1
|
Mittal K, Arini A, Basu N. Screening 800 putative endocrine disrupting chemicals in a representative mammal, bird, and fish using a neurochemical cell-free testing platform. CHEMOSPHERE 2024:142562. [PMID: 38851506 DOI: 10.1016/j.chemosphere.2024.142562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/26/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024]
Abstract
There is global demand for novel ecotoxicity testing tools that are based on alternative to animal models, have high throughput potential, and may be applicable to a wide diversity of taxa. Here we scaled up a microplate-based cell-free neurochemical testing platform to screen 800 putative endocrine disrupting chemicals from the U.S. Environmental Protection Agency's ToxCast e1k library against the glutamate (NMDA), muscarinic acetylcholine (mACh), and dopamine (D2) receptors. Each assay was tested in cellular membranes isolated from brain tissues from a representative bird (zebra finch = Taeniopygia castanotis), mammal (mink = Neogale vison), and fish (rainbow trout = Oncorhynchus mykiss). The primary objective of this short communication was to make the results database accessible, while also summarising key attributes of assay performance and presenting some initial observations. In total, 7,200 species-chemical-assay combinations were tested, of which 453 combinations were classified as a hit (radioligand binding changed by at least 3 standard deviations). There were some differences across species, and most hits were found for the D2 and NMDA receptors. The most active chemical was C.I. Solvent Yellow 14 followed by Diphenhydramine hydrochloride, Gentian Violet, SR271425, and Zamifenacin. Nine chemicals were tested across multiple plates with a mean relative standard deviation of the specific radioligand binding data being 24.6%. The results demonstrate that cell-free assays may serve as screening tool for large chemical libraries especially for ecological species not easily studied using traditional methods.
Collapse
Affiliation(s)
- Krittika Mittal
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Adeline Arini
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada
| | - Niladri Basu
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada.
| |
Collapse
|
2
|
Di Stefano M, Galati S, Piazza L, Granchi C, Mancini S, Fratini F, Macchia M, Poli G, Tuccinardi T. VenomPred 2.0: A Novel In Silico Platform for an Extended and Human Interpretable Toxicological Profiling of Small Molecules. J Chem Inf Model 2024; 64:2275-2289. [PMID: 37676238 PMCID: PMC11005041 DOI: 10.1021/acs.jcim.3c00692] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Indexed: 09/08/2023]
Abstract
The application of artificial intelligence and machine learning (ML) methods is becoming increasingly popular in computational toxicology and drug design; it is considered as a promising solution for assessing the safety profile of compounds, particularly in lead optimization and ADMET studies, and to meet the principles of the 3Rs, which calls for the replacement, reduction, and refinement of animal testing. In this context, we herein present the development of VenomPred 2.0 (http://www.mmvsl.it/wp/venompred2/), the new and improved version of our free of charge web tool for toxicological predictions, which now represents a powerful web-based platform for multifaceted and human-interpretable in silico toxicity profiling of chemicals. VenomPred 2.0 presents an extended set of toxicity endpoints (androgenicity, skin irritation, eye irritation, and acute oral toxicity, in addition to the already available carcinogenicity, mutagenicity, hepatotoxicity, and estrogenicity) that can be evaluated through an exhaustive consensus prediction strategy based on multiple ML models. Moreover, we also implemented a new utility based on the Shapley Additive exPlanations (SHAP) method that allows human interpretable toxicological profiling of small molecules, highlighting the features that strongly contribute to the toxicological predictions in order to derive structural toxicophores.
