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Kreutz A, Oyetade OB, Chang X, Hsieh JH, Behl M, Allen DG, Kleinstreuer NC, Hogberg HT. Integrated Approach for Testing and Assessment for Developmental Neurotoxicity (DNT) to Prioritize Aromatic Organophosphorus Flame Retardants. TOXICS 2024; 12:437. [PMID: 38922117 PMCID: PMC11209292 DOI: 10.3390/toxics12060437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024]
Abstract
Organophosphorus flame retardants (OPFRs) are abundant and persistent in the environment but have limited toxicity information. Their similarity in structure to organophosphate pesticides presents great concern for developmental neurotoxicity (DNT). However, current in vivo testing is not suitable to provide DNT information on the amount of OPFRs that lack data. Over the past decade, an in vitro battery was developed to enhance DNT assessment, consisting of assays that evaluate cellular processes in neurodevelopment and function. In this study, behavioral data of small model organisms were also included. To assess if these assays provide sufficient mechanistic coverage to prioritize chemicals for further testing and/or identify hazards, an integrated approach to testing and assessment (IATA) was developed with additional information from the Integrated Chemical Environment (ICE) and the literature. Human biomonitoring and exposure data were identified and physiologically-based toxicokinetic models were applied to relate in vitro toxicity data to human exposure based on maximum plasma concentration. Eight OPFRs were evaluated, including aromatic OPFRs (triphenyl phosphate (TPHP), isopropylated phenyl phosphate (IPP), 2-ethylhexyl diphenyl phosphate (EHDP), tricresyl phosphate (TMPP), isodecyl diphenyl phosphate (IDDP), tert-butylphenyl diphenyl phosphate (BPDP)) and halogenated FRs ((Tris(1,3-dichloro-2-propyl) phosphate (TDCIPP), tris(2-chloroethyl) phosphate (TCEP)). Two representative brominated flame retardants (BFRs) (2,2'4,4'-tetrabromodiphenyl ether (BDE-47) and 3,3',5,5'-tetrabromobisphenol A (TBBPA)) with known DNT potential were selected for toxicity benchmarking. Data from the DNT battery indicate that the aromatic OPFRs have activity at similar concentrations as the BFRs and should therefore be evaluated further. However, these assays provide limited information on the mechanism of the compounds. By integrating information from ICE and the literature, endocrine disruption was identified as a potential mechanism. This IATA case study indicates that human exposure to some OPFRs could lead to a plasma concentration similar to those exerting in vitro activities, indicating potential concern for human health.
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Affiliation(s)
- Anna Kreutz
- Inotiv, Research Triangle Park, NC 27560, USA; (A.K.); (O.B.O.); (X.C.); (D.G.A.)
| | - Oluwakemi B. Oyetade
- Inotiv, Research Triangle Park, NC 27560, USA; (A.K.); (O.B.O.); (X.C.); (D.G.A.)
| | - Xiaoqing Chang
- Inotiv, Research Triangle Park, NC 27560, USA; (A.K.); (O.B.O.); (X.C.); (D.G.A.)
| | - Jui-Hua Hsieh
- NIH/NIEHS/DTT/PTB, Research Triangle Park, NC 27560, USA;
| | - Mamta Behl
- Neurocrine Biosciences Inc., San Diego, CA 92130, USA;
| | - David G. Allen
- Inotiv, Research Triangle Park, NC 27560, USA; (A.K.); (O.B.O.); (X.C.); (D.G.A.)
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Chambers BA, Basili D, Word L, Baker N, Middleton A, Judson RS, Shah I. Searching for LINCS to Stress: Using Text Mining to Automate Reference Chemical Curation. Chem Res Toxicol 2024; 37:878-893. [PMID: 38736322 DOI: 10.1021/acs.chemrestox.3c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Adaptive stress response pathways (SRPs) restore cellular homeostasis following perturbation but may activate terminal outcomes like apoptosis, autophagy, or cellular senescence if disruption exceeds critical thresholds. Because SRPs hold the key to vital cellular tipping points, they are targeted for therapeutic interventions and assessed as biomarkers of toxicity. Hence, we are developing a public database of chemicals that perturb SRPs to enable new data-driven tools to improve public health. Here, we report on the automated text-mining pipeline we used to build and curate the first version of this database. We started with 100 reference SRP chemicals gathered from published biomarker studies to bootstrap the database. Second, we used information retrieval to find co-occurrences of reference chemicals with SRP terms in PubMed abstracts and determined pairwise mutual information thresholds to filter biologically relevant relationships. Third, we applied these thresholds to find 1206 putative SRP perturbagens within thousands of substances in the Library of Integrated Network-Based Cellular Signatures (LINCS). To assign SRP activity to LINCS chemicals, domain experts had to manually review at least three publications for each of 1206 chemicals out of 181,805 total abstracts. To accomplish this efficiently, we implemented a machine learning approach to predict SRP classifications from texts to prioritize abstracts. In 5-fold cross-validation testing with a corpus derived from the 100 reference chemicals, artificial neural networks performed the best (F1-macro = 0.678) and prioritized 2479/181,805 abstracts for expert review, which resulted in 457 chemicals annotated with SRP activities. An independent analysis of enriched mechanisms of action and chemical use class supported the text-mined chemical associations (p < 0.05): heat shock inducers were linked with HSP90 and DNA damage inducers to topoisomerase inhibition. This database will enable novel applications of LINCS data to evaluate SRP activities and to further develop tools for biomedical information extraction from the literature.
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Affiliation(s)
- Bryant A Chambers
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Danilo Basili
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Laura Word
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Nancy Baker
- Leidos, Research Triangle Park, North Carolina 27711, United States
| | - Alistair Middleton
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Richard S Judson
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Imran Shah
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
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Thorne D, McHugh D, Simms L, Lee KM, Fujimoto H, Moses S, Gaca M. Applying new approach methodologies to assess next-generation tobacco and nicotine products. FRONTIERS IN TOXICOLOGY 2024; 6:1376118. [PMID: 38938663 PMCID: PMC11208635 DOI: 10.3389/ftox.2024.1376118] [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: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 06/29/2024] Open
Abstract
In vitro toxicology research has accelerated with the use of in silico, computational approaches and human in vitro tissue systems, facilitating major improvements evaluating the safety and health risks of novel consumer products. Innovation in molecular and cellular biology has shifted testing paradigms, with less reliance on low-throughput animal data and greater use of medium- and high-throughput in vitro cellular screening approaches. These new approach methodologies (NAMs) are being implemented in other industry sectors for chemical testing, screening candidate drugs and prototype consumer products, driven by the need for reliable, human-relevant approaches. Routine toxicological methods are largely unchanged since development over 50 years ago, using high-doses and often employing in vivo testing. Several disadvantages are encountered conducting or extrapolating data from animal studies due to differences in metabolism or exposure. The last decade saw considerable advancement in the development of in vitro tools and capabilities, and the challenges of the next decade will be integrating these platforms into applied product testing and acceptance by regulatory bodies. Governmental and validation agencies have launched and applied frameworks and "roadmaps" to support agile validation and acceptance of NAMs. Next-generation tobacco and nicotine products (NGPs) have the potential to offer reduced risks to smokers compared to cigarettes. These include heated tobacco products (HTPs) that heat but do not burn tobacco; vapor products also termed electronic nicotine delivery systems (ENDS), that heat an e-liquid to produce an inhalable aerosol; oral smokeless tobacco products (e.g., Swedish-style snus) and tobacco-free oral nicotine pouches. With the increased availability of NGPs and the requirement of scientific studies to support regulatory approval, NAMs approaches can supplement the assessment of NGPs. This review explores how NAMs can be applied to assess NGPs, highlighting key considerations, including the use of appropriate in vitro model systems, deploying screening approaches for hazard identification, and the importance of test article characterization. The importance and opportunity for fit-for-purpose testing and method standardization are discussed, highlighting the value of industry and cross-industry collaborations. Supporting the development of methods that are accepted by regulatory bodies could lead to the implementation of NAMs for tobacco and nicotine NGP testing.
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Affiliation(s)
- David Thorne
- BAT (Investments) Ltd., Southampton, Hampshire, United Kingdom
| | - Damian McHugh
- PMI R&D Philip Morris Products S. A., Neuchâtel, Switzerland
| | - Liam Simms
- Imperial Brands, Bristol, United Kingdom
| | - K. Monica Lee
- Altria Client Services LLC, Richmond, VA, United States
| | | | | | - Marianna Gaca
- BAT (Investments) Ltd., Southampton, Hampshire, United Kingdom
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Wood A, Breffa C, Chaine C, Cubberley R, Dent M, Eichhorn J, Fayyaz S, Grimm FA, Houghton J, Kiwamoto R, Kukic P, Lee M, Malcomber S, Martin S, Nicol B, Reynolds J, Riley G, Scott S, Smith C, Westmoreland C, Wieland W, Williams M, Wolton K, Zellmann T, Gutsell S. Next generation risk assessment for occupational chemical safety - A real world example with sodium-2-hydroxyethane sulfonate. Toxicology 2024; 506:153835. [PMID: 38857863 DOI: 10.1016/j.tox.2024.153835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/07/2024] [Accepted: 05/15/2024] [Indexed: 06/12/2024]
Abstract
Next Generation Risk Assessment (NGRA) is an exposure-led approach to safety assessment that uses New Approach Methodologies (NAMs). Application of NGRA has been largely restricted to assessments of consumer use of cosmetics and is not currently implemented in occupational safety assessments, e.g. under EU REACH. By contrast, a large proportion of regulatory worker safety assessments are underpinned by toxicological studies using experimental animals. Consequently, occupational safety assessment represents an area that would benefit from increasing application of NGRA to safety decision making. Here, a workflow for conducting NGRA under an occupational safety context was developed, which is illustrated with a case study chemical; sodium 2-hydroxyethane sulphonate (sodium isethionate or SI). Exposures were estimated using a standard occupational exposure model following a comprehensive life cycle assessment of SI and considering factory-specific data. Outputs of this model were then used to estimate internal exposures using a Physiologically Based Kinetic (PBK) model, which was constructed with SI specific Absorption, Distribution, Metabolism and Excretion (ADME) data. PBK modelling indicated a worst-case plasma maximum concentration (Cmax) of 0.8 μM across the SI life cycle. SI bioactivity was assessed in a battery of NAMs relevant to systemic, reproductive, and developmental toxicity; a cell stress panel, high throughput transcriptomics in three cell lines (HepG2, HepaRG and MCF-7 cells), pharmacological profiling and specific assays relating to developmental toxicity (Reprotracker and devTOX quickPredict). Points of Departure (PoDs) for SI ranged from 104 to 5044 µM. Cmax values obtained from PBK modelling of occupational exposures to SI were compared with PoDs from the bioactivity assays to derive Bioactivity Exposure Ratios (BERs) which demonstrated the safety for workers exposed to SI under current levels of factory specific risk management. In summary, the tiered and iterative workflow developed here represents an opportunity for integrating non animal approaches for a large subset of substances for which systemic worker safety assessment is required. Such an approach could be followed to ensure that animal testing is only conducted as a "last resort" e.g. under EU REACH.
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Affiliation(s)
- Adam Wood
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK.
| | - Catherine Breffa
- Clariant Produkte (Deutschland) GmbH, Frankfurt am Main, Germany
| | - Caroline Chaine
- Vantage Specialty Chemicals, 3 rue Jules Guesde, Ris Orangis 91130, France
| | - Richard Cubberley
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Matthew Dent
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Joachim Eichhorn
- Clariant Produkte (Deutschland) GmbH, Frankfurt am Main, Germany
| | - Susann Fayyaz
- Clariant Produkte (Deutschland) GmbH, Frankfurt am Main, Germany
| | - Fabian A Grimm
- Clariant Produkte (Deutschland) GmbH, Frankfurt am Main, Germany
| | - Jade Houghton
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Reiko Kiwamoto
- Unilever, Bronland 14, Wageningen 6708 WH, the Netherlands
| | - Predrag Kukic
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - MoungSook Lee
- Clariant Produkte (Deutschland) GmbH, Frankfurt am Main, Germany
| | - Sophie Malcomber
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Suzanne Martin
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Beate Nicol
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Joe Reynolds
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Gordon Riley
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Sharon Scott
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Colin Smith
- ERM Ireland Limited, Ardilaun Court, St Stephen's Green, Dublin, Ireland
| | - Carl Westmoreland
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | | | - Mesha Williams
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Kathryn Wolton
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | | | - Steve Gutsell
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
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Mittal K, Arini A, Basu N. Screening 800 putative endocrine disrupting chemicals in a representative mammal, bird, and fish using a neurochemical cell-free testing platform. CHEMOSPHERE 2024; 362:142562. [PMID: 38851506 DOI: 10.1016/j.chemosphere.2024.142562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/26/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024]
Abstract
There is global demand for novel ecotoxicity testing tools that are based on alternative to animal models, have high throughput potential, and may be applicable to a wide diversity of taxa. Here we scaled up a microplate-based cell-free neurochemical testing platform to screen 800 putative endocrine disrupting chemicals from the U.S. Environmental Protection Agency's ToxCast e1k library against the glutamate (NMDA), muscarinic acetylcholine (mACh), and dopamine (D2) receptors. Each assay was tested in cellular membranes isolated from brain tissues from a representative bird (zebra finch = Taeniopygia castanotis), mammal (mink = Neogale vison), and fish (rainbow trout = Oncorhynchus mykiss). The primary objective of this short communication was to make the results database accessible, while also summarising key attributes of assay performance and presenting some initial observations. In total, 7200 species-chemical-assay combinations were tested, of which 453 combinations were classified as a hit (radioligand binding changed by at least 3 standard deviations). There were some differences across species, and most hits were found for the D2 and NMDA receptors. The most active chemical was C.I. Solvent Yellow 14 followed by Diphenhydramine hydrochloride, Gentian Violet, SR271425, and Zamifenacin. Nine chemicals were tested across multiple plates with a mean relative standard deviation of the specific radioligand binding data being 24.6%. The results demonstrate that cell-free assays may serve as screening tools for large chemical libraries especially for ecological species not easily studied using traditional methods.
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Affiliation(s)
- Krittika Mittal
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Adeline Arini
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Niladri Basu
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada.
