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Mastrolorito F, Togo MV, Gambacorta N, Trisciuzzi D, Giannuzzi V, Bonifazi F, Liantonio A, Imbrici P, De Luca A, Altomare CD, Ciriaco F, Amoroso N, Nicolotti O. TISBE: A Public Web Platform for the Consensus-Based Explainable Prediction of Developmental Toxicity. Chem Res Toxicol 2024; 37:323-339. [PMID: 38200616 DOI: 10.1021/acs.chemrestox.3c00310] [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: 01/12/2024]
Abstract
Despite being extremely relevant for the protection of prenatal and neonatal health, the developmental toxicity (Dev Tox) is a highly complex endpoint whose molecular rationale is still largely unknown. The lack of availability of high-quality data as well as robust nontesting methods makes its understanding even more difficult. Thus, the application of new explainable alternative methods is of utmost importance, with Dev Tox being one of the most animal-intensive research themes of regulatory toxicology. Descending from TIRESIA (Toxicology Intelligence and Regulatory Evaluations for Scientific and Industry Applications), the present work describes TISBE (TIRESIA Improved on Structure-Based Explainability), a new public web platform implementing four fundamental advancements for in silico analyses: a three times larger dataset, a transparent XAI (explainable artificial intelligence) framework employing a fragment-based fingerprint coding, a novel consensus classifier based on five independent machine learning models, and a new applicability domain (AD) method based on a double top-down approach for better estimating the prediction reliability. The training set (TS) includes as many as 1008 chemicals annotated with experimental toxicity values. Based on a 5-fold cross-validation, a median value of 0.410 for the Matthews correlation coefficient was calculated; TISBE was very effective, with a median value of sensitivity and specificity equal to 0.984 and 0.274, respectively. TISBE was applied on two external pools made of 1484 bioactive compounds and 85 pediatric drugs taken from ChEMBL (Chemical European Molecular Biology Laboratory) and TEDDY (Task-Force in Europe for Drug Development in the Young) repositories, respectively. Notably, TISBE gives users the option to clearly spot the molecular fragments responsible for the toxicity or the safety of a given chemical query and is available for free at https://prometheus.farmacia.uniba.it/tisbe.
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Affiliation(s)
- Fabrizio Mastrolorito
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Maria Vittoria Togo
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Nicola Gambacorta
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Viviana Giannuzzi
- Fondazione per la Ricerca Farmacologica Gianni Benzi Onlus, 70010 Valenzano (BA), Italy
| | - Fedele Bonifazi
- Fondazione per la Ricerca Farmacologica Gianni Benzi Onlus, 70010 Valenzano (BA), Italy
| | - Antonella Liantonio
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Paola Imbrici
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Annamaria De Luca
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Cosimo Damiano Altomare
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Fulvio Ciriaco
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
| | - Nicola Amoroso
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70125 Bari, Italy
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125 Bari, Italy
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2
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Hamm JT, Hsieh JH, Roberts GK, Collins B, Gorospe J, Sparrow B, Walker NJ, Truong L, Tanguay RL, Dyballa S, Miñana R, Schiavone V, Terriente J, Weiner A, Muriana A, Quevedo C, Ryan KR. Interlaboratory Study on Zebrafish in Toxicology: Systematic Evaluation of the Application of Zebrafish in Toxicology's (SEAZIT's) Evaluation of Developmental Toxicity. TOXICS 2024; 12:93. [PMID: 38276729 PMCID: PMC10820928 DOI: 10.3390/toxics12010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/04/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
Embryonic zebrafish represent a useful test system to screen substances for their ability to perturb development. The exposure scenarios, endpoints captured, and data analysis vary among the laboratories who conduct screening. A lack of harmonization impedes the comparison of the substance potency and toxicity outcomes across laboratories and may hinder the broader adoption of this model for regulatory use. The Systematic Evaluation of the Application of Zebrafish in Toxicology (SEAZIT) initiative was developed to investigate the sources of variability in toxicity testing. This initiative involved an interlaboratory study to determine whether experimental parameters altered the developmental toxicity of a set of 42 substances (3 tested in duplicate) in three diverse laboratories. An initial dose-range-finding study using in-house protocols was followed by a definitive study using four experimental conditions: chorion-on and chorion-off using both static and static renewal exposures. We observed reasonable agreement across the three laboratories as 33 of 42 test substances (78.6%) had the same activity call. However, the differences in potency seen using variable in-house protocols emphasizes the importance of harmonization of the exposure variables under evaluation in the second phase of this study. The outcome of the Def will facilitate future practical discussions on harmonization within the zebrafish research community.
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Affiliation(s)
- Jon T. Hamm
- Inotiv, P.O. Box 13501, Research Triangle Park, NC 27709, USA
| | - Jui-Hua Hsieh
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Georgia K. Roberts
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Bradley Collins
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Jenni Gorospe
- Battelle Memorial Institute, Columbus, OH 43201, USA
| | | | - Nigel J. Walker
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Lisa Truong
- Department of Environmental and Molecular Toxicology, The Sinnhuber Aquatic Research Laboratory, The Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, USA
| | - Robyn L. Tanguay
- Department of Environmental and Molecular Toxicology, The Sinnhuber Aquatic Research Laboratory, The Environmental Health Sciences Center, Oregon State University, Corvallis, OR 97331, USA
| | | | - Rafael Miñana
- ZeClinics SL., 08980 Barcelona, Spain
- CTI Laboratory Services Spain SL., 48160 Bilbao, Spain
| | | | | | - Andrea Weiner
- BBD BioPhenix SL. (Biobide), 20009 San Sebastian, Spain
| | | | - Celia Quevedo
- BBD BioPhenix SL. (Biobide), 20009 San Sebastian, Spain
| | - Kristen R. Ryan
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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3
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Pierro JD, Ahir BK, Baker NC, Kleinstreuer NC, Xia M, Knudsen TB. Computational model for fetal skeletal defects potentially linked to disruption of retinoic acid signaling. Front Pharmacol 2022; 13:971296. [PMID: 36172177 PMCID: PMC9511990 DOI: 10.3389/fphar.2022.971296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
All-trans retinoic acid (ATRA) gradients determine skeletal patterning morphogenesis and can be disrupted by diverse genetic or environmental factors during pregnancy, leading to fetal skeleton defects. Adverse Outcome Pathway (AOP) frameworks for ATRA metabolism, signaling, and homeostasis allow for the development of new approach methods (NAMs) for predictive toxicology with less reliance on animal testing. Here, a data-driven model was constructed to identify chemicals associated with both ATRA pathway bioactivity and prenatal skeletal defects. The phenotype data was culled from ToxRefDB prenatal developmental toxicity studies and produced a list of 363 ToxRefDB chemicals with altered skeletal observations. Defects were classified regionally as cranial, post-cranial axial, appendicular, and other (unspecified) features based on ToxRefDB descriptors. To build a multivariate statistical model, high-throughput screening bioactivity data from >8,070 chemicals in ToxCast/Tox21 across 10 in vitro assays relevant to the retinoid signaling system were evaluated and compared to literature-based candidate reference chemicals in the dataset. There were 48 chemicals identified for effects on both in vivo skeletal defects and in vitro ATRA pathway targets for computational modeling. The list included 28 chemicals with prior evidence of skeletal defects linked to retinoid toxicity and 20 chemicals without prior evidence. The combination of thoracic cage defects and DR5 (direct repeats of 5 nucleotides for RAR/RXR transactivation) disruption was the most frequently occurring phenotypic and target disturbance, respectively. This data model provides valuable AOP elucidation and validates current mechanistic understanding. These findings also shed light on potential avenues for new mechanistic discoveries related to ATRA pathway disruption and associated skeletal dysmorphogenesis due to environmental exposures.
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Affiliation(s)
- Jocylin D. Pierro
- Center for Computational Toxicology and Exposure (CCTE), Computational Toxicology and Bioinformatics Branch (CTBB), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park, NC, United States
| | - Bhavesh K. Ahir
- Eurofins Medical Device Testing, Lancaster, PA, United States
| | - Nancy C. Baker
- Scientific Computing and Data Curation Division (SCDCD), Leidos Contractor, Center for Computational Toxicology and Exposure (CCTE), USEPA/ORD, Research Triangle Park, NC, United States
| | - Nicole C. Kleinstreuer
- Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), National Toxicology Program, National Institutes of Health, Research Triangle Park, NC, United States
| | - Menghang Xia
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Thomas B. Knudsen
- Center for Computational Toxicology and Exposure (CCTE), Computational Toxicology and Bioinformatics Branch (CTBB), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park, NC, United States
- *Correspondence: Thomas B. Knudsen, , orcid.org/0000-0002-5036-596x
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Pla L, Kühne BA, Guardia-Escote L, Vázquez-Aristizabal P, Loreiro C, Flick B, Gratacós E, Barenys M, Illa M. Protocols for the Evaluation of Neurodevelopmental Alterations in Rabbit Models In Vitro and In Vivo. FRONTIERS IN TOXICOLOGY 2022; 4:918520. [PMID: 35936386 PMCID: PMC9355155 DOI: 10.3389/ftox.2022.918520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
The rabbit model is gaining importance in the field of neurodevelopmental evaluation due to its higher similarity to humans in terms of brain development and maturation than rodents. In this publication, we detailed 14 protocols covering toxicological relevant endpoints for the assessment of neurodevelopmental adverse effects in the rabbit species. These protocols include both in vitro and in vivo techniques, which also cover different evaluation time-points, the neonatal period, and long-term examinations at postnatal days (PNDs) 50–70. Specifically, the protocols (P) included are as follows: neurosphere preparation (GD30/PND0; P2) and neurosphere assay (P3), behavioral ontogeny (PND1; P4), brain obtaining and brain weight measurement at two different ages: PND1 (P5) and PND70 (P12), neurohistopathological evaluations after immersion fixation for neurons, astrocytes, oligodendrocytes and microglia (PND1; P6-9) or perfusion fixation (PND70; P12), motor activity (P11, open field), memory and sensory function (P11, object recognition test), learning (P10, Skinner box), and histological evaluation of plasticity (P13 and P14) through dendritic spines and perineuronal nets. The expected control values and their variabilities are presented together with the information on how to troubleshoot the most common issues related to each protocol. To sum up, this publication offers a comprehensive compilation of reliable protocols adapted to the rabbit model for neurodevelopmental assessment in toxicology.
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Affiliation(s)
- Laura Pla
- BCNatal-Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Déu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Center for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Britta Anna Kühne
- BCNatal-Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Déu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Center for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
- GRET, INSA-UB and Toxicology Unit, Pharmacology, Toxicology and Therapeutical Chemistry Department, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Laia Guardia-Escote
- GRET, INSA-UB and Toxicology Unit, Pharmacology, Toxicology and Therapeutical Chemistry Department, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
- Department of Psychology, Faculty of Psychology, Universitat Rovira i Virgili, Tarragona, Spain
| | - Paula Vázquez-Aristizabal
- BCNatal-Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Déu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Center for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
- GRET, INSA-UB and Toxicology Unit, Pharmacology, Toxicology and Therapeutical Chemistry Department, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Carla Loreiro
- BCNatal-Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Déu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Center for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Burkhard Flick
- Department of Toxicology, NUVISAN ICB GmbH, Berlin, Germany
| | - Eduard Gratacós
- BCNatal-Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Déu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Center for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
| | - Marta Barenys
- GRET, INSA-UB and Toxicology Unit, Pharmacology, Toxicology and Therapeutical Chemistry Department, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Miriam Illa
- BCNatal-Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Déu), Fetal i+D Fetal Medicine Research Center, IDIBAPS, University of Barcelona, Center for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Spain
- *Correspondence: Miriam Illa,
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Ciallella HL, Russo DP, Sharma S, Li Y, Sloter E, Sweet L, Huang H, Zhu H. Predicting Prenatal Developmental Toxicity Based On the Combination of Chemical Structures and Biological Data. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:5984-5998. [PMID: 35451820 PMCID: PMC9191745 DOI: 10.1021/acs.est.2c01040] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
For hazard identification, classification, and labeling purposes, animal testing guidelines are required by law to evaluate the developmental toxicity potential of new and existing chemical products. However, guideline developmental toxicity studies are costly, time-consuming, and require many laboratory animals. Computational modeling has emerged as a promising, animal-sparing, and cost-effective method for evaluating the developmental toxicity potential of chemicals, such as endocrine disruptors, without the use of animals. We aimed to develop a predictive and explainable computational model for developmental toxicants. To this end, a comprehensive dataset of 1244 chemicals with developmental toxicity classifications was curated from public repositories and literature sources. Data from 2140 toxicological high-throughput screening assays were extracted from PubChem and the ToxCast program for this dataset and combined with information about 834 chemical fragments to group assays based on their chemical-mechanistic relationships. This effort revealed two assay clusters containing 83 and 76 assays, respectively, with high positive predictive rates for developmental toxicants identified with animal testing guidelines (PPV = 72.4 and 77.3% during cross-validation). These two assay clusters can be used as developmental toxicity models and were applied to predict new chemicals for external validation. This study provides a new strategy for constructing alternative chemical developmental toxicity evaluations that can be replicated for other toxicity modeling studies.