Collapse
Affiliation(s)
- Miriana Di Stefano
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
- Department
of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Salvatore Galati
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Lisa Piazza
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Carlotta Granchi
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Simone Mancini
- Department
of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124 Pisa, Italy
| | - Filippo Fratini
- Department
of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124 Pisa, Italy
| | - Marco Macchia
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Giulio Poli
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Department
of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| |
Collapse
|
3
|
Glassmeyer ST, Burns EE, Focazio MJ, Furlong ET, Gribble MO, Jahne MA, Keely SP, Kennicutt AR, Kolpin DW, Medlock Kakaley EK, Pfaller SL. Water, Water Everywhere, but Every Drop Unique: Challenges in the Science to Understand the Role of Contaminants of Emerging Concern in the Management of Drinking Water Supplies. GEOHEALTH 2023; 7:e2022GH000716. [PMID: 38155731 PMCID: PMC10753268 DOI: 10.1029/2022gh000716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 12/30/2023]
Abstract
The protection and management of water resources continues to be challenged by multiple and ongoing factors such as shifts in demographic, social, economic, and public health requirements. Physical limitations placed on access to potable supplies include natural and human-caused factors such as aquifer depletion, aging infrastructure, saltwater intrusion, floods, and drought. These factors, although varying in magnitude, spatial extent, and timing, can exacerbate the potential for contaminants of concern (CECs) to be present in sources of drinking water, infrastructure, premise plumbing and associated tap water. This monograph examines how current and emerging scientific efforts and technologies increase our understanding of the range of CECs and drinking water issues facing current and future populations. It is not intended to be read in one sitting, but is instead a starting point for scientists wanting to learn more about the issues surrounding CECs. This text discusses the topical evolution CECs over time (Section 1), improvements in measuring chemical and microbial CECs, through both analysis of concentration and toxicity (Section 2) and modeling CEC exposure and fate (Section 3), forms of treatment effective at removing chemical and microbial CECs (Section 4), and potential for human health impacts from exposure to CECs (Section 5). The paper concludes with how changes to water quantity, both scarcity and surpluses, could affect water quality (Section 6). Taken together, these sections document the past 25 years of CEC research and the regulatory response to these contaminants, the current work to identify and monitor CECs and mitigate exposure, and the challenges facing the future.
Collapse
Affiliation(s)
- Susan T. Glassmeyer
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
| | | | - Michael J. Focazio
- Retired, Environmental Health ProgramEcosystems Mission AreaU.S. Geological SurveyRestonVAUSA
| | - Edward T. Furlong
- Emeritus, Strategic Laboratory Sciences BranchLaboratory & Analytical Services DivisionU.S. Geological SurveyDenverCOUSA
| | - Matthew O. Gribble
- Gangarosa Department of Environmental HealthRollins School of Public HealthEmory UniversityAtlantaGAUSA
| | - Michael A. Jahne
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
| | - Scott P. Keely
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
| | - Alison R. Kennicutt
- Department of Civil and Mechanical EngineeringYork College of PennsylvaniaYorkPAUSA
| | - Dana W. Kolpin
- U.S. Geological SurveyCentral Midwest Water Science CenterIowa CityIAUSA
| | | | - Stacy L. Pfaller
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
| |
Collapse
|
4
|
Eytcheson SA, Olker JH, Friedman KP, Hornung MW, Degitz SJ. Assessing utility of thyroid in vitro screening assays through comparisons to observed impacts in vivo. Regul Toxicol Pharmacol 2023; 144:105491. [PMID: 37666444 DOI: 10.1016/j.yrtph.2023.105491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 08/22/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
To better understand endocrine disruption, the U.S. Environmental Protection Agency's (USEPA) Endocrine Disruptor Screening Program (EDSP) utilizes a two-tiered approach to investigate the potential of a chemical to interact with the estrogen, androgen, or thyroid systems. As in vivo testing lacks the throughput to address data gaps on endocrine bioactivity for thousands of chemicals, in vitro high-throughput screening (HTS) methods are being developed to screen larger chemical libraries. The primary objective of this work was to investigate for how many of the 52 chemicals with weight-of-evidence (WoE) determinations from EDSP Tier 1 screening there are available in vitro HTS data supporting a thyroid impact. HTS data from the USEPA ToxCast program and the EDSP WoE were collected for this analysis. Considering the complexity of endocrine disruption and interpreting HTS data, concordance between in vitro activity and in vivo effects ranges from 58 to 78%. Based on this evaluation, we conclude that the current suite of HTS assays is beneficial for prioritizing chemicals for further inquiry; however, without a more detailed analysis, one cannot conclude whether HTS results are the primary mode-of-action. Furthermore, development of in vitro assays for additional thyroid-relevant molecular initiating events is required to effectively predict in vivo thyroid impacts.