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6
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Martin MM, Carpenter AF, Shafer TJ, Paul Friedman K, Carstens KE. Chemical effects on neural network activity: Comparison of acute versus network formation exposure in microelectrode array assays. Toxicology 2024; 505:153842. [PMID: 38788893 DOI: 10.1016/j.tox.2024.153842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/08/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
New approach methodologies (NAMs) can address information gaps on potential neurotoxicity or developmental neurotoxicity hazard for data-poor chemicals. Two assays have been previously developed using microelectrode arrays (MEA), a technology which measures neural activity. The MEA acute network function assay (AcN) uses dissociated rat cortical cells cultured at postnatal day 0 and evaluates network activity during a 40-minute chemical exposure on day in vitro (DIV)13 or 15. In contrast, the MEA network formation assay (NFA) uses a developmental exposure paradigm spanning DIV0 through DIV12. Measures of network activity over time at DIV5, 7, 9, and 12 in the NFA are reduced to an estimated area under the curve to facilitate concentration-response evaluation. Here, we evaluated the hypothesis that chemicals with effects in the AcN also perturb the NFA by examining quantitative and qualitative concordance between assays. Out of 243 chemicals screened in both assays, we observed 70.3% concordance between the AcN and NFA after eliminating activity inferred to be cytotoxic (selective activity), with the majority of discordance explained by chemicals that altered selective activity in the AcN but not NFA. The NFA detected more active chemicals when evaluating activity associated with cytotoxicity. Median potency values were lower in the NFA compared to the AcN, but within-chemical potency values were not uniformly lower in the NFA than the AcN. Lastly, the AcN and NFA captured unique bioactivity fingerprints; the AcN was more informative for identifying chemicals with a shared mode of action, while the NFA provided information relevant to developmental exposure. Taken together, this analysis provides a rationale for using both approaches for chemical evaluation with consideration of the context of use, such as screening/ prioritization, hazard identification, or to address questions regarding biological mechanism or function.
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Affiliation(s)
- Melissa M Martin
- Computational Toxicology & Bioinformatics Branch, Biomolecular and Computational Toxicology Division, CCTE/ORD, US. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Amy F Carpenter
- Computational Toxicology & Bioinformatics Branch, Biomolecular and Computational Toxicology Division, CCTE/ORD, US. Environmental Protection Agency, Research Triangle Park, NC 27711, USA; Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, USA
| | - Timothy J Shafer
- Computational Toxicology & Bioinformatics Branch, Biomolecular and Computational Toxicology Division, CCTE/ORD, US. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Katie Paul Friedman
- Computational Toxicology & Bioinformatics Branch, Biomolecular and Computational Toxicology Division, CCTE/ORD, US. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Kelly E Carstens
- Computational Toxicology & Bioinformatics Branch, Biomolecular and Computational Toxicology Division, CCTE/ORD, US. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
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7
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Charlton-Sevcik AK, Collom C, Liu JY, Hsieh YL, Stark N, Ede JD, Shatkin JA, Sayes CM. The impact of surface functionalization of cellulose following simulated digestion and gastrointestinal cell-based model exposure. Int J Biol Macromol 2024; 271:132603. [PMID: 38788877 DOI: 10.1016/j.ijbiomac.2024.132603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Surface-functionalized cellulose materials are developed for various purposes, including food additives and food contact materials. A new biologically relevant testing strategy has been developed based on guidance from the European Food Safety Authority to demonstrate the safety of several next-generation surface-functionalized cellulose materials. This strategy involves a complex three-stage simulated digestion to compare the health effects of thirteen novel different types of cellulose. The physical and chemical properties of surface-functionalized fibrillated celluloses differed depending on the type, amount, and location of functional groups such as sulfonate, TEMPO-oxidized carboxy, and periodate-chlorite oxidized dicarboxylic acid celluloses. Despite exposure to gastrointestinal fluids, the celluloses maintained their physicochemical properties, such as negative surface charges and high length-to-width/thickness aspect ratios. An established intestinal co-culture model was used to measure cytotoxicity, barrier integrity, oxidative stress, and pro-inflammatory response to create a toxicological profile for these unique materials. We conclude that the C6 carboxylated cellulose nanofibrils by TEMPO-oxidation induced the most toxicity in the biological model used in this study and that the observed effects were most prominent at the 4-hour post-exposure time point.
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Affiliation(s)
- Amanda K Charlton-Sevcik
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798-7266, USA
| | - Clancy Collom
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798-7266, USA
| | - James Y Liu
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798-7266, USA
| | | | | | - James D Ede
- Vireo Advisors, LLC, Boston, MA 02130-4323, USA
| | | | - Christie M Sayes
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798-7266, USA.
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Groff L, Williams A, Shah I, Patlewicz G. MetSim: Integrated Programmatic Access and Pathway Management for Xenobiotic Metabolism Simulators. Chem Res Toxicol 2024; 37:685-697. [PMID: 38598715 DOI: 10.1021/acs.chemrestox.3c00398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Xenobiotic metabolism is a key consideration in evaluating the hazards and risks posed by environmental chemicals. A number of software tools exist that are capable of simulating metabolites, but each reports its predictions in a different format and with varying levels of detail. This makes comparing the performance and coverage of the tools a practical challenge. To address this shortcoming, we developed a metabolic simulation framework called MetSim, which comprises three main components. A graph-based schema was developed to allow metabolism information to be harmonized. The schema was implemented in MongoDB to store and retrieve metabolic graphs for subsequent analysis. MetSim currently includes an application programming interface for four metabolic simulators: BioTransformer, the OECD Toolbox, EPA's chemical transformation simulator (CTS), and tissue metabolism simulator (TIMES). Lastly, MetSim provides functions to help evaluate simulator performance for specific data sets. In this study, a set of 112 drugs with 432 reported metabolites were compiled, and predictions were made using the 4 simulators. Fifty-nine of the 112 drugs were taken from the Small Molecule Pathway Database, with the remainder sourced from the literature. The human models within BioTransformer and CTS (Phase I only) and the rat models within TIMES and the OECD Toolbox (Phase I only) were used to make predictions for the chemicals in the data set. The recall and precision (recall, precision) ranked in order of highest recall for each individual tool were CTS (0.54, 0.017), BioTransformer (0.50, 0.008), Toolbox in vitro (0.40, 0.144), TIMES in vivo (0.40, 0.133), Toolbox in vivo (0.40, 0.118), and TIMES in vitro (0.39, 0.128). Combining all of the model predictions together increased the overall recall (0.73, 0.008). MetSim enabled insights into the performance and coverage of in silico metabolic simulators to be more efficiently derived, which in turn should aid future efforts to evaluate other data sets.
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Affiliation(s)
- Louis Groff
- Center for Computational Toxicology and Exposure (CCTE), Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Antony Williams
- Center for Computational Toxicology and Exposure (CCTE), Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Imran Shah
- Center for Computational Toxicology and Exposure (CCTE), Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Grace Patlewicz
- Center for Computational Toxicology and Exposure (CCTE), Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
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Henriquez JE, Badwaik VD, Bianchi E, Chen W, Corvaro M, LaRocca J, Lunsman TD, Zu C, Johnson KJ. From Pipeline to Plant Protection Products: Using New Approach Methodologies (NAMs) in Agrochemical Safety Assessment. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10710-10724. [PMID: 38688008 DOI: 10.1021/acs.jafc.4c00958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The human population will be approximately 9.7 billion by 2050, and food security has been identified as one of the key issues facing the global population. Agrochemicals are an important tool available to farmers that enable high crop yields and continued access to healthy foods, but the average new agrochemical active ingredient takes more than ten years, 350 million dollars, and 20,000 animals to develop and register. The time, monetary, and animal costs incentivize the use of New Approach Methodologies (NAMs) in early-stage screening to prioritize chemical candidates. This review outlines NAMs that are currently available or can be adapted for use in early-stage screening agrochemical programs. It covers new in vitro screens that are on the horizon in key areas of regulatory concern. Overall, early-stage screening with NAMs enables the prioritization of development for agrochemicals without human and environmental health concerns through a more directed, agile, and iterative development program before animal-based regulatory testing is even considered.
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Affiliation(s)
| | - Vivek D Badwaik
- Corteva Agriscience, Indianapolis, Indiana 46268, United States
| | - Enrica Bianchi
- Corteva Agriscience, Indianapolis, Indiana 46268, United States
| | - Wei Chen
- Corteva Agriscience, Indianapolis, Indiana 46268, United States
| | | | - Jessica LaRocca
- Corteva Agriscience, Indianapolis, Indiana 46268, United States
| | | | - Chengli Zu
- Corteva Agriscience, Indianapolis, Indiana 46268, United States
| | - Kamin J Johnson
- Corteva Agriscience, Indianapolis, Indiana 46268, United States
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Luo YS, Ying RY, Chen XT, Yeh YJ, Wei CC, Chan CC. Integrating high-throughput phenotypic profiling and transcriptomic analyses to predict the hepatosteatosis effects induced by per- and polyfluoroalkyl substances. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133891. [PMID: 38457971 DOI: 10.1016/j.jhazmat.2024.133891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/18/2024] [Accepted: 02/23/2024] [Indexed: 03/10/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) is a large compound class (n > 12,000) that is extensively present in food, drinking water, and aquatic environments. Reduced serum triglycerides and hepatosteatosis appear to be the common phenotypes for different PFAS chemicals. However, the hepatosteatosis potential of most PFAS chemicals remains largely unknown. This study aims to investigate PFAS-induced hepatosteatosis using in vitro high-throughput phenotype profiling (HTPP) and high-throughput transcriptomic (HTTr) data. We quantified the in vitro hepatosteatosis effects and mitochondrial damage using high-content imaging, curated the transcriptomic data from the Gene Expression Omnibus (GEO) database, and then calculated the point of departure (POD) values for HTPP phenotypes or HTTr transcripts, using the Bayesian benchmark dose modeling approach. Our results indicated that PFAS compounds with fully saturated C-F bonds, sulfur- and nitrogen-containing functional groups, and a fluorinated carbon chain length greater than 8 have the potential to produce biological effects consistent with hepatosteatosis. PFAS primarily induced hepatosteatosis via disturbance in lipid transport and storage. The potency rankings of PFAS compounds are highly concordant among in vitro HTPP, HTTr, and in vivo hepatosteatosis phenotypes (ρ = 0.60-0.73). In conclusion, integrating the information from in vitro HTPP and HTTr analyses can accurately project in vivo hepatosteatosis effects induced by PFAS compounds.
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Affiliation(s)
- Yu-Syuan Luo
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, Taipei City, Taiwan; Master of Public Health Program, College of Public Health, National Taiwan University, Taipei City, Taiwan.
| | - Ren-Yan Ying
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, Taipei City, Taiwan
| | - Xsuan-Ting Chen
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, Taipei City, Taiwan; Department of Public Health, College of Public Health, National Taiwan University, Taipei City, Taiwan
| | - Yu-Jia Yeh
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, Taipei City, Taiwan
| | - Chia-Cheng Wei
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, Taipei City, Taiwan; Department of Public Health, College of Public Health, National Taiwan University, Taipei City, Taiwan
| | - Chang-Chuan Chan
- Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei City, Taiwan
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11
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Seal S, Trapotsi MA, Spjuth O, Singh S, Carreras-Puigvert J, Greene N, Bender A, Carpenter AE. A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. ARXIV 2024:arXiv:2405.02767v1. [PMID: 38745696 PMCID: PMC11092692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions. Here, we systematically review the substantial methodological advancements and applications of Cell Painting. Advancements include improvements in the Cell Painting protocol, assay adaptations for different types of perturbations and applications, and improved methodologies for feature extraction, quality control, and batch effect correction. Moreover, machine learning methods recently surpassed classical approaches in their ability to extract biologically useful information from Cell Painting images. Cell Painting data have been used alone or in combination with other -omics data to decipher the mechanism of action of a compound, its toxicity profile, and many other biological effects. Overall, key methodological advances have expanded Cell Painting's ability to capture cellular responses to various perturbations. Future advances will likely lie in advancing computational and experimental techniques, developing new publicly available datasets, and integrating them with other high-content data types.
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Affiliation(s)
- Srijit Seal
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Maria-Anna Trapotsi
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Shantanu Singh
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Jordi Carreras-Puigvert
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Nigel Greene
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Andreas Bender
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Anne E. Carpenter
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
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12
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Corton JC, Matteo G, Chorley B, Liu J, Vallanat B, Everett L, Atlas E, Meier MJ, Williams A, Yauk CL. A 50-gene biomarker identifies estrogen receptor-modulating chemicals in a microarray compendium. Chem Biol Interact 2024; 394:110952. [PMID: 38570061 DOI: 10.1016/j.cbi.2024.110952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/01/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024]
Abstract
High throughput transcriptomics (HTTr) profiling has the potential to rapidly and comprehensively identify molecular targets of environmental chemicals that can be linked to adverse outcomes. We describe here the construction and characterization of a 50-gene expression biomarker designed to identify estrogen receptor (ER) active chemicals in HTTr datasets. Using microarray comparisons, the genes in the biomarker were identified as those that exhibited consistent directional changes when ER was activated (4 ER agonists; 4 ESR1 gene constitutively active mutants) and opposite directional changes when ER was suppressed (4 antagonist treatments; 4 ESR1 knockdown experiments). The biomarker was evaluated as a predictive tool using the Running Fisher algorithm by comparison to annotated gene expression microarray datasets including those evaluating the transcriptional effects of hormones and chemicals in MCF-7 cells. Depending on the reference dataset used, the biomarker had a predictive accuracy for activation of up to 96%. To demonstrate applicability for HTTr data analysis, the biomarker was used to identify ER activators in a set of 15 chemicals that are considered potential bisphenol A (BPA) alternatives examined at up to 10 concentrations in MCF-7 cells and analyzed by full-genome TempO-Seq. Using benchmark dose (BMD) modeling, the biomarker genes stratified the ER potency of BPA alternatives consistent with previous studies. These results demonstrate that the ER biomarker can be used to accurately identify ER activators in transcript profile data derived from MCF-7 cells.
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Affiliation(s)
- J Christopher Corton
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Geronimo Matteo
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada; Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Brian Chorley
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Jie Liu
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Beena Vallanat
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Logan Everett
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
| | - Ella Atlas
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada.
| | - Matthew J Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada.
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada.
| | - Carole Lyn Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
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13
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Flynn K, Le M, Hazemi M, Biales A, Bencic DC, Blackwell BR, Bush K, Flick R, Hoang JX, Martinson J, Morshead M, Rodriguez KS, Stacy E, Villeneuve DL. Comparing Transcriptomic Points of Departure to Apical Effect Concentrations For Larval Fathead Minnow Exposed to Chemicals with Four Different Modes Of Action. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2024; 86:346-362. [PMID: 38743081 DOI: 10.1007/s00244-024-01064-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
It is postulated that below a transcriptomic-based point of departure, adverse effects are unlikely to occur, thereby providing a chemical concentration to use in screening level hazard assessment. The present study extends previous work describing a high-throughput fathead minnow assay that can provide full transcriptomic data after exposure to a test chemical. One-day post-hatch fathead minnows were exposed to ten concentrations of three representatives of four chemical modes of action: organophosphates, ecdysone receptor agonists, plant photosystem II inhibitors, and estrogen receptor agonists for 24 h. Concentration response modeling was performed on whole body gene expression data from each exposure, using measured chemical concentrations when available. Transcriptomic points of departure in larval fathead minnow were lower than apical effect concentrations across fish species but not always lower than toxic effect concentrations in other aquatic taxa like crustaceans and insects. The point of departure was highly dependent on measured chemical concentration which were often lower than the nominal concentration. Differentially expressed genes between chemicals within modes of action were compared and often showed statistically significant overlap. In addition, reproducibility between identical exposures using a positive control chemical (CuSO4) and variability associated with the transcriptomic point of departure using in silico sampling were considered. Results extend a transcriptomic-compatible fathead minnow high-throughput assay for possible use in ecological hazard screening.
