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Kaplan BLF, Hoberman AM, Slikker W, Smith MA, Corsini E, Knudsen TB, Marty MS, Sobrian SK, Fitzpatrick SC, Ratner MH, Mendrick DL. Protecting Human and Animal Health: The Road from Animal Models to New Approach Methods. Pharmacol Rev 2024; 76:251-266. [PMID: 38351072 PMCID: PMC10877708 DOI: 10.1124/pharmrev.123.000967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/18/2023] [Accepted: 12/01/2023] [Indexed: 02/16/2024] Open
Abstract
Animals and animal models have been invaluable for our current understanding of human and animal biology, including physiology, pharmacology, biochemistry, and disease pathology. However, there are increasing concerns with continued use of animals in basic biomedical, pharmacological, and regulatory research to provide safety assessments for drugs and chemicals. There are concerns that animals do not provide sufficient information on toxicity and/or efficacy to protect the target population, so scientists are utilizing the principles of replacement, reduction, and refinement (the 3Rs) and increasing the development and application of new approach methods (NAMs). NAMs are any technology, methodology, approach, or assay used to understand the effects and mechanisms of drugs or chemicals, with specific focus on applying the 3Rs. Although progress has been made in several areas with NAMs, complete replacement of animal models with NAMs is not yet attainable. The road to NAMs requires additional development, increased use, and, for regulatory decision making, usually formal validation. Moreover, it is likely that replacement of animal models with NAMs will require multiple assays to ensure sufficient biologic coverage. The purpose of this manuscript is to provide a balanced view of the current state of the use of animal models and NAMs as approaches to development, safety, efficacy, and toxicity testing of drugs and chemicals. Animals do not provide all needed information nor do NAMs, but each can elucidate key pieces of the puzzle of human and animal biology and contribute to the goal of protecting human and animal health. SIGNIFICANCE STATEMENT: Data from traditional animal studies have predominantly been used to inform human health safety and efficacy. Although it is unlikely that all animal studies will be able to be replaced, with the continued advancement in new approach methods (NAMs), it is possible that sometime in the future, NAMs will likely be an important component by which the discovery, efficacy, and toxicity testing of drugs and chemicals is conducted and regulatory decisions are made.
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Affiliation(s)
- Barbara L F Kaplan
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Alan M Hoberman
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - William Slikker
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Mary Alice Smith
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Emanuela Corsini
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Thomas B Knudsen
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - M Sue Marty
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Sonya K Sobrian
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Suzanne C Fitzpatrick
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Marcia H Ratner
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
| | - Donna L Mendrick
- Center for Environmental Health Sciences, Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi (B.L.F.K.); Charles River Laboratories, Inc., Horsham, Pennsylvania (A.M.H.); Retired, National Center for Toxicological Research, Jefferson, Arkansas (W.S.); University of Georgia, Athens, Georgia (M.A.S.); Department of Pharmacological and Biomolecular Sciences, 'Rodolfo Paoletti' Università degli Studi di Milano, Milan, Italy (E.C.); US Environmental Protection Agency, Research Triangle Park, North Carolina (T.B.K.); Dow, Inc., Midland, Michigan (M.S.M.); Howard University College of Medicine, Washington DC (S.K.S.); Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland (S.C.F.); Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts (M.H.R.); and National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, Maryland (D.L.M.)
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Basu M, Howdeshell KL, Rasmussen SA, Rychlik KA, Knudsen TB, Shuey DL, Slikker W. Society for birth defects research and prevention's multidisciplinary research needs workshop 2022: A call to action. Birth Defects Res 2023; 115:959-966. [PMID: 37218073 PMCID: PMC10641708 DOI: 10.1002/bdr2.2186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 04/21/2023] [Indexed: 05/24/2023]
Abstract
The Society for Birth Defects Research and Prevention (BDRP) strives to understand and protect against potential hazards to developing embryos, fetuses, children, and adults by bringing together scientific knowledge from diverse fields. The theme of 62nd Annual Meeting of BDRP, "From Bench to Bedside and Back Again", represented the cutting-edge research areas of high relevance to public health and significance in the fields of birth defects research and surveillance. The multidisciplinary Research Needs Workshop (RNW) convened at the Annual Meeting continues to identify pressing knowledge gaps and encourage interdisciplinary research initiatives. The multidisciplinary RNW was first introduced at the 2018 annual meeting to provide an opportunity for annual meeting attendees to participate in breakout discussions on emerging topics in birth defects research and to foster collaboration between basic researchers, clinicians, epidemiologists, drug developers, industry partners, funding agencies, and regulators to discuss state-of-the-art methods and innovative projects. Initially, a list of workshop topics was compiled by the RNW planning committee and circulated among the members of BDRP to obtain the most popular topics for the Workshop discussions. Based on the pre-meeting survey results, the top three discussion topics selected were, A) Inclusion of pregnant and lactating women in clinical trials. When, why, and how? B) Building multidisciplinary teams across disciplines: What cross-training is needed? And C) Challenges in applications of Artificial Intelligence (AI) and machine learning for risk factor analysis in birth defects research. This report summarizes the key highlights of the RNW workshop and specific topic discussions.
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Affiliation(s)
- Madhumita Basu
- Center for Cardiovascular Research and Heart Center, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- MelliCell Inc. Newton, Massachusetts, United States of America
| | - Kembra L. Howdeshell
- Division of Translational Toxicology, National Institute of Environmental Health Sciences (NIEHS), North Carolina, United States of America
| | - Sonja A. Rasmussen
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kristal A. Rychlik
- Public Health Program, School of Exercise and Sport Science, University of Mary Hardin-Baylor, Belton, Texas, United States of America
| | - Thomas B. Knudsen
- US Environmental Protection Agency, Center for Computational Toxicology and Exposure, Research Triangle Park, North Carolina, United States of America
| | - Dana L. Shuey
- Incyte Corporation, Wilmington, Delaware, United States of America
| | - William Slikker
- Retired, Formerly of the Office of the Director, National Center for Toxicological Research, US Food and Drug Administration (FDA), Jefferson, Arkansas, United States of America
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Chang X, Palmer J, Lumen A, Lee UJ, Ceger P, Mansouri K, Sprankle C, Donley E, Bell S, Knudsen TB, Wambaugh J, Cook B, Allen D, Kleinstreuer N. Quantitative in vitro to in vivo extrapolation for developmental toxicity potency of valproic acid analogues. Birth Defects Res 2022; 114:1037-1055. [PMID: 35532929 PMCID: PMC9790683 DOI: 10.1002/bdr2.2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND The developmental toxicity potential (dTP) concentration from the devTOX quickPredict (devTOXqP ) assay, a metabolomics-based human induced pluripotent stem cell assay, predicts a chemical's developmental toxicity potency. Here, in vitro to in vivo extrapolation (IVIVE) approaches were applied to address whether the devTOXqP assay could quantitatively predict in vivo developmental toxicity lowest effect levels (LELs) for the prototypical teratogen valproic acid (VPA) and a group of structural analogues. METHODS VPA and a series of structural analogues were tested with the devTOXqP assay to determine dTP concentration and we estimated the equivalent administered doses (EADs) that would lead to plasma concentrations equivalent to the in vitro dTP concentrations. The EADs were compared to the LELs in rat developmental toxicity studies, human clinical doses, and EADs reported using other in vitro assays. To evaluate the impact of different pharmacokinetic (PK) models on IVIVE outcomes, we compared EADs predicted using various open-source and commercially available PK and physiologically based PK (PBPK) models. To evaluate the effect of in vitro kinetics, an equilibrium distribution model was applied to translate dTP concentrations to free medium concentrations before subsequent IVIVE analyses. RESULTS The EAD estimates for the VPA analogues based on different PK/PBPK models were quantitatively similar to in vivo data from both rats and humans, where available, and the derived rank order of the chemicals was consistent with observed in vivo developmental toxicity. Different models were identified that provided accurate predictions for rat prenatal LELs and conservative estimates of human safe exposure. The impact of in vitro kinetics on EAD estimates is chemical-dependent. EADs from this study were within range of predicted doses from other in vitro and model organism data. CONCLUSIONS This study highlights the importance of pharmacokinetic considerations when using in vitro assays and demonstrates the utility of the devTOXqP human stem cell-based platform to quantitatively assess a chemical's developmental toxicity potency.