Collapse
Affiliation(s)
- Stephanie A Eytcheson
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA; U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Duluth, MN, 55804, USA
| | - Jennifer H Olker
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Duluth, MN, 55804, USA
| | - Katie Paul Friedman
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Biomolecular and Computational Toxicology Division, Research Triangle Park, NC, 27711, USA
| | - Michael W Hornung
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Duluth, MN, 55804, USA
| | - Sigmund J Degitz
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Duluth, MN, 55804, USA.
| |
Collapse
|
5
|
Luo YS, Chen Z, Hsieh NH, Lin TE. Chemical and biological assessments of environmental mixtures: A review of current trends, advances, and future perspectives. JOURNAL OF HAZARDOUS MATERIALS 2022; 432:128658. [PMID: 35290896 DOI: 10.1016/j.jhazmat.2022.128658] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/21/2022] [Accepted: 03/07/2022] [Indexed: 05/28/2023]
Abstract
Considering the chemical complexity and toxicity data gaps of environmental mixtures, most studies evaluate the chemical risk individually. However, humans are usually exposed to a cocktail of chemicals in real life. Mixture health assessment remains to be a research area having significant knowledge gaps. Characterization of chemical composition and bioactivity/toxicity are the two critical aspects of mixture health assessments. This review seeks to introduce the recent progress and tools for the chemical and biological characterization of environmental mixtures. The state-of-the-art techniques include the sampling, extraction, rapid detection methods, and the in vitro, in vivo, and in silico approaches to generate the toxicity data of an environmental mixture. Application of these novel methods, or new approach methodologies (NAMs), has increased the throughput of generating chemical and toxicity data for mixtures and thus refined the mixture health assessment. Combined with computational methods, the chemical and biological information would shed light on identifying the bioactive/toxic components in an environmental mixture.
Collapse
Affiliation(s)
- Yu-Syuan Luo
- Institute of Food Safety and Health, College of Public Health, National Taiwan University, Taipei City, Taiwan.
| | - Zunwei Chen
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nan-Hung Hsieh
- Interdisciplinary Faculty of Toxicology and Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Tzu-En Lin
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| |
Collapse
|
6
|
Robitaille J, Denslow ND, Escher BI, Kurita-Oyamada HG, Marlatt V, Martyniuk CJ, Navarro-Martín L, Prosser R, Sanderson T, Yargeau V, Langlois VS. Towards regulation of Endocrine Disrupting chemicals (EDCs) in water resources using bioassays - A guide to developing a testing strategy. ENVIRONMENTAL RESEARCH 2022; 205:112483. [PMID: 34863984 DOI: 10.1016/j.envres.2021.112483] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are found in every environmental medium and are chemically diverse. Their presence in water resources can negatively impact the health of both human and wildlife. Currently, there are no mandatory screening mandates or regulations for EDC levels in complex water samples globally. Bioassays, which allow quantifying in vivo or in vitro biological effects of chemicals are used commonly to assess acute toxicity in water. The existing OECD framework to identify single-compound EDCs offers a set of bioassays that are validated for the Estrogen-, Androgen-, and Thyroid hormones, and for Steroidogenesis pathways (EATS). In this review, we discussed bioassays that could be potentially used to screen EDCs in water resources, including in vivo and in vitro bioassays using invertebrates, fish, amphibians, and/or mammalians species. Strengths and weaknesses of samples preparation for complex water samples are discussed. We also review how to calculate the Effect-Based Trigger values, which could serve as thresholds to determine if a given water sample poses a risk based on existing quality standards. This work aims to assist governments and regulatory agencies in developing a testing strategy towards regulation of EDCs in water resources worldwide. The main recommendations include 1) opting for internationally validated cell reporter in vitro bioassays to reduce animal use & cost; 2) testing for cell viability (a critical parameter) when using in vitro bioassays; and 3) evaluating the recovery of the water sample preparation method selected. This review also highlights future research avenues for the EDC screening revolution (e.g., 3D tissue culture, transgenic animals, OMICs, and Adverse Outcome Pathways (AOPs)).