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Affiliation(s)
- Kevin Flynn
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, US EPA GLTED, 6201 Congdon Blvd, Duluth, MN, 55804, USA.
| | - Michelle Le
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - Monique Hazemi
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - Adam Biales
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Cincinnati, OH, 45220, USA
| | - David C Bencic
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Cincinnati, OH, 45220, USA
| | - Brett R Blackwell
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Kendra Bush
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - Robert Flick
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Cincinnati, OH, 45220, USA
| | - John X Hoang
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - John Martinson
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Cincinnati, OH, 45220, USA
| | - Mackenzie Morshead
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - Kelvin Santana Rodriguez
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - Emma Stacy
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, US EPA GLTED, 6201 Congdon Blvd, Duluth, MN, 55804, USA
| | - Daniel L Villeneuve
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, US EPA GLTED, 6201 Congdon Blvd, Duluth, MN, 55804, USA
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14
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Foley B, Hopperstad K, Gamble J, Lynn SG, Thomas RS, Deisenroth C. Technical evaluation and standardization of the human thyroid microtissue assay. Toxicol Sci 2024; 199:89-107. [PMID: 38310358 DOI: 10.1093/toxsci/kfae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024] Open
Abstract
The success and sustainability of U.S. EPA efforts to reduce, refine, and replace in vivo animal testing depends on the ability to translate toxicokinetic and toxicodynamic data from in vitro and in silico new approach methods (NAMs) to human-relevant exposures and health outcomes. Organotypic culture models employing primary human cells enable consideration of human health effects and inter-individual variability but present significant challenges for test method standardization, transferability, and validation. Increasing confidence in the information provided by these in vitro NAMs requires setting appropriate performance standards and benchmarks, defined by the context of use, to consider human biology and mechanistic relevance without animal data. The human thyroid microtissue (hTMT) assay utilizes primary human thyrocytes to reproduce structural and functional features of the thyroid gland that enable testing for potential thyroid-disrupting chemicals. As a variable-donor assay platform, conventional principles for assay performance standardization need to be balanced with the ability to predict a range of human responses. The objectives of this study were to (1) define the technical parameters for optimal donor procurement, primary thyrocyte qualification, and performance in the hTMT assay, and (2) set benchmark ranges for reference chemical responses. Thyrocytes derived from a cohort of 32 demographically diverse euthyroid donors were characterized across a battery of endpoints to evaluate morphological and functional variability. Reference chemical responses were profiled to evaluate the range and chemical-specific variability of donor-dependent effects within the cohort. The data-informed minimum acceptance criteria for donor qualification and set benchmark parameters for method transfer proficiency testing and validation of assay performance.
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Affiliation(s)
- Briana Foley
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Kristen Hopperstad
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - John Gamble
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee 37831, USA
| | - Scott G Lynn
- Office of Pesticide Programs, U.S. Environmental Protection Agency, Washington, District of Columbia 20460, USA
| | - Russell S Thomas
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
| | - Chad Deisenroth
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
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15
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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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16
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Smith MN, Stump S, van Bergen SK, Davies HG, Fanning E, Eaton R, Manahan CC, Sergent A, Zarker K. A Hazard-Based Framework for Identifying Safer Alternatives to Classes of Chemicals: A Case Study on Phthalates in Consumer Products. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:45002. [PMID: 38683745 PMCID: PMC11057665 DOI: 10.1289/ehp13549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 03/11/2024] [Accepted: 03/28/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Humans are exposed to hazardous chemicals found in consumer products. In 2019, the Pollution Prevention for Healthy People and Puget Sound Act was passed in Washington State. This law is meant to reduce hazardous chemicals in consumer products and protect human health and the environment. The law directs the Washington State Department of Ecology to assess chemicals and chemical classes found in products, determine whether there are safer alternatives, and make regulatory determinations. OBJECTIVES To implement the law, the Department of Ecology developed a hazard-based framework for identifying safer alternatives to classes of chemicals. METHODS We developed a hazard-based framework, termed the "Criteria for Safer," to set a transparent bar for determining whether new chemical alternatives are safer than existing classes of chemicals. Our "Criteria for Safer" is a framework that builds on existing hazard assessment methodologies and published approaches for assessing chemicals and chemical classes. DISCUSSION We describe implementation of our criteria using a case study on the phthalates chemical class in two categories of consumer products: vinyl flooring and fragrances used in personal care and beauty products. Additional context and considerations that guided our decision-making process are also discussed, as well as benefits and limitations of our approach. This paper gives insight into our development and implementation of a hazard-based framework to address classes of chemicals in consumer products and will aid others working to build and employ similar approaches. https://doi.org/10.1289/EHP13549.
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Affiliation(s)
- Marissa N. Smith
- Hazardous Waste & Toxics Reduction, Washington State Department of Ecology, Lacey, Washington, USA
| | - Sascha Stump
- Hazardous Waste & Toxics Reduction, Washington State Department of Ecology, Lacey, Washington, USA
| | - Saskia K. van Bergen
- Hazardous Waste & Toxics Reduction, Washington State Department of Ecology, Lacey, Washington, USA
| | - Holly G. Davies
- Environmental Public Health Sciences, Washington State Department of Health, Tumwater, Washington, USA
| | - Elinor Fanning
- Environmental Public Health Sciences, Washington State Department of Health, Tumwater, Washington, USA
| | - Rae Eaton
- Hazardous Waste & Toxics Reduction, Washington State Department of Ecology, Lacey, Washington, USA
| | - Craig C. Manahan
- Hazardous Waste & Toxics Reduction, Washington State Department of Ecology, Lacey, Washington, USA
| | - Amber Sergent
- Hazardous Waste & Toxics Reduction, Washington State Department of Ecology, Lacey, Washington, USA
| | - Ken Zarker
- Hazardous Waste & Toxics Reduction, Washington State Department of Ecology, Lacey, Washington, USA
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17
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Du XY, Yang JY. Biomimetic microfluidic chips for toxicity assessment of environmental pollutants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170745. [PMID: 38340832 DOI: 10.1016/j.scitotenv.2024.170745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/31/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Various types of pollutants widely present in environmental media, including synthetic and natural chemicals, physical pollutants such as radioactive substances, ultraviolet rays, and noise, as well as biological organisms, pose a huge threat to public health. Therefore, it is crucial to accurately and effectively explore the human physiological responses and toxicity mechanisms of pollutants to prevent diseases caused by pollutants. The emerging toxicological testing method biomimetic microfluidic chips (BMCs) exhibit great potential in environmental pollutant toxicity assessment due to their superior biomimetic properties. The BMCs are divided into cell-on-chips and organ-on-chips based on the distinctions in bionic simulation levels. Herein, we first summarize the characteristics, emergence and development history, composition and structure, and application fields of BMCs. Then, with a focus on the toxicity mechanisms of pollutants, we review the applications and advances of the BMCs in the toxicity assessment of physical, chemical, and biological pollutants, respectively, highlighting its potential and development prospects in environmental toxicology testing. Finally, the opportunities and challenges for further use of BMCs are discussed.
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Affiliation(s)
- Xin-Yue Du
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China
| | - Jin-Yan Yang
- College of Architecture and Environment, Sichuan University, Chengdu 610065, China..
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18
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Ostovich E, Klaper R. Using a Novel Multiplexed Algal Cytological Imaging (MACI) Assay and Machine Learning as a Way to Characterize Complex Phenotypes in Plant-Type Organisms. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4894-4903. [PMID: 38446593 DOI: 10.1021/acs.est.3c07733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
High-throughput phenotypic profiling assays, popular for their ability to characterize alternations in single-cell morphological feature data, have been useful in recent years for predicting cellular targets and mechanisms of action (MoAs) for different chemicals and novel drugs. However, this approach has not been extensively used in environmental toxicology due to the lack of studies and established methods for performing this kind of assay in environmentally relevant species. Here, we developed a multiplexed algal cytological imaging (MACI) assay, based on the subcellular structures of the unicellular microalgae, Raphidocelis subcapitata, a toxicology and ecological model species. Several different herbicides and antibiotics with unique MoAs were exposed to R. subcapitata cells, and MACI was used to characterize cellular impacts by measuring subtle changes in their morphological features, including metrics of area, shape, quantity, fluorescence intensity, and granularity of individual subcellular components. This study demonstrates that MACI offers a quick and effective framework for characterizing complex phenotypic responses to environmental chemicals that can be used for determining their MoAs and identifying their cellular targets in plant-type organisms.
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Affiliation(s)
- Eric Ostovich
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53204, United States
| | - Rebecca Klaper
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53204, United States
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19
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Ebmeyer J, Najjar A, Lange D, Boettcher M, Voß S, Brandmair K, Meinhardt J, Kuehnl J, Hewitt NJ, Krueger CT, Schepky A. Next generation risk assessment: an ab initio case study to assess the systemic safety of the cosmetic ingredient, benzyl salicylate, after dermal exposure. Front Pharmacol 2024; 15:1345992. [PMID: 38515841 PMCID: PMC10955127 DOI: 10.3389/fphar.2024.1345992] [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: 11/28/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
We performed an ab initio next-generation risk assessment (NGRA) for a fragrance ingredient, benzyl salicylate (BSal), to demonstrate how cosmetic ingredients can be evaluated for systemic toxicity endpoints based on non-animal approaches. New approach methodologies (NAMs) used to predict the internal exposure included skin absorption assays, hepatocyte metabolism, and physiologically based pharmacokinetic (PBPK) modeling, and potential toxicodynamic effects were assessed using pharmacology profiling, ToxProfiler cell stress assay, transcriptomics in HepG2 and MCF-7 cells, ReproTracker developmental and reproductive toxicology (DART) assays, and cytotoxicity assays in human kidney cells. The outcome of the NGRA was compared to that of the traditional risk assessment approach based on animal data. The identification of the toxicologically critical entity was a critical step that directed the workflow and the selection of chemicals for PBPK modeling and testing in bioassays. The traditional risk assessment and NGRA identified salicylic acid (SA) as the "toxdriver." A deterministic PBPK model for a single-day application of 1.54 g face cream containing 0.5% BSal estimated the Cmax for BSal (1 nM) to be much lower than that of its major in vitro metabolite, SA (93.2 nM). Therefore, SA was tested using toxicodynamics bioassays. The lowest points of departure (PoDs) were obtained from the toxicogenomics assays. The interpretation of these results by two companies and methods were similar (SA only results in significant gene deregulation in HepG2 cells), but PoD differed (213 μM and 10.6 µM). A probabilistic PBPK model for repeated applications of the face cream estimated the highest Cmax of SA to be 630 nM. The resulting margins of internal exposure (MoIE) using the PoDs were 338 and 16, which were more conservative than those derived from external exposure and in vivo PoDs (margin of safety values were 9,705). In conclusion, both traditional and ab initio NGRA approaches concluded that the daily application of BSal in a cosmetic leave-on face cream at 0.5% is safe for humans. The processing and interpretation of toxicogenomics data can lead to different PoDs, which can subsequently affect the calculation of the MoIE. This case study supports the use of NAMs in a tiered NGRA ab initio approach.
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20
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Villeneuve DL, Blackwell BR, Bush K, Harrill J, Harris F, Hazemi M, Le M, Stacy E, Flynn KM. Transcriptomics-Based Points of Departure for Daphnia magna Exposed to 18 Per- and Polyfluoroalkyl Substances. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 38450772 DOI: 10.1002/etc.5838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/08/2024] [Accepted: 01/27/2024] [Indexed: 03/08/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) represent a large group of contaminants of concern based on their widespread use, environmental persistence, and potential toxicity. Many traditional models for estimating toxicity, bioaccumulation, and other toxicological properties are not well suited for PFAS. Consequently, there is a need to generate hazard information for PFAS in an efficient and cost-effective manner. In the present study, Daphnia magna were exposed to multiple concentrations of 22 different PFAS for 24 h in a 96-well plate format. Following exposure, whole-body RNA was extracted and extracts, each representing five exposed individuals, were subjected to RNA sequencing. Following analytical measurements to verify PFAS exposure concentrations and quality control on processed cDNA libraries for sequencing, concentration-response modeling was applied to the data sets for 18 of the tested compounds, and the concentration at which a concerted molecular response occurred (transcriptomic point of departure; tPOD) was calculated. The tPODs, based on measured concentrations of PFAS, generally ranged from 0.03 to 0.58 µM (9.9-350 µg/L; interquartile range). In most cases, these concentrations were two orders of magnitude lower than similarly calculated tPODs for human cell lines exposed to PFAS. They were also lower than apical effect concentrations reported for seven PFAS for which some crustacean or invertebrate toxicity data were available, although there were a few exceptions. Despite being lower than most other available hazard benchmarks, D. magna tPODs were, on average, four orders of magnitude greater than the maximum aqueous concentrations of PFAS measured in Great Lakes tributaries. Overall, this high-throughput transcriptomics assay with D. magna holds promise as a component of a tiered hazard evaluation strategy employing new approach methodologies. Environ Toxicol Chem 2024;00:1-16. © 2024 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Daniel L Villeneuve
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, USA
| | - Brett R Blackwell
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, USA
- Bioscience Division, Biochemistry and Biotechnology Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kendra Bush
- Oak Ridge Institute for Science and Education Research Participant at US EPA, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Joshua Harrill
- Biomolecular and Computational Toxicology Division, United States Environmental Protection Agency, NC, USA
| | - Felix Harris
- Oak Ridge Institute for Science and Education Research Participant at US EPA, Biomolecular and Computational Toxicology Division, Oak Ridge, NC, USA
| | - Monique Hazemi
- Oak Ridge Institute for Science and Education Research Participant at US EPA, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Michelle Le
- Oak Ridge Institute for Science and Education Research Participant at US EPA, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Emma Stacy
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, USA
| | - Kevin M Flynn
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, USA
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21
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Kleinstreuer N, Hartung T. Artificial intelligence (AI)-it's the end of the tox as we know it (and I feel fine). Arch Toxicol 2024; 98:735-754. [PMID: 38244040 PMCID: PMC10861653 DOI: 10.1007/s00204-023-03666-2] [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: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024]
Abstract
The rapid progress of AI impacts diverse scientific disciplines, including toxicology, and has the potential to transform chemical safety evaluation. Toxicology has evolved from an empirical science focused on observing apical outcomes of chemical exposure, to a data-rich field ripe for AI integration. The volume, variety and velocity of toxicological data from legacy studies, literature, high-throughput assays, sensor technologies and omics approaches create opportunities but also complexities that AI can help address. In particular, machine learning is well suited to handle and integrate large, heterogeneous datasets that are both structured and unstructured-a key challenge in modern toxicology. AI methods like deep neural networks, large language models, and natural language processing have successfully predicted toxicity endpoints, analyzed high-throughput data, extracted facts from literature, and generated synthetic data. Beyond automating data capture, analysis, and prediction, AI techniques show promise for accelerating quantitative risk assessment by providing probabilistic outputs to capture uncertainties. AI also enables explanation methods to unravel mechanisms and increase trust in modeled predictions. However, issues like model interpretability, data biases, and transparency currently limit regulatory endorsement of AI. Multidisciplinary collaboration is needed to ensure development of interpretable, robust, and human-centered AI systems. Rather than just automating human tasks at scale, transformative AI can catalyze innovation in how evidence is gathered, data are generated, hypotheses are formed and tested, and tasks are performed to usher new paradigms in chemical safety assessment. Used judiciously, AI has immense potential to advance toxicology into a more predictive, mechanism-based, and evidence-integrated scientific discipline to better safeguard human and environmental wellbeing across diverse populations.