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Affiliation(s)
| | | | - Annie Lumen
- National Center for Toxicological ResearchU.S. Food and Drug AdministrationJeffersonArkansasUSA,Present address:
Clinical Pharmacology, Modeling and SimulationsAmgenSouth San FranciscoCaliforniaUSA
| | - Un Jung Lee
- National Center for Toxicological ResearchU.S. Food and Drug AdministrationJeffersonArkansasUSA,Present address:
Albert Einstein College of MedicineBronxNew YorkUSA
| | | | - Kamel Mansouri
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological MethodsNational Institute of Environmental Health SciencesResearch Triangle ParkNorth CarolinaUSA
| | | | | | | | - Thomas B. Knudsen
- Center for Computational Toxicology and ExposureEnvironmental Protection AgencyResearch Triangle ParkNorth CarolinaUSA
| | - John Wambaugh
- Center for Computational Toxicology and ExposureEnvironmental Protection AgencyResearch Triangle ParkNorth CarolinaUSA
| | | | | | - Nicole Kleinstreuer
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological MethodsNational Institute of Environmental Health SciencesResearch Triangle ParkNorth CarolinaUSA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Baker NC, Pierro JD, Taylor LW, Knudsen TB. Identifying candidate reference chemicals for in vitro testing of the retinoid pathway for predictive developmental toxicity. ALTEX 2022; 40:217–236. [PMID: 35796328 PMCID: PMC10765368 DOI: 10.14573/altex.2202231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022]
Abstract
Evaluating chemicals for potential in vivo toxicity based on their in vitro bioactivity profile is an important step toward animal- free testing. A compendium of reference chemicals and data describing their bioactivity on specific molecular targets, cellular pathways, and biological processes is needed to bolster confidence in the predictive value of in vitro hazard detection. Endogenous signaling by all-trans retinoic acid (ATRA) is an important pathway in developmental processes and toxicities. Employing data extraction methods and advanced literature extraction tools, we assembled a set of candidate reference chemicals with demonstrated activity on ten protein family targets in the retinoid system. The compendium was culled from Protein Data Bank, ChEMBL, ToxCast/Tox21, and the biomedical literature in PubMed. Finally, we performed a case study on one chemical in our collection, citral, an inhibitor of endogenous ATRA production, to determine whether the literature supports an adverse outcome pathway explaining the compound’s developmental toxicity initiated by disruption of the retinoid pathway. We also deliver an updated Abstract Sifter tool populated with these reference compounds and complex search terms designed to query the literature for the downstream consequences to support concordance with targeted retinoid pathway disruption.
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Affiliation(s)
| | - Jocylin D. Pierro
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Laura W. Taylor
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Thomas B. Knudsen
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
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Piersma AH, Baker NC, Daston GP, Flick B, Fujiwara M, Knudsen TB, Spielmann H, Suzuki N, Tsaioun K, Kojima H. Pluripotent Stem Cell Assays: Modalities and Applications For Predictive Developmental Toxicity. Curr Res Toxicol 2022; 3:100074. [PMID: 35633891 PMCID: PMC9130094 DOI: 10.1016/j.crtox.2022.100074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/21/2022] [Accepted: 05/09/2022] [Indexed: 12/02/2022] Open
Abstract
A systematic scoping review of the literature evaluated the embryonic stem cell test (EST). 1533 publications included 18 publications testing 10 or more compounds in human or mouse EST. Selected case examples included 5-fluorouracil, thalidomide, and caffeine. Applicability, limitations, and recommendations for further work are discussed.
This manuscript provides a review focused on embryonic stem cell-based models and their place within the landscape of alternative developmental toxicity assays. Against the background of the principles of developmental toxicology, the wide diversity of alternative methods using pluripotent stem cells developed in this area over the past half century is reviewed. In order to provide an overview of available models, a systematic scoping review was conducted following a published protocol with inclusion criteria, which were applied to select the assays. Critical aspects including biological domain, readout endpoint, availability of standardized protocols, chemical domain, reproducibility and predictive power of each assay are described in detail, in order to review the applicability and limitations of the platform in general and progress moving forward to implementation. The horizon of innovative routes of promoting regulatory implementation of alternative methods is scanned, and recommendations for further work are given.
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Whaley P, Blaauboer BJ, Brozek J, Cohen Hubal EA, Hair K, Kacew S, Knudsen TB, Kwiatkowski CF, Mellor DT, Olshan AF, Page MJ, Rooney AA, Radke EG, Shamseer L, Tsaioun K, Tugwell P, Wikoff D, Woodruff TJ. Improving the quality of toxicology and environmental health systematic reviews: What journal editors can do. ALTEX 2021; 38:513-522. [PMID: 34164697 DOI: 10.14573/altex.2106111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 11/23/2022]
Abstract
Systematic reviews are fast increasing in prevalence in the toxicology and environmental health literature. However, how well these complex research projects are being conducted and reported is unclear. Since editors have an essential role in ensuring the scientific quality of manuscripts being published in their journals, a workshop was convened where editors, systematic review practitioners, and research quality control experts could discuss what editors can do to ensure the systematic reviews they publish are of sufficient scientific quality. Interventions were explored along four themes: setting standards; reviewing protocols; optimizing editorial workflows; and measuring the effectiveness of editorial interventions. In total, 58 editorial interventions were proposed. Of these, 26 were shortlisted for being potentially effective, and 5 were prioritized as short-term actions that editors could relatively easily take to improve the quality of published systematic reviews. Recent progress in improving systematic reviews is summarized, and outstanding challenges to further progress are highlighted.
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Affiliation(s)
- Paul Whaley
- Evidence-based Toxicology Collaboration at Johns Hopkins Bloomberg School of Public Health, Baltimore, USA,Lancaster Environment Centre, Lancaster University, United Kingdom
| | - Bas J Blaauboer
- Institute for Risk Assessment Sciences, div. of Toxicology, Utrecht University, Utrecht, The Netherlands
| | - Jan Brozek
- Department of Clinical Epidemiology and Biostatistics, McMaster University Health Sciences Centre, Hamilton, ON, Canada
| | - Elaine A Cohen Hubal
- US EPA, Office of Research and Development, Center for Public Health and Environmental Assessment, Research Triangle Park, NC, USA
| | - Kaitlyn Hair
- CAMARADES, University of Edinburgh, Centre for Clinical Brain Sciences, Edinburgh, United Kingdom
| | - Sam Kacew
- McLaughlin Centre for Risk Assessment, University of Ottawa, Ottawa, ON, Canada
| | - Thomas B Knudsen
- US EPA, Office of Research and Development, Center for Computational Toxicology and Exposure, Research Triangle Park, NC, USA
| | | | | | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew J Page
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Andrew A Rooney
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Elizabeth G Radke
- Center for Public Health and Environmental Assessment, United States Environmental Protection Agency, Washington, DC, USA
| | - Larissa Shamseer
- Knowledge Translation Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Katya Tsaioun
- Evidence-based Toxicology Collaboration at Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Peter Tugwell
- Department of Medicine and School of Epidemiology University of Ottawa, ON, Canada
| | | | - Tracey J Woodruff
- Program on Reproductive Health and the Environment, University of California San Francisco, San Francisco, CA, USA
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Knudsen TB, Spielmann M, Megason SG, Faustman EM. Single-cell profiling for advancing birth defects research and prevention. Birth Defects Res 2021; 113:546-559. [PMID: 33496083 PMCID: PMC8562675 DOI: 10.1002/bdr2.1870] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/10/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022]
Abstract
Cellular analysis of developmental processes and toxicities has traditionally entailed bulk methods (e.g., transcriptomics) that lack single cell resolution or tissue localization methods (e.g., immunostaining) that allow only a few genes to be monitored in each experiment. Recent technological advances have enabled interrogation of genomic function at the single-cell level, providing new opportunities to unravel developmental pathways and processes with unprecedented resolution. Here, we review emerging technologies of single-cell RNA-sequencing (scRNA-seq) to globally characterize the gene expression sets of different cell types and how different cell types emerge from earlier cell states in development. Cell atlases of experimental embryology and human embryogenesis at single-cell resolution will provide an encyclopedia of genes that define key stages from gastrulation to organogenesis. This technology, combined with computational models to discover key organizational principles, was recognized by Science magazine as the "Breakthrough of the year" for 2018 due to transformative potential on the way we study how human cells mature over a lifetime, how tissues regenerate, and how cells change in diseases (e.g., patient-derived organoids to screen disease-specific targets and design precision therapy). Profiling transcriptomes at the single-cell level can fulfill the need for greater detail in the molecular progression of all cell lineages, from pluripotency to adulthood and how cell-cell signaling pathways control progression at every step. Translational opportunities emerge for elucidating pathogenesis of genetic birth defects with cellular precision and improvements for predictive toxicology of chemical teratogenesis.
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Affiliation(s)
- Thomas B Knudsen
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Malte Spielmann
- Human Molecular Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Elaine M Faustman
- Department of Environmental & Occupational Health Sciences, University of Washington, School of Public Health, Seattle, Washington, USA
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10
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Knudsen TB, Fitzpatrick SC, De Abrew KN, Birnbaum LS, Chappelle A, Daston GP, Dolinoy DC, Elder A, Euling S, Faustman EM, Fedinick KP, Franzosa JA, Haggard DE, Haws L, Kleinstreuer NC, Buck Louis GM, Mendrick DL, Rudel R, Saili KS, Schug TT, Tanguay RL, Turley AE, Wetmore BA, White KW, Zurlinden TJ. FutureTox IV Workshop Summary: Predictive Toxicology for Healthy Children. Toxicol Sci 2021; 180:198-211. [PMID: 33555348 PMCID: PMC8041457 DOI: 10.1093/toxsci/kfab013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
FutureTox IV, a Society of Toxicology Contemporary Concepts in Toxicology workshop, was held in November 2018. Building upon FutureTox I, II, and III, this conference focused on the latest science and technology for in vitro profiling and in silico modeling as it relates to predictive developmental and reproductive toxicity (DART). Publicly available high-throughput screening data sets are now available for broad in vitro profiling of bioactivities across large inventories of chemicals. Coupling this vast amount of mechanistic data with a deeper understanding of molecular embryology and post-natal development lays the groundwork for using new approach methodologies (NAMs) to evaluate chemical toxicity, drug efficacy, and safety assessment for embryo-fetal development. NAM is a term recently adopted in reference to any technology, methodology, approach, or combination thereof that can be used to provide information on chemical hazard and risk assessment to avoid the use of intact animals (U.S. Environmental Protection Agency [EPA], Strategic plan to promote the development and implementation of alternative test methods within the tsca program, 2018, https://www.epa.gov/sites/production/files/2018-06/documents/epa_alt_strat_plan_6-20-18_clean_final.pdf). There are challenges to implementing NAMs to evaluate chemicals for developmental toxicity compared with adult toxicity. This forum article reviews the 2018 workshop activities, highlighting challenges and opportunities for applying NAMs for adverse pregnancy outcomes (eg, preterm labor, malformations, low birth weight) as well as disorders manifesting postnatally (eg, neurodevelopmental impairment, breast cancer, cardiovascular disease, fertility). DART is an important concern for different regulatory statutes and test guidelines. Leveraging advancements in such approaches and the accompanying efficiencies to detecting potential hazards to human development are the unifying concepts toward implementing NAMs in DART testing. Although use of NAMs for higher level regulatory decision making is still on the horizon, the conference highlighted novel testing platforms and computational models that cover multiple levels of biological organization, with the unique temporal dynamics of embryonic development, and novel approaches for estimating toxicokinetic parameters essential in supporting in vitro to in vivo extrapolation.