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Affiliation(s)
- Heather L. Ciallella
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08103, USA
| | - Daniel P. Russo
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08103, USA
- Department of Chemistry, Rutgers University, Camden, NJ, 08102, USA
| | - Swati Sharma
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08103, USA
| | - Yafan Li
- The Lubrizol Corporation, Wickliffe, OH, 44092, USA
| | - Eddie Sloter
- The Lubrizol Corporation, Wickliffe, OH, 44092, USA
| | - Len Sweet
- The Lubrizol Corporation, Wickliffe, OH, 44092, USA
| | - Heng Huang
- Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Hao Zhu
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, 08103, USA
- Department of Chemistry, Rutgers University, Camden, NJ, 08102, USA
- Corresponding Author333 Hao Zhu, 201 South Broadway, Joint Health Sciences Center, Rutgers University, Camden, New Jersey 08103; Telephone: (856) 225-6781;
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van der Voet M, Teunis M, Louter-van de Haar J, Stigter N, Bhalla D, Rooseboom M, Wever KE, Krul C, Pieters R, Wildwater M, van Noort V. Towards a reporting guideline for developmental and reproductive toxicology testing in C. elegans and other nematodes. Toxicol Res (Camb) 2021; 10:1202-1210. [PMID: 34950447 PMCID: PMC8692742 DOI: 10.1093/toxres/tfab109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 10/07/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
Implementation of reliable methodologies allowing Reduction, Refinement, and Replacement (3Rs) of animal testing is a process that takes several decades and is still not complete. Reliable methods are essential for regulatory hazard assessment of chemicals where differences in test protocol can influence the test outcomes and thus affect the confidence in the predictive value of the organisms used as an alternative for mammals. Although test guidelines are common for mammalian studies, they are scarce for non-vertebrate organisms that would allow for the 3Rs of animal testing. Here, we present a set of 30 reporting criteria as the basis for such a guideline for Developmental and Reproductive Toxicology (DART) testing in the nematode Caenorhabditis elegans. Small organisms like C. elegans are upcoming in new approach methodologies for hazard assessment; thus, reliable and robust test protocols are urgently needed. A literature assessment of the fulfilment of the reporting criteria demonstrates that although studies describe methodological details, essential information such as compound purity and lot/batch number or type of container is often not reported. The formulated set of reporting criteria for C. elegans testing can be used by (i) researchers to describe essential experimental details (ii) data scientists that aggregate information to assess data quality and include data in aggregated databases (iii) regulators to assess study data for inclusion in regulatory hazard assessment of chemicals.
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Affiliation(s)
| | - Marc Teunis
- Utrecht University of Applied Sciences, Innovative testing in Life Sciences & Chemistry, 3584 CH, Utrecht, the Netherlands
| | - Johanna Louter-van de Haar
- Utrecht University of Applied Sciences, Innovative testing in Life Sciences & Chemistry, 3584 CH, Utrecht, the Netherlands
| | - Nienke Stigter
- Utrecht University of Applied Sciences, Innovative testing in Life Sciences & Chemistry, 3584 CH, Utrecht, the Netherlands
| | - Diksha Bhalla
- KU Leuven, Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, 3001, Leuven, Belgium
| | - Martijn Rooseboom
- Toxicology group Shell International B.V., 2596 HR, The Hague, the Netherlands
| | - Kimberley E Wever
- Radboud University Medical Center, Radboud Institute for Health Sciences, Department for Health Evidence, 6525 GA, Nijmegen, the Netherlands
| | - Cyrille Krul
- Utrecht University of Applied Sciences, Innovative testing in Life Sciences & Chemistry, 3584 CH, Utrecht, the Netherlands
| | - Raymond Pieters
- Utrecht University of Applied Sciences, Innovative testing in Life Sciences & Chemistry, 3584 CH, Utrecht, the Netherlands
- Utrecht University, Institute for Risk Assessment Sciences, 3584 CM, Utrecht, the Netherlands
| | | | - Vera van Noort
- KU Leuven, Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, 3001, Leuven, Belgium
- Leiden University, Institute of Biology Leiden, 2333 BE, Leiden, the Netherlands
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7
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Zurlinden TJ, Saili KS, Rush N, Kothiya P, Judson RS, Houck KA, Hunter ES, Baker NC, Palmer JA, Thomas RS, Knudsen TB. Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity. Toxicol Sci 2021; 174:189-209. [PMID: 32073639 DOI: 10.1093/toxsci/kfaa014] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Stemina devTOX quickPredict platform is a human pluripotent stem cell-based assay that predicts the developmental toxicity potential based on changes in cellular metabolism following chemical exposure [Palmer, J. A., Smith, A. M., Egnash, L. A., Conard, K. R., West, P. R., Burrier, R. E., Donley, E. L. R., and Kirchner, F. R. (2013). Establishment and assessment of a new human embryonic stem cell-based biomarker assay for developmental toxicity screening. Birth Defects Res. B Dev. Reprod. Toxicol. 98, 343-363]. Using this assay, we screened 1065 ToxCast phase I and II chemicals in single-concentration or concentration-response for the targeted biomarker (ratio of ornithine to cystine secreted or consumed from the media). The dataset from the Stemina (STM) assay is annotated in the ToxCast portfolio as STM. Major findings from the analysis of ToxCast_STM dataset include (1) 19% of 1065 chemicals yielded a prediction of developmental toxicity, (2) assay performance reached 79%-82% accuracy with high specificity (> 84%) but modest sensitivity (< 67%) when compared with in vivo animal models of human prenatal developmental toxicity, (3) sensitivity improved as more stringent weights of evidence requirements were applied to the animal studies, and (4) statistical analysis of the most potent chemical hits on specific biochemical targets in ToxCast revealed positive and negative associations with the STM response, providing insights into the mechanistic underpinnings of the targeted endpoint and its biological domain. The results of this study will be useful to improving our ability to predict in vivo developmental toxicants based on in vitro data and in silico models.
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Affiliation(s)
| | | | | | | | | | | | - E Sidney Hunter
- National Health and Environmental Effects Research Laboratory (NHEERL), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park, North Carolina
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8
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Knudsen TB, Pierro JD, Baker NC. Retinoid signaling in skeletal development: Scoping the system for predictive toxicology. Reprod Toxicol 2021; 99:109-130. [DOI: 10.1016/j.reprotox.2020.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/15/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]
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9
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Knudsen TB, Spencer RM, Pierro JD, Baker NC. Computational Biology and in silico Toxicodynamics. CURRENT OPINION IN TOXICOLOGY 2020; 23-24:119-126. [PMID: 36561131 PMCID: PMC9770085 DOI: 10.1016/j.cotox.2020.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
New approach methodologies (NAMs) refer to any non-animal technology, methodology, approach, or combination thereof that can be used to provide information on chemical hazard and risk assessment that avoids the use of intact animals. A spectrum of in silico models is needed for the integrated analysis of various domains in toxicology to improve predictivity and reduce animal testing. This review focuses on in silico approaches, computer models, and computational intelligence for developmental and reproductive toxicity (predictive DART), providing a means to measure toxicodynamics in simulated systems for quantitative prediction of adverse outcomes phenotypes.
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Affiliation(s)
- Thomas B. Knudsen
- Center for Computational Toxicology and Exposure (CCTE), Biomolecular and Computational Toxicology Division (BCTD), Computational Toxicology and Bioinformatics Branch (CTBB), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park NC 27711,Corresponding author:
| | - Richard M. Spencer
- General Dynamics, Contractor, Environmental Modeling and Visualization Laboratory (EMVL), US EPA/ORD, Research Triangle Park NC 27711
| | - Jocylin D. Pierro
- Center for Computational Toxicology and Exposure (CCTE), Biomolecular and Computational Toxicology Division (BCTD), Computational Toxicology and Bioinformatics Branch (CTBB), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park NC 27711
| | - Nancy C. Baker
- Leidos Contractor, Center for Computational Toxicology and Exposure (CCTE), Scientific Computing and Data Curation Division (SCDCD), USEPA/ORD, Research Triangle Park NC 27711
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10
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Vegosen L, Martin TM. An automated framework for compiling and integrating chemical hazard data. CLEAN TECHNOLOGIES AND ENVIRONMENTAL POLICY 2020; 22:441-458. [PMID: 33867908 PMCID: PMC8048128 DOI: 10.1007/s10098-019-01795-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/13/2019] [Indexed: 05/07/2023]
Abstract
Comparative chemical hazard assessment, which compares hazards for several endpoints across several chemicals, can be used for a variety of purposes including alternatives assessment and the prioritization of chemicals for further assessment. A new framework was developed to compile and integrate chemical hazard data for several human health and ecotoxicity endpoints from public online sources including hazardous chemical lists, Globally Harmonized System hazard codes (H-codes) or hazard categories from government health agencies, experimental quantitative toxicity values, and predicted values using Quantitative Structure-Activity Relationship (QSAR) models. QSAR model predictions were obtained using EPA's Toxicity Estimation Software Tool. Java programming was used to download hazard data, convert data from each source into a consistent score record format, and store the data in a database. Scoring criteria based on the EPA's Design for the Environment Program Alternatives Assessment Criteria for Hazard Evaluation were used to determine ordinal hazard scores (i.e., low, medium, high, or very high) for each score record. Different methodologies were assessed for integrating data from multiple sources into one score for each hazard endpoint for each chemical. The chemical hazard assessment (CHA) Database developed in this study currently contains more than 990,000 score records for more than 85,000 chemicals. The CHA Database and the methods used in its development may contribute to several cheminformatics, public health, and environmental activities.
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Affiliation(s)
- Leora Vegosen
- Oak Ridge Institute for Science and Education, 100 ORAU Way, Oak Ridge, TN 37830, USA
- National Risk Management Research Laboratory, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
| | - Todd M. Martin
- National Risk Management Research Laboratory, U.S. Environmental Protection Agency, 26 W. Martin Luther King Dr., Cincinnati, OH 45268, USA
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11
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Yamaguchi A, Uchida M, Ishibashi H, Hirano M, Ichikawa N, Arizono K, Koyama J, Tominaga N. Potential mechanisms underlying embryonic developmental toxicity caused by benzo[a]pyrene in Japanese medaka (Oryzias latipes). CHEMOSPHERE 2020; 242:125243. [PMID: 31704526 DOI: 10.1016/j.chemosphere.2019.125243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/25/2019] [Accepted: 10/26/2019] [Indexed: 06/10/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs), such as benzo[a]pyrene (BaP), are widely distributed in air, water, and sediments; however, limited data are available regarding their potential adverse effects on the early life stages of fish. In this study, we evaluated the embryonic teratogenicity and developmental toxicity of BaP in Japanese medaka (Oryzias latipes) using a nanosecond pulsed electric field (nsPEF) technique and predicted their molecular mechanisms via transcriptome analysis. The gas chromatography/mass spectrometry analyses revealed that the BaP was efficiently incorporated into the embryos by nsPEF treatment. The embryos incorporating BaP presented typical teratogenic and developmental effects, such as cardiovascular abnormalities, developmental abnormalities, and curvature of backbone. DNA microarray analysis revealed several unique upregulated genes, such as those involved in cardiovascular diseases, various cellular processes, and neural development. Furthermore, the gene set enrichment and network analyses found several genes and hub proteins involved in the developmental effects of BaP on the embryos. These findings suggest a potential mechanism of teratogenicity and developmental toxicity caused by exposure to BaP. The nsPEF and transcriptome analyses in combination can be effective for evaluating the potential effects of chemical substances on medaka embryos.
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Affiliation(s)
- Akemi Yamaguchi
- Department of Creative Engineering, National Institute of Technology, Ariake College, 150 Higashi-Hagio, Omuta, Fukuoka, 836-8585, Japan
| | - Masaya Uchida
- Department of Creative Engineering, National Institute of Technology, Ariake College, 150 Higashi-Hagio, Omuta, Fukuoka, 836-8585, Japan
| | - Hiroshi Ishibashi
- Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, 790-8566, Japan
| | - Masashi Hirano
- Department of Biological and Chemical Systems Engineering, National Institute of Technology, Kumamoto College, 2627 Hirayama-shinmachi, Yatsushiro, Kumamoto, 866-8501, Japan
| | - Nobuhiro Ichikawa
- College of Pharmaceutical Sciences, Department of Pharmacy, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Koji Arizono
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, 3-1-100 Higashi-ku, Tsukide, Kumamoto, 862-8502, Japan
| | - Jiro Koyama
- Faculty of Fisheries, Kagoshima University, 4-50-20 Shimoarata, Kagoshima, 890-0056, Japan
| | - Nobuaki Tominaga
- Department of Creative Engineering, National Institute of Technology, Ariake College, 150 Higashi-Hagio, Omuta, Fukuoka, 836-8585, Japan.