Collapse
Affiliation(s)
- Julie Robitaille
- Centre Eau Terre Environnement, Institut National de La Recherche Scientifique (INRS), Quebec City, QC, Canada
| | | | - Beate I Escher
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany; Eberhard Karls University Tübingen, Tübingen, Germany
| | | | - Vicki Marlatt
- Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | | | - Thomas Sanderson
- Centre Armand-Frappier Santé Biotechnologie, INRS, Laval, QC, Canada
| | | | - Valerie S Langlois
- Centre Eau Terre Environnement, Institut National de La Recherche Scientifique (INRS), Quebec City, QC, Canada.
| |
Collapse
|
7
|
Grouping of chemicals into mode of action classes by automated effect pattern analysis using the zebrafish embryo toxicity test. Arch Toxicol 2022; 96:1353-1369. [PMID: 35254489 PMCID: PMC9013687 DOI: 10.1007/s00204-022-03253-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/15/2022] [Indexed: 11/17/2022]
Abstract
A central element of high throughput screens for chemical effect assessment using zebrafish is the assessment and quantification of phenotypic changes. By application of an automated and more unbiased analysis of these changes using image analysis, patterns of phenotypes may be associated with the mode of action (MoA) of the exposure chemical. The aim of our study was to explore to what extent compounds can be grouped according to their anticipated toxicological or pharmacological mode of action using an automated quantitative multi-endpoint zebrafish test. Chemical-response signatures for 30 endpoints, covering phenotypic and functional features, were generated for 25 chemicals assigned to 8 broad MoA classes. Unsupervised clustering of the profiling data demonstrated that chemicals were partially grouped by their main MoA. Analysis with a supervised clustering technique such as a partial least squares discriminant analysis (PLS-DA) allowed to identify markers with a strong potential to discriminate between MoAs such as mandibular arch malformation observed for compounds interfering with retinoic acid signaling. The capacity for discriminating MoAs was also benchmarked to an available battery of in vitro toxicity data obtained from ToxCast library indicating a partially similar performance. Further, we discussed to which extent the collected dataset indicated indeed differences for compounds with presumably similar MoA or whether other factors such as toxicokinetic differences could have an important impact on the determined response patterns.
Collapse
|
8
|
Ciallella HL, Russo DP, Aleksunes LM, Grimm FA, Zhu H. Revealing Adverse Outcome Pathways from Public High-Throughput Screening Data to Evaluate New Toxicants by a Knowledge-Based Deep Neural Network Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10875-10887. [PMID: 34304572 PMCID: PMC8713073 DOI: 10.1021/acs.est.1c02656] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Traditional experimental testing to identify endocrine disruptors that enhance estrogenic signaling relies on expensive and labor-intensive experiments. We sought to design a knowledge-based deep neural network (k-DNN) approach to reveal and organize public high-throughput screening data for compounds with nuclear estrogen receptor α and β (ERα and ERβ) binding potentials. The target activity was rodent uterotrophic bioactivity driven by ERα/ERβ activations. After training, the resultant network successfully inferred critical relationships among ERα/ERβ target bioassays, shown as weights of 6521 edges between 1071 neurons. The resultant network uses an adverse outcome pathway (AOP) framework to mimic the signaling pathway initiated by ERα and identify compounds that mimic endogenous estrogens (i.e., estrogen mimetics). The k-DNN can predict estrogen mimetics by activating neurons representing several events in the ERα/ERβ signaling pathway. Therefore, this virtual pathway model, starting from a compound's chemistry initiating ERα activation and ending with rodent uterotrophic bioactivity, can efficiently and accurately prioritize new estrogen mimetics (AUC = 0.864-0.927). This k-DNN method is a potential universal computational toxicology strategy to utilize public high-throughput screening data to characterize hazards and prioritize potentially toxic compounds.