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Affiliation(s)
| | - Thomas Hartung
- Bloomberg School of Public Health, Doerenkamp-Zbinden Chair for Evidence-Based Toxicology, Center for Alternatives to Animal Testing (CAAT), Johns Hopkins University, Baltimore, MD, USA.
- CAAT-Europe, University of Konstanz, Constance, Germany.
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22
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Ankley GT, Berninger JP, Maloney EM, Olker JH, Schaupp CM, Villeneuve DL, LaLone CA. Linking Mechanistic Effects of Pharmaceuticals and Personal Care Products to Ecologically Relevant Outcomes: A Decade of Progress. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:537-548. [PMID: 35735070 PMCID: PMC11036122 DOI: 10.1002/etc.5416] [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] [Received: 04/21/2022] [Revised: 06/02/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
There are insufficient toxicity data to assess the ecological risks of many pharmaceuticals and personal care products (PPCPs). While data limitations are not uncommon for contaminants of environmental concern, PPCPs are somewhat unique in that an a priori understanding of their biological activities in conjunction with measurements of molecular, biochemical, or histological responses could provide a foundation for understanding mode(s) of action and predicting potential adverse apical effects. Over the past decade significant progress has been made in the development of new approach methodologies (NAMs) to efficiently quantify these types of endpoints using computational models and pathway-based in vitro and in vivo assays. The availability of open-access knowledgebases to curate biological response (including NAM) data and sophisticated bioinformatics tools to help interpret the information also has significantly increased. Finally, advances in the development and implementation of the adverse outcome pathway framework provide the critical conceptual underpinnings needed to translate NAM data into predictions of the ecologically relevant outcomes required by risk assessors and managers. The evolution and convergence of these various data streams, tools, and concepts provides the basis for a fundamental change in how ecological risks of PPCPs can be pragmatically assessed. Environ Toxicol Chem 2024;43:537-548. © 2022 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Gerald T Ankley
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, Minnesota, USA
| | - Jason P Berninger
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, Minnesota, USA
| | - Erin M Maloney
- University of Minnesota-Duluth, Integrated Biological Sciences Program, Duluth, Minnesota, USA
| | - Jennifer H Olker
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, Minnesota, USA
| | | | - Daniel L Villeneuve
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, Minnesota, USA
| | - Carlie A LaLone
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, Minnesota, USA
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23
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Browne P, Paul Friedman K, Boekelheide K, Thomas RS. Adverse effects in traditional and alternative toxicity tests. Regul Toxicol Pharmacol 2024; 148:105579. [PMID: 38309424 PMCID: PMC11062625 DOI: 10.1016/j.yrtph.2024.105579] [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: 10/06/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/05/2024]
Abstract
Chemical safety assessment begins with defining the lowest level of chemical that alters one or more measured endpoints. This critical effect level, along with factors to account for uncertainty, is used to derive limits for human exposure. In the absence of data regarding the specific mechanisms or biological pathways affected, non-specific endpoints such as body weight and non-target organ weight changes are used to set critical effect levels. Specific apical endpoints such as impaired reproductive function or altered neurodevelopment have also been used to set chemical safety limits; however, in test guidelines designed for specific apical effect(s), concurrently measured non-specific endpoints may be equally or more sensitive than specific endpoints. This means that rather than predicting a specific toxicological response, animal data are often used to develop protective critical effect levels, without assuming the same change would be observed in humans. This manuscript is intended to encourage a rethinking of how adverse chemical effects are interpreted: non-specific endpoints from in vivo toxicological studies data are often used to derive points of departure for use with safety assessment factors to create recommended exposure levels that are broadly protective but not necessarily target-specific.
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Affiliation(s)
- Patience Browne
- Environment Health and Safety Division Environmental Directorate, Organisation for Economic and Cooperative Development (OECD), 2 rue André Pascal, Paris Cedex 16, 75775, France.
| | - Katie Paul Friedman
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Kim Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Russell S Thomas
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
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24
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Villeneuve DL, Bush K, Hazemi M, Hoang JX, Le M, Blackwell BR, Stacy E, Flynn KM. Derivation of Transcriptomics-Based Points of Departure for 20 Per- or Polyfluoroalkyl Substances Using a Larval Fathead Minnow (Pimephales promelas) Reduced Transcriptome Assay. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 38415853 DOI: 10.1002/etc.5825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/18/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
Traditional toxicity testing has been unable to keep pace with the introduction of new chemicals into commerce. Consequently, there are limited or no toxicity data for many chemicals to which fish and wildlife may be exposed. Per- and polyfluoroalkyl substances (PFAS) are emblematic of this issue in that ecological hazards of most PFAS remain uncharacterized. The present study employed a high-throughput assay to identify the concentration at which 20 PFAS, with diverse properties, elicited a concerted gene expression response (termed a transcriptomics-based point of departure [tPOD]) in larval fathead minnows (Pimephales promelas; 5-6 days postfertilization) exposed for 24 h. Based on a reduced transcriptome approach that measured whole-body expression of 1832 genes, the median tPOD for the 20 PFAS tested was 10 µM. Longer-chain carboxylic acids (12-13 C-F); an eight-C-F dialcohol, N-alkyl sulfonamide; and telomer sulfonic acid were among the most potent PFAS, eliciting gene expression responses at concentrations <1 µM. With a few exceptions, larval fathead minnow tPODs were concordant with those based on whole-transcriptome response in human cell lines. However, larval fathead minnow tPODs were often greater than those for Daphnia magna exposed to the same PFAS. The tPODs overlapped concentrations at which other sublethal effects have been reported in fish (available for 10 PFAS). Nonetheless, fathead minnow tPODs were orders of magnitude higher than aqueous PFAS concentrations detected in tributaries of the North American Great Lakes, suggesting a substantial margin of safety. Overall, results broadly support the use of a fathead minnow larval transcriptomics assay to derive screening-level potency estimates for use in ecological risk-based prioritization. Environ Toxicol Chem 2024;00:1-16. © 2024 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Daniel L Villeneuve
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota
| | - Kendra Bush
- Research Participant at Great Lakes Toxicology and Ecology Division, Oak Ridge Institute for Science and Education, Duluth, Minnesota, USA
| | - Monique Hazemi
- Research Participant at Great Lakes Toxicology and Ecology Division, Oak Ridge Institute for Science and Education, Duluth, Minnesota, USA
| | - John X Hoang
- Research Participant at Great Lakes Toxicology and Ecology Division, Oak Ridge Institute for Science and Education, Duluth, Minnesota, USA
| | - Michelle Le
- Research Participant at Great Lakes Toxicology and Ecology Division, Oak Ridge Institute for Science and Education, Duluth, Minnesota, USA
| | - Brett R Blackwell
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota
- Bioscience Division, Biochemistry and Biotechnology Group, Los Alamos National Laboratory, Los Alamos, Minnesota, USA
| | - Emma Stacy
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota
| | - Kevin M Flynn
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota
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25
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Rusyn I, Wright FA. Ten years of using key characteristics of human carcinogens to organize and evaluate mechanistic evidence in IARC Monographs on the identification of carcinogenic hazards to humans: Patterns and associations. Toxicol Sci 2024; 198:141-154. [PMID: 38141214 PMCID: PMC10901152 DOI: 10.1093/toxsci/kfad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2023] Open
Abstract
Systematic review and evaluation of mechanistic evidence using the Key Characteristics approach was proposed by the International Agency for Research on Cancer (IARC) in 2012 and used by the IARC Monographs Working Groups since 2015. Key Characteristics are 10 features of agents known to cause cancer in humans. From 2015 to 2022, a total of 19 Monographs (73 agents combined) used Key Characteristics for cancer hazard classification. We hypothesized that a retrospective analysis of applications of the Key Characteristics approach to cancer hazard classification using heterogenous mechanistic data on diverse agents would be informative for systematic reviews in decision-making. We extracted information on the conclusions, data types, and the role mechanistic data played in the cancer hazard classification from each Monograph. Statistical analyses identified patterns in the use of Key Characteristics, as well as trends and correlations among Key Characteristics, data types, and ultimate decisions. Despite gaps in data for many agents and Key Characteristics, several significant results emerged. Mechanistic data from in vivo animal, in vitro animal, and in vitro human studies were most impactful in concluding that an agent could cause cancer via a Key Characteristic. To exclude the involvement of a Key Characteristic, data from large-scale systematic in vitro testing programs such as ToxCast, were most informative. Overall, increased availability of systemized data streams, such as human in vitro data, would provide the basis for more confident and informed conclusions about both positive and negative associations and inform expert judgments on cancer hazard.
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Affiliation(s)
- Ivan Rusyn
- Department of Veterinary Pharmacology and Physiology, Texas A&M University, College Station, Texas 77843, USA
| | - Fred A Wright
- Department of Statistics, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27606, USA
- Department of Biological Sciences, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27606, USA
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26
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Silva MH. Investigating open access new approach methods (NAM) to assess biological points of departure: A case study with 4 neurotoxic pesticides. Curr Res Toxicol 2024; 6:100156. [PMID: 38404712 PMCID: PMC10891343 DOI: 10.1016/j.crtox.2024.100156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/28/2023] [Accepted: 02/09/2024] [Indexed: 02/27/2024] Open
Abstract
Open access new approach methods (NAM) in the US EPA ToxCast program and NTP Integrated Chemical Environment (ICE) were used to investigate activities of four neurotoxic pesticides: endosulfan, fipronil, propyzamide and carbaryl. Concordance of in vivo regulatory points of departure (POD) adjusted for interspecies extrapolation (AdjPOD) to modelled human Administered Equivalent Dose (AEDHuman) was assessed using 3-compartment or Adult/Fetal PBTK in vitro to in vivo extrapolation. Model inputs were from Tier 1 (High throughput transcriptomics: HTTr, high throughput phenotypic profiling: HTPP) and Tier 2 (single target: ToxCast) assays. HTTr identified gene expression signatures associated with potential neurotoxicity for endosulfan, propyzamide and carbaryl in non-neuronal MCF-7 and HepaRG cells. The HTPP assay in U-2 OS cells detected potent effects on DNA endpoints for endosulfan and carbaryl, and mitochondria with fipronil (propyzamide was inactive). The most potent ToxCast assays were concordant with specific components of each chemical mode of action (MOA). Predictive adult IVIVE models produced fold differences (FD) < 10 between the AEDHuman and the measured in vivo AdjPOD. The 3-compartment model was concordant (i.e., smallest FD) for endosulfan, fipronil and carbaryl, and PBTK was concordant for propyzamide. The most potent AEDHuman predictions for each chemical showed HTTr, HTPP and ToxCast were mainly concordant with in vivo AdjPODs but assays were less concordant with MOAs. This was likely due to the cell types used for testing and/or lack of metabolic capabilities and pathways available in vivo. The Fetal PBTK model had larger FDs than adult models and was less predictive overall.
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27
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Kaplan BLF, Hoberman AM, Slikker W, Smith MA, Corsini E, Knudsen TB, Marty MS, Sobrian SK, Fitzpatrick SC, Ratner MH, Mendrick DL. Protecting Human and Animal Health: The Road from Animal Models to New Approach Methods. Pharmacol Rev 2024; 76:251-266. [PMID: 38351072 PMCID: PMC10877708 DOI: 10.1124/pharmrev.123.000967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/18/2023] [Accepted: 12/01/2023] [Indexed: 02/16/2024] Open
Abstract
Animals and animal models have been invaluable for our current understanding of human and animal biology, including physiology, pharmacology, biochemistry, and disease pathology. However, there are increasing concerns with continued use of animals in basic biomedical, pharmacological, and regulatory research to provide safety assessments for drugs and chemicals. There are concerns that animals do not provide sufficient information on toxicity and/or efficacy to protect the target population, so scientists are utilizing the principles of replacement, reduction, and refinement (the 3Rs) and increasing the development and application of new approach methods (NAMs). NAMs are any technology, methodology, approach, or assay used to understand the effects and mechanisms of drugs or chemicals, with specific focus on applying the 3Rs. Although progress has been made in several areas with NAMs, complete replacement of animal models with NAMs is not yet attainable. The road to NAMs requires additional development, increased use, and, for regulatory decision making, usually formal validation. Moreover, it is likely that replacement of animal models with NAMs will require multiple assays to ensure sufficient biologic coverage. The purpose of this manuscript is to provide a balanced view of the current state of the use of animal models and NAMs as approaches to development, safety, efficacy, and toxicity testing of drugs and chemicals. Animals do not provide all needed information nor do NAMs, but each can elucidate key pieces of the puzzle of human and animal biology and contribute to the goal of protecting human and animal health. SIGNIFICANCE STATEMENT: Data from traditional animal studies have predominantly been used to inform human health safety and efficacy. Although it is unlikely that all animal studies will be able to be replaced, with the continued advancement in new approach methods (NAMs), it is possible that sometime in the future, NAMs will likely be an important component by which the discovery, efficacy, and toxicity testing of drugs and chemicals is conducted and regulatory decisions are made.