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12
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Clements JM, Hawkes RG, Jones D, Adjei A, Chambers T, Simon L, Stemplewski H, Berry N, Price S, Pirmohamed M, Piersma AH, Waxenecker G, Barrow P, Beekhuijzen MEW, Fowkes A, Prior H, Sewell F. Predicting the safety of medicines in pregnancy: A workshop report. Reprod Toxicol 2020; 93:199-210. [PMID: 32126282 DOI: 10.1016/j.reprotox.2020.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/10/2020] [Accepted: 02/26/2020] [Indexed: 01/05/2023]
Abstract
The framework for developmental toxicity testing has remained largely unchanged for over 50 years and although it remains invaluable in assessing potential risks in pregnancy, knowledge gaps exist, and some outcomes do not necessarily correlate with clinical experience. Advances in omics, in silico approaches and alternative assays are providing opportunities to enhance our understanding of embryo-fetal development and the prediction of potential risks associated with the use of medicines in pregnancy. A workshop organised by the Medicines and Healthcare products Regulatory Agency (MHRA), "Predicting the Safety of Medicines in Pregnancy - a New Era?", was attended by delegates representing regulatory authorities, academia, industry, patients, funding bodies and software developers to consider how to improve the quality of and access to nonclinical developmental toxicity data and how to use this data to better predict the safety of medicines in human pregnancy. The workshop delegates concluded that based on comparative data to date alternative methodologies are currently no more predictive than conventional methods and not qualified for use in regulatory submissions. To advance the development and qualification of alternative methodologies, there is a requirement for better coordinated multidisciplinary cross-sector interactions coupled with data sharing. Furthermore, a better understanding of human developmental biology and the incorporation of this knowledge into the development of alternative methodologies is essential to enhance the prediction of adverse outcomes for human development. The output of the workshop was a series of recommendations aimed at supporting multidisciplinary efforts to develop and validate these alternative methodologies.
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Affiliation(s)
- J M Clements
- Medicines and Healthcare products Regulatory Agency, London, UK
| | - R G Hawkes
- Medicines and Healthcare products Regulatory Agency, London, UK.
| | - D Jones
- Medicines and Healthcare products Regulatory Agency, London, UK
| | - A Adjei
- Medicines and Healthcare products Regulatory Agency, London, UK
| | - T Chambers
- Medicines and Healthcare products Regulatory Agency, London, UK
| | - L Simon
- Medicines and Healthcare products Regulatory Agency, London, UK
| | - H Stemplewski
- Medicines and Healthcare products Regulatory Agency, London, UK
| | - N Berry
- National Institute for Biological Standards and Control, Potters Bar, UK
| | | | | | - A H Piersma
- National Institute for Public Health and the Environment (RIVM), Center for Health Protection, Bilthoven, Netherlands
| | - G Waxenecker
- Austrian Medicines and Medical Devices Agency, Vienna, Austria
| | - P Barrow
- Roche Pharmaceutical Research and Early Development, Basel, Switzerland
| | | | | | - H Prior
- National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), London, UK
| | - F Sewell
- National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), London, UK
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13
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Watford S, Ly Pham L, Wignall J, Shin R, Martin MT, Friedman KP. ToxRefDB version 2.0: Improved utility for predictive and retrospective toxicology analyses. Reprod Toxicol 2019; 89:145-158. [PMID: 31340180 PMCID: PMC6944327 DOI: 10.1016/j.reprotox.2019.07.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/31/2019] [Accepted: 07/12/2019] [Indexed: 02/08/2023]
Abstract
The Toxicity Reference Database (ToxRefDB) structures information from over 5000 in vivo toxicity studies, conducted largely to guidelines or specifications from the US Environmental Protection Agency and the National Toxicology Program, into a public resource for training and validation of predictive models. Herein, ToxRefDB version 2.0 (ToxRefDBv2) development is described. Endpoints were annotated (e.g. required, not required) according to guidelines for subacute, subchronic, chronic, developmental, and multigenerational reproductive designs, distinguishing negative responses from untested. Quantitative data were extracted, and dose-response modeling for nearly 28,000 datasets from nearly 400 endpoints using Benchmark Dose (BMD) Modeling Software were generated and stored. Implementation of controlled vocabulary improved data quality; standardization to guideline requirements and cross-referencing with United Medical Language System (UMLS) connects ToxRefDBv2 observations to vocabularies linked to UMLS, including PubMed medical subject headings. ToxRefDBv2 allows for increased connections to other resources and has greatly enhanced quantitative and qualitative utility for predictive toxicology.
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Affiliation(s)
- Sean Watford
- ORAU, Contractor to U.S. Environmental Protection Agency through the National Student Services Contract, United States; National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency, United States
| | - Ly Ly Pham
- ORAU, Contractor to U.S. Environmental Protection Agency through the National Student Services Contract, United States; ORISE Postdoctoral Research Participant, United States
| | | | | | - Matthew T Martin
- ORAU, Contractor to U.S. Environmental Protection Agency through the National Student Services Contract, United States; Currently at Drug Safety Research and Development, Global Investigative Toxicology, Pfizer, Groton, CT, United States
| | - Katie Paul Friedman
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency, United States.
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14
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Fritsche E, Barenys M, Klose J, Masjosthusmann S, Nimtz L, Schmuck M, Wuttke S, Tigges J. Development of the Concept for Stem Cell-Based Developmental Neurotoxicity Evaluation. Toxicol Sci 2019; 165:14-20. [PMID: 29982725 DOI: 10.1093/toxsci/kfy175] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Human brain development consists of a series of complex spatiotemporal processes that if disturbed by chemical exposure causes irreversible impairments of the nervous system. To evaluate a chemical disturbance in an alternative assay, the concept evolved that the complex procedure of brain development can be disassembled into several neurodevelopmental endpoints which can be represented by a combination of different alternative assays. In this review article, we provide a scientific rationale for the neurodevelopmental endpoints that are currently chosen to establish assays with human stem/and progenitor cells. Assays covering these major neurodevelopmental endpoints are thought to assemble as building blocks of a DNT testing battery.
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Affiliation(s)
- Ellen Fritsche
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany.,Heinrich Heine University, 40225 Düsseldorf, Germany
| | | | - Jördis Klose
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Stefan Masjosthusmann
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Laura Nimtz
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Martin Schmuck
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Saskia Wuttke
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Julia Tigges
- IUF - Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
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15
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Baker NC, Sipes NS, Franzosa J, Belair DG, Abbott BD, Judson RS, Knudsen TB. Characterizing cleft palate toxicants using ToxCast data, chemical structure, and the biomedical literature. Birth Defects Res 2019; 112:19-39. [PMID: 31471948 DOI: 10.1002/bdr2.1581] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/11/2022]
Abstract
Cleft palate has been linked to both genetic and environmental factors that perturb key events during palatal morphogenesis. As a developmental outcome, it presents a challenging, mechanistically complex endpoint for predictive modeling. A data set of 500 chemicals evaluated for their ability to induce cleft palate in animal prenatal developmental studies was compiled from Toxicity Reference Database and the biomedical literature, which included 63 cleft palate active and 437 inactive chemicals. To characterize the potential molecular targets for chemical-induced cleft palate, we mined the ToxCast high-throughput screening database for patterns and linkages in bioactivity profiles and chemical structural descriptors. ToxCast assay results were filtered for cytotoxicity and grouped by target gene activity to produce a "gene score." Following unsuccessful attempts to derive a global prediction model using structural and gene score descriptors, hierarchical clustering was applied to the set of 63 cleft palate positives to extract local structure-bioactivity clusters for follow-up study. Patterns of enrichment were confirmed on the complete data set, that is, including cleft palate inactives, and putative molecular initiating events identified. The clusters corresponded to ToxCast assays for cytochrome P450s, G-protein coupled receptors, retinoic acid receptors, the glucocorticoid receptor, and tyrosine kinases/phosphatases. These patterns and linkages were organized into preliminary decision trees and the resulting inferences were mapped to a putative adverse outcome pathway framework for cleft palate supported by literature evidence of current mechanistic understanding. This general data-driven approach offers a promising avenue for mining chemical-bioassay drivers of complex developmental endpoints where data are often limited.
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Affiliation(s)
| | - Nisha S Sipes
- NIEHS Division of the National Toxicology Program, Research Triangle Park, North Carolina
| | - Jill Franzosa
- IOAA CSS, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | - David G Belair
- NHEERL, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Barbara D Abbott
- NHEERL, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Richard S Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Thomas B Knudsen
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
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16
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Kim M, Jeong J, Kim H, Choi J. High-throughput COPAS assay for screening of developmental and reproductive toxicity of nanoparticles using the nematode Caenorhabditis elegans. J Appl Toxicol 2019; 39:1470-1479. [PMID: 31287177 DOI: 10.1002/jat.3833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/25/2022]
Abstract
With the rapid advancement and numerous applications of engineered nanomaterials (ENMs) in science and technology, their effects on animal health, environment and safety should be considered carefully. However, quick assessment of their effects on developmental and reproductive health and an understanding of how they cause such adverse toxic effects remain challenging, because of the fast-growing number of ENMs and the limitations of the different toxicity assays currently in use as well as lack of suitable animal model systems. In this study, we performed a high-throughput complex object parametric analyzer and sorter (COPAS) assay for assessing the developmental and reproductive toxicity of ENMs using Caenorhabditis elegans and provide descriptions of the data and their subsequent analysis. The results showed significant reproductive and developmental toxicity potential of different ENMs. We assessed the usefulness of this method in terms of error-free data, user-friendliness and results being consistent with those of visual, molecular and cellular studies. Moreover, the COPAS Biosort system could be used on a larger scale to screen thousands of chemicals, drugs, pharmaceuticals and ENMs. This study also indicates that the COPAS-based high-throughput screening system is highly reliable for the assessment of toxicity and health risks of NMs.
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Affiliation(s)
- MinA Kim
- School of Environmental Engineering, University of Seoul, Dongdaemun-gu, Seoul, South Korea
| | - Jaeseong Jeong
- School of Environmental Engineering, University of Seoul, Dongdaemun-gu, Seoul, South Korea
| | - Heejin Kim
- School of Environmental Engineering, University of Seoul, Dongdaemun-gu, Seoul, South Korea
| | - Jinhee Choi
- School of Environmental Engineering, University of Seoul, Dongdaemun-gu, Seoul, South Korea
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17
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Fry RC, Bangma J, Szilagyi J, Rager JE. Developing novel in vitro methods for the risk assessment of developmental and placental toxicants in the environment. Toxicol Appl Pharmacol 2019; 378:114635. [PMID: 31233757 DOI: 10.1016/j.taap.2019.114635] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 01/12/2023]
Abstract
During pregnancy, the placenta is critical for the regulation of maternal homeostasis and fetal growth and development. Exposures to environmental chemicals during pregnancy can be detrimental to the health of the placenta and therefore adversely impact maternal and fetal health. Though research on placental-derived developmental toxicity is expanding, testing is limited by the resources required for traditional test methods based on whole animal experimentation. Alternative strategies utilizing in vitro methods are well suited to contribute to more efficient screening of chemical toxicity and identification of biological mechanisms underlying toxicity outcomes. This review aims to summarize methods that can be used to evaluate toxicity resulting from exposures during the prenatal period, with a focus on newer in vitro methods centered on placental toxicity. The following key aspects are reviewed: (i) traditional test methods based on animal developmental toxicity testing, (ii) in vitro methods using monocultures and explant models, as well as more recently developed methods, including co-cultures, placenta-on-a-chip, and 3-dimensional (3D) cell models, (iii) endpoints that are commonly measured using in vitro designs, and (iv) the translation of in vitro methods into chemical evaluations and risk assessment applications. We conclude that findings from in vitro placental models can contribute to the screening of potentially hazardous chemicals, elucidation of chemical mechanism of action, incorporation into adverse outcome pathways, estimation of doses eliciting toxicity, derivation of extrapolation factors, and characterization of overall risk of adverse outcomes, representing key components of chemical regulation in the 21st century.
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Affiliation(s)
- Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Toxicology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jacqueline Bangma
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - John Szilagyi
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Julia E Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Toxicology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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18
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Braakhuis HM, Theunissen PT, Slob W, Rorije E, Piersma AH. Testing developmental toxicity in a second species: are the differences due to species or replication error? Regul Toxicol Pharmacol 2019; 107:104410. [PMID: 31226390 DOI: 10.1016/j.yrtph.2019.104410] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 11/20/2022]
Abstract
Developmental toxicity studies for chemical and pharmaceutical safety are primarily performed in rats. Regulatory frameworks may require testing in a second, non-rodent species, for which the rabbit is usually chosen. This study shows that differences in NOAELs or LOAELs (N(L)OAELs) observed between rat and rabbit developmental toxicity studies performed according to OECD guidelines could just as well be caused by study replication errors, and not necessarily by differences in species sensitivity. This conclusion follows from an analysis of a database with rat and rabbit developmental toxicity studies for over 1000 industrial chemicals, pesticides, veterinary drugs and human pharmaceuticals, which included 143 compounds with multiple oral rat studies and 124 compounds with multiple oral rabbit studies. Our analysis confirms earlier findings that, on average over all compounds, rat and rabbit do not differ in sensitivity to developmental effects. There is substantial scatter in the correlation plots comparing rat and rabbit developmental N(L)OAELs, which is easily interpreted as species differences for individual compounds. However, for compounds tested twice in the same species, these N(L)OAELs may differ up to a factor of 25. Thus, potential interspecies differences in developmental N(L)OAEL will be overwhelmed by the reproducibility error, rendering the added value of a second species study questionable. As N(L)OAELs serve as point of departure (POD) for setting health-based guidance values in risk assessment, the large reproducibility error of N(L)OAELs should be taken into account by the introduction of an additional uncertainty factor. It is recommended to aim for reducing the reproducibility error by applying dose-response (BMD) analysis, optimize study designs and harmonize study protocols.
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Affiliation(s)
- Hedwig M Braakhuis
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Wout Slob
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Emiel Rorije
- Centre for Safety of Substances and Products, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Aldert H Piersma
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands; Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.