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Affiliation(s)
- Thomas B Knudsen
- U.S. Environmental Protection Agency, ORD, Research Triangle Park, North Carolina, USA
| | | | | | - Linda S Birnbaum
- National Institute of Environmental Health Science, NIH, Research Triangle Park, North Carolina, USA
| | - Anne Chappelle
- Chappelle Toxicology Consulting, LLC, Chadds Ford, Pennsylvania, USA
| | | | | | - Alison Elder
- University of Rochester, Rochester, New York, USA
| | - Susan Euling
- U.S. Environmental Protection Agency, Office of Children’s Health Protection, Washington, District of Columbia, USA
| | | | | | - Jill A Franzosa
- U.S. Environmental Protection Agency, ORD, Research Triangle Park, North Carolina, USA
| | - Derik E Haggard
- U.S. Environmental Protection Agency, ORD, Research Triangle Park, North Carolina, USA
- Oak Ridge Institute for Science and Education (ORISE);, Texas, USA
| | | | | | | | - Donna L Mendrick
- U.S. Food and Drug Administration, NCTR, Silver Spring, Maryland, USA
| | | | - Katerine S Saili
- U.S. Environmental Protection Agency, ORD, Research Triangle Park, North Carolina, USA
| | - Thaddeus T Schug
- National Institute of Environmental Health Science, NIH, Research Triangle Park, North Carolina, USA
| | | | | | - Barbara A Wetmore
- U.S. Environmental Protection Agency, ORD, Research Triangle Park, North Carolina, USA
| | - Kimberly W White
- American Chemistry Council, Washington, District of Columbia, USA
| | - Todd J Zurlinden
- U.S. Environmental Protection Agency, ORD, Research Triangle Park, North Carolina, USA
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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] [What about the content of this article? (0)] [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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12
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Stadler HS, Peters CA, Sturm RM, Baker LA, Best CJM, Bird VY, Geller F, Hoshizaki DK, Knudsen TB, Norton JM, Romao RLP, Cohn MJ. Meeting report on the NIDDK/AUA Workshop on Congenital Anomalies of External Genitalia: challenges and opportunities for translational research. J Pediatr Urol 2020; 16:791-804. [PMID: 33097421 PMCID: PMC7885182 DOI: 10.1016/j.jpurol.2020.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 09/10/2020] [Accepted: 09/13/2020] [Indexed: 01/02/2023]
Abstract
Congenital anomalies of the external genitalia (CAEG) are a prevalent and serious public health concern with lifelong impacts on the urinary function, sexual health, fertility, tumor development, and psychosocial wellbeing of affected individuals. Complications of treatment are frequent, and data reflecting long-term outcomes in adulthood are limited. To identify a path forward to improve treatments and realize the possibility of preventing CAEG, the National Institute of Diabetes and Digestive and Kidney Diseases and the American Urological Association convened researchers from a range of disciplines to coordinate research efforts to fully understand the different etiologies of these common conditions, subsequent variation in clinical phenotypes, and best practices for long term surgical success. Meeting participants concluded that a central data hub for clinical evaluations, including collection of DNA samples from patients and their parents, and short interviews to determine familial penetrance (small pedigrees), would accelerate research in this field. Such a centralized datahub will advance efforts to develop detailed multi-dimensional phenotyping and will enable access to genome sequence analyses and associated metadata to define the genetic bases for these conditions. Inclusion of tissue samples and integration of clinical studies with basic research using human cells and animal models will advance efforts to identify the developmental mechanisms that are disrupted during development and will add cellular and molecular granularity to phenotyping CAEG. While the discussion focuses heavily on hypospadias, this can be seen as a potential template for other conditions in the realm of CAEG, including cryptorchidism or the exstrophy-epispadias complex. Taken together with long-term clinical follow-up, these data could inform surgical choices and improve likelihood for long-term success.
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Affiliation(s)
- H Scott Stadler
- Department of Skeletal Biology, Shriners Hospital for Children, 3101 SW Sam Jackson Park Road, Portland, OR, Oregon Health & Science University, Department of Orthopaedics and Rehabilitation, Portland, 97239, OR, USA.
| | - Craig A Peters
- Department of Urology, University of Texas Southwestern, 5323 Harry Hines Blvd., Dallas, 75390-9110, TX, USA; Pediatric Urology, Children's Health System Texas, University of Texas Southwestern, Dallas, 75390, TX, USA.
| | - Renea M Sturm
- Department of Urology, Division of Pediatric Urology, University of California Los Angeles, 200 Medical Plaza #170, Los Angeles, 90095, CA, USA
| | - Linda A Baker
- Department of Urology, University of Texas Southwestern, 5323 Harry Hines Blvd., Dallas, 75390-9110, TX, USA
| | - Carolyn J M Best
- American Urological Association, 1000 Corporate Boulevard, Linthicum, 21090, MD, USA
| | - Victoria Y Bird
- Department of Urology, University of Florida, Gainesville, 32610, FL, USA; National Medical Association and Research Group, 5745 SW 75th Street, #507, Gainesville, 32608, FL, USA
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, 5 Artillerivej, Copenhagen S, DK-2300, Denmark
| | - Deborah K Hoshizaki
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 6707 Democracy Boulevard, Bethesda, 20892, MD, USA
| | - Thomas B Knudsen
- US Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Research Triangle Park, 27711, NC, USA
| | - Jenna M Norton
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 6707 Democracy Boulevard, Bethesda, 20892, MD, USA
| | - Rodrigo L P Romao
- Departments of Surgery and Urology, IWK Health Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Martin J Cohn
- Department of Molecular Genetics and Microbiology, Department of Biology, And UF Genetics Institute, University of Florida, PO Box 103610, Gainesville, 32610, FL, USA.
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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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14
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Heusinkveld HJ, Staal YCM, Baker NC, Daston G, Knudsen TB, Piersma A. An ontology for developmental processes and toxicities of neural tube closure. Reprod Toxicol 2020; 99:160-167. [PMID: 32926990 PMCID: PMC10083840 DOI: 10.1016/j.reprotox.2020.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/12/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023]
Abstract
In recent years, the development and implementation of animal-free approaches to chemical and pharmaceutical hazard and risk assessment has taken off. Alternative approaches are being developed starting from the perspective of human biology and physiology. Neural tube closure is a vital step that occurs early in human development. Correct closure of the neural tube depends on a complex interplay between proteins along a number of protein concentration gradients. The sensitivity of neural tube closure to chemical disturbance of signalling pathways such as the retinoid pathway, is well known. To map the pathways underlying neural tube closure, literature data on the molecular regulation of neural tube closure were collected. As the process of neural tube closure is highly conserved in vertebrates, the extensive literature available for the mouse was used whilst considering its relevance for humans. Thus, important cell compartments, regulatory pathways, and protein interactions essential for neural tube closure under physiological circumstances were identified and mapped. An understanding of aberrant processes leading to neural tube defects (NTDs) requires detailed maps of neural tube embryology, including the complex genetic signals and responses underlying critical cellular dynamical and biomechanical processes. The retinoid signaling pathway serves as a case study for this ontology because of well-defined crosstalk with the genetic control of neural tube patterning and morphogenesis. It is a known target for mechanistically-diverse chemical structures that disrupt neural tube closure The data presented in this manuscript will set the stage for constructing mathematical models and computer simulation of neural tube closure for human-relevant AOPs and predictive toxicology.