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Affiliation(s)
- Barbara L F Kaplan
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Alan M Hoberman
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - William Slikker
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Mary Alice Smith
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Emanuela Corsini
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Thomas B Knudsen
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - M Sue Marty
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Sonya K Sobrian
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Suzanne C Fitzpatrick
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Marcia H Ratner
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Donna L Mendrick
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
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Li H, Seada H, Madnick S, Zhao H, Chen Z, Li F, Zhu F, Hall S, Boekelheide K. Machine learning-assisted high-content imaging analysis of 3D MCF7 microtissues for estrogenic effect prediction. Sci Rep 2024; 14:2999. [PMID: 38316851 PMCID: PMC10844358 DOI: 10.1038/s41598-024-53323-6] [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: 09/11/2023] [Accepted: 01/30/2024] [Indexed: 02/07/2024] Open
Abstract
Endocrine-disrupting chemicals (EDCs) pose a significant threat to human well-being and the ecosystem. However, in managing the many thousands of uncharacterized chemical entities, the high-throughput screening of EDCs using relevant biological endpoints remains challenging. Three-dimensional (3D) culture technology enables the development of more physiologically relevant systems in more realistic biochemical microenvironments. The high-content and quantitative imaging techniques enable quantifying endpoints associated with cell morphology, cell-cell interaction, and microtissue organization. In the present study, 3D microtissues formed by MCF-7 breast cancer cells were exposed to the model EDCs estradiol (E2) and propyl pyrazole triol (PPT). A 3D imaging and image analysis pipeline was established to extract quantitative image features from estrogen-exposed microtissues. Moreover, a machine-learning classification model was built using estrogenic-associated differential imaging features. Based on 140 common differential image features found between the E2 and PPT group, the classification model predicted E2 and PPT exposure with AUC-ROC at 0.9528 and 0.9513, respectively. Deep learning-assisted analysis software was developed to characterize microtissue gland lumen formation. The fully automated tool can accurately characterize the number of identified lumens and the total luminal volume of each microtissue. Overall, the current study established an integrated approach by combining non-supervised image feature profiling and supervised luminal volume characterization, which reflected the complexity of functional ER signaling and highlighted a promising conceptual framework for estrogenic EDC risk assessment.
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Affiliation(s)
- Hui Li
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China.
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Providence, RI, 02903, USA.
| | - Haitham Seada
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Providence, RI, 02903, USA
| | - Samantha Madnick
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Providence, RI, 02903, USA
| | - He Zhao
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China
| | - Zhaozeng Chen
- College of Pharmaceutical Sciences, Center for Drug Safety Evaluation and Research of Zhejiang University, Zhejiang University, 866 Yuhangtang Rd, Hangzhou, 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Susan Hall
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Providence, RI, 02903, USA
| | - Kim Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Providence, RI, 02903, USA.
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29
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Tao TP, Brandmair K, Gerlach S, Przibilla J, Schepky A, Marx U, Hewitt NJ, Maschmeyer I, Kühnl J. Application of a skin and liver Chip2 microphysiological model to investigate the route-dependent toxicokinetics and toxicodynamics of consumer-relevant doses of genistein. J Appl Toxicol 2024; 44:287-300. [PMID: 37700462 DOI: 10.1002/jat.4540] [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: 07/19/2023] [Revised: 08/25/2023] [Accepted: 08/27/2023] [Indexed: 09/14/2023]
Abstract
The HUMMIC skin-liver Chip2 microphysiological system using EpiDerm™ and HepaRG and stellate liver spheroids was used to evaluate the route-specific metabolism and toxicodynamic effects of genistein. Human-relevant exposure levels were compared: 60 nM representing the plasma concentration expected after topical application of a cosmetic product and 1 μM representing measured plasma concentrations after ingesting soya products. Genistein was applied as single and repeated topical and/or systemic doses. The kinetics of genistein and its metabolites were measured over 5 days. Toxicodynamic effects were measured using transcriptional analyses of skin and liver organoids harvested on Days 2 and 5. Route-specific differences in genistein's bioavailability were observed, with first-pass metabolism (sulfation) occurring in the skin after topical application. Only repeated application of 1 μM, resembling daily oral intake of soya products, induced statistically significant changes in gene expression in liver organoids only. This was concomitant with a much higher systemic concentration of genistein which was not reached in any other dosing scenario. This suggests that single or low doses of genistein are rapidly metabolised which limits its toxicodynamic effects on the liver and skin. Therefore, by facilitating longer and/or repeated applications, the Chip2 can support safety assessments by linking relevant gene modulation with systemically available parent or metabolite(s). The rate of metabolism was in accordance with the short half-life observed in in vivo in humans, thus supporting the relevance of the findings. In conclusion, the skin-liver Chip2 provides route-specific information on metabolic fate and toxicodynamics that may be relevant to safety assessment.
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30
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Reale E, Zare Jeddi M, Paini A, Connolly A, Duca R, Cubadda F, Benfenati E, Bessems J, S Galea K, Dirven H, Santonen T, M Koch H, Jones K, Sams C, Viegas S, Kyriaki M, Campisi L, David A, Antignac JP, B Hopf N. Human biomonitoring and toxicokinetics as key building blocks for next generation risk assessment. ENVIRONMENT INTERNATIONAL 2024; 184:108474. [PMID: 38350256 DOI: 10.1016/j.envint.2024.108474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/15/2023] [Accepted: 02/01/2024] [Indexed: 02/15/2024]
Abstract
Human health risk assessment is historically built upon animal testing, often following Organisation for Economic Co-operation and Development (OECD) test guidelines and exposure assessments. Using combinations of human relevant in vitro models, chemical analysis and computational (in silico) approaches bring advantages compared to animal studies. These include a greater focus on the human species and on molecular mechanisms and kinetics, identification of Adverse Outcome Pathways and downstream Key Events as well as the possibility of addressing susceptible populations and additional endpoints. Much of the advancement and progress made in the Next Generation Risk Assessment (NGRA) have been primarily focused on new approach methodologies (NAMs) and physiologically based kinetic (PBK) modelling without incorporating human biomonitoring (HBM). The integration of toxicokinetics (TK) and PBK modelling is an essential component of NGRA. PBK models are essential for describing in quantitative terms the TK processes with a focus on the effective dose at the expected target site. Furthermore, the need for PBK models is amplified by the increasing scientific and regulatory interest in aggregate and cumulative exposure as well as interactions of chemicals in mixtures. Since incorporating HBM data strengthens approaches and reduces uncertainties in risk assessment, here we elaborate on the integrated use of TK, PBK modelling and HBM in chemical risk assessment highlighting opportunities as well as challenges and limitations. Examples are provided where HBM and TK/PBK modelling can be used in both exposure assessment and hazard characterization shifting from external exposure and animal dose/response assays to animal-free, internal exposure-based NGRA.
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Affiliation(s)
- Elena Reale
- Centre for Primary Care and Public Health (Unisanté), University of Lausanne, Switzerland
| | - Maryam Zare Jeddi
- National Institute for Public Health and the Environment (RIVM), the Netherlands
| | | | - Alison Connolly
- UCD Centre for Safety & Health at Work, School of Public Health, Physiotherapy, and Sports Science, University College Dublin, D04 V1W8, Dublin, Ireland for Climate and Air Pollution Studies, Physics, School of Natural Science and the Ryan Institute, National University of Ireland, University Road, Galway H91 CF50, Ireland
| | - Radu Duca
- Unit Environmental Hygiene and Human Biological Monitoring, Department of Health Protection, Laboratoire national de santé (LNS), 1, Rue Louis Rech, 3555 Dudelange, Luxembourg; Environment and Health, Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 35, 3000 Leuven, Belgium
| | - Francesco Cubadda
- Istituto Superiore di Sanità - National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
| | - Emilio Benfenati
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Mario Negri 2, 20156 Milano, Italy
| | - Jos Bessems
- VITO HEALTH, Flemish Institute for Technological Research, 2400 Mol, Belgium
| | - Karen S Galea
- Institute of Occupational Medicine (IOM), Research Avenue North, Riccarton, Edinburgh EH14 4AP, UK
| | - Hubert Dirven
- Department of Climate and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Tiina Santonen
- Finnish Institute of Occupational Health (FIOH), P.O. Box 40, FI-00032 Työterveyslaitos, Finland
| | - Holger M Koch
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bürkle-de-la-Camp-Platz 1, 44789 Bochum, Germany
| | - Kate Jones
- HSE - Health and Safety Executive, Harpur Hill, Buxton SK17 9JN, UK
| | - Craig Sams
- HSE - Health and Safety Executive, Harpur Hill, Buxton SK17 9JN, UK
| | - Susana Viegas
- NOVA National School of Public Health, Public Health Research Centre, Comprehensive Health Research Center, CHRC, NOVA University Lisbon, Lisbon, Portugal
| | - Machera Kyriaki
- Benaki Phytopathological Institute, 8, Stephanou Delta Street, 14561 Kifissia, Athens, Greece
| | - Luca Campisi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; Flashpoint srl, Via Norvegia 56, 56021 Cascina (PI), Italy
| | - Arthur David
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, F-35000 Rennes, France
| | | | - Nancy B Hopf
- Centre for Primary Care and Public Health (Unisanté), University of Lausanne, Switzerland.
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31
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Isaacs KK, Wall JT, Paul Friedman K, Franzosa JA, Goeden H, Williams AJ, Dionisio KL, Lambert JC, Linnenbrink M, Singh A, Wambaugh JF, Bogdan AR, Greene C. Screening for drinking water contaminants of concern using an automated exposure-focused workflow. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2024; 34:136-147. [PMID: 37193773 PMCID: PMC11131037 DOI: 10.1038/s41370-023-00552-y] [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] [Received: 10/05/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND The number of chemicals present in the environment exceeds the capacity of government bodies to characterize risk. Therefore, data-informed and reproducible processes are needed for identifying chemicals for further assessment. The Minnesota Department of Health (MDH), under its Contaminants of Emerging Concern (CEC) initiative, uses a standardized process to screen potential drinking water contaminants based on toxicity and exposure potential. OBJECTIVE Recently, MDH partnered with the U.S. Environmental Protection Agency (EPA) Office of Research and Development (ORD) to accelerate the screening process via development of an automated workflow accessing relevant exposure data, including exposure new approach methodologies (NAMs) from ORD's ExpoCast project. METHODS The workflow incorporated information from 27 data sources related to persistence and fate, release potential, water occurrence, and exposure potential, making use of ORD tools for harmonization of chemical names and identifiers. The workflow also incorporated data and criteria specific to Minnesota and MDH's regulatory authority. The collected data were used to score chemicals using quantitative algorithms developed by MDH. The workflow was applied to 1867 case study chemicals, including 82 chemicals that were previously manually evaluated by MDH. RESULTS Evaluation of the automated and manual results for these 82 chemicals indicated reasonable agreement between the scores although agreement depended on data availability; automated scores were lower than manual scores for chemicals with fewer available data. Case study chemicals with high exposure scores included disinfection by-products, pharmaceuticals, consumer product chemicals, per- and polyfluoroalkyl substances, pesticides, and metals. Scores were integrated with in vitro bioactivity data to assess the feasibility of using NAMs for further risk prioritization. SIGNIFICANCE This workflow will allow MDH to accelerate exposure screening and expand the number of chemicals examined, freeing resources for in-depth assessments. The workflow will be useful in screening large libraries of chemicals for candidates for the CEC program.
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Affiliation(s)
- Kristin K Isaacs
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, Durham, NC, 27711, USA.
| | - Jonathan T Wall
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, Durham, NC, 27711, USA
| | - Katie Paul Friedman
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, Durham, NC, 27711, USA
| | - Jill A Franzosa
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, Durham, NC, 27711, USA
| | - Helen Goeden
- Minnesota Department of Health, 625 Robert St. N, St. Paul, MN, 55155, USA
| | - Antony J Williams
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, Durham, NC, 27711, USA
| | - Kathie L Dionisio
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, Durham, NC, 27711, USA
| | - Jason C Lambert
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, Durham, NC, 27711, USA
| | - Monica Linnenbrink
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, Durham, NC, 27711, USA
| | - Amar Singh
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, Durham, NC, 27711, USA
| | - John F Wambaugh
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, 109 TW Alexander Drive, Research Triangle Park, Durham, NC, 27711, USA
| | - Alexander R Bogdan
- Minnesota Department of Health, 625 Robert St. N, St. Paul, MN, 55155, USA
| | - Christopher Greene
- Minnesota Department of Health, 625 Robert St. N, St. Paul, MN, 55155, USA
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32
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Harrill JA, Everett LJ, Haggard DE, Bundy JL, Willis CM, Shah I, Friedman KP, Basili D, Middleton A, Judson RS. Exploring the effects of experimental parameters and data modeling approaches on in vitro transcriptomic point-of-departure estimates. Toxicology 2024; 501:153694. [PMID: 38043774 DOI: 10.1016/j.tox.2023.153694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Multiple new approach methods (NAMs) are being developed to rapidly screen large numbers of chemicals to aid in hazard evaluation and risk assessments. High-throughput transcriptomics (HTTr) in human cell lines has been proposed as a first-tier screening approach for determining the types of bioactivity a chemical can cause (activation of specific targets vs. generalized cell stress) and for calculating transcriptional points of departure (tPODs) based on changes in gene expression. In the present study, we examine a range of computational methods to calculate tPODs from HTTr data, using six data sets in which MCF7 cells cultured in two different media formulations were treated with a panel of 44 chemicals for 3 different exposure durations (6, 12, 24 hr). The tPOD calculation methods use data at the level of individual genes and gene set signatures, and compare data processed using the ToxCast Pipeline 2 (tcplfit2), BMDExpress and PLIER (Pathway Level Information ExtractoR). Methods were evaluated by comparing to in vitro PODs from a validated set of high-throughput screening (HTS) assays for a set of estrogenic compounds. Key findings include: (1) for a given chemical and set of experimental conditions, tPODs calculated by different methods can vary by several orders of magnitude; (2) tPODs are at least as sensitive to computational methods as to experimental conditions; (3) in comparison to an external reference set of PODs, some methods give generally higher values, principally PLIER and BMDExpress; and (4) the tPODs from HTTr in this one cell type are mostly higher than the overall PODs from a broad battery of targeted in vitro ToxCast assays, reflecting the need to test chemicals in multiple cell types and readout technologies for in vitro hazard screening.
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Affiliation(s)
- Joshua A Harrill
- Center for Computational Toxicology and Exposure, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Logan J Everett
- Center for Computational Toxicology and Exposure, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Derik E Haggard
- Center for Computational Toxicology and Exposure, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, USA; Oak Ridge Institute for Science and Education (ORISE), USA
| | - Joseph L Bundy
- Center for Computational Toxicology and Exposure, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Clinton M Willis
- Center for Computational Toxicology and Exposure, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, USA; Oak Ridge Associated Universities (ORAU), USA
| | - Imran Shah
- Center for Computational Toxicology and Exposure, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Katie Paul Friedman
- Center for Computational Toxicology and Exposure, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Danilo Basili
- Unilever Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Alistair Middleton
- Unilever Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Richard S Judson
- Center for Computational Toxicology and Exposure, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, USA.