Collapse
Affiliation(s)
- Heather L Ciallella
- Center for Computational and Integrative Biology, Rutgers University Camden, Camden, New Jersey 08103, United States
| | - Daniel P Russo
- Center for Computational and Integrative Biology, Rutgers University Camden, Camden, New Jersey 08103, United States
- Department of Chemistry, Rutgers University Camden, Camden, New Jersey 08102, United States
| | - Lauren M Aleksunes
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Fabian A Grimm
- ExxonMobil Biomedical Sciences, Inc., Annandale, New Jersey 08801, United States
| | - Hao Zhu
- Center for Computational and Integrative Biology, Rutgers University Camden, Camden, New Jersey 08103, United States
- Department of Chemistry, Rutgers University Camden, Camden, New Jersey 08102, United States
| |
Collapse
|
9
|
Zurlinden TJ, Saili KS, Rush N, Kothiya P, Judson RS, Houck KA, Hunter ES, Baker NC, Palmer JA, Thomas RS, Knudsen TB. Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity. Toxicol Sci 2021; 174:189-209. [PMID: 32073639 DOI: 10.1093/toxsci/kfaa014] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The Stemina devTOX quickPredict platform is a human pluripotent stem cell-based assay that predicts the developmental toxicity potential based on changes in cellular metabolism following chemical exposure [Palmer, J. A., Smith, A. M., Egnash, L. A., Conard, K. R., West, P. R., Burrier, R. E., Donley, E. L. R., and Kirchner, F. R. (2013). Establishment and assessment of a new human embryonic stem cell-based biomarker assay for developmental toxicity screening. Birth Defects Res. B Dev. Reprod. Toxicol. 98, 343-363]. Using this assay, we screened 1065 ToxCast phase I and II chemicals in single-concentration or concentration-response for the targeted biomarker (ratio of ornithine to cystine secreted or consumed from the media). The dataset from the Stemina (STM) assay is annotated in the ToxCast portfolio as STM. Major findings from the analysis of ToxCast_STM dataset include (1) 19% of 1065 chemicals yielded a prediction of developmental toxicity, (2) assay performance reached 79%-82% accuracy with high specificity (> 84%) but modest sensitivity (< 67%) when compared with in vivo animal models of human prenatal developmental toxicity, (3) sensitivity improved as more stringent weights of evidence requirements were applied to the animal studies, and (4) statistical analysis of the most potent chemical hits on specific biochemical targets in ToxCast revealed positive and negative associations with the STM response, providing insights into the mechanistic underpinnings of the targeted endpoint and its biological domain. The results of this study will be useful to improving our ability to predict in vivo developmental toxicants based on in vitro data and in silico models.
Collapse
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
| | | | | | | | | |
Collapse
|
10
|
Ciallella HL, Russo DP, Aleksunes LM, Grimm FA, Zhu H. Predictive modeling of estrogen receptor agonism, antagonism, and binding activities using machine- and deep-learning approaches. J Transl Med 2021; 101:490-502. [PMID: 32778734 PMCID: PMC7873171 DOI: 10.1038/s41374-020-00477-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/19/2020] [Accepted: 07/21/2020] [Indexed: 11/23/2022] Open
Abstract
As defined by the World Health Organization, an endocrine disruptor is an exogenous substance or mixture that alters function(s) of the endocrine system and consequently causes adverse health effects in an intact organism, its progeny, or (sub)populations. Traditional experimental testing regimens to identify toxicants that induce endocrine disruption can be expensive and time-consuming. Computational modeling has emerged as a promising and cost-effective alternative method for screening and prioritizing potentially endocrine-active compounds. The efficient identification of suitable chemical descriptors and machine-learning algorithms, including deep learning, is a considerable challenge for computational toxicology studies. Here, we sought to apply classic machine-learning algorithms and deep-learning approaches to a panel of over 7500 compounds tested against 18 Toxicity Forecaster assays related to nuclear estrogen receptor (ERα and ERβ) activity. Three binary fingerprints (Extended Connectivity FingerPrints, Functional Connectivity FingerPrints, and Molecular ACCess System) were used as chemical descriptors in this study. Each descriptor was combined with four machine-learning and two deep- learning (normal and multitask neural networks) approaches to construct models for all 18 ER assays. The resulting model performance was evaluated using the area under the receiver- operating curve (AUC) values obtained from a fivefold cross-validation procedure. The results showed that individual models have AUC values that range from 0.56 to 0.86. External validation was conducted using two additional sets of compounds (n = 592 and n = 966) with established interactions with nuclear ER demonstrated through experimentation. An agonist, antagonist, or binding score was determined for each compound by averaging its predicted probabilities in relevant assay models as an external validation, yielding AUC values ranging from 0.63 to 0.91. The results suggest that multitask neural networks offer advantages when modeling mechanistically related endpoints. Consensus predictions based on the average values of individual models remain the best modeling strategy for computational toxicity evaluations.
Collapse
Affiliation(s)
- Heather L Ciallella
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Daniel P Russo
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Lauren M Aleksunes
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA
| | - Fabian A Grimm
- ExxonMobil Biomedical Sciences, Inc., Annandale, NJ, USA
| | - Hao Zhu
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA.