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Affiliation(s)
- Harm J Heusinkveld
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
| | - Yvonne C M Staal
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - George Daston
- Global Product Stewardship, The Procter & Gamble Company, Cincinnati, OH USA
| | - Thomas B Knudsen
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research Triangle Park NC 27711, USA
| | - Aldert Piersma
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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15
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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. Corrigendum to: "Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity". Toxicol Sci 2020; 177:301. [PMID: 32529217 DOI: 10.1093/toxsci/kfaa064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Knudsen TB, Vinken M. Excellence paves the way with Current Research in Toxicology. Curr Res Toxicol 2020; 1:iv. [PMID: 34345846 PMCID: PMC8320605 DOI: 10.1016/j.crtox.2020.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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17
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Mahony C, Ashton RS, Birk B, Boobis AR, Cull T, Daston GP, Ewart L, Knudsen TB, Manou I, Maurer-Stroh S, Margiotta-Casaluci L, Müller BP, Nordlund P, Roberts RA, Steger-Hartmann T, Vandenbossche E, Viant MR, Vinken M, Whelan M, Zvonimir Z, Cronin MTD. New ideas for non-animal approaches to predict repeated-dose systemic toxicity: Report from an EPAA Blue Sky Workshop. Regul Toxicol Pharmacol 2020; 114:104668. [PMID: 32335207 DOI: 10.1016/j.yrtph.2020.104668] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 02/09/2023]
Abstract
The European Partnership for Alternative Approaches to Animal Testing (EPAA) convened a 'Blue Sky Workshop' on new ideas for non-animal approaches to predict repeated-dose systemic toxicity. The aim of the Workshop was to formulate strategic ideas to improve and increase the applicability, implementation and acceptance of modern non-animal methods to determine systemic toxicity. The Workshop concluded that good progress is being made to assess repeated dose toxicity without animals taking advantage of existing knowledge in toxicology, thresholds of toxicological concern, adverse outcome pathways and read-across workflows. These approaches can be supported by New Approach Methodologies (NAMs) utilising modern molecular technologies and computational methods. Recommendations from the Workshop were based around the needs for better chemical safety assessment: how to strengthen the evidence base for decision making; to develop, standardise and harmonise NAMs for human toxicity; and the improvement in the applicability and acceptance of novel techniques. "Disruptive thinking" is required to reconsider chemical legislation, validation of NAMs and the opportunities to move away from reliance on animal tests. Case study practices and data sharing, ensuring reproducibility of NAMs, were viewed as crucial to the improvement of non-animal test approaches for systemic toxicity.
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Affiliation(s)
| | - Randolph S Ashton
- Department of Biomedical Engineering & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, 53715, USA.
| | - Barbara Birk
- BASF SE, Experimental Toxicology and Ecology, Carl-Bosch-Straβe 38, 67056, Ludwigshafen, Germany.
| | - Alan R Boobis
- National Heart & Lung Institute, Imperial College London, London, W12 0NN, UK.
| | - Tom Cull
- Unilever, Colworth Science Park, Sharnbrook, Bedford, MK44 1LQ, UK.
| | - George P Daston
- Mason Business Center, The Procter & Gamble Company, Cincinnati, OH, 45040, USA.
| | - Lorna Ewart
- Veroli Consulting Limited, Cambridge, UK; Emulate Inc, 27 Dry Dock Avenue, Boston, MA, 02210, USA.
| | - Thomas B Knudsen
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Research Triangle Park, NC, 27711, USA.
| | - Irene Manou
- European Partnership for Alternative Approaches to Animal Testing (EPAA) Industry Secretariat, Belgium.
| | - Sebastian Maurer-Stroh
- Innovations in Chemical and Food Safety, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore.
| | | | | | - Pär Nordlund
- Department of Oncology and Pathology, Karolinska Institutet, 17177, Stockholm, Sweden; Institute of Molecular and Cellular Biology, A*STAR, 61 Biopolis Drive, 138673, Singapore.
| | - Ruth A Roberts
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Thomas Steger-Hartmann
- Investigational Toxicology, Bayer AG, Pharmaceuticals, Müllerstraβe 178, 13353, Berlin, Germany.
| | | | - Mark R Viant
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Mathieu Vinken
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium.
| | - Maurice Whelan
- European Commission, Joint Research Centre (JRC), Italy.
| | - Zvonar Zvonimir
- European Partnership for Alternative Approaches to Animal Testing (EPAA) Industry Secretariat, Belgium.
| | - Mark T D Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK.
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Wei Z, Sakamuru S, Zhang L, Zhao J, Huang R, Kleinstreuer NC, Chen Y, Shu Y, Knudsen TB, Xia M. Identification and Profiling of Environmental Chemicals That Inhibit the TGFβ/SMAD Signaling Pathway. Chem Res Toxicol 2019; 32:2433-2444. [PMID: 31652400 PMCID: PMC7341485 DOI: 10.1021/acs.chemrestox.9b00228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The transforming growth factor beta (TGFβ) superfamily of secreted signaling molecules and their cognate receptors regulate cell fate and behaviors relevant to many developmental and disease processes. Disruption of TGFβ signaling during embryonic development can, for example, affect morphogenesis and differentiation through complex pathways that may be SMAD (Small Mothers Against Decapentaplegic) dependent or SMAD independent. In the present study, the SMAD Binding Element (SBE)-beta lactamase (bla) HEK 293T cell line, which responds to the activation of the SMAD2/3/4 complex, was used in a quantitative high-throughput screening (qHTS) assay to identify potential TGFβ disruptors in the Tox21 10K compound library. From the primary screening we identified several kinase inhibitors, organometallic compounds, and dithiocarbamates (DTCs) that inhibited TGFβ1-induced SMAD signaling of reporter gene activation independent of cytotoxicity. Counterscreen of SBE antagonists on human embryonic neural stem cells demonstrated cytotoxicity, providing additional evidence to support evaluation of these compounds for developmental toxicity. We profiled the inhibitory patterns of putative SBE antagonists toward other developmental signaling pathways, including wingless-related integration site (WNT), retinoic acid α receptor (RAR), and sonic hedgehog (SHH). The profiling results from SBE-bla assay identify chemicals that disrupt TGFβ/SMAD signaling as part of an integrated qHTS approach for prioritizing putative developmental toxicants.
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Affiliation(s)
- Zhengxi Wei
- National Center for Advancing Translational Sciences, National Institutes of Health, MD, USA
| | - Srilatha Sakamuru
- National Center for Advancing Translational Sciences, National Institutes of Health, MD, USA
| | - Li Zhang
- National Center for Advancing Translational Sciences, National Institutes of Health, MD, USA
| | - Jinghua Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, MD, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, MD, USA
| | - Nicole C. Kleinstreuer
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Yanling Chen
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Yan Shu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Thomas B. Knudsen
- National Center for Computational Toxicology, Office of Research and Development, United States Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, MD, USA
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19
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Knudsen TB. Symposium: “Digitalisation meets Pathology and Developmental Toxicology”. Reprod Toxicol 2019. [DOI: 10.1016/j.reprotox.2019.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Piersma AH, Baker NC, Burgoon LD, Daston G, Knudsen TB, Staal YC. An AOP-based ontology for spina bifida caused by disturbance in retinoic acid signaling. Reprod Toxicol 2018. [DOI: 10.1016/j.reprotox.2018.06.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Stapleton PA, Wingard CJ, Nurkiewicz TR, Holloway AC, Zelikoff JT, Knudsen TB, Rogers LK. Cardiopulmonary consequences of gestational toxicant exposure: Symposium overview at the 56th annual SOT meeting, Baltimore, MD. Reprod Toxicol 2018; 79:16-20. [PMID: 29709519 DOI: 10.1016/j.reprotox.2018.04.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/09/2018] [Accepted: 04/24/2018] [Indexed: 01/17/2023]
Abstract
Xenobiotic exposures affect the maternal and/or in utero environment resulting in impairments in fetal development. During the period of rapid fetal growth, developing cardiovascular systems are especially vulnerable to their environment. Furthermore, fetal exposures can evoke changes in epigenetic signatures that result in permanent modifications in gene expression. This symposium focused on the intersection between maternal and fetal exposure and the developing cardiovascular system. The impact of maternal exposures on prenatal development is of major concern for regulatory agencies given the unique vulnerability of the embryo/fetus to environmental factors, the importance of vascular biology to maternal-fetal interactions, and the adverse consequences of vascular disruption to children's health. Speakers provided data from diverse exposures: nanomaterials, particulate matter or air pollution (PM2.5), nicotine, and environmental chemicals. The current findings related to susceptible gestational windows for cardiovascular development and epigenetic, transcriptomic, toxicokinetic, and toxicodynamic changes in vascular physiology and cardiac function. In response to these concerns, new concepts in predictive modeling and risk assessment associated with in utero exposures were presented as future avenues of research within developmental toxicology. Finally, current applications using an Adverse Outcome Pathway framework for developmental toxicity were presented to integrate data from in vitro profiling of chemical libraries (e.g. ToxCast™) with computational models for in silico toxicology. In summary, this symposium addressed the significant threats to cardiovascular health that are associated with fetal/perinatal exposures, and offered new insights into the predictive, mechanistic, and risk assessment strategies in developmental toxicology.
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Affiliation(s)
- Phoebe A Stapleton
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA.
| | - Christopher J Wingard
- College of Health Professions, School of Movement and Rehabilitation Sciences, Bellarmine University, Louisville, KY, USA
| | - Timothy R Nurkiewicz
- Department of Physiology, Pharmacology, and Neuroscience, Toxicology Working Group, West Virginia University, Morgantown, WV, USA
| | - Alison C Holloway
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, Ontario, Canada
| | - Judith T Zelikoff
- New York University School of Medicine, Dept. of Environmental Medicine, 57 Old Forge Road, Tuxedo, NY, USA
| | - Thomas B Knudsen
- National Center for Computational Toxicology, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Lynette K Rogers
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA.