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Ivan de Ávila R, Fentem J, Villela I, Somlo D, Fusco Almeida AM, Mendes-Giannini MJS, Di Pietro Micali Canavez A, Bosquetti B, Catarino CM, Schuck DC, Valadares BN, Facchini G, Marigliani B, Migliorini Figueira AC, Hickson R, Leme DM, Tagliati C, de Souza LCR, Maria Engler SS, Gaspar Cordeiro LR, Koepp J, Granjeiro JM, de Mello Brandao H, Munk M, Antunes de Mattos K, Pedralli B, Siqueira Furtuoso Rodrigues MM, Stival AC, Andrade J, Brito LB, Marques Dos Santos TR, Leite J, Garcia da Silva AC, Valadares MC. Brazilian National Network of Alternative Methods (RENAMA) 10th Anniversary: Meeting of the Associated Laboratories, May 2022. Altern Lab Anim 2024; 52:60-68. [PMID: 38061994 DOI: 10.1177/02611929231218378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The Brazilian National Network of Alternative Methods (RENAMA), which is linked to the Ministry of Science, Technology and Innovation, is currently comprised of 51 laboratories from CROs, academia, industry and government. RENAMA's aim is to develop and validate new approach methodologies (NAMs), as well as train researchers and disseminate information on their use - thus reducing Brazilian, and consequently Latin American, dependence on external technology. Moreover, it promotes the adoption of NAMs by educators and trained researchers, as well as the implementation of good laboratory practice (GLP) and the use of certified products. The RENAMA network started its activities in 2012, and was originally comprised of three central laboratories - the National Institute of Metrology, Quality and Technology (INMETRO); the National Institute of Quality Control in Health (INCQS); and the National Brazilian Biosciences Laboratory (LNBio) - and ten associated laboratories. In 2022, RENAMA celebrated its 10th anniversary, a milestone commemorated by the organisation of a meeting attended by different stakeholders, including the RENAMA-associated laboratories, academia, non-governmental organisations and industry. Ninety-six participants attended the meeting, held on 26 May 2022 in Balneário Camboriú, SC, Brazil, as part of the programme of the XXIII Brazilian Congress of Toxicology 2022. Significant moments of the RENAMA were remembered, and new goals and discussion themes were established. The lectures highlighted recent innovations in the toxicological sciences that have translated into the assessment of consumer product safety through the use of human-relevant NAMs instead of the use of existing animal-based approaches. The challenges and opportunities in accepting such practices for regulatory purposes were also presented and discussed.
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Affiliation(s)
- Renato Ivan de Ávila
- Unilever's Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Bedfordshire, UK
| | - Julia Fentem
- Unilever's Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Bedfordshire, UK
| | - Izabel Villela
- InnVitro Support and Management in Toxicology, Porto Alegre, Brazil
| | - Debora Somlo
- Unilever Brazil Industrial Ltda, WTorre Morumbi, São Paulo, Brazil
| | - Ana Marisa Fusco Almeida
- Laboratory of Proteomics and Clinical Mycology, Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, São Paulo State University, Araraquara, Brazil
| | - Maria José S Mendes-Giannini
- Laboratory of Proteomics and Clinical Mycology, Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, São Paulo State University, Araraquara, Brazil
| | | | - Bruna Bosquetti
- Safety Assessment Management, Grupo Boticário, Curitiba, Brazil
| | | | | | | | | | - Bianca Marigliani
- Research and Toxicology Department, Humane Society International (HSI), Rio de Janeiro, Brazil
| | | | | | | | - Carlos Tagliati
- Lab Tox, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Janice Koepp
- Biocelltis Biotechnology SA, Florianópolis, Brazil
| | - Jose Mauro Granjeiro
- National Institute of Metrology, Quality and Technology, Fluminense Federal University, Rio de Janeiro, Brazil
| | - Humberto de Mello Brandao
- Innovation Laboratory in Nanobiotechnology and Advanced Materials for Livestock Embrapa Gado de Leite, Juiz de Fora, Brazil
| | - Michele Munk
- Federal University of Juiz de Fora, Juiz de Fora, Brazil
| | - Katherine Antunes de Mattos
- Microbiological Control Laboratory, Quality Control Department, Bio-Manguinhos, Fiocruz, Rio de Janeiro, Brazil
| | - Bruna Pedralli
- Laboratory of Education and Research in In vitro Toxicology, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | | | - Ana Clara Stival
- Laboratory of Education and Research in In vitro Toxicology, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Jordana Andrade
- Laboratory of Education and Research in In vitro Toxicology, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Lara Barroso Brito
- Laboratory of Education and Research in In vitro Toxicology, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Thais Rosa Marques Dos Santos
- Laboratory of Education and Research in In vitro Toxicology, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Jacqueline Leite
- Laboratory of Education and Research in In vitro Toxicology, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
- Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Artur Christian Garcia da Silva
- Laboratory of Education and Research in In vitro Toxicology, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
| | - Marize Campos Valadares
- Laboratory of Education and Research in In vitro Toxicology, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Brazil
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Chen P, Li Y, Long Q, Zuo T, Zhang Z, Guo J, Xu D, Li K, Liu S, Li S, Yin J, Chang L, Kukic P, Liddell M, Tulum L, Carmichael P, Peng S, Li J, Zhang Q, Xu P. The phosphoproteome is a first responder in tiered cellular adaptation to chemical stress followed by proteomics and transcriptomics alteration. CHEMOSPHERE 2023; 344:140329. [PMID: 37783352 DOI: 10.1016/j.chemosphere.2023.140329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/04/2023]
Abstract
Next-generation risk assessment (NGRA) for environmental chemicals involves a weight of evidence (WoE) framework integrating a suite of new approach methodologies (NAMs) based on points of departure (PoD) obtained from in vitro assays. Among existing NAMs, the omic-based technologies are of particular importance based on the premise that any apical endpoint change indicative of impaired health must be underpinned by some alterations at the omics level, such as transcriptome, proteome, metabolome, epigenome and genome. Transcriptomic assay plays a leading role in providing relatively conservative PoDs compared with apical endpoints. However, it is unclear whether and how parameters measured with other omics techniques predict the cellular response to chemical perturbations, especially at exposure levels below the transcriptomically defined PoD. Multi-omics coverage may provide additional sensitive or confirmative biomarkers to complement and reduce the uncertainty in safety decisions made using targeted and transcriptomics assays. In the present study, we conducted multi-omics studies of transcriptomics, proteomics and phosphoproteomics on two prototype compounds, coumarin and 2,4-dichlorophenoxyacetic acid (2,4-D), with multiple chemical concentrations and time points, to understand the sensitivity of the three omics techniques in response to chemically-induced changes in HepG2. We demonstrated that, phosphoproteomics alterations occur not only earlier in time, but also more sensitive to lower concentrations than proteomics and transcriptomics when the HepG2 cells were exposed to various chemical treatments. The phosphoproteomics changes appear to approach maximum when the transcriptomics alterations begin to initiate. Therefore, it is proximal to the very early effects induced by chemical exposure. We concluded that phosphoproteomics can be utilized to provide a more complete coverage of chemical-induced cellular alteration and supplement transcriptomics-based health safety decision making.
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Affiliation(s)
- Peiru Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Yuan Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Department of Biomedicine, Medical College, Guizhou University, Guiyang, 550025, China; Guizhou Provincial People's Hospital, Affiliated Hospital of Guizhou University, Guiyang, 550002, China
| | - Qi Long
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; School of Basic Medicine, Anhui Medical University, Hefei, 230032, China
| | - Tao Zuo
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Jiabin Guo
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Danyang Xu
- Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Kaixuan Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Shu Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Suzhen Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; School of Basic Medicine, Anhui Medical University, Hefei, 230032, China
| | - Jian Yin
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Lei Chang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Predrag Kukic
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Mark Liddell
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Liz Tulum
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Paul Carmichael
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Shuangqing Peng
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Jin Li
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK.
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, USA, GA, 30322.
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China; Department of Biomedicine, Medical College, Guizhou University, Guiyang, 550025, China; School of Basic Medicine, Anhui Medical University, Hefei, 230032, China; Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang, 110122, China.
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Decrane R, Stoker T, Murr A, Ford J, El-Masri H. Cross species extrapolation of the disruption of thyroid hormone synthesis by oxyfluorfen using in vitro data, physiologically based pharmacokinetic (PBPK), and thyroid hormone kinetics models. Curr Res Toxicol 2023; 5:100138. [PMID: 38074188 PMCID: PMC10697989 DOI: 10.1016/j.crtox.2023.100138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 03/22/2024] Open
Abstract
The thyroid hormones play key roles in physiological processes such as regulation of the metabolic and cardiac systems as well as the development of the brain and surrounding sympathetic nervous system. Recent efforts to screen environmental chemicals for their ability to alter thyroid hormone synthesis, transport, metabolism and/or function have identified novel chemicals that target key processes in the thyroid pathway. One newly identified chemical, oxyfluorfen, is a diphenyl-ether herbicide used for control of annual broadleaf and grassy weeds in a variety of tree fruit, nut, vine, and field crops. Using in vitro high-throughput screening (HTS) assays, oxyfluorofen was identified to be a potent inhibitor of the thyroidal sodium-iodide symporter (NIS). To quantitatively assess this inhibition mechanism in vivo, we extrapolated in vitro NIS inhibition data to in vivo disruption of thyroid hormones synthesis in rats using physiologically based pharmacokinetic (PBPK) and thyroid hormone kinetics models. The overall computational model (chemical PBPK and THs kinetic sub-models) was calibrated against in vivo data for the levels of oxyfluorfen in thyroid tissue and serum and against serum levels of thyroid hormones triiodothyronine (T3) and thyroxine (T4) in rats. The rat thyroid model was then extrapolated to humans using human in vitro HTS data for NIS inhibition and the chemical specific hepatic clearance rate in humans. The overall species extrapolated PBPK-thyroid kinetics model can be used to predict dose-response (% drop in thyroid serum levels compared to homeostasis) relationships in humans. These relationships can be used to estimate points of departure for health risks related to a drop in serum levels of TH hormones based on HTS assays in vitro to in vivo extrapolation (IVIVE), toxicokinetics, and physiological principles.
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Dong G, Wang N, Xu T, Liang J, Qiao R, Yin D, Lin S. Deep Learning-Enabled Morphometric Analysis for Toxicity Screening Using Zebrafish Larvae. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:18127-18138. [PMID: 36971266 DOI: 10.1021/acs.est.3c00593] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Toxicology studies heavily rely on morphometric analysis to detect abnormalities and diagnose disease processes. The emergence of ever-increasing varieties of environmental pollutants makes it difficult to perform timely assessments, especially using in vivo models. Herein, we propose a deep learning-based morphometric analysis (DLMA) to quantitatively identify eight abnormal phenotypes (head hemorrhage, jaw malformation, uninflated swim bladder, pericardial edema, yolk edema, bent spine, dead, unhatched) and eight vital organ features (eye, head, jaw, heart, yolk, swim bladder, body length, and curvature) of zebrafish larvae. A data set composed of 2532 bright-field micrographs of zebrafish larvae at 120 h post fertilization was generated from toxicity screening of three categories of chemicals, i.e., endocrine disruptors (perfluorooctanesulfonate and bisphenol A), heavy metals (CdCl2 and PbI2), and emerging organic pollutants (acetaminophen, 2,7-dibromocarbazole, 3-monobromocarbazo, 3,6-dibromocarbazole, and 1,3,6,8-tetrabromocarbazo). Two typical deep learning models, one-stage and two-stage models (TensorMask, Mask R-CNN), were trained to implement phenotypic feature classification and segmentation. The accuracy was statistically validated with a mean average precision >0.93 in unlabeled data sets and a mean accuracy >0.86 in previously published data sets. Such a method effectively enables subjective morphometric analysis of zebrafish larvae to achieve efficient hazard identification of both chemicals and environmental pollutants.
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Affiliation(s)
- Gongqing Dong
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, China
- Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Nan Wang
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, China
- Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Ting Xu
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, China
- Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Jingyu Liang
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, China
- Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Ruxia Qiao
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, China
- Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Daqiang Yin
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, China
- Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
| | - Sijie Lin
- College of Environmental Science and Engineering, Biomedical Multidisciplinary Innovation Research Institute, Shanghai East Hospital, Tongji University, Shanghai 200092, China
- Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai 200092, China
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Li H, Seada H, Madnick S, Zhao H, Chen Z, Li F, Zhu F, Hall S, Boekelheide K. Machine Learning-Assisted High-Content Imaging Analysis of 3D MCF7 Microtissues for Estrogenic Effect Prediction. RESEARCH SQUARE 2023:rs.3.rs-3343627. [PMID: 37886543 PMCID: PMC10602099 DOI: 10.21203/rs.3.rs-3343627/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Endocrine-disrupting chemicals (EDCs) pose a significant threat to human well-being and the ecosystem. However, in managing the many thousands of uncharacterized chemical entities, the high-throughput screening of EDCs using relevant biological endpoints remains challenging. Three-dimensional (3D) culture technology enables the development of more physiologically relevant systems in more realistic biochemical microenvironments. The high-content and quantitative imaging techniques enable quantifying endpoints associated with cell morphology, cell-cell interaction, and microtissue organization. In the present study, 3D microtissues formed by MCF-7 breast cancer cells were exposed to the model EDCs estradiol (E2) and propyl pyrazole triol (PPT). A 3D imaging and image analysis pipeline was established to extract quantitative image features from estrogen-exposed microtissues. Moreover, a machine-learning classification model was built using estrogenic-associated differential imaging features. Based on 140 common differential image features found between the E2 and PPT group, the classification model predicted E2 and PPT exposure with AUC-ROC at 0.9528 and 0.9513, respectively. Deep learning-assisted analysis software was developed to characterize microtissue gland lumen formation. The fully automated tool can accurately characterize the number of identified lumens and the total luminal volume of each microtissue. Overall, the current study established an integrated approach by combining non-supervised image feature profiling and supervised luminal volume characterization, which reflected the complexity of functional ER signaling and highlighted a promising conceptual framework for estrogenic EDC risk assessment.
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38
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Eytcheson SA, Olker JH, Friedman KP, Hornung MW, Degitz SJ. Assessing utility of thyroid in vitro screening assays through comparisons to observed impacts in vivo. Regul Toxicol Pharmacol 2023; 144:105491. [PMID: 37666444 DOI: 10.1016/j.yrtph.2023.105491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 08/22/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
To better understand endocrine disruption, the U.S. Environmental Protection Agency's (USEPA) Endocrine Disruptor Screening Program (EDSP) utilizes a two-tiered approach to investigate the potential of a chemical to interact with the estrogen, androgen, or thyroid systems. As in vivo testing lacks the throughput to address data gaps on endocrine bioactivity for thousands of chemicals, in vitro high-throughput screening (HTS) methods are being developed to screen larger chemical libraries. The primary objective of this work was to investigate for how many of the 52 chemicals with weight-of-evidence (WoE) determinations from EDSP Tier 1 screening there are available in vitro HTS data supporting a thyroid impact. HTS data from the USEPA ToxCast program and the EDSP WoE were collected for this analysis. Considering the complexity of endocrine disruption and interpreting HTS data, concordance between in vitro activity and in vivo effects ranges from 58 to 78%. Based on this evaluation, we conclude that the current suite of HTS assays is beneficial for prioritizing chemicals for further inquiry; however, without a more detailed analysis, one cannot conclude whether HTS results are the primary mode-of-action. Furthermore, development of in vitro assays for additional thyroid-relevant molecular initiating events is required to effectively predict in vivo thyroid impacts.
