Avramova S, Jeliazkova N. Ambit-SMIRKS: a software module for reaction representation, reaction search and structure transformation. J Cheminform 2018; 10:42. [PMID: 30128804 PMCID: PMC6102164 DOI: 10.1186/s13321-018-0295-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/11/2018] [Indexed: 11/15/2022] Open
Abstract
Ambit-SMIRKS is an open source software, enabling structure transformation via the SMIRKS language and implemented as an extension of Ambit-SMARTS. As part of the Ambit project it builds on top of The Chemistry Development Kit (The CDK). Ambit-SMIRKS provides the following functionalities: parsing of SMIRKS linear notations into internal reaction (transformation) representations based on The CDK objects, application of the stored reactions against target (reactant) molecules for actual transformation of the target chemical objects, reaction searching, stereo information handling, product post-processing, etc. The transformations can be applied on various sites of the reactant molecule in several modes: single, non-overlapping, non-identical, non-homomorphic or externally specified list of sites utilizing efficient substructure searching algorithm. Ambit-SMIRKS handles the molecules stereo information and supports basic chemical stereo elements implemented in The CDK library. The full SMARTS logical expressions syntax for reactions specification is supported, including recursive SMARTS expressions as well as additional syntax extensions. Since its initial development for the purpose of metabolite generation within Toxtree, the Ambit-SMIRKS module was used in various chemoinformatics projects, both developed by the authors of the package and by external teams. We show several use cases of the Ambit-SMIRKS software including standardization of large chemical databases and pathway transformation database and prediction. Ambit-SMIRKS is distributed as a Java library under LGPL license. More information on use cases and applications, including download links is available at http://ambit.sourceforge.net/smirks .
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Affiliation(s)
- Nikolay Kochev
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 24 Tsar Assen St., 4000 Plovdiv, Bulgaria
- Ideaconsult Ltd, 4 A. Kanchev Str., 1000 Sofia, Bulgaria
| | - Svetlana Avramova
- Department of Analytical Chemistry and Computer Chemistry, University of Plovdiv, 24 Tsar Assen St., 4000 Plovdiv, Bulgaria
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18
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Limonciel A, Ates G, Carta G, Wilmes A, Watzele M, Shepard PJ, VanSteenhouse HC, Seligmann B, Yeakley JM, van de Water B, Vinken M, Jennings P. Comparison of base-line and chemical-induced transcriptomic responses in HepaRG and RPTEC/TERT1 cells using TempO-Seq. Arch Toxicol 2018; 92:2517-2531. [PMID: 30008028 PMCID: PMC6063331 DOI: 10.1007/s00204-018-2256-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 07/04/2018] [Indexed: 12/21/2022]
Abstract
The utilisation of genome-wide transcriptomics has played a pivotal role in advancing the field of toxicology, allowing the mapping of transcriptional signatures to chemical exposures. These activities have uncovered several transcriptionally regulated pathways that can be utilised for assessing the perturbation impact of a chemical and also the identification of toxic mode of action. However, current transcriptomic platforms are not very amenable to high-throughput workflows due to, high cost, complexities in sample preparation and relatively complex bioinformatic analysis. Thus, transcriptomic investigations are usually limited in dose and time dimensions and are, therefore, not optimal for implementation in risk assessment workflows. In this study, we investigated a new cost-effective, transcriptomic assay, TempO-Seq, which alleviates the aforementioned limitations. This technique was evaluated in a 6-compound screen, utilising differentiated kidney (RPTEC/TERT1) and liver (HepaRG) cells and compared to non-transcriptomic label-free sensitive endpoints of chemical-induced disturbances, namely phase contrast morphology, xCELLigence and glycolysis. Non-proliferating cell monolayers were exposed to six sub-lethal concentrations of each compound for 24 h. The results show that utilising a 2839 gene panel, it is possible to discriminate basal tissue-specific signatures, generate dose-response relationships and to discriminate compound-specific and cell type-specific responses. This study also reiterates previous findings that chemical-induced transcriptomic alterations occur prior to cytotoxicity and that transcriptomics provides in depth mechanistic information of the effects of chemicals on cellular transcriptional responses. TempO-Seq is a robust transcriptomic platform that is well suited for in vitro toxicity experiments.
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Affiliation(s)
- Alice Limonciel
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Gamze Ates
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Giada Carta
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Anja Wilmes
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Manfred Watzele
- Roche Diagnostics GmbH, Nonnenwald 2, 82377, Penzberg, Germany
| | - Peter J Shepard
- BioSpyder Technologies, Inc., 5922 Farnsworth Ct Ste 102, Carlsbad, CA, 92008, USA
| | | | - Bruce Seligmann
- BioSpyder Technologies, Inc., 5922 Farnsworth Ct Ste 102, Carlsbad, CA, 92008, USA
| | - Joanne M Yeakley
- BioSpyder Technologies, Inc., 5922 Farnsworth Ct Ste 102, Carlsbad, CA, 92008, USA
| | - Bob van de Water
- Division of Toxicology, Leiden Academic Center for Drug Research, Leiden University, PO Box 9503, 2300 RA, Leiden, The Netherlands
| | - Mathieu Vinken
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium.
| | - Paul Jennings
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
- Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, 6020, Innsbruck, Austria.
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