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25
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Knudsen TB. Computational embryology as an integrative platform for predictive DART. Reprod Toxicol 2017. [DOI: 10.1016/j.reprotox.2017.06.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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26
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Abstract
Microphysiological systems (MPS) and computer simulation models that recapitulate the underlying biology and toxicology of critical developmental transitions are emerging tools for developmental effects assessment of drugs/chemicals. Opportunities and challenges exist for their application to alternative, more public health relevant and efficient chemical toxicity testing methods. This is especially pertinent to children's health research and the evaluation of complex embryological and reproductive impacts of drug/chemical exposure. Scaling these technologies to higher throughput is a key challenge and drives the need for in silico models for quantitative prediction of developmental toxicity to inform safety assessments. One example is cellular agent-based models, constructed from extant embryology, that produce data useful to simulate critical developmental transitions and thereby predict phenotypic consequences of disruption in silico. Biologically inspired MPS models built from human induced pluripotent stem (iPS)-derived cells and synthetic matrices that recapitulate organ-specific physiologies and native tissue architectures are providing exciting new research opportunities to advance the assessment of developmental toxicity and offer the possibility of deriving a full 'human on a chip' system, or a 'Homunculus.' Impact statement This 'commentary' summarizes research needs and opportunities for engineered MPS models for developmental and reproductive toxicity testing. Emerging concepts can be taken forward to a virtual tissue modeling framework for assessing chemical (and non-chemical) stressors on human development. These models will advance children's health research, both basic and translational and new ways to evaluate complex embryological and reproductive impacts of drug and chemical exposures to inform safety assessments.
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Affiliation(s)
- T B Knudsen
- 1 National Center for Computational Toxicology/EPA, Research Triangle Park, NC 27711, USA
| | - B Klieforth
- 2 National Center for Environmental Research/EPA, Washington, DC 20460, USA
| | - W Slikker
- 3 National Center for Toxicological Research/FDA, Jefferson, AR 72079, USA
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27
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Ellis-Hutchings RG, Settivari RS, McCoy AT, Kleinstreuer N, Franzosa J, Knudsen TB, Carney EW. Embryonic vascular disruption adverse outcomes: Linking high throughput signaling signatures with functional consequences. Reprod Toxicol 2017; 70:82-96. [PMID: 28527947 DOI: 10.1016/j.reprotox.2017.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Embryonic vascular disruption is an important adverse outcome pathway (AOP) as chemical disruption of cardiovascular development induces broad prenatal defects. High throughput screening (HTS) assays aid AOP development although linking in vitro data to in vivo apical endpoints remains challenging. This study evaluated two anti-angiogenic agents, 5HPP-33 and TNP-470, across the ToxCastDB HTS assay platform and anchored the results to complex in vitro functional assays: the rat aortic explant assay (AEA), rat whole embryo culture (WEC), and the zebrafish embryotoxicity (ZET) assay. Both were identified as putative vascular disruptive compounds (pVDCs) in ToxCastDB and disrupted angiogenesis and embryogenesis in the functional assays. Differences were observed in potency and adverse effects: 5HPP-33 was embryolethal (WEC and ZET); TNP-470 produced caudal defects at lower concentrations. This study demonstrates how a tiered approach using HTS signatures and complex functional in vitro assays might be used to prioritize further in vivo developmental toxicity testing.
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Affiliation(s)
- Robert G Ellis-Hutchings
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, 1803 Building, Midland, MI 48674, United States.
| | - Raja S Settivari
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, 1803 Building, Midland, MI 48674, United States
| | - Alene T McCoy
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, 1803 Building, Midland, MI 48674, United States
| | - Nicole Kleinstreuer
- National Toxicology Program Interagency Center for Evaluation of Alternative Toxicological Methods, Research Triangle Park, NC, 27711, United States
| | - Jill Franzosa
- National Center for Computational Toxicology, Office of Research and Development, United States Environmental Protection Agency, Research Triangle Park, NC, 27711, United States
| | - Thomas B Knudsen
- National Center for Computational Toxicology, Office of Research and Development, United States Environmental Protection Agency, Research Triangle Park, NC, 27711, United States
| | - Edward W Carney
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, 1803 Building, Midland, MI 48674, United States
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Abstract
Morphogenetic events are driven by cell-generated physical forces and complex cellular dynamics. To improve our capacity to predict developmental effects from chemical-induced cellular alterations, we built a multicellular agent-based model in CompuCell3D that recapitulates the cellular networks and collective cell behavior underlying growth and fusion of the mammalian secondary palate. The model incorporated multiple signaling pathways (TGFβ, BMP, FGF, EGF, and SHH) in a biological framework to recapitulate morphogenetic events from palatal outgrowth through midline fusion. It effectively simulated higher-level phenotypes (e.g., midline contact, medial edge seam (MES) breakdown, mesenchymal confluence, and fusion defects) in response to genetic or environmental perturbations. Perturbation analysis of various control features revealed model functionality with respect to cell signaling systems and feedback loops for growth and fusion, diverse individual cell behaviors and collective cellular behavior leading to physical contact and midline fusion, and quantitative analysis of the TGF/EGF switch that controls MES breakdown-a key event in morphogenetic fusion. The virtual palate model was then executed with theoretical chemical perturbation scenarios to simulate switch behavior leading to a disruption of fusion following chronic (e.g., dioxin) and acute (e.g., retinoic acid) chemical exposures. This computer model adds to similar systems models toward an integrative "virtual embryo" for simulation and quantitative prediction of adverse developmental outcomes following genetic perturbation and/or environmental disruption.
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Affiliation(s)
- M Shane Hutson
- Department of Physics & Astronomy, Department of Biological Sciences and Vanderbilt Institute for Integrative Biosystem Research & Education, Vanderbilt University , Nashville, Tennessee 37235, United States.,Oak Ridge Institute for Science & Education , Oak Ridge, Tennessee 37832, United States
| | - Maxwell C K Leung
- Oak Ridge Institute for Science & Education , Oak Ridge, Tennessee 37832, United States
| | - Nancy C Baker
- Leidos , Research Triangle Park, Durham, North Carolina 27711 United States
| | - Richard M Spencer
- Leidos , 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 , Research Triangle Park, Durham, North Carolina 27711, United States
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29
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Houck KA, Judson RS, Knudsen TB, Martin MT, Richard AM, Crofton KM, Simeonov A, Paules RS, Bucher JR, Thomas RS. Comment on "On the Utility of ToxCast™ and ToxPi as Methods for Identifying New Obesogens". Environ Health Perspect 2017; 125:A8-A11. [PMID: 28055944 PMCID: PMC5226707 DOI: 10.1289/ehp881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Keith A. Houck
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Richard S. Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Thomas B. Knudsen
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Matthew T. Martin
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Ann M. Richard
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Kevin M. Crofton
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Richard S. Paules
- National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - John R. Bucher
- National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Russell S. Thomas
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
- Address correspondence to R.S. Thomas, National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27705 USA. Telephone: 919-541-5776. E-mail:
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30
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Juberg DR, Knudsen TB, Sander M, Beck NB, Faustman EM, Mendrick DL, Fowle JR, Hartung T, Tice RR, Lemazurier E, Becker RA, Fitzpatrick SC, Daston GP, Harrill A, Hines RN, Keller DA, Lipscomb JC, Watson D, Bahadori T, Crofton KM. FutureTox III: Bridges for Translation. Toxicol Sci 2016; 155:22-31. [PMID: 27780885 DOI: 10.1093/toxsci/kfw194] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Future Tox III, a Society of Toxicology Contemporary Concepts in Toxicology workshop, was held in November 2015. Building upon Future Tox I and II, Future Tox III was focused on developing the high throughput risk assessment paradigm and taking the science of in vitro data and in silico models forward to explore the question-what progress is being made to address challenges in implementing the emerging big-data toolbox for risk assessment and regulatory decision-making. This article reports on the outcome of the workshop including 2 examples of where advancements in predictive toxicology approaches are being applied within Federal agencies, where opportunities remain within the exposome and AOP domains, and how collectively the toxicology community across multiple sectors can continue to bridge the translation from historical approaches to Tox21 implementation relative to risk assessment and regulatory decision-making.
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Affiliation(s)
| | - Thomas B Knudsen
- US Environmental Protection Agency, Research Triangle Park, North Carolina
| | | | - Nancy B Beck
- American Chemistry Council, Washington, The District of Columbia
| | | | | | - John R Fowle
- Science to Inform, LLC, Pittsboro, North Carolina
| | - Thomas Hartung
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Raymond R Tice
- National Toxicology Program/National Institute of Environmental Health Sciences, Durham, North Carolina
| | | | - Richard A Becker
- American Chemistry Council, Washington, The District of Columbia
| | | | | | - Alison Harrill
- University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Ronald N Hines
- US Environmental Protection Agency, Research Triangle Park, North Carolina
| | | | | | | | - Tina Bahadori
- US Environmental Protection Agency, Washington, The District of Columbia
| | - Kevin M Crofton
- US Environmental Protection Agency, Research Triangle Park, North Carolina
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31
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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] [What about the content of this article? (0)] [Affiliation(s)] [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: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Makris SL, Scott CS, Fox J, Knudsen TB, Hotchkiss AK, Arzuaga X, Euling SY, Powers CM, Jinot J, Hogan KA, Abbott BD, Hunter ES, Narotsky MG. A systematic evaluation of the potential effects of trichloroethylene exposure on cardiac development. Reprod Toxicol 2016; 65:321-358. [PMID: 27575429 PMCID: PMC9113522 DOI: 10.1016/j.reprotox.2016.08.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 07/27/2016] [Accepted: 08/25/2016] [Indexed: 11/26/2022]
Abstract
The 2011 EPA trichloroethylene (TCE) IRIS assessment, used developmental cardiac defects from a controversial drinking water study in rats (Johnson et al. [51]), along with several other studies/endpoints to derive reference values. An updated literature search of TCE-related developmental cardiac defects was conducted. Study quality, strengths, and limitations were assessed. A putative adverse outcome pathway (AOP) construct was developed to explore key events for the most commonly observed cardiac dysmorphologies, particularly those involved with epithelial-mesenchymal transition (EMT) of endothelial origin (EndMT); several candidate pathways were identified. A hypothesis-driven weight-of-evidence analysis of epidemiological, toxicological, in vitro, in ovo, and mechanistic/AOP data concluded that TCE has the potential to cause cardiac defects in humans when exposure occurs at sufficient doses during a sensitive window of fetal development. The study by Johnson et al. [51] was reaffirmed as suitable for hazard characterization and reference value derivation, though acknowledging study limitations and uncertainties.