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19
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Thomas RS, Bahadori T, Buckley TJ, Cowden J, Deisenroth C, Dionisio KL, Frithsen JB, Grulke CM, Gwinn MR, Harrill JA, Higuchi M, Houck KA, Hughes MF, Hunter ES, Isaacs KK, Judson RS, Knudsen TB, Lambert JC, Linnenbrink M, Martin TM, Newton SR, Padilla S, Patlewicz G, Paul-Friedman K, Phillips KA, Richard AM, Sams R, Shafer TJ, Setzer RW, Shah I, Simmons JE, Simmons SO, Singh A, Sobus JR, Strynar M, Swank A, Tornero-Valez R, Ulrich EM, Villeneuve DL, Wambaugh JF, Wetmore BA, Williams AJ. The Next Generation Blueprint of Computational Toxicology at the U.S. Environmental Protection Agency. Toxicol Sci 2019; 169:317-332. [PMID: 30835285 PMCID: PMC6542711 DOI: 10.1093/toxsci/kfz058] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The U.S. Environmental Protection Agency (EPA) is faced with the challenge of efficiently and credibly evaluating chemical safety often with limited or no available toxicity data. The expanding number of chemicals found in commerce and the environment, coupled with time and resource requirements for traditional toxicity testing and exposure characterization, continue to underscore the need for new approaches. In 2005, EPA charted a new course to address this challenge by embracing computational toxicology (CompTox) and investing in the technologies and capabilities to push the field forward. The return on this investment has been demonstrated through results and applications across a range of human and environmental health problems, as well as initial application to regulatory decision-making within programs such as the EPA's Endocrine Disruptor Screening Program. The CompTox initiative at EPA is more than a decade old. This manuscript presents a blueprint to guide the strategic and operational direction over the next 5 years. The primary goal is to obtain broader acceptance of the CompTox approaches for application to higher tier regulatory decisions, such as chemical assessments. To achieve this goal, the blueprint expands and refines the use of high-throughput and computational modeling approaches to transform the components in chemical risk assessment, while systematically addressing key challenges that have hindered progress. In addition, the blueprint outlines additional investments in cross-cutting efforts to characterize uncertainty and variability, develop software and information technology tools, provide outreach and training, and establish scientific confidence for application to different public health and environmental regulatory decisions.
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Affiliation(s)
- Russell S. Thomas
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Tina Bahadori
- National Center for Environmental Assessment, Office of Research and Development, US Environmental Protection Agency
| | - Timothy J. Buckley
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - John Cowden
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Chad Deisenroth
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Kathie L. Dionisio
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Jeffrey B. Frithsen
- Chemical Safety for Sustainability National Research Program, Office of Research and Development, US Environmental Protection Agency
| | - Christopher M. Grulke
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Maureen R. Gwinn
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Joshua A. Harrill
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Mark Higuchi
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Keith A. Houck
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Michael F. Hughes
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - E. Sidney Hunter
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Kristin K. Isaacs
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Richard S. Judson
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Thomas B. Knudsen
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Jason C. Lambert
- National Center for Environmental Assessment, Office of Research and Development, US Environmental Protection Agency
| | - Monica Linnenbrink
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Todd M. Martin
- National Risk Management Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Seth R. Newton
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Stephanie Padilla
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Grace Patlewicz
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Katie Paul-Friedman
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Katherine A. Phillips
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Ann M. Richard
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Reeder Sams
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Timothy J. Shafer
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - R. Woodrow Setzer
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Imran Shah
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Jane E. Simmons
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Steven O. Simmons
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Amar Singh
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Jon R. Sobus
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Mark Strynar
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Adam Swank
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Rogelio Tornero-Valez
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Elin M. Ulrich
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Daniel L Villeneuve
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - John F. Wambaugh
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Barbara A. Wetmore
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Antony J. Williams
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
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20
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Estimating uncertainty in the context of new approach methodologies for potential use in chemical safety evaluation. CURRENT OPINION IN TOXICOLOGY 2019. [DOI: 10.1016/j.cotox.2019.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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21
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Abstract
The more than 80,000 chemicals in commerce present a challenge for hazard assessments that toxicity testing in the 21st century strives to address through high-throughput screening (HTS) assays. Assessing chemical effects on human development adds an additional layer of complexity to the screening, with a need to capture complex and dynamic events essential for proper embryo-fetal development. HTS data from ToxCast/Tox21 informs systems toxicology models, which incorporate molecular targets and biological pathways into mechanistic models describing the effects of chemicals on human cells, 3D organotypic culture models, and small model organisms. Adverse Outcome Pathways (AOPs) provide a useful framework for integrating the evidence derived from these in silico and in vitro systems to inform chemical hazard characterization. To illustrate this formulation, we have built an AOP for developmental toxicity through a mode of action linked to embryonic vascular disruption (Aop43). Here, we review the model for quantitative prediction of developmental vascular toxicity from ToxCast HTS data and compare the HTS results to functional vascular development assays in complex cell systems, virtual tissues, and small model organisms. ToxCast HTS predictions from several published and unpublished assays covering different aspects of the angiogenic cycle were generated for a test set of 38 chemicals representing a range of putative vascular disrupting compounds (pVDCs). Results boost confidence in the capacity to predict adverse developmental outcomes from HTS in vitro data and model computational dynamics for in silico reconstruction of developmental systems biology. Finally, we demonstrate the integration of the AOP and developmental systems toxicology to investigate the unique modes of action of two angiogenesis inhibitors.
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Honda GS, Pearce RG, Pham LL, Setzer RW, Wetmore BA, Sipes NS, Gilbert J, Franz B, Thomas RS, Wambaugh JF. Using the concordance of in vitro and in vivo data to evaluate extrapolation assumptions. PLoS One 2019; 14:e0217564. [PMID: 31136631 PMCID: PMC6538186 DOI: 10.1371/journal.pone.0217564] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/14/2019] [Indexed: 12/16/2022] Open
Abstract
Linking in vitro bioactivity and in vivo toxicity on a dose basis enables the use of high-throughput in vitro assays as an alternative to traditional animal studies. In this study, we evaluated assumptions in the use of a high-throughput, physiologically based toxicokinetic (PBTK) model to relate in vitro bioactivity and rat in vivo toxicity data. The fraction unbound in plasma (fup) and intrinsic hepatic clearance (Clint) were measured for rats (for 67 and 77 chemicals, respectively), combined with fup and Clint literature data for 97 chemicals, and incorporated in the PBTK model. Of these chemicals, 84 had corresponding in vitro ToxCast bioactivity data and in vivo toxicity data. For each possible comparison of in vitro and in vivo endpoint, the concordance between the in vivo and in vitro data was evaluated by a regression analysis. For a base set of assumptions, the PBTK results were more frequently better associated than either the results from a “random” model parameterization or direct comparison of the “untransformed” values of AC50 and dose (performed best in 51%, 28%, and 21% of cases, respectively). We also investigated several assumptions in the application of PBTK for IVIVE, including clearance and internal dose selection. One of the better assumptions sets–restrictive clearance and comparing free in vivo venous plasma concentration with free in vitro concentration–outperformed the random and untransformed results in 71% of the in vitro-in vivo endpoint comparisons. These results demonstrate that applying PBTK improves our ability to observe the association between in vitro bioactivity and in vivo toxicity data in general. This suggests that potency values from in vitro screening should be transformed using in vitro-in vivo extrapolation (IVIVE) to build potentially better machine learning and other statistical models for predicting in vivo toxicity in humans.
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Affiliation(s)
- Gregory S. Honda
- National Center for Computational Toxicology, U.S. EPA, Research Triangle Park, North Carolina, United States of America
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | - Robert G. Pearce
- National Center for Computational Toxicology, U.S. EPA, Research Triangle Park, North Carolina, United States of America
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | - Ly L. Pham
- National Center for Computational Toxicology, U.S. EPA, Research Triangle Park, North Carolina, United States of America
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | - R. W. Setzer
- National Center for Computational Toxicology, U.S. EPA, Research Triangle Park, North Carolina, United States of America
| | - Barbara A. Wetmore
- National Exposure Research Laboratory, U.S. EPA, Research Triangle Park, North Carolina, United States of America
| | - Nisha S. Sipes
- Division of the National Toxicology Program, NIEHS, Research Triangle Park, North Carolina, United States of America
| | - Jon Gilbert
- Cyprotex, Watertown, MA, United States of America
| | - Briana Franz
- Cyprotex, Watertown, MA, United States of America
| | - Russell S. Thomas
- National Center for Computational Toxicology, U.S. EPA, Research Triangle Park, North Carolina, United States of America
| | - John F. Wambaugh
- National Center for Computational Toxicology, U.S. EPA, Research Triangle Park, North Carolina, United States of America
- * E-mail:
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23
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From mRNA Expression of Drug Disposition Genes to In Vivo Assessment of CYP-Mediated Biotransformation during Zebrafish Embryonic and Larval Development. Int J Mol Sci 2018; 19:ijms19123976. [PMID: 30544719 PMCID: PMC6321216 DOI: 10.3390/ijms19123976] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 12/07/2018] [Indexed: 12/14/2022] Open
Abstract
The zebrafish (Danio rerio) embryo is currently explored as an alternative for developmental toxicity testing. As maternal metabolism is lacking in this model, knowledge of the disposition of xenobiotics during zebrafish organogenesis is pivotal in order to correctly interpret the outcome of teratogenicity assays. Therefore, the aim of this study was to assess cytochrome P450 (CYP) activity in zebrafish embryos and larvae until 14 d post-fertilization (dpf) by using a non-specific CYP substrate, i.e., benzyloxy-methyl-resorufin (BOMR) and a CYP1-specific substrate, i.e., 7-ethoxyresorufin (ER). Moreover, the constitutive mRNA expression of CYP1A, CYP1B1, CYP1C1, CYP1C2, CYP2K6, CYP3A65, CYP3C1, phase II enzymes uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) and sulfotransferase 1st1 (SULT1ST1), and an ATP-binding cassette (ABC) drug transporter, i.e., abcb4, was assessed during zebrafish development until 32 dpf by means of quantitative PCR (qPCR). The present study showed that trancripts and/or the activity of these proteins involved in disposition of xenobiotics are generally low to undetectable before 72 h post-fertilization (hpf), which has to be taken into account in teratogenicity testing. Full capacity appears to be reached by the end of organogenesis (i.e., 120 hpf), although CYP1-except CYP1A-and SULT1ST1 were shown to be already mature in early embryonic development.
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Saili KS, Zurlinden TJ, Schwab AJ, Silvin A, Baker NC, Hunter ES, Ginhoux F, Knudsen TB. Blood-brain barrier development: Systems modeling and predictive toxicology. Birth Defects Res 2018; 109:1680-1710. [PMID: 29251840 DOI: 10.1002/bdr2.1180] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/12/2017] [Indexed: 01/17/2023]
Abstract
The blood-brain barrier (BBB) serves as a gateway for passage of drugs, chemicals, nutrients, metabolites, and hormones between vascular and neural compartments in the brain. Here, we review BBB development with regard to the microphysiology of the neurovascular unit (NVU) and the impact of BBB disruption on brain development. Our focus is on modeling these complex systems. Extant in silico models are available as tools to predict the probability of drug/chemical passage across the BBB; in vitro platforms for high-throughput screening and high-content imaging provide novel data streams for profiling chemical-biological interactions; and engineered human cell-based microphysiological systems provide empirical models with which to investigate the dynamics of NVU function. Computational models are needed that bring together kinetic and dynamic aspects of NVU function across gestation and under various physiological and toxicological scenarios. This integration will inform adverse outcome pathways to reduce uncertainty in translating in vitro data and in silico models for use in risk assessments that aim to protect neurodevelopmental health.
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Affiliation(s)
- Katerine S Saili
- National Center for Computational Toxicology (NCCT); U.S. Environmental Protection Agency, Office of Research and Development, Research Triangle Park, North Carolina 27711
| | - Todd J Zurlinden
- National Center for Computational Toxicology (NCCT); U.S. Environmental Protection Agency, Office of Research and Development, Research Triangle Park, North Carolina 27711
| | - Andrew J Schwab
- National Health and Environmental Effects Research Laboratory (NHEERL), U.S. Environmental Protection Agency, Office of Research and Development, Research Triangle Park, North Carolina 27711
| | - Aymeric Silvin
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 138648, Singapore
| | - Nancy C Baker
- Leidos, contractor to NCCT, Research Triangle Park, North Carolina 27711
| | - E Sidney Hunter
- National Health and Environmental Effects Research Laboratory (NHEERL), U.S. Environmental Protection Agency, Office of Research and Development, Research Triangle Park, North Carolina 27711
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 138648, Singapore
| | - Thomas B Knudsen
- National Center for Computational Toxicology (NCCT); U.S. Environmental Protection Agency, Office of Research and Development, Research Triangle Park, North Carolina 27711
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25
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Phillips KA, Yau A, Favela KA, Isaacs KK, McEachran A, Grulke C, Richard AM, Williams AJ, Sobus JR, Thomas RS, Wambaugh JF. Suspect Screening Analysis of Chemicals in Consumer Products. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3125-3135. [PMID: 29405058 PMCID: PMC6168952 DOI: 10.1021/acs.est.7b04781] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A two-dimensional gas chromatography-time-of-flight/mass spectrometry (GC×GC-TOF/MS) suspect screening analysis method was used to rapidly characterize chemicals in 100 consumer products-which included formulations (e.g., shampoos, paints), articles (e.g., upholsteries, shower curtains), and foods (cereals)-and therefore supports broader efforts to prioritize chemicals based on potential human health risks. Analyses yielded 4270 unique chemical signatures across the products, with 1602 signatures tentatively identified using the National Institute of Standards and Technology 2008 spectral database. Chemical standards confirmed the presence of 119 compounds. Of the 1602 tentatively identified chemicals, 1404 were not present in a public database of known consumer product chemicals. Reported data and model predictions of chemical functional use were applied to evaluate the tentative chemical identifications. Estimated chemical concentrations were compared to manufacturer-reported values and other measured data. Chemical presence and concentration data can now be used to improve estimates of chemical exposure, and refine estimates of risk posed to human health and the environment.