- Department of Chemistry, Rutgers University, Camden, NJ, USA.
| |
Collapse
|
11
|
Zorn KM, Foil DH, Lane TR, Hillwalker W, Feifarek DJ, Jones F, Klaren WD, Brinkman AM, Ekins S. Comparing Machine Learning Models for Aromatase (P450 19A1). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:15546-15555. [PMID: 33207874 PMCID: PMC8194505 DOI: 10.1021/acs.est.0c05771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Aromatase, or cytochrome P450 19A1, catalyzes the aromatization of androgens to estrogens within the body. Changes in the activity of this enzyme can produce hormonal imbalances that can be detrimental to sexual and skeletal development. Inhibition of this enzyme can occur with drugs and natural products as well as environmental chemicals. Therefore, predicting potential endocrine disruption via exogenous chemicals requires that aromatase inhibition be considered in addition to androgen and estrogen pathway interference. Bayesian machine learning methods can be used for prospective prediction from the molecular structure without the need for experimental data. Herein, the generation and evaluation of multiple machine learning models utilizing different sources of aromatase inhibition data are described. These models are applied to two test sets for external validation with molecules relevant to drug discovery from the public domain. In addition, the performance of multiple machine learning algorithms was evaluated by comparing internal five-fold cross-validation statistics of the training data. These methods to predict aromatase inhibition from molecular structure, when used in concert with estrogen and androgen machine learning models, allow for a more holistic assessment of endocrine-disrupting potential of chemicals with limited empirical data and enable the reduction of the use of hazardous substances.
Collapse
Affiliation(s)
- Kimberley M. Zorn
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA
| | - Daniel H. Foil
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA
| | - Thomas R. Lane
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA
| | - Wendy Hillwalker
- Global Product Safety, SC Johnson and Son, Inc., Racine, WI, USA
| | | | - Frank Jones
- Global Product Safety, SC Johnson and Son, Inc., Racine, WI, USA
| | | | | | - Sean Ekins
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, USA
| |
Collapse
|
12
|
Zorn KM, Foil DH, Lane TR, Russo DP, Hillwalker W, Feifarek DJ, Jones F, Klaren WD, Brinkman AM, Ekins S. Machine Learning Models for Estrogen Receptor Bioactivity and Endocrine Disruption Prediction. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:12202-12213. [PMID: 32857505 PMCID: PMC8194504 DOI: 10.1021/acs.est.0c03982] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The U.S. Environmental Protection Agency (EPA) periodically releases in vitro data across a variety of targets, including the estrogen receptor (ER). In 2015, the EPA used these data to construct mathematical models of ER agonist and antagonist pathways to prioritize chemicals for endocrine disruption testing. However, mathematical models require in vitro data prior to predicting estrogenic activity, but machine learning methods are capable of prospective prediction from the molecular structure alone. The current study describes the generation and evaluation of Bayesian machine learning models grouped by the EPA's ER agonist pathway model using multiple data types with proprietary software, Assay Central. External predictions with three test sets of in vitro and in vivo reference chemicals with agonist activity classifications were compared to previous mathematical model publications. Training data sets were subjected to additional machine learning algorithms and compared with rank normalized scores of internal five-fold cross-validation statistics. External predictions were found to be comparable or superior to previous studies published by the EPA. When assessing six additional algorithms for the training data sets, Assay Central performed similarly at a reduced computational cost. This study demonstrates that machine learning can prioritize chemicals for future in vitro and in vivo testing of ER agonism.