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Judson R, Houck K, Martin M, Richard AM, Knudsen TB, Shah I, Little S, Wambaugh J, Setzer RW, Kothiya P, Phuong J, Filer D, Smith D, Reif D, Rotroff D, Kleinstreuer N, Sipes N, Xia M, Huang R, Crofton K, Thomas RS. Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space. Toxicol Sci 2016; 153:409. [PMID: 27605417 PMCID: PMC7297301 DOI: 10.1093/toxsci/kfw148] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Knudsen TB. Computational modeling and simulation of developmental toxicity. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.06.1245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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. Environ Health Perspect 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Shah I, Setzer RW, Jack J, Houck KA, Judson RS, Knudsen TB, Liu J, Martin MT, Reif DM, Richard AM, Thomas RS, Crofton KM, Dix DJ, Kavlock RJ. Using ToxCast™ Data to Reconstruct Dynamic Cell State Trajectories and Estimate Toxicological Points of Departure. Environ Health Perspect 2016; 124:910-9. [PMID: 26473631 PMCID: PMC4937847 DOI: 10.1289/ehp.1409029] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/12/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND High-content imaging (HCI) allows simultaneous measurement of multiple cellular phenotypic changes and is an important tool for evaluating the biological activity of chemicals. OBJECTIVES Our goal was to analyze dynamic cellular changes using HCI to identify the "tipping point" at which the cells did not show recovery towards a normal phenotypic state. METHODS HCI was used to evaluate the effects of 967 chemicals (in concentrations ranging from 0.4 to 200 μM) on HepG2 cells over a 72-hr exposure period. The HCI end points included p53, c-Jun, histone H2A.x, α-tubulin, histone H3, alpha tubulin, mitochondrial membrane potential, mitochondrial mass, cell cycle arrest, nuclear size, and cell number. A computational model was developed to interpret HCI responses as cell-state trajectories. RESULTS Analysis of cell-state trajectories showed that 336 chemicals produced tipping points and that HepG2 cells were resilient to the effects of 334 chemicals up to the highest concentration (200 μM) and duration (72 hr) tested. Tipping points were identified as concentration-dependent transitions in system recovery, and the corresponding critical concentrations were generally between 5 and 15 times (25th and 75th percentiles, respectively) lower than the concentration that produced any significant effect on HepG2 cells. The remaining 297 chemicals require more data before they can be placed in either of these categories. CONCLUSIONS These findings show the utility of HCI data for reconstructing cell state trajectories and provide insight into the adaptation and resilience of in vitro cellular systems based on tipping points. Cellular tipping points could be used to define a point of departure for risk-based prioritization of environmental chemicals. CITATION Shah I, Setzer RW, Jack J, Houck KA, Judson RS, Knudsen TB, Liu J, Martin MT, Reif DM, Richard AM, Thomas RS, Crofton KM, Dix DJ, Kavlock RJ. 2016. Using ToxCast™ data to reconstruct dynamic cell state trajectories and estimate toxicological points of departure. Environ Health Perspect 124:910-919; http://dx.doi.org/10.1289/ehp.1409029.
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Affiliation(s)
- Imran Shah
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - R. Woodrow Setzer
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - John Jack
- Department of Statistics, North Carolina State University, Raleigh, North Carolina, USA
| | - Keith A. Houck
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Richard S. Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Thomas B. Knudsen
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Jie Liu
- Oak Ridge Institute for Science Education (ORISE), U.S. Department of Energy, Oak Ridge, Tennessee, USA
| | - Matthew T. Martin
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - David M. Reif
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Ann M. Richard
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Russell S. Thomas
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Kevin M. Crofton
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - David J. Dix
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Robert J. Kavlock
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
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Judson R, Houck K, Martin M, Richard AM, Knudsen TB, Shah I, Little S, Wambaugh J, Woodrow Setzer R, Kothiya P, Phuong J, Filer D, Smith D, Reif D, Rotroff D, Kleinstreuer N, Sipes N, Xia M, Huang R, Crofton K, Thomas RS. Editor's Highlight: Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space. Toxicol Sci 2016; 152:323-39. [PMID: 27208079 DOI: 10.1093/toxsci/kfw092] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Chemical toxicity can arise from disruption of specific biomolecular functions or through more generalized cell stress and cytotoxicity-mediated processes. Here, responses of 1060 chemicals including pharmaceuticals, natural products, pesticidals, consumer, and industrial chemicals across a battery of 815 in vitro assay endpoints from 7 high-throughput assay technology platforms were analyzed in order to distinguish between these types of activities. Both cell-based and cell-free assays showed a rapid increase in the frequency of responses at concentrations where cell stress/cytotoxicity responses were observed in cell-based assays. Chemicals that were positive on at least 2 viability/cytotoxicity assays within the concentration range tested (typically up to 100 μM) activated a median of 12% of assay endpoints whereas those that were not cytotoxic in this concentration range activated 1.3% of the assays endpoints. The results suggest that activity can be broadly divided into: (1) specific biomolecular interactions against one or more targets (eg, receptors or enzymes) at concentrations below which overt cytotoxicity-associated activity is observed; and (2) activity associated with cell stress or cytotoxicity, which may result from triggering specific cell stress pathways, chemical reactivity, physico-chemical disruption of proteins or membranes, or broad low-affinity non-covalent interactions. Chemicals showing a greater number of specific biomolecular interactions are generally designed to be bioactive (pharmaceuticals or pesticidal active ingredients), whereas intentional food-use chemicals tended to show the fewest specific interactions. The analyses presented here provide context for use of these data in ongoing studies to predict in vivo toxicity from chemicals lacking extensive hazard assessment.
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Affiliation(s)
- Richard Judson
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina;
| | - Keith Houck
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Matt Martin
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Ann M Richard
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Thomas B Knudsen
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Imran Shah
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Stephen Little
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - John Wambaugh
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - R Woodrow Setzer
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Parth Kothiya
- Contractor to the U.S. EPA National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Jimmy Phuong
- Contractor to the U.S. EPA National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Dayne Filer
- ORISE Fellow at the U.S. EPA National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Doris Smith
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - David Reif
- Department of Statistics, North Carolina State University, Raleigh, North Carolina
| | - Daniel Rotroff
- Department of Statistics, North Carolina State University, Raleigh, North Carolina
| | | | - Nisha Sipes
- National Toxicology Program, Research Triangle Park, North Carolina
| | - Menghang Xia
- NIH National Center for Advancing Translational Sciences, Rockville, Maryland
| | - Ruili Huang
- NIH National Center for Advancing Translational Sciences, Rockville, Maryland
| | - Kevin Crofton
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
| | - Russell S Thomas
- *U.S. EPA, National Center for Computational Toxicology, Research Triangle Park, North Carolina
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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] [What about the content of this article? (0)] [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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Judson RS, Magpantay FM, Chickarmane V, Haskell C, Tania N, Taylor J, Xia M, Huang R, Rotroff DM, Filer DL, Houck KA, Martin MT, Sipes N, Richard AM, Mansouri K, Setzer RW, Knudsen TB, Crofton KM, Thomas RS. Integrated Model of Chemical Perturbations of a Biological Pathway Using 18 In Vitro High-Throughput Screening Assays for the Estrogen Receptor. Toxicol Sci 2015; 148:137-54. [PMID: 26272952 DOI: 10.1093/toxsci/kfv168] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We demonstrate a computational network model that integrates 18 in vitro, high-throughput screening assays measuring estrogen receptor (ER) binding, dimerization, chromatin binding, transcriptional activation, and ER-dependent cell proliferation. The network model uses activity patterns across the in vitro assays to predict whether a chemical is an ER agonist or antagonist, or is otherwise influencing the assays through a manner dependent on the physics and chemistry of the technology platform ("assay interference"). The method is applied to a library of 1812 commercial and environmental chemicals, including 45 ER positive and negative reference chemicals. Among the reference chemicals, the network model correctly identified the agonists and antagonists with the exception of very weak compounds whose activity was outside the concentration range tested. The model agonist score also correlated with the expected potency class of the active reference chemicals. Of the 1812 chemicals evaluated, 111 (6.1%) were predicted to be strongly ER active in agonist or antagonist mode. This dataset and model were also used to begin a systematic investigation of assay interference. The most prominent cause of false-positive activity (activity in an assay that is likely not due to interaction of the chemical with ER) is cytotoxicity. The model provides the ability to prioritize a large set of important environmental chemicals with human exposure potential for additional in vivo endocrine testing. Finally, this model is generalizable to any molecular pathway for which there are multiple upstream and downstream assays available.