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Affiliation(s)
- Katherine A. Phillips
- National Exposure Research Laboratory U.S. Environmental Protection Agency, Office of Research and Development, 109 T. W. Alexander Drive, RTP, NC USA 27711
| | - Alice Yau
- Southwest Research Institute, San Antonio, TX
| | | | - Kristin K. Isaacs
- National Exposure Research Laboratory U.S. Environmental Protection Agency, Office of Research and Development, 109 T. W. Alexander Drive, RTP, NC USA 27711
| | - Andrew McEachran
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, USA 37830
- National Center for Computational Toxicology U.S. Environmental Protection Agency, Office of Research and Development, 109 T. W. Alexander Drive, RTP, NC USA 27711
| | - Christopher Grulke
- National Center for Computational Toxicology U.S. Environmental Protection Agency, Office of Research and Development, 109 T. W. Alexander Drive, RTP, NC USA 27711
| | - Ann M. Richard
- National Center for Computational Toxicology U.S. Environmental Protection Agency, Office of Research and Development, 109 T. W. Alexander Drive, RTP, NC USA 27711
| | - Antony J. Williams
- National Center for Computational Toxicology U.S. Environmental Protection Agency, Office of Research and Development, 109 T. W. Alexander Drive, RTP, NC USA 27711
| | - Jon R. Sobus
- National Exposure Research Laboratory U.S. Environmental Protection Agency, Office of Research and Development, 109 T. W. Alexander Drive, RTP, NC USA 27711
| | - Russell S. Thomas
- National Center for Computational Toxicology U.S. Environmental Protection Agency, Office of Research and Development, 109 T. W. Alexander Drive, RTP, NC USA 27711
| | - John F. Wambaugh
- National Center for Computational Toxicology U.S. Environmental Protection Agency, Office of Research and Development, 109 T. W. Alexander Drive, RTP, NC USA 27711
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26
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Truong L, Ouedraogo G, Pham L, Clouzeau J, Loisel-Joubert S, Blanchet D, Noçairi H, Setzer W, Judson R, Grulke C, Mansouri K, Martin M. Predicting in vivo effect levels for repeat-dose systemic toxicity using chemical, biological, kinetic and study covariates. Arch Toxicol 2018; 92:587-600. [PMID: 29075892 PMCID: PMC5818596 DOI: 10.1007/s00204-017-2067-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/18/2017] [Indexed: 11/29/2022]
Abstract
In an effort to address a major challenge in chemical safety assessment, alternative approaches for characterizing systemic effect levels, a predictive model was developed. Systemic effect levels were curated from ToxRefDB, HESS-DB and COSMOS-DB from numerous study types totaling 4379 in vivo studies for 1247 chemicals. Observed systemic effects in mammalian models are a complex function of chemical dynamics, kinetics, and inter- and intra-individual variability. To address this complex problem, systemic effect levels were modeled at the study-level by leveraging study covariates (e.g., study type, strain, administration route) in addition to multiple descriptor sets, including chemical (ToxPrint, PaDEL, and Physchem), biological (ToxCast), and kinetic descriptors. Using random forest modeling with cross-validation and external validation procedures, study-level covariates alone accounted for approximately 15% of the variance reducing the root mean squared error (RMSE) from 0.96 log10 to 0.85 log10 mg/kg/day, providing a baseline performance metric (lower expectation of model performance). A consensus model developed using a combination of study-level covariates, chemical, biological, and kinetic descriptors explained a total of 43% of the variance with an RMSE of 0.69 log10 mg/kg/day. A benchmark model (upper expectation of model performance) was also developed with an RMSE of 0.5 log10 mg/kg/day by incorporating study-level covariates and the mean effect level per chemical. To achieve a representative chemical-level prediction, the minimum study-level predicted and observed effect level per chemical were compared reducing the RMSE from 1.0 to 0.73 log10 mg/kg/day, equivalent to 87% of predictions falling within an order-of-magnitude of the observed value. Although biological descriptors did not improve model performance, the final model was enriched for biological descriptors that indicated xenobiotic metabolism gene expression, oxidative stress, and cytotoxicity, demonstrating the importance of accounting for kinetics and non-specific bioactivity in predicting systemic effect levels. Herein, we generated an externally predictive model of systemic effect levels for use as a safety assessment tool and have generated forward predictions for over 30,000 chemicals.
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Affiliation(s)
- Lisa Truong
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
- Currently at Oregon State University, Corvallis, USA
| | - Gladys Ouedraogo
- L'Oréal Safety Research Department, 1 Avenue E. Schueller, 93600, Aulnay-Sous-Bois, France
| | - LyLy Pham
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Jacques Clouzeau
- L'Oréal Safety Research Department, 1 Avenue E. Schueller, 93600, Aulnay-Sous-Bois, France
| | - Sophie Loisel-Joubert
- L'Oréal Safety Research Department, 1 Avenue E. Schueller, 93600, Aulnay-Sous-Bois, France
| | - Delphine Blanchet
- L'Oréal Safety Research Department, 1 Avenue E. Schueller, 93600, Aulnay-Sous-Bois, France
| | - Hicham Noçairi
- L'Oréal Safety Research Department, 1 Avenue E. Schueller, 93600, Aulnay-Sous-Bois, France
| | - Woodrow Setzer
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Richard Judson
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Chris Grulke
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Kamel Mansouri
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
- Currently at Scitovation LLC, Research Triangle Park, NC, USA
| | - Matthew Martin
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, 27711, USA.
- Currently at Pfizer, Inc, Drug Safety Research and Development, 445 Eastern Point Road, MS 8274-1224, Groton, CT, 06340, USA.
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27
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Teixidó E, Krupp E, Amberg A, Czich A, Scholz S. Species-specific developmental toxicity in rats and rabbits: Generation of a reference compound list for development of alternative testing approaches. Reprod Toxicol 2018; 76:93-102. [PMID: 29409988 DOI: 10.1016/j.reprotox.2018.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/05/2017] [Accepted: 01/26/2018] [Indexed: 11/19/2022]
Abstract
For regulatory information requirements, developmental toxicity testing is often conducted in two mammalian species. In order to provide a set of reference compounds that could be used to explore alternative approaches to supersede testing in a second species, a retrospective data analysis was conducted. The aim was to identify compounds for which species sensitivity differences between rats and rabbits are not caused by maternal toxicity or toxicokinetic differences. A total of 330 compounds were analysed and classified according to their species-specific differences. A lack of concordance between rat and rabbit was observed in 24% of the compounds, of which 10% were found to be selective developmental toxicants in one of the species. In contrast to previously published analyses the presented comparison is based entirely on publically data allowing validating and comparing alternative approaches for developmental toxicity testing. Furthermore, this list could be useful to identify mechanisms leading to species differences.
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Affiliation(s)
- E Teixidó
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| | - E Krupp
- Sanofi-Aventis Deutschland GmbH, Preclinical Safety, Industriepark Hoechst, D-65926, Frankfurt am Main, Germany
| | - A Amberg
- Sanofi-Aventis Deutschland GmbH, Preclinical Safety, Industriepark Hoechst, D-65926, Frankfurt am Main, Germany
| | - A Czich
- Sanofi-Aventis Deutschland GmbH, Preclinical Safety, Industriepark Hoechst, D-65926, Frankfurt am Main, Germany
| | - S Scholz
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
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28
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Baker N, Boobis A, Burgoon L, Carney E, Currie R, Fritsche E, Knudsen T, Laffont M, Piersma AH, Poole A, Schneider S, Daston G. Building a developmental toxicity ontology. Birth Defects Res 2018; 110:502-518. [DOI: 10.1002/bdr2.1189] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nancy Baker
- Lockheed Martin, Research Triangle Park; Piedmont North Carolina
| | - Alan Boobis
- Department of Medicine; Imperial College London; London United Kingdom
| | - Lyle Burgoon
- U.S. Army Engineer Research and Development Center; Raleigh-Durham North Carolina
| | | | | | | | - Thomas Knudsen
- U.S. Environmental Protection Agency; Research Triangle Park; Piedmont North Carolina
| | - Madeleine Laffont
- European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC); Brussels Belgium
| | - Aldert H. Piersma
- Center for Health Protection; National Institute for Public Health and the Environment (RIVM), Bilthoven, and Institute for Risk Assessment Sciences (IRAS), Utrecht University; Utrecht The Netherlands
| | - Alan Poole
- European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC); Brussels Belgium
| | | | - George Daston
- Central Product Safety Department; The Procter & Gamble Company; Mason Ohio
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29
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Yamaguchi A, Ishibashi H, Kono S, Iida M, Uchida M, Arizono K, Tominaga N. Nanosecond pulsed electric field incorporation technique to predict molecular mechanisms of teratogenicity and developmental toxicity of estradiol-17β on medaka embryos. J Appl Toxicol 2017; 38:714-723. [PMID: 29280155 DOI: 10.1002/jat.3579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/23/2017] [Accepted: 11/23/2017] [Indexed: 01/08/2023]
Abstract
Herein, we propose using a nanosecond pulsed electric field (nsPEF) technique to assess teratogenicity and embryonic developmental toxicity of estradiol-17β (E2 ) and predict the molecular mechanisms of teratogenicity and embryonic developmental defects caused by E2 on medaka (Oryzias latipes). The 5 hour post-fertilization embryos were exposed to co-treatment with 10 μm E2 and nsPEF for 2 hours and then continuously cultured under non-E2 and nsPEF conditions until hatching. Results documented that the time to hatching of embryos was significantly delayed in comparison to the control group and that typical abnormal embryo development, such as the delay of blood vessel formation, was observed. For DNA microarray analysis, 6 day post-fertilization embryos that had been continuously cultured under the non-E2 and nsPEF condition after 2 hour co-treatments were used. DNA microarray analysis identified 542 upregulated genes and one downregulated gene in the 6 day post-fertilization embryos. Furthermore, bioinformatic analyses using differentially expressed genes revealed that E2 exposure affected various gene ontology terms, such as response to hormone stimulus. The network analysis also documented that the estrogen receptor α in the mitogen-activated protein kinase signaling pathway may be involved in regulating several transcription factors, such as FOX, AKT1 and epidermal growth factor receptor. These results suggest that our nsPEF technique is a powerful tool for assessing teratogenicity and embryonic developmental toxicity of E2 and predict their molecular mechanisms in medaka embryos.
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Affiliation(s)
- Akemi Yamaguchi
- Department of Creative Engineering, National Institute of Technology, Ariake College, 150 Higashi-Hagio, Omuta, Fukuoka, 836-8585, Japan
| | - Hiroshi Ishibashi
- Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, 790-8566, Japan
| | - Susumu Kono
- Department of Creative Engineering, National Institute of Technology, Ariake College, 150 Higashi-Hagio, Omuta, Fukuoka, 836-8585, Japan
| | - Midori Iida
- Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-0067, Japan
| | - Masaya Uchida
- Department of Creative Engineering, National Institute of Technology, Ariake College, 150 Higashi-Hagio, Omuta, Fukuoka, 836-8585, Japan.,Mizuki Biotech, Co., Ltd., 1-1 Hyakunenkouen, Kurume, Fukuoka, 839-0864, Japan
| | - Koji Arizono
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, 3-1-100 Tsukide, Higashi-ku, Kumamoto, 862-8502, Japan
| | - Nobuaki Tominaga
- Department of Creative Engineering, National Institute of Technology, Ariake College, 150 Higashi-Hagio, Omuta, Fukuoka, 836-8585, Japan
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30
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Beekhuijzen M. The era of 3Rs implementation in developmental and reproductive toxicity (DART) testing: Current overview and future perspectives. Reprod Toxicol 2017; 72:86-96. [PMID: 28552675 DOI: 10.1016/j.reprotox.2017.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/07/2017] [Accepted: 05/19/2017] [Indexed: 11/29/2022]
Abstract
Since adoption of the first globally implemented guidelines for developmental and reproductive toxicity (DART) testing for pharmaceuticals, industrial chemicals and agrochemicals, many years passed without major updates. However in recent years, significant changes in these guidelines have been made or are being implemented. These changes have been guided by the ethical drive to reduce, refine and replace (3R) animal testing, as well as the addition of endocrine disruptor relevant endpoints. Recent applied improvements have focused on reduction and refinement. Ongoing scientific and technical innovations will provide the means for replacement of animal testing in the future and will improve predictivity in humans. The aim of this review is to provide an overview of ongoing global DART endeavors in respect to the 3Rs, with an outlook towards future advances in DART testing aspiring to reduce animal testing to a minimum and the supreme ambition towards animal-free hazard and risk assessment.