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Affiliation(s)
- Stephanie A Eytcheson
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA; U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Duluth, MN, 55804, USA
| | - Jennifer H Olker
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Duluth, MN, 55804, USA
| | - Katie Paul Friedman
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, Research Triangle Park, NC, 27711, USA
| | - Michael W Hornung
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Duluth, MN, 55804, USA
| | - Sigmund J Degitz
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Duluth, MN, 55804, USA.
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Garnovskaya M, Feshuk M, Stewart W, Friedman KP, Thomas RS, Deisenroth C. Evaluation of a high-throughput H295R homogenous time resolved fluorescence assay for androgen and estrogen steroidogenesis screening. Toxicol In Vitro 2023; 92:105659. [PMID: 37557933 PMCID: PMC10903741 DOI: 10.1016/j.tiv.2023.105659] [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: 04/28/2023] [Revised: 07/06/2023] [Accepted: 08/06/2023] [Indexed: 08/11/2023]
Abstract
The H295R test guideline assay evaluates the effect of test substances on synthesis of 17β-estradiol (E2) and testosterone (T). The objective of this study was to leverage commercial immunoassay technology to develop a more efficient H295R assay to measure E2 and T levels in 384-well format. The resulting Homogenous Time Resolved Fluorescence assay platform (H295R-HTRF) was evaluated against a training set of 36 chemicals derived from the OECD inter-laboratory validation study, EPA guideline 890.1200 aromatase assay, and azole fungicides active in the HT-H295R assay. Quality control performance criteria were met for all conditions except E2 synthesis inhibition where low basal hormone synthesis was observed. Five proficiency chemicals were active for both the E2 and T endpoints, consistent with guideline classifications. Of the nine OECD core reference chemicals, 9/9 were concordant with outcomes for E2 and 7/9 for T. Likewise, 9/13 and 11/13 OECD supplemental chemicals were concordant with anticipated effects for E2 and T, respectively. Of the 10 azole fungicides screened, 7/10 for E2 and 8/10 for T exhibited concordant outcomes for inhibition. Generally, all active chemicals in the training set demonstrated equivalent or greater potency in the H295R-HTRF assay, supporting the sensitivity of the platform. The adaptation of HTRF technology to the H295R model provides an efficient way to evaluate E2 and T modulators in accordance with guideline specifications.
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Affiliation(s)
- Maria Garnovskaya
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States
| | - Madison Feshuk
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States
| | - Wendy Stewart
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States
| | - Katie Paul Friedman
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States
| | - Russell S Thomas
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States
| | - Chad Deisenroth
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, United States.
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Martin R, Hazemi M, Flynn K, Villeneuve D, Wehmas L. Short-Term Transcriptomic Points of Departure Are Consistent with Chronic Points of Departure for Three Organophosphate Pesticides across Mouse and Fathead Minnow. TOXICS 2023; 11:820. [PMID: 37888672 PMCID: PMC10611195 DOI: 10.3390/toxics11100820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023]
Abstract
New approach methods (NAMs) can reduce the need for chronic animal studies. Here, we apply benchmark dose (concentration) (BMD(C))-response modeling to transcriptomic changes in the liver of mice and in fathead minnow larvae after short-term exposures (7 days and 1 day, respectively) to several dose/concentrations of three organophosphate pesticides (OPPs): fenthion, methidathion, and parathion. The mouse liver transcriptional points of departure (TPODs) for fenthion, methidathion, and parathion were 0.009, 0.093, and 0.046 mg/Kg-bw/day, while the fathead minnow larva TPODs were 0.007, 0.115, and 0.046 mg/L, respectively. The TPODs were consistent across both species and reflected the relative potencies from traditional chronic toxicity studies with fenthion identified as the most potent. Moreover, the mouse liver TPODs were more sensitive than or within a 10-fold difference from the chronic apical points of departure (APODs) for mammals, while the fathead minnow larva TPODs were within an 18-fold difference from the chronic APODs for fish species. Short-term exposure to OPPs significantly impacted acetylcholinesterase mRNA abundance (FDR p-value <0.05, |fold change| ≥2) and canonical pathways (IPA, p-value <0.05) associated with organism death and neurological/immune dysfunctions, indicating the conservation of key events related to OPP toxicity. Together, these results build confidence in using short-term, molecular-based assays for the characterization of chemical toxicity and risk, thereby reducing reliance on chronic animal studies.
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Affiliation(s)
- Rubia Martin
- Office of Research and Development, Center for Computational Toxicology and Exposure, Chemical Characterization and Exposure Division, Oak Ridge Institute for Science and Education, U.S. Environmental Protection Agency, Durham, NC 27709, USA;
| | - Monique Hazemi
- Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Ecology Division, Oak Ridge Institute for Science and Education, U.S. Environmental Protection Agency, Duluth, MN 55804, USA;
| | - Kevin Flynn
- Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Ecology Division, U.S. Environmental Protection Agency, Duluth, MN 55804, USA; (K.F.); (D.V.)
| | - Daniel Villeneuve
- Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Ecology Division, U.S. Environmental Protection Agency, Duluth, MN 55804, USA; (K.F.); (D.V.)
| | - Leah Wehmas
- Office of Research and Development, Center for Computational Toxicology and Exposure, Chemical Characterization and Exposure Division, U.S. Environmental Protection Agency, Durham, NC 27709, USA
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Schaupp CM, Maloney EM, Mattingly K, Olker JH, Villeneuve DL. Comparison of in silico, in vitro, and in vivo toxicity benchmarks suggests a role for ToxCast data in ecological hazard assessment. Toxicol Sci 2023; 195:145-154. [PMID: 37490521 PMCID: PMC11217893 DOI: 10.1093/toxsci/kfad072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Abstract
Large repositories of in vitro bioactivity data such as US EPA's Toxicity Forecaster (ToxCast) provide a wealth of publicly accessible toxicity information for thousands of chemicals. These data can be used to calculate point-of-departure (POD) estimates via concentration-response modeling that may serve as lower bound, protective estimates of in vivo effects. However, the data are predominantly based on mammalian models and discussions to date about their utility have largely focused on potential integration into human hazard assessment, rather than application to ecological risk assessment. The goal of the present study was to compare PODs based on (1) quantitative structure-activity relationships (QSARs), (2) the 5th centile of the activity concentration at cutoff (ACC), and (3) lower-bound cytotoxic burst (LCB) from ToxCast, with the distribution of in vivo PODs compiled in the Ecotoxicology Knowledgebase (ECOTOX). While overall correlation between ToxCast ACC5 and ECOTOX PODs for 649 chemicals was weak, there were significant associations among PODs based on LCB and ECOTOX, LCB and QSARs, and ECOTOX and QSARs. Certain classes of compounds showed moderate correlation across datasets (eg, antimicrobials/disinfectants), while others, such as organophosphate insecticides, did not. Unsurprisingly, more precise classifications of the data based on ECOTOX effect and endpoint type (eg, apical vs biochemical; acute vs chronic) had a significant effect on overall relationships. Results of this research help to define appropriate roles for data from new approach methodologies in chemical prioritization and screening of ecological hazards.
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Affiliation(s)
- Christopher M. Schaupp
- Oak Ridge Institute for Science and Education, US EPA, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Erin M. Maloney
- University of Minnesota-Duluth, Integrated Biological Sciences Program, Duluth, MN, USA
| | - Kali Mattingly
- Spec-Pro Professional Services, 6201 Congdon Blvd, Duluth, MN, 55804, USA
| | - Jennifer H. Olker
- US Environmental Protection Agency, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Daniel L. Villeneuve
- US Environmental Protection Agency, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
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Feshuk M, Kolaczkowski L, Dunham K, Davidson-Fritz SE, Carstens KE, Brown J, Judson RS, Paul Friedman K. The ToxCast pipeline: updates to curve-fitting approaches and database structure. FRONTIERS IN TOXICOLOGY 2023; 5:1275980. [PMID: 37808181 PMCID: PMC10552852 DOI: 10.3389/ftox.2023.1275980] [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: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction: The US Environmental Protection Agency Toxicity Forecaster (ToxCast) program makes in vitro medium- and high-throughput screening assay data publicly available for prioritization and hazard characterization of thousands of chemicals. The assays employ a variety of technologies to evaluate the effects of chemical exposure on diverse biological targets, from distinct proteins to more complex cellular processes like mitochondrial toxicity, nuclear receptor signaling, immune responses, and developmental toxicity. The ToxCast data pipeline (tcpl) is an open-source R package that stores, manages, curve-fits, and visualizes ToxCast data and populates the linked MySQL Database, invitrodb. Methods: Herein we describe major updates to tcpl and invitrodb to accommodate a new curve-fitting approach. The original tcpl curve-fitting models (constant, Hill, and gain-loss models) have been expanded to include Polynomial 1 (Linear), Polynomial 2 (Quadratic), Power, Exponential 2, Exponential 3, Exponential 4, and Exponential 5 based on BMDExpress and encoded by the R package dependency, tcplfit2. Inclusion of these models impacted invitrodb (beta version v4.0) and tcpl v3 in several ways: (1) long-format storage of generic modeling parameters to permit additional curve-fitting models; (2) updated logic for winning model selection; (3) continuous hit calling logic; and (4) removal of redundant endpoints as a result of bidirectional fitting. Results and discussion: Overall, the hit call and potency estimates were largely consistent between invitrodb v3.5 and 4.0. Tcpl and invitrodb provide a standard for consistent and reproducible curve-fitting and data management for diverse, targeted in vitro assay data with readily available documentation, thus enabling sharing and use of these data in myriad toxicology applications. The software and database updates described herein promote comparability across multiple tiers of data within the US Environmental Protection Agency CompTox Blueprint.
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Affiliation(s)
- M. Feshuk
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - L. Kolaczkowski
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
- National Student Services Contractor, Oak Ridge Associated Universities, Oak Ridge, TN, United States
| | - K. Dunham
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
- National Student Services Contractor, Oak Ridge Associated Universities, Oak Ridge, TN, United States
| | - S. E. Davidson-Fritz
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - K. E. Carstens
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - J. Brown
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - R. S. Judson
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - K. Paul Friedman
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
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Li H, Madnick S, Zhao H, Hall S, Amin A, Dent MP, Boekelheide K. A novel co-culture model of human prostate epithelial and stromal cells for androgenic and antiandrogenic screening. Toxicol In Vitro 2023; 91:105624. [PMID: 37230229 PMCID: PMC10527365 DOI: 10.1016/j.tiv.2023.105624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 05/07/2023] [Accepted: 05/21/2023] [Indexed: 05/27/2023]
Abstract
The risk assessment of endocrine-disrupting chemicals (EDCs) greatly relies on in vitro screening. A 3-dimensional (3D) in vitro prostate model that can reflect physiologically-relevant prostate epithelial and stromal crosstalk can significantly advance the current androgen assessment. This study built a prostate epithelial and stromal co-culture microtissue model with BHPrE and BHPrS cells in scaffold-free hydrogels. The optimal 3D co-culture condition was defined, and responses of the microtissue to androgen (dihydrotestosterone, DHT) and anti-androgen (flutamide) exposure were characterized using molecular and image profiling techniques. The co-culture prostate microtissue maintained a stable structure for up to seven days and presented molecular and morphological features of the early developmental stage of the human prostate. The cytokeratin 5/6 (CK5/6) and cytokeratin 18 (CK18) immunohistochemical staining indicated epithelial heterogeneity and differentiation in these microtissues. The prostate-related gene expression profiling did not efficiently differentiate androgen and anti-androgen exposure. However, a cluster of distinctive 3D image features was identified and could be applied in the androgenic and anti-androgenic effect prediction. Overall, the current study established a co-culture prostate model that provided an alternative strategy for (anti-)androgenic EDC safety assessment and highlighted the potential and advantage of utilizing image features to predict endpoints in chemical screening.
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Affiliation(s)
- Hui Li
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China; Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - Samantha Madnick
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - He Zhao
- Center for Drug Safety Evaluation and Research of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Susan Hall
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Ali Amin
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Matthew P Dent
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Bedfordshire MK44 1LQ, UK
| | - Kim Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
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44
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Russo D, Aleksunes LM, Goyak K, Qian H, Zhu H. Integrating Concentration-Dependent Toxicity Data and Toxicokinetics To Inform Hepatotoxicity Response Pathways. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12291-12301. [PMID: 37566783 PMCID: PMC10448720 DOI: 10.1021/acs.est.3c02792] [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] [Received: 04/13/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023]
Abstract
Failure of animal models to predict hepatotoxicity in humans has created a push to develop biological pathway-based alternatives, such as those that use in vitro assays. Public screening programs (e.g., ToxCast/Tox21 programs) have tested thousands of chemicals using in vitro high-throughput screening (HTS) assays. Developing pathway-based models for simple biological pathways, such as endocrine disruption, has proven successful, but development remains a challenge for complex toxicities like hepatotoxicity, due to the many biological events involved. To this goal, we aimed to develop a computational strategy for developing pathway-based models for complex toxicities. Using a database of 2171 chemicals with human hepatotoxicity classifications, we identified 157 out of 1600+ ToxCast/Tox21 HTS assays to be associated with human hepatotoxicity. Then, a computational framework was used to group these assays by biological target or mechanisms into 52 key event (KE) models of hepatotoxicity. KE model output is a KE score summarizing chemical potency against a hepatotoxicity-relevant biological target or mechanism. Grouping hepatotoxic chemicals based on the chemical structure revealed chemical classes with high KE scores plausibly informing their hepatotoxicity mechanisms. Using KE scores and supervised learning to predict in vivo hepatotoxicity, including toxicokinetic information, improved the predictive performance. This new approach can be a universal computational toxicology strategy for various chemical toxicity evaluations.