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Affiliation(s)
- Richard S Judson
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711;
| | | | - Vijay Chickarmane
- Division of Biology, California Institute of Technology, Pasadena, California 91125
| | - Cymra Haskell
- §Department of Mathematics, University of Southern California, Los Angeles, California 90089
| | - Nessy Tania
- Department of Mathematics, Smith College, Northampton, Massachusetts 01063
| | - Jean Taylor
- Courant Institute, New York University, New York New York 10012
| | - Menghang Xia
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, Rockville, Maryland 20892
| | - Ruili Huang
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, Rockville, Maryland 20892
| | - Daniel M Rotroff
- Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27607
| | - Dayne L Filer
- **ORISE Fellow at the U.S. EPA, Research Triangle Park, North Carolina 27711
| | - Keith A Houck
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Matthew T Martin
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Nisha Sipes
- NIH National Toxicology Program, Research Triangle Park, North Carolina 27711
| | - Ann M Richard
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Kamel Mansouri
- **ORISE Fellow at the U.S. EPA, Research Triangle Park, North Carolina 27711
| | - R Woodrow Setzer
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Thomas B Knudsen
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Kevin M Crofton
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Russell S Thomas
- *U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
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Abstract
Risk assessment, in the context of public health, is the process of quantifying the probability of a harmful effect to individuals or populations from human activities. With increasing public health concern regarding the potential risks associated with chemical exposure, there is a need for more predictive and accurate approaches to risk assessment. Developing such an approach requires a mechanistic understanding of the process by which xenobiotic substances perturb biological systems and lead to toxicity. Supplementing the shortfalls of traditional risk assessment with mechanistic biological data has been widely discussed but not routinely implemented in the evaluation of chemical exposure. These mechanistic approaches to risk assessment have been generally referred to as systems toxicology. This Symposium Overview article summarizes 4 talks presented at the 35th Annual Meeting of the American College of Toxicology.
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Affiliation(s)
- John Michael Sauer
- Predictive Safety Testing Consortium (PSTC), Critical Path Institute, Tucson, AZ, USA
| | - Thomas Hartung
- Bloomberg School of Public Health, John Hopkins University, Baltimore, MD, USA
| | | | - Thomas B Knudsen
- US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Julia Hoeng
- Philip Morris International R&D, Neuchâtel, Switzerland
| | - A Wallace Hayes
- Harvard University, Cambridge, MA, USA University of Massachusetts School of Public Health, Amherst, MA, USA
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Knudsen TB, Keller DA, Sander M, Carney EW, Doerrer NG, Eaton DL, Fitzpatrick SC, Hastings KL, Mendrick DL, Tice RR, Watkins PB, Whelan M. FutureTox II: in vitro data and in silico models for predictive toxicology. Toxicol Sci 2015; 143:256-67. [PMID: 25628403 PMCID: PMC4318934 DOI: 10.1093/toxsci/kfu234] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
FutureTox II, a Society of Toxicology Contemporary Concepts in Toxicology workshop, was held in January, 2014. The meeting goals were to review and discuss the state of the science in toxicology in the context of implementing the NRC 21st century vision of predicting in vivo responses from in vitro and in silico data, and to define the goals for the future. Presentations and discussions were held on priority concerns such as predicting and modeling of metabolism, cell growth and differentiation, effects on sensitive subpopulations, and integrating data into risk assessment. Emerging trends in technologies such as stem cell-derived human cells, 3D organotypic culture models, mathematical modeling of cellular processes and morphogenesis, adverse outcome pathway development, and high-content imaging of in vivo systems were discussed. Although advances in moving towards an in vitro/in silico based risk assessment paradigm were apparent, knowledge gaps in these areas and limitations of technologies were identified. Specific recommendations were made for future directions and research needs in the areas of hepatotoxicity, cancer prediction, developmental toxicity, and regulatory toxicology.
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Affiliation(s)
- Thomas B Knudsen
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
| | - Douglas A Keller
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
| | - Miriam Sander
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
| | - Edward W Carney
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
| | - Nancy G Doerrer
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
| | - David L Eaton
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
| | - Suzanne Compton Fitzpatrick
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
| | - Kenneth L Hastings
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
| | - Donna L Mendrick
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
| | - Raymond R Tice
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
| | - Paul B Watkins
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
| | - Maurice Whelan
- United States Environmental Protection Agency, Research Triangle Park, North Carolina 27711, Sanofi, Bridgewater, New Jersey 08807, Page One Editorial Services, Boulder, Colorado 80304, Dow Chemical Company, Midland, Michigan 48674, Health and Environmental Sciences Institute, Washington, District of Columbia 20005, University of Washington, Seattle, Washington 98105, United States Food and Drug Administration, Silver Spring, Maryland 20993, Sanofi, Bethesda, Maryland 20814, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, University of North Carolina, Chapel Hill, North Carolina 27599, The Hamner Institutes, Research Triangle Park, North Carolina 27709, and European Commission Joint Research Centre, I-21027 Ispra, Italy
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Knudsen TB. Identifying key events in AOPs for embryonic disruption using computational toxicology. Reprod Toxicol 2014. [DOI: 10.1016/j.reprotox.2014.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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45
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Rotroff DM, Martin MT, Dix DJ, Filer DL, Houck KA, Knudsen TB, Sipes NS, Reif DM, Xia M, Huang R, Judson RS. Predictive endocrine testing in the 21st century using in vitro assays of estrogen receptor signaling responses. Environ Sci Technol 2014; 48:8706-8716. [PMID: 24960280 DOI: 10.1021/es502676e] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Thousands of environmental chemicals are subject to regulatory review for their potential to be endocrine disruptors (ED). In vitro high-throughput screening (HTS) assays have emerged as a potential tool for prioritizing chemicals for ED-related whole-animal tests. In this study, 1814 chemicals including pesticide active and inert ingredients, industrial chemicals, food additives, and pharmaceuticals were evaluated in a panel of 13 in vitro HTS assays. The panel of in vitro assays interrogated multiple end points related to estrogen receptor (ER) signaling, namely binding, agonist, antagonist, and cell growth responses. The results from the in vitro assays were used to create an ER Interaction Score. For 36 reference chemicals, an ER Interaction Score >0 showed 100% sensitivity and 87.5% specificity for classifying potential ER activity. The magnitude of the ER Interaction Score was significantly related to the potency classification of the reference chemicals (p < 0.0001). ERα/ERβ selectivity was also evaluated, but relatively few chemicals showed significant selectivity for a specific isoform. When applied to a broader set of chemicals with in vivo uterotrophic data, the ER Interaction Scores showed 91% sensitivity and 65% specificity. Overall, this study provides a novel method for combining in vitro concentration response data from multiple assays and, when applied to a large set of ER data, accurately predicted estrogenic responses and demonstrated its utility for chemical prioritization.
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Affiliation(s)
- Daniel M Rotroff
- Department of Environmental Sciences and Engineering, University of North Carolina , Chapel Hill, North Carolina 27514, United States
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Green ML, Pisano MM, Prough RA, Knudsen TB. Release of targeted p53 from the mitochondrion as an early signal during mitochondrial dysfunction. Cell Signal 2013; 25:2383-90. [PMID: 23899557 PMCID: PMC3826263 DOI: 10.1016/j.cellsig.2013.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 07/08/2013] [Accepted: 07/19/2013] [Indexed: 01/28/2023]
Abstract
Increased accumulation of p53 tumor suppressor protein is an early response to low-level stressors. To investigate the fate of mitochondrial-sequestered p53, mouse embryonic fibroblast cells (MEFs) on a p53-deficient genetic background were transfected with p53-EGFP fusion protein led by a sense (m53-EGFP) or antisense (c53-EGFP) mitochondrial import signal. Rotenone exposure (100nM, 1h) triggered the translocation of m53-EGFP from the mitochondrion to the nucleus, thus shifting the transfected cells from a mitochondrial p53 to a nuclear p53 state. Antibodies for p53 serine phosphorylation or lysine acetylation indicated a different post-translational status of recombinant p53 in the nucleus and mitochondrion, respectively. These data suggest that cycling of p53 through the mitochondria may establish a direct pathway for p53 signaling from the mitochondria to the nucleus during mitochondrial dysfunction. PK11195, a pharmacological ligand of mitochondrial TSPO (formerly known as the peripheral-type benzodiazepine receptor), partially suppressed the release of mitochondria-sequestered p53. These findings support the notion that p53 function mediates a direct signaling pathway from the mitochondria to nucleus during mitochondrial dysfunction.
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Affiliation(s)
- M L Green
- Department of Molecular, Cellular and Craniofacial Biology, University of Louisville, 501 S. Preston St., Louisville, KY 40202, USA; Department of Biochemistry and Molecular Biology, University of Louisville School of Medicine, Louisville, KY 40292, USA.