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31
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Judson RS, Martin MT, Patlewicz G, Wood CE. Retrospective mining of toxicology data to discover multispecies and chemical class effects: Anemia as a case study. Regul Toxicol Pharmacol 2017; 86:74-92. [PMID: 28242142 DOI: 10.1016/j.yrtph.2017.02.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/19/2016] [Accepted: 02/18/2017] [Indexed: 12/13/2022]
Abstract
Predictive toxicity models rely on large amounts of accurate in vivo data. Here, we analyze the quality of in vivo data from the U.S. EPA Toxicity Reference Database (ToxRefDB), using chemical-induced anemia as an example. Considerations include variation in experimental conditions, changes in terminology over time, distinguishing negative from missing results, observer and diagnostic bias, and data transcription errors. Within ToxRefDB, we use hematological data on 658 chemicals tested in one or more of 1738 studies (subchronic rat or chronic rat, mouse, or dog). Anemia was reported most frequently in the rat subchronic studies, followed by chronic studies in dog, rat, and then mouse. Concordance between studies for a positive finding of anemia (same chemical, different laboratories) ranged from 90% (rat subchronic predicting rat chronic) to 40% (mouse chronic predicting rat chronic). Concordance increased with manual curation by 20% on average. We identified 49 chemicals that showed an anemia phenotype in at least two species. These included 14 aniline moiety-containing compounds that were further analyzed for their potential to be metabolically transformed into substituted anilines, which are known anemia-causing chemicals. This analysis should help inform future use of in vivo databases for model development.
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Affiliation(s)
- Richard S Judson
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA.
| | - Matthew T Martin
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Grace Patlewicz
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Charles E Wood
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
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32
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Theunissen PT, Beken S, Beyer B, Breslin WJ, Cappon GD, Chen CL, Chmielewski G, de Schaepdrijver L, Enright B, Foreman JE, Harrouk W, Hew KW, Hoberman AM, Y Hui J, Knudsen TB, Laffan SB, Makris SL, Martin M, McNerney ME, Siezen CL, Stanislaus DJ, Stewart J, Thompson KE, Tornesi B, Van der Laan JW, Weinbauer GF, Wood S, Piersma AH. Comparing rat and rabbit embryo-fetal developmental toxicity data for 379 pharmaceuticals: on systemic dose and developmental effects. Crit Rev Toxicol 2016; 47:402-414. [PMID: 27766926 DOI: 10.1080/10408444.2016.1224808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A database of embryo-fetal developmental toxicity (EFDT) studies of 379 pharmaceutical compounds in rat and rabbit was analyzed for species differences based on toxicokinetic parameters of area under the curve (AUC) and maximum concentration (Cmax) at the developmental lowest adverse effect level (dLOAEL). For the vast majority of cases (83% based on AUC of n = 283), dLOAELs in rats and rabbits were within the same order of magnitude (less than 10-fold different) when compared based on available data on AUC and Cmax exposures. For 13.5% of the compounds the rabbit was more sensitive and for 3.5% of compounds the rat was more sensitive when compared based on AUC exposures. For 12% of the compounds the rabbit was more sensitive and for 1.3% of compounds the rat was more sensitive based on Cmax exposures. When evaluated based on human equivalent dose (HED) conversion using standard factors, the rat and rabbit were equally sensitive. The relative extent of embryo-fetal toxicity in the presence of maternal toxicity was not different between species. Overall effect severity incidences were distributed similarly in rat and rabbit studies. Individual rat and rabbit strains did not show a different general distribution of systemic exposure LOAELs as compared to all strains combined for each species. There were no apparent species differences in the occurrence of embryo-fetal variations. Based on power of detection and given differences in the nature of developmental effects between rat and rabbit study outcomes for individual compounds, EFDT studies in two species have added value over single studies.
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Affiliation(s)
- Peter T Theunissen
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , The Netherlands.,b Medicines Evaluation Board , Utrecht , The Netherlands.,c Innovative Testing in Life Sciences and Chemistry , University of Applied Sciences Utrecht (HU) , Utrecht , The Netherlands
| | - Sonia Beken
- d Federal Agency for Medicines and Health Products , Brussels , Belgium
| | | | - William J Breslin
- f Lilly Research Laboratories, Lilly Corporate Center , Indianapolis , IN , USA
| | - Gregg D Cappon
- g Pfizer Worldwide Research & Development , Groton , CT , USA
| | - Connie L Chen
- h ILSI-Health and Environmental Sciences Institute , Washington , DC , USA
| | | | | | | | | | - Wafa Harrouk
- m US Food & Drug Administration , Silver Spring , MD , USA
| | - Kok-Wah Hew
- n Takeda Pharmaceutical Company , Deerfield , IL , USA
| | - Alan M Hoberman
- o Preclinical Services , Charles-River Laboratories , Horsham , PA , USA
| | | | - Thomas B Knudsen
- q US Environmental Protection Agency, National Center for Computational Toxicology , Research Triangle Park , NC , USA
| | - Susan B Laffan
- r Safety Assessment , GlaxoSmithKline , King of Prussia , PA , USA
| | - Susan L Makris
- s National Center for Environmental Assessment, US Environmental Protection Agency , Washington , DC , USA
| | - Matthew Martin
- q US Environmental Protection Agency, National Center for Computational Toxicology , Research Triangle Park , NC , USA
| | | | | | | | - Jane Stewart
- u Drug Safety & Metabolism , AstraZeneca , Macclesfield , UK
| | - Kary E Thompson
- t Drug Safety Evaluation , Bristol-Myers Squibb , New Brunswick , NJ , USA
| | | | - Jan Willem Van der Laan
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , The Netherlands.,b Medicines Evaluation Board , Utrecht , The Netherlands
| | | | - Sandra Wood
- w Merck Research Laboratories , Upper Gwynedd , PA , USA
| | - Aldert H Piersma
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , The Netherlands.,x Faculty of Veterinary Sciences , Institute for Risk Assessment Sciences, Utrecht University , Utrecht , The Netherlands
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Theunissen PT, Beken S, Beyer BK, Breslin WJ, Cappon GD, Chen CL, Chmielewski G, De Schaepdrijver L, Enright B, Foreman JE, Harrouk W, Hew KW, Hoberman AM, Hui JY, Knudsen TB, Laffan SB, Makris SL, Martin M, McNerney ME, Siezen CL, Stanislaus DJ, Stewart J, Thompson KE, Tornesi B, Van der Laan JW, Weinbauer GF, Wood S, Piersma AH. Comparison of rat and rabbit embryo-fetal developmental toxicity data for 379 pharmaceuticals: on the nature and severity of developmental effects. Crit Rev Toxicol 2016; 46:900-910. [PMID: 27848393 PMCID: PMC8865449 DOI: 10.1080/10408444.2016.1224807] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regulatory non-clinical safety testing of human pharmaceuticals typically requires embryo–fetal developmental toxicity (EFDT) testing in two species (one rodent and one non-rodent). The question has been raised whether under some conditions EFDT testing could be limited to one species, or whether the testing in a second species could be decided on a case-by-case basis. As part of a consortium initiative, we built and queried a database of 379 compounds with EFDT studies (in both rat and rabbit animal models) conducted for marketed and non-marketed pharmaceuticals for their potential for adverse developmental and maternal outcomes, including EFDT incidence and the nature and severity of adverse findings. Manifestation of EFDT in either one or both species was demonstrated for 282 compounds (74%). EFDT was detected in only one species (rat or rabbit) in almost a third (31%, 118 compounds), with 58% (68 compounds) of rat studies and 42% (50 compounds) of rabbit studies identifying an EFDT signal. For 24 compounds (6%), fetal malformations were observed in one species (rat or rabbit) in the absence of any EFDT in the second species. In general, growth retardation, fetal variations, and malformations were more prominent in the rat, whereas embryo–fetal death was observed more often in the rabbit. Discordance across species may be attributed to factors such as maternal toxicity, study design differences, pharmacokinetic differences, and pharmacologic relevance of species. The current analysis suggests that in general both species are equally sensitive on the basis of an overall EFDT LOAEL comparison, but selective EFDT toxicity in one species is not uncommon. Also, there appear to be species differences in the prevalence of various EFDT manifestations (i.e. embryo–fetal death, growth retardation, and dysmorphogenesis) between rat and rabbit, suggesting that the use of both species has a higher probability of detecting developmental toxicants than either one alone.
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Affiliation(s)
- Peter T Theunissen
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , The Netherlands.,b Medicines Evaluation Board , Utrecht , The Netherlands.,c Innovative Testing in Life Sciences and Chemistry, University of Applied Sciences Utrecht (HU) , Utrecht , The Netherlands
| | - Sonja Beken
- d Federal Agency for Medicines and Health Products , Brussels , Belgium
| | | | - William J Breslin
- f Lilly Research Laboratories , Lilly Corporate Center , Indianapolis , IN , USA
| | - Gregg D Cappon
- g Pfizer Worldwide Research & Development , Groton , CT , USA
| | - Connie L Chen
- h ILSI-Health and Environmental Sciences Institute , Washington , DC , USA
| | | | | | | | | | - Wafa Harrouk
- m U.S. Food & Drug Administration , Silver Spring , MD , USA
| | - Kok-Wah Hew
- n Takeda Pharmaceutical Company , Deerfield , IL , USA
| | - Alan M Hoberman
- o Charles-River Laboratories, Preclinical Services , Horsham , PA , USA
| | | | - Thomas B Knudsen
- q U.S. Environmental Protection Agency, National Center for Computational Toxicology, Research Triangle Park , NC , USA
| | - Susan B Laffan
- r Safety Assessment, GlaxoSmithKline , King of Prussia , PA , USA
| | - Susan L Makris
- s U.S. Environmental Protection Agency, National Center for Environmental Assessment , Washington , DC , USA
| | - Matt Martin
- q U.S. Environmental Protection Agency, National Center for Computational Toxicology, Research Triangle Park , NC , USA
| | | | | | | | - Jane Stewart
- u Drug Safety & Metabolism, AstraZeneca , Macclesfield , UK
| | - Kary E Thompson
- t Drug Safety Evaluation, Bristol-Myers Squibb , New Brunswick , NJ , USA
| | | | - Jan Willem Van der Laan
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , The Netherlands.,b Medicines Evaluation Board , Utrecht , The Netherlands
| | | | - Sandra Wood
- w Merck Research Laboratories , Upper Gwynedd , Pennsylvania , USA
| | - Aldert H Piersma
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , The Netherlands.,x Institute for Risk Assessment Sciences, Faculty of Veterinary Sciences , Utrecht University , Utrecht , The Netherlands
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Richard AM, Judson RS, Houck KA, Grulke CM, Volarath P, Thillainadarajah I, Yang C, Rathman J, Martin MT, Wambaugh JF, Knudsen TB, Kancherla J, Mansouri K, Patlewicz G, Williams AJ, Little SB, Crofton KM, Thomas RS. ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology. Chem Res Toxicol 2016; 29:1225-51. [PMID: 27367298 DOI: 10.1021/acs.chemrestox.6b00135] [Citation(s) in RCA: 381] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The U.S. Environmental Protection Agency's (EPA) ToxCast program is testing a large library of Agency-relevant chemicals using in vitro high-throughput screening (HTS) approaches to support the development of improved toxicity prediction models. Launched in 2007, Phase I of the program screened 310 chemicals, mostly pesticides, across hundreds of ToxCast assay end points. In Phase II, the ToxCast library was expanded to 1878 chemicals, culminating in the public release of screening data at the end of 2013. Subsequent expansion in Phase III has resulted in more than 3800 chemicals actively undergoing ToxCast screening, 96% of which are also being screened in the multi-Agency Tox21 project. The chemical library unpinning these efforts plays a central role in defining the scope and potential application of ToxCast HTS results. The history of the phased construction of EPA's ToxCast library is reviewed, followed by a survey of the library contents from several different vantage points. CAS Registry Numbers are used to assess ToxCast library coverage of important toxicity, regulatory, and exposure inventories. Structure-based representations of ToxCast chemicals are then used to compute physicochemical properties, substructural features, and structural alerts for toxicity and biotransformation. Cheminformatics approaches using these varied representations are applied to defining the boundaries of HTS testability, evaluating chemical diversity, and comparing the ToxCast library to potential target application inventories, such as used in EPA's Endocrine Disruption Screening Program (EDSP). Through several examples, the ToxCast chemical library is demonstrated to provide comprehensive coverage of the knowledge domains and target inventories of potential interest to EPA. Furthermore, the varied representations and approaches presented here define local chemistry domains potentially worthy of further investigation (e.g., not currently covered in the testing library or defined by toxicity "alerts") to strategically support data mining and predictive toxicology modeling moving forward.