Collapse
Affiliation(s)
- Kimberley M Zorn
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Daniel H Foil
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Thomas R Lane
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| | - Daniel P Russo
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, United States
| | - Wendy Hillwalker
- Global Product Safety, SC Johnson and Son, Inc., Racine, Wisconsin 53404, United States
| | - David J Feifarek
- Global Product Safety, SC Johnson and Son, Inc., Racine, Wisconsin 53404, United States
| | - Frank Jones
- Global Product Safety, SC Johnson and Son, Inc., Racine, Wisconsin 53404, United States
| | - William D Klaren
- Global Product Safety, SC Johnson and Son, Inc., Racine, Wisconsin 53404, United States
| | - Ashley M Brinkman
- Global Product Safety, SC Johnson and Son, Inc., Racine, Wisconsin 53404, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, North Carolina 27606, United States
| |
Collapse
|
13
|
Ren XM, Kuo Y, Blumberg B. Agrochemicals and obesity. Mol Cell Endocrinol 2020; 515:110926. [PMID: 32619583 PMCID: PMC7484009 DOI: 10.1016/j.mce.2020.110926] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 06/11/2020] [Accepted: 06/23/2020] [Indexed: 12/11/2022]
Abstract
Obesity has become a very large concern worldwide, reaching pandemic proportions over the past several decades. Lifestyle factors, such as excess caloric intake and decreased physical activity, together with genetic predispositions, are well-known factors related to obesity. There is accumulating evidence suggesting that exposure to some environmental chemicals during critical windows of development may contribute to the rapid increase in the incidence of obesity. Agrochemicals are a class of chemicals extensively used in agriculture, which have been widely detected in human. There is now considerable evidence linking human exposure to agrochemicals with obesity. This review summarizes human epidemiological evidence and experimental animal studies supporting the association between agrochemical exposure and obesity and outlines possible mechanistic underpinnings for this link.
Collapse
Affiliation(s)
- Xiao-Min Ren
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697-2300, USA
| | - Yun Kuo
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697-2300, USA
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697-2300, USA; Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA; Department of Biomedical Engineering, University of California, Irvine, CA, USA.
| |
Collapse
|
14
|
Jaladanki CK, He Y, Zhao LN, Maurer-Stroh S, Loo LH, Song H, Fan H. Virtual screening of potentially endocrine-disrupting chemicals against nuclear receptors and its application to identify PPARγ-bound fatty acids. Arch Toxicol 2020; 95:355-374. [PMID: 32909075 PMCID: PMC7811525 DOI: 10.1007/s00204-020-02897-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022]
Abstract
Nuclear receptors (NRs) are key regulators of energy homeostasis, body development, and sexual reproduction. Xenobiotics binding to NRs may disrupt natural hormonal systems and induce undesired adverse effects in the body. However, many chemicals of concerns have limited or no experimental data on their potential or lack-of-potential endocrine-disrupting effects. Here, we propose a virtual screening method based on molecular docking for predicting potential endocrine-disrupting chemicals (EDCs) that bind to NRs. For 12 NRs, we systematically analyzed how multiple crystal structures can be used to distinguish actives and inactives found in previous high-throughput experiments. Our method is based on (i) consensus docking scores from multiple structures at a single functional state (agonist-bound or antagonist-bound), (ii) multiple functional states (agonist-bound and antagonist-bound), and (iii) multiple pockets (orthosteric site and alternative sites) of these NRs. We found that the consensus enrichment from multiple structures is better than or comparable to the best enrichment from a single structure. The discriminating power of this consensus strategy was further enhanced by a chemical similarity-weighted scoring scheme, yielding better or comparable enrichment for all studied NRs. Applying this optimized method, we screened 252 fatty acids against peroxisome proliferator-activated receptor gamma (PPARγ) and successfully identified 3 previously unknown fatty acids with Kd = 100-250 μM including two furan fatty acids: furannonanoic acid (FNA) and furanundecanoic acid (FUA), and one cyclopropane fatty acid: phytomonic acid (PTA). These results suggested that the proposed method can be used to rapidly screen and prioritize potential EDCs for further experimental evaluations.
Collapse
Affiliation(s)
- Chaitanya K Jaladanki
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
- Toxicity Mode-of-Action Discovery (ToxMAD) Platform, Innovations in Food and Chemical Safety Programme, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Yang He
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Li Na Zhao
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
- Toxicity Mode-of-Action Discovery (ToxMAD) Platform, Innovations in Food and Chemical Safety Programme, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Lit-Hsin Loo
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
- Toxicity Mode-of-Action Discovery (ToxMAD) Platform, Innovations in Food and Chemical Safety Programme, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Haiwei Song
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore.