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Affiliation(s)
- Daniel
P. Russo
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Lauren M. Aleksunes
- Department
of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Katy Goyak
- ExxonMobil
Biomedical Sciences, Inc., Annandale, New Jersey 08801, United States
| | - Hua Qian
- ExxonMobil
Biomedical Sciences, Inc., Annandale, New Jersey 08801, United States
| | - Hao Zhu
- Department
of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
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Buckley TJ, Egeghy PP, Isaacs K, Richard AM, Ring C, Sayre RR, Sobus JR, Thomas RS, Ulrich EM, Wambaugh JF, Williams AJ. Cutting-edge computational chemical exposure research at the U.S. Environmental Protection Agency. ENVIRONMENT INTERNATIONAL 2023; 178:108097. [PMID: 37478680 PMCID: PMC10588682 DOI: 10.1016/j.envint.2023.108097] [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] [Received: 03/21/2023] [Revised: 06/05/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
Exposure science is evolving from its traditional "after the fact" and "one chemical at a time" approach to forecasting chemical exposures rapidly enough to keep pace with the constantly expanding landscape of chemicals and exposures. In this article, we provide an overview of the approaches, accomplishments, and plans for advancing computational exposure science within the U.S. Environmental Protection Agency's Office of Research and Development (EPA/ORD). First, to characterize the universe of chemicals in commerce and the environment, a carefully curated, web-accessible chemical resource has been created. This DSSTox database unambiguously identifies >1.2 million unique substances reflecting potential environmental and human exposures and includes computationally accessible links to each compound's corresponding data resources. Next, EPA is developing, applying, and evaluating predictive exposure models. These models increasingly rely on data, computational tools like quantitative structure activity relationship (QSAR) models, and machine learning/artificial intelligence to provide timely and efficient prediction of chemical exposure (and associated uncertainty) for thousands of chemicals at a time. Integral to this modeling effort, EPA is developing data resources across the exposure continuum that includes application of high-resolution mass spectrometry (HRMS) non-targeted analysis (NTA) methods providing measurement capability at scale with the number of chemicals in commerce. These research efforts are integrated and well-tailored to support population exposure assessment to prioritize chemicals for exposure as a critical input to risk management. In addition, the exposure forecasts will allow a wide variety of stakeholders to explore sustainable initiatives like green chemistry to achieve economic, social, and environmental prosperity and protection of future generations.
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Affiliation(s)
- Timothy J Buckley
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States.
| | - Peter P Egeghy
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Kristin Isaacs
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Ann M Richard
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Caroline Ring
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Risa R Sayre
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Jon R Sobus
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Russell S Thomas
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Elin M Ulrich
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - John F Wambaugh
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Antony J Williams
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
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Schmeisser S, Miccoli A, von Bergen M, Berggren E, Braeuning A, Busch W, Desaintes C, Gourmelon A, Grafström R, Harrill J, Hartung T, Herzler M, Kass GEN, Kleinstreuer N, Leist M, Luijten M, Marx-Stoelting P, Poetz O, van Ravenzwaay B, Roggeband R, Rogiers V, Roth A, Sanders P, Thomas RS, Marie Vinggaard A, Vinken M, van de Water B, Luch A, Tralau T. New approach methodologies in human regulatory toxicology - Not if, but how and when! ENVIRONMENT INTERNATIONAL 2023; 178:108082. [PMID: 37422975 PMCID: PMC10858683 DOI: 10.1016/j.envint.2023.108082] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
The predominantly animal-centric approach of chemical safety assessment has increasingly come under pressure. Society is questioning overall performance, sustainability, continued relevance for human health risk assessment and ethics of this system, demanding a change of paradigm. At the same time, the scientific toolbox used for risk assessment is continuously enriched by the development of "New Approach Methodologies" (NAMs). While this term does not define the age or the state of readiness of the innovation, it covers a wide range of methods, including quantitative structure-activity relationship (QSAR) predictions, high-throughput screening (HTS) bioassays, omics applications, cell cultures, organoids, microphysiological systems (MPS), machine learning models and artificial intelligence (AI). In addition to promising faster and more efficient toxicity testing, NAMs have the potential to fundamentally transform today's regulatory work by allowing more human-relevant decision-making in terms of both hazard and exposure assessment. Yet, several obstacles hamper a broader application of NAMs in current regulatory risk assessment. Constraints in addressing repeated-dose toxicity, with particular reference to the chronic toxicity, and hesitance from relevant stakeholders, are major challenges for the implementation of NAMs in a broader context. Moreover, issues regarding predictivity, reproducibility and quantification need to be addressed and regulatory and legislative frameworks need to be adapted to NAMs. The conceptual perspective presented here has its focus on hazard assessment and is grounded on the main findings and conclusions from a symposium and workshop held in Berlin in November 2021. It intends to provide further insights into how NAMs can be gradually integrated into chemical risk assessment aimed at protection of human health, until eventually the current paradigm is replaced by an animal-free "Next Generation Risk Assessment" (NGRA).
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Affiliation(s)
| | - Andrea Miccoli
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany; National Research Council, Ancona, Italy
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Leipzig, Germany
| | | | - Albert Braeuning
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Wibke Busch
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Christian Desaintes
- European Commission (EC), Directorate General for Research and Innovation (RTD), Brussels, Belgium
| | - Anne Gourmelon
- Organisation for Economic Cooperation and Development (OECD), Environment Directorate, Paris, France
| | | | - Joshua Harrill
- Center for Computational Toxicology and Exposure (CCTE), United States Environmental Protection Agency (US EPA), Durham, USA
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health Baltimore MD USA, CAAT-Europe, University of Konstanz, Konstanz, Germany
| | - Matthias Herzler
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | | | - Nicole Kleinstreuer
- NTP Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), National Institute of Environmental Health Sciences (NIEHS), Durham, USA
| | - Marcel Leist
- CAAT‑Europe and Department of Biology, University of Konstanz, Konstanz, Germany
| | - Mirjam Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Oliver Poetz
- NMI Natural and Medical Science Institute at the University of Tuebingen, Reutlingen, Germany; SIGNATOPE GmbH, Reutlingen, Germany
| | | | - Rob Roggeband
- European Partnership for Alternative Approaches to Animal Testing (EPAA), Procter and Gamble Services Company NV/SA, Strombeek-Bever, Belgium
| | - Vera Rogiers
- Scientific Committee on Consumer Safety (SCCS), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Adrian Roth
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Pascal Sanders
- Fougeres Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Fougères, France France
| | - Russell S Thomas
- Center for Computational Toxicology and Exposure (CCTE), United States Environmental Protection Agency (US EPA), Durham, USA
| | | | | | | | - Andreas Luch
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Tewes Tralau
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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47
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Rusyn I, Wright FA. Ten Years of Using Key Characteristics of Human Carcinogens to Organize and Evaluate Mechanistic Evidence in IARC Monographs on the Identification of Carcinogenic Hazards to Humans: Patterns and Associations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548354. [PMID: 37503163 PMCID: PMC10369858 DOI: 10.1101/2023.07.11.548354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Systematic review and evaluation of the mechanistic evidence only recently been instituted in cancer hazard identification step of decision-making. One example of organizing and evaluating mechanistic evidence is the Key Characteristics approach of the International Agency for Research on Cancer (IARC) Monographs on the Identification of Carcinogenic Hazards to Humans. The Key Characteristics of Human Carcinogens were proposed almost 10 years ago and have been used in every IARC Monograph since 2015. We investigated the patterns and associations in the use of Key Characteristics by the independent expert Working Groups. We examined 19 Monographs (2015-2022) that evaluated 73 agents. We extracted information on the conclusions by each Working Group on the strength of evidence for agent-Key Characteristic combinations, data types that were available for decisions, and the role mechanistic data played in the final cancer hazard classification. We conducted both descriptive and association analyses within and across data types. We found that IARC Working Groups were cautious when evaluating mechanistic evidence: for only ∼13% of the agents was strong evidence assigned for any Key Characteristic. Genotoxicity and cell proliferation were most data-rich, while little evidence was available for DNA repair and immortalization Key Characteristics. Analysis of the associations among Key Characteristics revealed that only chemical's metabolic activation was significantly co-occurring with genotoxicity and cell proliferation/death. Evidence from exposed humans was limited, while mechanistic evidence from rodent studies in vivo was often available. Only genotoxicity and cell proliferation/death were strongly associated with decisions on whether mechanistic data was impactful on the final cancer hazard classification. The practice of using the Key Characteristics approach is now well-established at IARC Monographs and other government agencies and the analyses presented herein will inform the future use of mechanistic evidence in regulatory decision-making.
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48
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Suciu I, Pamies D, Peruzzo R, Wirtz PH, Smirnova L, Pallocca G, Hauck C, Cronin MTD, Hengstler JG, Brunner T, Hartung T, Amelio I, Leist M. G × E interactions as a basis for toxicological uncertainty. Arch Toxicol 2023; 97:2035-2049. [PMID: 37258688 PMCID: PMC10256652 DOI: 10.1007/s00204-023-03500-9] [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: 03/15/2023] [Accepted: 04/17/2023] [Indexed: 06/02/2023]
Abstract
To transfer toxicological findings from model systems, e.g. animals, to humans, standardized safety factors are applied to account for intra-species and inter-species variabilities. An alternative approach would be to measure and model the actual compound-specific uncertainties. This biological concept assumes that all observed toxicities depend not only on the exposure situation (environment = E), but also on the genetic (G) background of the model (G × E). As a quantitative discipline, toxicology needs to move beyond merely qualitative G × E concepts. Research programs are required that determine the major biological variabilities affecting toxicity and categorize their relative weights and contributions. In a complementary approach, detailed case studies need to explore the role of genetic backgrounds in the adverse effects of defined chemicals. In addition, current understanding of the selection and propagation of adverse outcome pathways (AOP) in different biological environments is very limited. To improve understanding, a particular focus is required on modulatory and counter-regulatory steps. For quantitative approaches to address uncertainties, the concept of "genetic" influence needs a more precise definition. What is usually meant by this term in the context of G × E are the protein functions encoded by the genes. Besides the gene sequence, the regulation of the gene expression and function should also be accounted for. The widened concept of past and present "gene expression" influences is summarized here as Ge. Also, the concept of "environment" needs some re-consideration in situations where exposure timing (Et) is pivotal: prolonged or repeated exposure to the insult (chemical, physical, life style) affects Ge. This implies that it changes the model system. The interaction of Ge with Et might be denoted as Ge × Et. We provide here general explanations and specific examples for this concept and show how it could be applied in the context of New Approach Methodologies (NAM).
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Affiliation(s)
- Ilinca Suciu
- In Vitro Toxicology and Biomedicine, Department Inaugurated By the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Constance, Germany
| | - David Pamies
- Department of Biological Sciences, University of Lausanne, 1005, Lausanne, Switzerland
| | - Roberta Peruzzo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Petra H Wirtz
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78457, Constance, Germany
- Biological Work and Health Psychology, Department of Psychology, University of Konstanz, 78457, Constance, Germany
| | - Lena Smirnova
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | | | - Christof Hauck
- Department of Cell Biology, University of Konstanz, 78457, Constance, Germany
| | - Mark T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Technical University Dortmund, 44139, Dortmund, Germany
| | - Thomas Brunner
- Biochemical Pharmacology, Department of Biology, University of Konstanz, 78457, Constance, Germany
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- CAAT Europe, University of Konstanz, 78457, Constance, Germany
| | - Ivano Amelio
- Division for Systems Toxicology, Department of Biology, University of Konstanz, 78457, Constance, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department Inaugurated By the Doerenkamp-Zbinden Foundation, University of Konstanz, Universitaetsstr. 10, 78457, Constance, Germany.
- CAAT Europe, University of Konstanz, 78457, Constance, Germany.
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49
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Kim D, Jeong J, Choi J. Exploring the potential of ToxCast™ data for mechanism-based prioritization of chemicals in regulatory context: Case study with priority existing chemicals (PECs) under K-REACH. Regul Toxicol Pharmacol 2023:105439. [PMID: 37392832 DOI: 10.1016/j.yrtph.2023.105439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/26/2023] [Accepted: 06/29/2023] [Indexed: 07/03/2023]
Abstract
Recent studies have highlighted the potential of ToxCast™ database to mechanism-based prioritization of chemicals. To explore the applicability of ToxCast data in the context of regulatory inventory chemicals, we screened 510 priority existing chemicals (PECs) regulated under the Act on the Registration and Evaluation of Chemical Substances (K-REACH) using ToxCast bioassays. In our analysis, a hit-call data matrix containing 298984 chemical-gene interactions was computed for 949 bioassays with the intended target genes, which enabled the identification of the putative toxicity mechanisms. Based on the reactivity to the chemicals, we analyzed 412 bioassays whose intended target gene families were cytochrome P450, oxidoreductase, transporter, nuclear receptor, steroid hormone, and DNA-binding. We also identified 141 chemicals based on their reactivity in the bioassays. These chemicals are mainly in consumer products including colorants, preservatives, air fresheners, and detergents. Our analysis revealed that in vitro bioactivities were involved in the relevant mechanisms inducing in vivo toxicity; however, this was not sufficient to predict more hazardous chemicals. Overall, the current results point to a potential and limitation in using ToxCast data for chemical prioritization in regulatory context in the absence of suitable in vivo data.
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Affiliation(s)
- Donghyeon Kim
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Jaeseong Jeong
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, 163 Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea.
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50
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Tsai HHD, House JS, Wright FA, Chiu WA, Rusyn I. A tiered testing strategy based on in vitro phenotypic and transcriptomic data for selecting representative petroleum UVCBs for toxicity evaluation in vivo. Toxicol Sci 2023; 193:219-233. [PMID: 37079747 PMCID: PMC10230285 DOI: 10.1093/toxsci/kfad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Hazard evaluation of substances of "unknown or variable composition, complex reaction products and biological materials" (UVCBs) remains a major challenge in regulatory science because their chemical composition is difficult to ascertain. Petroleum substances are representative UVCBs and human cell-based data have been previously used to substantiate their groupings for regulatory submissions. We hypothesized that a combination of phenotypic and transcriptomic data could be integrated to make decisions as to selection of group-representative worst-case petroleum UVCBs for subsequent toxicity evaluation in vivo. We used data obtained from 141 substances from 16 manufacturing categories previously tested in 6 human cell types (induced pluripotent stem cell [iPSC]-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, and MCF7 and A375 cell lines). Benchmark doses for gene-substance combinations were calculated, and both transcriptomic and phenotype-derived points of departure (PODs) were obtained. Correlation analysis and machine learning were used to assess associations between phenotypic and transcriptional PODs and to determine the most informative cell types and assays, thus representing a cost-effective integrated testing strategy. We found that 2 cell types-iPSC-derived-hepatocytes and -cardiomyocytes-contributed the most informative and protective PODs and may be used to inform selection of representative petroleum UVCBs for further toxicity evaluation in vivo. Overall, although the use of new approach methodologies to prioritize UVCBs has not been widely adopted, our study proposes a tiered testing strategy based on iPSC-derived hepatocytes and cardiomyocytes to inform selection of representative worst-case petroleum UVCBs from each manufacturing category for further toxicity evaluation in vivo.
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Affiliation(s)
- Han-Hsuan Doris Tsai
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - John S House
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Fred A Wright
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, USA
- Department of Biological Sciences and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, USA
| | - Weihsueh A Chiu
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
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