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Affiliation(s)
- Ann M Richard
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Richard S Judson
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Keith A Houck
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Christopher M Grulke
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Patra Volarath
- Center for Food Safety and Nutrition, U.S. Food and Drug Administration , 5100 Paint Branch Parkway, College Park, Maryland 20740, United States
| | - Inthirany Thillainadarajah
- Senior Environmental Employment Program, U.S. Environmental Protection Agency , Research Triangle Park, Durham, North Carolina 27711, United States
| | - Chihae Yang
- Molecular Networks GmbH , Henkestraße 91, 91052 Erlangen, Germany.,Altamira, LLC , 1455 Candlewood Drive, Columbus, Ohio 43235, United States
| | - James Rathman
- Altamira, LLC , 1455 Candlewood Drive, Columbus, Ohio 43235, United States.,Department of Chemical and Biomolecular Engineering, The Ohio State University , 151 W. Woodruff Avenue, Columbus, Ohio 43210, United States
| | - Matthew T Martin
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - John F Wambaugh
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Thomas B Knudsen
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Jayaram Kancherla
- ORISE Fellow, U.S. Environmental Protection Agency, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Kamel Mansouri
- ORISE Fellow, U.S. Environmental Protection Agency, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Grace Patlewicz
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Antony J Williams
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Stephen B Little
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Kevin M Crofton
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
| | - Russell S Thomas
- National Center for Computational Toxicology, Office of Research & Development, U.S. Environmental Protection Agency , Mail Code B205-01, Research Triangle Park, Durham, North Carolina 27711, United States
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Leung MC, Phuong J, Baker NC, Sipes NS, Klinefelter GR, Martin MT, McLaurin KW, Setzer RW, Darney SP, Judson RS, Knudsen TB. Systems Toxicology of Male Reproductive Development: Profiling 774 Chemicals for Molecular Targets and Adverse Outcomes. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:1050-61. [PMID: 26662846 PMCID: PMC4937872 DOI: 10.1289/ehp.1510385] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/24/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Trends in male reproductive health have been reported for increased rates of testicular germ cell tumors, low semen quality, cryptorchidism, and hypospadias, which have been associated with prenatal environmental chemical exposure based on human and animal studies. OBJECTIVE In the present study we aimed to identify significant correlations between environmental chemicals, molecular targets, and adverse outcomes across a broad chemical landscape with emphasis on developmental toxicity of the male reproductive system. METHODS We used U.S. EPA's animal study database (ToxRefDB) and a comprehensive literature analysis to identify 774 chemicals that have been evaluated for adverse effects on male reproductive parameters, and then used U.S. EPA's in vitro high-throughput screening (HTS) database (ToxCastDB) to profile their bioactivity across approximately 800 molecular and cellular features. RESULTS A phenotypic hierarchy of testicular atrophy, sperm effects, tumors, and malformations, a composite resembling the human testicular dysgenesis syndrome (TDS) hypothesis, was observed in 281 chemicals. A subset of 54 chemicals with male developmental consequences had in vitro bioactivity on molecular targets that could be condensed into 156 gene annotations in a bipartite network. CONCLUSION Computational modeling of available in vivo and in vitro data for chemicals that produce adverse effects on male reproductive end points revealed a phenotypic hierarchy across animal studies consistent with the human TDS hypothesis. We confirmed the known role of estrogen and androgen signaling pathways in rodent TDS, and importantly, broadened the list of molecular targets to include retinoic acid signaling, vascular remodeling proteins, G-protein coupled receptors (GPCRs), and cytochrome P450s. CITATION Leung MC, Phuong J, Baker NC, Sipes NS, Klinefelter GR, Martin MT, McLaurin KW, Setzer RW, Darney SP, Judson RS, Knudsen TB. 2016. Systems toxicology of male reproductive development: profiling 774 chemicals for molecular targets and adverse outcomes. Environ Health Perspect 124:1050-1061; http://dx.doi.org/10.1289/ehp.1510385.
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Affiliation(s)
- Maxwell C.K. Leung
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
- National Center for Computational Toxicology, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
- Address correspondence to M.C.K. Leung, U.S. Environmental Protection Agency, 109 T.W. Alexander Dr., Research Triangle Park, NC 27711 USA. Telephone: (919) 541-2721. E-mail: , or T.B. Knudsen, U.S. Environmental Protection Agency, 109 T.W. Alexander Dr., Research Triangle Park, NC 27711 USA. Telephone: (919) 541-9776. E-mail:
| | - Jimmy Phuong
- National Center for Computational Toxicology, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
| | | | - Nisha S. Sipes
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
- National Center for Computational Toxicology, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
| | - Gary R. Klinefelter
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Research Triangle Park, North Carolina
| | - Matthew T. Martin
- National Center for Computational Toxicology, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
| | - Keith W. McLaurin
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
- National Center for Computational Toxicology, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
| | - R. Woodrow Setzer
- National Center for Computational Toxicology, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
| | - Sally Perreault Darney
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Research Triangle Park, North Carolina
| | - Richard S. Judson
- National Center for Computational Toxicology, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
| | - Thomas B. Knudsen
- National Center for Computational Toxicology, U.S. Environmental Protection Agency (EPA), Research Triangle Park, North Carolina
- Address correspondence to M.C.K. Leung, U.S. Environmental Protection Agency, 109 T.W. Alexander Dr., Research Triangle Park, NC 27711 USA. Telephone: (919) 541-2721. E-mail: , or T.B. Knudsen, U.S. Environmental Protection Agency, 109 T.W. Alexander Dr., Research Triangle Park, NC 27711 USA. Telephone: (919) 541-9776. E-mail:
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Boyd WA, Smith MV, Co CA, Pirone JR, Rice JR, Shockley KR, Freedman JH. Developmental Effects of the ToxCast™ Phase I and Phase II Chemicals in Caenorhabditis elegans and Corresponding Responses in Zebrafish, Rats, and Rabbits. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:586-93. [PMID: 26496690 PMCID: PMC4858399 DOI: 10.1289/ehp.1409645] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 10/08/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Modern toxicology is shifting from an observational to a mechanistic science. As part of this shift, high-throughput toxicity assays are being developed using alternative, nonmammalian species to prioritize chemicals and develop prediction models of human toxicity. METHODS The nematode Caenorhabditis elegans (C. elegans) was used to screen the U.S. Environmental Protection Agency's (EPA's) ToxCast™ Phase I and Phase II libraries, which contain 292 and 676 chemicals, respectively, for chemicals leading to decreased larval development and growth. Chemical toxicity was evaluated using three parameters: a biologically defined effect size threshold, half-maximal activity concentration (AC50), and lowest effective concentration (LEC). RESULTS Across both the Phase I and Phase II libraries, 62% of the chemicals were classified as active ≤ 200 μM in the C. elegans assay. Chemical activities and potencies in C. elegans were compared with those from two zebrafish embryonic development toxicity studies and developmental toxicity data for rats and rabbits. Concordance of chemical activity was higher between C. elegans and one zebrafish assay across Phase I chemicals (79%) than with a second zebrafish assay (59%). Using C. elegans or zebrafish to predict rat or rabbit developmental toxicity resulted in balanced accuracies (the average value of the sensitivity and specificity for an assay) ranging from 45% to 53%, slightly lower than the concordance between rat and rabbit (58%). CONCLUSIONS Here, we present an assay that quantitatively and reliably describes the effects of chemical toxicants on C. elegans growth and development. We found significant overlap in the activity of chemicals in the ToxCast™ libraries between C. elegans and zebrafish developmental screens. Incorporating C. elegans toxicological assays as part of a battery of in vitro and in vivo assays provides additional information for the development of models to predict a chemical's potential toxicity to humans. CITATION Boyd WA, Smith MV, Co CA, Pirone JR, Rice JR, Shockley KR, Freedman JH. 2016. Developmental effects of the ToxCast™ Phase I and II chemicals in Caenorhabditis elegans and corresponding responses in zebrafish, rats, and rabbits. Environ Health Perspect 124:586-593; http://dx.doi.org/10.1289/ehp.1409645.
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Affiliation(s)
- Windy A. Boyd
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | | | - Caroll A. Co
- Social & Scientific Systems Inc., Durham, North Carolina, USA
| | - Jason R. Pirone
- Social & Scientific Systems Inc., Durham, North Carolina, USA
| | - Julie R. Rice
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | | | - Jonathan H. Freedman
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
- Laboratory of Toxicology and Pharmacology, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina, USA
- Address correspondence to J.H. Freedman, Department of Toxicology and Pharmacology, University of Louisville School of Medicine, Room 1300, HSC-A, 500 S. Preston St., Louisville, KY 40202 USA (current address). Telephone: (502) 852-5348. E-mail:
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Basant N, Gupta S, Singh KP. In silico prediction of the developmental toxicity of diverse organic chemicals in rodents for regulatory purposes. Toxicol Res (Camb) 2016; 5:773-787. [PMID: 30090388 PMCID: PMC6061034 DOI: 10.1039/c5tx00493d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/10/2016] [Indexed: 11/21/2022] Open
Abstract
The experimental determination of the developmental toxicity potential (LEL) of chemicals is not only tedious, time and resource intensive, but it also involves unethical tests on animals. In this study, we have established quantitative structure activity relationship (QSAR) models for predicting the developmental toxicity potential of chemicals in rodents following the OECD guidelines. Accordingly, decision tree forest (DTF) and decision tree boost (DTB) based local (L-QSAR), global (G-QSAR) and interspecies quantitative structure activity-activity relationship (ISC QSAAR) models were developed for estimating the LEL (lowest effective level) dose of chemicals for developmental toxicity in rats and rabbits. The structural features of chemicals responsible for developmental toxicity in rodents were extracted and used in QSAR/QSAAR analysis. The external predictive power of the developed models was evaluated through the internal and external validation procedures. In test data, the L-QSAR models (DTF, DTB) yielded R2 values of >0.846 (rat) and >0.906 (rabbit), whereas in G-QSAR, the correlation value was >0.870 between the measured and predicted endpoint values. In ISC QSAAR models, the R2 values in test data were 0.830 (DTF) and 0.927 (DTB), respectively. Values of various statistical validation coefficients derived from the test data (except rm2 in DTF based rat L-QSAR and ISC QSAAR models) were above their respective threshold limits, thus putting a high confidence in this analysis. The prediction quality of the developed QSAR/QSAAR models was also assessed using the mean absolute error (MAE) criteria and found good. The applicability domains of the constructed models were defined using the descriptor range, leverage, and standardization approaches. The results suggest that the developed QSAR/QSAAR models can reliably predict the developmental toxicity potential of structurally diverse chemicals in rodents, generating useful toxicity data for risk assessment in humans.
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Affiliation(s)
| | - Shikha Gupta
- Environmental Chemistry Division , CSIR-Indian Institute of Toxicology Research , Post Box 80 , Mahatma Gandhi Marg , Lucknow-226 001 , India . ;
| | - Kunwar P Singh
- Environmental Chemistry Division , CSIR-Indian Institute of Toxicology Research , Post Box 80 , Mahatma Gandhi Marg , Lucknow-226 001 , India . ;
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Harlow PH, Perry SJ, Widdison S, Daniels S, Bondo E, Lamberth C, Currie RA, Flemming AJ. The nematode Caenorhabditis elegans as a tool to predict chemical activity on mammalian development and identify mechanisms influencing toxicological outcome. Sci Rep 2016; 6:22965. [PMID: 26987796 PMCID: PMC4796825 DOI: 10.1038/srep22965] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/19/2016] [Indexed: 01/08/2023] Open
Abstract
To determine whether a C. elegans bioassay could predict mammalian developmental activity, we selected diverse compounds known and known not to elicit such activity and measured their effect on C. elegans egg viability. 89% of compounds that reduced C. elegans egg viability also had mammalian developmental activity. Conversely only 25% of compounds found not to reduce egg viability in C. elegans were also inactive in mammals. We conclude that the C. elegans egg viability assay is an accurate positive predictor, but an inaccurate negative predictor, of mammalian developmental activity. We then evaluated C. elegans as a tool to identify mechanisms affecting toxicological outcomes among related compounds. The difference in developmental activity of structurally related fungicides in C. elegans correlated with their rate of metabolism. Knockdown of the cytochrome P450s cyp-35A3 and cyp-35A4 increased the toxicity to C. elegans of the least developmentally active compounds to the level of the most developmentally active. This indicated that these P450s were involved in the greater rate of metabolism of the less toxic of these compounds. We conclude that C. elegans based approaches can predict mammalian developmental activity and can yield plausible hypotheses for factors affecting the biological potency of compounds in mammals.