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Hao R, Bondesson M, Singh AV, Riu A, McCollum CW, Knudsen TB, Gorelick DA, Gustafsson JÅ. Identification of estrogen target genes during zebrafish embryonic development through transcriptomic analysis. PLoS One 2013; 8:e79020. [PMID: 24223173 PMCID: PMC3819264 DOI: 10.1371/journal.pone.0079020] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 09/17/2013] [Indexed: 12/26/2022] Open
Abstract
Estrogen signaling is important for vertebrate embryonic development. Here we have used zebrafish (Danio rerio) as a vertebrate model to analyze estrogen signaling during development. Zebrafish embryos were exposed to 1 µM 17β-estradiol (E2) or vehicle from 3 hours to 4 days post fertilization (dpf), harvested at 1, 2, 3 and 4 dpf, and subjected to RNA extraction for transcriptome analysis using microarrays. Differentially expressed genes by E2-treatment were analyzed with hierarchical clustering followed by biological process and tissue enrichment analysis. Markedly distinct sets of genes were up and down-regulated by E2 at the four different time points. Among these genes, only the well-known estrogenic marker vtg1 was co-regulated at all time points. Despite this, the biological functional categories targeted by E2 were relatively similar throughout zebrafish development. According to knowledge-based tissue enrichment, estrogen responsive genes were clustered mainly in the liver, pancreas and brain. This was in line with the developmental dynamics of estrogen-target tissues that were visualized using transgenic zebrafish containing estrogen responsive elements driving the expression of GFP (Tg(5xERE:GFP)). Finally, the identified embryonic estrogen-responsive genes were compared to already published estrogen-responsive genes identified in male adult zebrafish (Gene Expression Omnibus database). The expressions of a few genes were co-regulated by E2 in both embryonic and adult zebrafish. These could potentially be used as estrogenic biomarkers for exposure to estrogens or estrogenic endocrine disruptors in zebrafish. In conclusion, our data suggests that estrogen effects on early embryonic zebrafish development are stage- and tissue- specific.
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Affiliation(s)
- Ruixin Hao
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Maria Bondesson
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail:
| | - Amar V. Singh
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Anne Riu
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Catherine W. McCollum
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Thomas B. Knudsen
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Daniel A. Gorelick
- Department of Embryology, Carnegie Institute for Science, Baltimore, Maryland, United States of America
| | - Jan-Åke Gustafsson
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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Wambaugh JF, Setzer RW, Reif DM, Gangwal S, Mitchell-Blackwood J, Arnot JA, Joliet O, Frame A, Rabinowitz J, Knudsen TB, Judson RS, Egeghy P, Vallero D, Cohen Hubal EA. High-throughput models for exposure-based chemical prioritization in the ExpoCast project. Environ Sci Technol 2013; 47:8479-88. [PMID: 23758710 DOI: 10.1021/es400482g] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The United States Environmental Protection Agency (U.S. EPA) must characterize potential risks to human health and the environment associated with manufacture and use of thousands of chemicals. High-throughput screening (HTS) for biological activity allows the ToxCast research program to prioritize chemical inventories for potential hazard. Similar capabilities for estimating exposure potential would support rapid risk-based prioritization for chemicals with limited information; here, we propose a framework for high-throughput exposure assessment. To demonstrate application, an analysis was conducted that predicts human exposure potential for chemicals and estimates uncertainty in these predictions by comparison to biomonitoring data. We evaluated 1936 chemicals using far-field mass balance human exposure models (USEtox and RAIDAR) and an indicator for indoor and/or consumer use. These predictions were compared to exposures inferred by Bayesian analysis from urine concentrations for 82 chemicals reported in the National Health and Nutrition Examination Survey (NHANES). Joint regression on all factors provided a calibrated consensus prediction, the variance of which serves as an empirical determination of uncertainty for prioritization on absolute exposure potential. Information on use was found to be most predictive; generally, chemicals above the limit of detection in NHANES had consumer/indoor use. Coupled with hazard HTS, exposure HTS can place risk earlier in decision processes. High-priority chemicals become targets for further data collection.
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Affiliation(s)
- John F Wambaugh
- National Center for Computational Toxicology, United States Environmental Protection Agency , Research Triangle Park, North Carolina 27711, United States.
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Sipes NS, Martin MT, Kothiya P, Reif DM, Judson RS, Richard AM, Houck K, Dix DJ, Kavlock RJ, Knudsen TB. Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem Res Toxicol 2013; 26:878-95. [PMID: 23611293 PMCID: PMC3685188 DOI: 10.1021/tx400021f] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Indexed: 11/30/2022]
Abstract
Understanding potential health risks is a significant challenge due to the large numbers of diverse chemicals with poorly characterized exposures and mechanisms of toxicities. The present study analyzes 976 chemicals (including failed pharmaceuticals, alternative plasticizers, food additives, and pesticides) in Phases I and II of the U.S. EPA's ToxCast project across 331 cell-free enzymatic and ligand-binding high-throughput screening (HTS) assays. Half-maximal activity concentrations (AC50) were identified for 729 chemicals in 256 assays (7,135 chemical-assay pairs). Some of the most commonly affected assays were CYPs (CYP2C9 and CYP2C19), transporters (mitochondrial TSPO, norepinephrine, and dopaminergic), and GPCRs (aminergic). Heavy metals, surfactants, and dithiocarbamate fungicides showed promiscuous but distinctly different patterns of activity, whereas many of the pharmaceutical compounds showed promiscuous activity across GPCRs. Literature analysis confirmed >50% of the activities for the most potent chemical-assay pairs (54) but also revealed 10 missed interactions. Twenty-two chemicals with known estrogenic activity were correctly identified for the majority (77%), missing only the weaker interactions. In many cases, novel findings for previously unreported chemical-target combinations clustered with known chemical-target interactions. Results from this large inventory of chemical-biological interactions can inform read-across methods as well as link potential targets to molecular initiating events in adverse outcome pathways for diverse toxicities.
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Affiliation(s)
- Nisha S. Sipes
- National
Center for Computational Toxicology, Office
of Research and Development, U.S. Environmental Protection
Agency, Research Triangle Park, North Carolina 27711,
United States
| | - Matthew T. Martin
- National
Center for Computational Toxicology, Office
of Research and Development, U.S. Environmental Protection
Agency, Research Triangle Park, North Carolina 27711,
United States
| | - Parth Kothiya
- National
Center for Computational Toxicology, Office
of Research and Development, U.S. Environmental Protection
Agency, Research Triangle Park, North Carolina 27711,
United States
| | - David M. Reif
- National
Center for Computational Toxicology, Office
of Research and Development, U.S. Environmental Protection
Agency, Research Triangle Park, North Carolina 27711,
United States
| | - Richard S. Judson
- National
Center for Computational Toxicology, Office
of Research and Development, U.S. Environmental Protection
Agency, Research Triangle Park, North Carolina 27711,
United States
| | - Ann M. Richard
- National
Center for Computational Toxicology, Office
of Research and Development, U.S. Environmental Protection
Agency, Research Triangle Park, North Carolina 27711,
United States
| | - Keith
A. Houck
- National
Center for Computational Toxicology, Office
of Research and Development, U.S. Environmental Protection
Agency, Research Triangle Park, North Carolina 27711,
United States
| | - David J. Dix
- National
Center for Computational Toxicology, Office
of Research and Development, U.S. Environmental Protection
Agency, Research Triangle Park, North Carolina 27711,
United States
| | - Robert J. Kavlock
- National
Center for Computational Toxicology, Office
of Research and Development, U.S. Environmental Protection
Agency, Research Triangle Park, North Carolina 27711,
United States
| | - Thomas B. Knudsen
- National
Center for Computational Toxicology, Office
of Research and Development, U.S. Environmental Protection
Agency, Research Triangle Park, North Carolina 27711,
United States
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50
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Sipes NS, Martin MT, Kothiya P, Reif DM, Judson RS, Richard AM, Houck KA, Dix DJ, Kavlock RJ, Knudsen TB. Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. Chem Res Toxicol 2013; 26:878-895. [PMID: 23611293 DOI: 10.1021/tx400021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Understanding potential health risks is a significant challenge due to the large numbers of diverse chemicals with poorly characterized exposures and mechanisms of toxicities. The present study analyzes 976 chemicals (including failed pharmaceuticals, alternative plasticizers, food additives, and pesticides) in Phases I and II of the U.S. EPA's ToxCast project across 331 cell-free enzymatic and ligand-binding high-throughput screening (HTS) assays. Half-maximal activity concentrations (AC50) were identified for 729 chemicals in 256 assays (7,135 chemical-assay pairs). Some of the most commonly affected assays were CYPs (CYP2C9 and CYP2C19), transporters (mitochondrial TSPO, norepinephrine, and dopaminergic), and GPCRs (aminergic). Heavy metals, surfactants, and dithiocarbamate fungicides showed promiscuous but distinctly different patterns of activity, whereas many of the pharmaceutical compounds showed promiscuous activity across GPCRs. Literature analysis confirmed >50% of the activities for the most potent chemical-assay pairs (54) but also revealed 10 missed interactions. Twenty-two chemicals with known estrogenic activity were correctly identified for the majority (77%), missing only the weaker interactions. In many cases, novel findings for previously unreported chemical-target combinations clustered with known chemical-target interactions. Results from this large inventory of chemical-biological interactions can inform read-across methods as well as link potential targets to molecular initiating events in adverse outcome pathways for diverse toxicities.
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Affiliation(s)
- Nisha S Sipes
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA.
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