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Affiliation(s)
- Philippa H Harlow
- Syngenta Ltd., Jealott's Hill Research Station, Bracknell, Berkshire, RG42 6EY, UK
| | - Simon J Perry
- Syngenta Ltd., Jealott's Hill Research Station, Bracknell, Berkshire, RG42 6EY, UK
| | - Stephanie Widdison
- General Bioinformatics, Jealott's Hill Research Station, Bracknell, Berkshire, RG42 6EY, UK
| | - Shannon Daniels
- Syngenta, 3054 East Cornwallis Road, Research Triangle Park, NC 27709-2257, USA
| | - Eddie Bondo
- Syngenta, 3054 East Cornwallis Road, Research Triangle Park, NC 27709-2257, USA
| | - Clemens Lamberth
- Syngenta Crop Protection AG, Chemical Research, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - Richard A Currie
- Syngenta Ltd., Jealott's Hill Research Station, Bracknell, Berkshire, RG42 6EY, UK
| | - Anthony J Flemming
- Syngenta Ltd., Jealott's Hill Research Station, Bracknell, Berkshire, RG42 6EY, UK
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Rychert M, Wilkins C. The challenge of a ban on animal testing for the development of a regulated legal market for new psychoactive substances (NPS) (‘legal highs’) in New Zealand: Issues and options for resolution. THE INTERNATIONAL JOURNAL OF DRUG POLICY 2015; 26:1273-8. [DOI: 10.1016/j.drugpo.2015.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/05/2015] [Indexed: 11/28/2022]
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Hu B, Gifford E, Wang H, Bailey W, Johnson T. Analysis of the ToxCast Chemical-Assay Space Using the Comparative Toxicogenomics Database. Chem Res Toxicol 2015; 28:2210-23. [PMID: 26505644 DOI: 10.1021/acs.chemrestox.5b00369] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Many studies have attempted to predict in vivo hazards based on the ToxCast in vitro assay results with the goal of using these predictions to prioritize compounds for conventional toxicity testing. Most of these conventional studies rely on in vivo end points observed using preclinical species (e.g., mice and rats). Although the preclinical animal studies provide valuable insights, there can often be significant disconnects between these studies and safety concerns in humans. One way to address these concerns, for an admittedly more limited set of compounds, is to explore relationships between the in vitro data from human cell lines and observations from human related studies. The Comparative Toxicogenomics Database (CTD; http://ctdbase.org ) is a rich source of data linking chemicals to human diseases/adverse events and pathways. In this study we explored the relationships between ToxCast chemicals, their ToxCast in vitro test results, and their annotations of human disease/adverse event end points as captured in the CTD database. We mined these associations to identify potentially interesting, statistically significant in vitro assay and in vivo toxicity correlations. To the best of our knowledge, this is one of the first studies analyzing the relationships between the ToxCast in vitro assays results and the CTD disease/adverse event end point annotations. The in vitro profiles identified in this analysis may prove useful for prioritizing compounds for toxicity testing, suggesting mechanisms of toxicity, and forecasting potential in vivo human drug induced injury.
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Affiliation(s)
- Bingjie Hu
- Structural Chemistry, Merck Research Laboratories, Merck & Co. , West Point, Pennsylvania 19486, United States
| | - Eric Gifford
- Structural Chemistry, Merck Research Laboratories, Merck & Co. , West Point, Pennsylvania 19486, United States
| | - Huijun Wang
- Structural Chemistry, Merck Research Laboratories, Merck & Co. , Kenilworth, New Jersey 07033, United States
| | - Wendy Bailey
- Safety Assessment and Laboratory Animal Resources, Merck Research Laboratories, Merck & Co. , West Point, Pennsylvania 19486, United States
| | - Timothy Johnson
- Safety Assessment and Laboratory Animal Resources, Merck Research Laboratories, Merck & Co. , West Point, Pennsylvania 19486, United States
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Solecki R, Rauch M, Gall A, Buschmann J, Clark R, Fuchs A, Kan H, Heinrich V, Kellner R, Knudsen TB, Li W, Makris SL, Ooshima Y, Paumgartten F, Piersma AH, Schönfelder G, Oelgeschläger M, Schaefer C, Shiota K, Ulbrich B, Ding X, Chahoud I. Continuing harmonization of terminology and innovations for methodologies in developmental toxicology: Report of the 8th Berlin Workshop on Developmental Toxicity, 14–16 May 2014. Reprod Toxicol 2015; 57:140-6. [DOI: 10.1016/j.reprotox.2015.06.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 02/17/2015] [Accepted: 06/03/2015] [Indexed: 11/29/2022]
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Kim H, Kim JH, Kim SY, Jo D, Park HJ, Kim J, Jung S, Kim HS, Lee K. Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PLoS One 2015; 10:e0136698. [PMID: 26335687 PMCID: PMC4559398 DOI: 10.1371/journal.pone.0136698] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/05/2015] [Indexed: 11/19/2022] Open
Abstract
Undesirable toxicity is one of the main reasons for withdrawing drugs from the market or eliminating them as candidates in clinical trials. Although numerous studies have attempted to identify biomarkers capable of predicting pharmacotoxicity, few have attempted to discover robust biomarkers that are coherent across various species and experimental settings. To identify such biomarkers, we conducted meta-analyses of massive gene expression profiles for 6,567 in vivo rat samples and 453 compounds. After applying rigorous feature reduction procedures, our analyses identified 18 genes to be related with toxicity upon comparisons of untreated versus treated and innocuous versus toxic specimens of kidney, liver and heart tissue. We then independently validated these genes in human cell lines. In doing so, we found several of these genes to be coherently regulated in both in vivo rat specimens and in human cell lines. Specifically, mRNA expression of neuronal regeneration-related protein was robustly down-regulated in both liver and kidney cells, while mRNA expression of cathepsin D was commonly up-regulated in liver cells after exposure to toxic concentrations of chemical compounds. Use of these novel toxicity biomarkers may enhance the efficiency of screening for safe lead compounds in early-phase drug development prior to animal testing.
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Affiliation(s)
- Hyosil Kim
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Ju-Hwa Kim
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - So Youn Kim
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
| | - Deokyeon Jo
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
| | - Ho Jun Park
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
| | - Jihyun Kim
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
| | - Sungwon Jung
- Department of Genome Medicine and Science, School of Medicine, Gachon University, Incheon, Korea
- * E-mail: (HSK); (SJ)
| | - Hyun Seok Kim
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
- * E-mail: (HSK); (SJ)
| | - KiYoung Lee
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
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43
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Tonk ECM, Pennings JLA, Piersma AH. An adverse outcome pathway framework for neural tube and axial defects mediated by modulation of retinoic acid homeostasis. Reprod Toxicol 2014; 55:104-13. [PMID: 25461899 DOI: 10.1016/j.reprotox.2014.10.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/12/2014] [Accepted: 10/07/2014] [Indexed: 11/29/2022]
Abstract
Developmental toxicity can be caused through a multitude of mechanisms and can therefore not be captured through a single simple mechanistic paradigm. However, it may be possible to define a selected group of overarching mechanisms that might allow detection of the vast majority of developmental toxicants. Against this background, we have explored the usefulness of retinoic acid mediated regulation of neural tube and axial patterning as a general mechanism that, when perturbed, may result in manifestations of developmental toxicity that may cover a large part of malformations known to occur in experimental animals and in man. Through a literature survey, we have identified key genes in the regulation of retinoic acid homeostasis, as well as marker genes of neural tube and axial patterning, that may be used to detect developmental toxicants in in vitro systems. A retinoic acid-neural tube/axial patterning adverse outcome pathway (RA-NTA AOP) framework was designed. The framework was tested against existing data of flusilazole exposure in the rat whole embryo culture, the zebrafish embryotoxicity test, and the embryonic stem cell test. Flusilazole is known to interact with retinoic acid homeostasis, and induced common and unique NTA marker gene changes in the three test systems. Flusilazole-induced changes were similar in directionality to gene expression responses after retinoic acid exposure. It is suggested that the RA-NTA framework may provide a general tool to define mechanistic pathways and biomarkers of developmental toxicity that may be used in alternative in vitro assays for the detection of embryotoxic compounds.
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Affiliation(s)
- Elisa C M Tonk
- Center for Health Protection, National Institute for Public Health and The Environment (RIVM), P.O. Box 1, 3720BA Bilthoven, The Netherlands
| | - Jeroen L A Pennings
- Center for Health Protection, National Institute for Public Health and The Environment (RIVM), P.O. Box 1, 3720BA Bilthoven, The Netherlands
| | - Aldert H Piersma
- Center for Health Protection, National Institute for Public Health and The Environment (RIVM), P.O. Box 1, 3720BA Bilthoven, The Netherlands; Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands.
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Theunissen P, Beken S, Cappon G, Chen C, Hoberman A, van der Laan J, Stewart J, Piersma A. Toward a comparative retrospective analysis of rat and rabbit developmental toxicity studies for pharmaceutical compounds. Reprod Toxicol 2014; 47:27-32. [DOI: 10.1016/j.reprotox.2014.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Judson R, Houck K, Martin M, Knudsen T, Thomas RS, Sipes N, Shah I, Wambaugh J, Crofton K. In vitro and modelling approaches to risk assessment from the U.S. Environmental Protection Agency ToxCast programme. Basic Clin Pharmacol Toxicol 2014; 115:69-76. [PMID: 24684691 DOI: 10.1111/bcpt.12239] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 03/24/2014] [Indexed: 12/24/2022]
Abstract
A significant challenge in toxicology is the 'too many chemicals' problem. Human beings and environmental species are exposed to tens of thousands of chemicals, only a small percentage of which have been tested thoroughly using standard in vivo test methods. This study reviews several approaches that are being developed to deal with this problem by the U.S. Environmental Protection Agency, under the umbrella of the ToxCast programme (http://epa.gov/ncct/toxcast/). The overall approach is broken into seven tasks: (i) identifying biological pathways that, when perturbed, can lead to toxicity; (ii) developing high-throughput in vitro assays to test chemical perturbations of these pathways; (iii) identifying the universe of chemicals with likely human or ecological exposure; (iv) testing as many of these chemicals as possible in the relevant in vitro assays; (v) developing hazard models that take the results of these tests and identify chemicals as being potential toxicants; (vi) generating toxicokinetics data on these chemicals to predict the doses at which these hazard pathways would be activated; and (vii) developing exposure models to identify chemicals for which these hazardous dose levels could be achieved. This overall strategy is described and briefly illustrated with recent examples from the ToxCast programme.
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Affiliation(s)
- Richard Judson
- U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, NC, USA
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Sensitivity of different generations and developmental stages in studies on reproductive toxicity. Toxicol Lett 2014; 226:245-55. [DOI: 10.1016/j.toxlet.2014.01.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 01/27/2014] [Accepted: 01/29/2014] [Indexed: 11/19/2022]
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47
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Fourches D. Cheminformatics: At the Crossroad of Eras. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2014. [DOI: 10.1007/978-94-017-9257-8_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Shah F, Greene N. Analysis of Pfizer Compounds in EPA’s ToxCast Chemicals-Assay Space. Chem Res Toxicol 2013; 27:86-98. [DOI: 10.1021/tx400343t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Falgun Shah
- Compound Safety Prediction, Pfizer Global Research & Development, 558 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Nigel Greene
- Compound Safety Prediction, Pfizer Global Research & Development, 558 Eastern Point Road, Groton, Connecticut 06340, United States
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49
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Thomas RS, Philbert MA, Auerbach SS, Wetmore BA, Devito MJ, Cote I, Rowlands JC, Whelan MP, Hays SM, Andersen ME, Meek MEB, Reiter LW, Lambert JC, Clewell HJ, Stephens ML, Zhao QJ, Wesselkamper SC, Flowers L, Carney EW, Pastoor TP, Petersen DD, Yauk CL, Nong A. Incorporating new technologies into toxicity testing and risk assessment: moving from 21st century vision to a data-driven framework. Toxicol Sci 2013; 136:4-18. [PMID: 23958734 PMCID: PMC3829570 DOI: 10.1093/toxsci/kft178] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Based on existing data and previous work, a series of studies is proposed as a basis toward a pragmatic early step in transforming toxicity testing. These studies were assembled into a data-driven framework that invokes successive tiers of testing with margin of exposure (MOE) as the primary metric. The first tier of the framework integrates data from high-throughput in vitro assays, in vitro-to-in vivo extrapolation (IVIVE) pharmacokinetic modeling, and exposure modeling. The in vitro assays are used to separate chemicals based on their relative selectivity in interacting with biological targets and identify the concentration at which these interactions occur. The IVIVE modeling converts in vitro concentrations into external dose for calculation of the point of departure (POD) and comparisons to human exposure estimates to yield a MOE. The second tier involves short-term in vivo studies, expanded pharmacokinetic evaluations, and refined human exposure estimates. The results from the second tier studies provide more accurate estimates of the POD and the MOE. The third tier contains the traditional animal studies currently used to assess chemical safety. In each tier, the POD for selective chemicals is based primarily on endpoints associated with a proposed mode of action, whereas the POD for nonselective chemicals is based on potential biological perturbation. Based on the MOE, a significant percentage of chemicals evaluated in the first 2 tiers could be eliminated from further testing. The framework provides a risk-based and animal-sparing approach to evaluate chemical safety, drawing broadly from previous experience but incorporating technological advances to increase efficiency.
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Affiliation(s)
- Russell S Thomas
- * The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709
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Allard P, Kleinstreuer NC, Knudsen TB, Colaiácovo MP. A C. elegans screening platform for the rapid assessment of chemical disruption of germline function. ENVIRONMENTAL HEALTH PERSPECTIVES 2013; 121:717-24. [PMID: 23603051 PMCID: PMC3672921 DOI: 10.1289/ehp.1206301] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 04/18/2013] [Indexed: 05/19/2023]
Abstract
BACKGROUND Despite the developmental impact of chromosome segregation errors, we lack the tools to assess environmental effects on the integrity of the germline in animals. OBJECTIVES We developed an assay in Caenorhabditis elegans that fluorescently marks aneuploid embryos after chemical exposure. METHODS We qualified the predictive value of the assay against chemotherapeutic agents as well as environmental compounds from the ToxCast Phase I library by comparing results from the C. elegans assay with the comprehensive mammalian in vivo end point data from the ToxRef database. RESULTS The assay was highly predictive of mammalian reproductive toxicities, with a 69% maximum balanced accuracy. We confirmed the effect of select compounds on germline integrity by monitoring germline apoptosis and meiotic progression. CONCLUSIONS This C. elegans assay provides a comprehensive strategy for assessing environmental effects on germline function.
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Affiliation(s)
- Patrick Allard
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115 , USA
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