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore.
| |
Collapse
|
15
|
Use of computational toxicology (CompTox) tools to predict in vivo toxicity for risk assessment. Regul Toxicol Pharmacol 2020; 116:104724. [PMID: 32640296 DOI: 10.1016/j.yrtph.2020.104724] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/20/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022]
Abstract
Computational Toxicology tools were used to predict toxicity for three pesticides: propyzamide (PZ), carbaryl (CB) and chlorpyrifos (CPF). The tools used included: a) ToxCast/Tox21 assays (AC50 s μM: concentration 50% maximum activity); b) in vitro-to-in vivo extrapolation (IVIVE) using ToxCast/Tox21 AC50s to predict administered equivalent doses (AED: mg/kg/d) to compare to known in vivo Lowest-Observed-Effect-Level (LOEL)/Benchmark Dose (BMD); c) high throughput toxicokinetics population based (HTTK-Pop) using AC50s for endpoints associated with the mode of action (MOA) to predict age-adjusted AED for comparison with in vivo LOEL/BMDs. ToxCast/Tox21 active-hit-calls for each chemical were predictive of targets associated with each MOA, however, assays directly relevant to the MOAs for each chemical were limited. IVIVE AEDs were predictive of in vivo LOEL/BMD10s for all three pesticides. HTTK-Pop was predictive of in vivo LOEL/BMD10s for PZ and CPF but not for CB after human age adjustments 11-15 (PZ) and 6-10 (CB) or 6-10 and 11-20 (CPF) corresponding to treated rat ages (in vivo endpoints). The predictions of computational tools are useful for risk assessment to identify targets in chemical MOAs and to support in vivo endpoints. Data can also aid is decisions about the need for further studies.
Collapse
|
16
|
Andrews FV, Kim SM, Edwards L, Schlezinger JJ. Identifying adipogenic chemicals: Disparate effects in 3T3-L1, OP9 and primary mesenchymal multipotent cell models. Toxicol In Vitro 2020; 67:104904. [PMID: 32473317 DOI: 10.1016/j.tiv.2020.104904] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 12/19/2022]
Abstract
3T3-L1 pre-adipocytes are used commonly to identify new adipogens, but this cell line has been shown to produce variable results. Here, potential adipogenic chemicals (identified in the ToxCast dataset using the Toxicological Priority Index) were tested for their ability to induce adipocyte differentiation in 3T3-L1 cells, OP9 cells and primary mouse bone marrow multipotent stromal cells (BM-MSC). Ten of the 36 potential adipogens stimulated lipid accumulation in at least one model (novel: fenthion, quinoxyfen, prallethrin, allethrin, pyrimethanil, tebuconzaole, 2,4,6-tris (tert-butyl)phenol; known: fentin, pioglitazone, 3,3',5,5'-tetrabromobisphenol A). Only prallethrin and pioglitazone enhanced lipid accumulation in all models. OP9 cells were significantly more sensitive to chemicals known to activate PPARγ through RXR than the other models. Coordinate effects on adipocyte and osteoblast differentiation were investigated further in BM-MSCs. Lipid accumulation was correlated with the ability to stimulate expression of the PPARγ target gene, Plin1. Induction of lipid accumulation also was associated with reduction in alkaline phosphatase activity. Allethrin, prallethrin, and quinoxyfen strongly suppressed osteogenic gene expression. BM-MSCs were useful in coordinately investigating pro-adipogenic and anti-osteogenic effects. Overall, the results show that additional models should be used in conjunction with 3T3-L1 cells to identify a broader spectrum of adipogens and their coordinate effects on osteogenesis.
Collapse
Affiliation(s)
- Faye V Andrews
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA
| | - Stephanie M Kim
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA
| | - Lariah Edwards
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA
| | - Jennifer J Schlezinger
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA.
| |
Collapse
|
17
|
Leung MCK, Meyer JN. Mitochondria as a target of organophosphate and carbamate pesticides: Revisiting common mechanisms of action with new approach methodologies. Reprod Toxicol 2019; 89:83-92. [PMID: 31315019 PMCID: PMC6766410 DOI: 10.1016/j.reprotox.2019.07.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 06/19/2019] [Accepted: 07/09/2019] [Indexed: 01/01/2023]
Abstract
Mitochondrial toxicity has been proposed as a potential cause of developmental defects in humans. We evaluated 51 organophosphate and carbamate pesticides using the U.S. EPA ToxCast and Tox21 databases. Only a small number of them bind directly to cholinesterases in the parent form. The hydrophobicity of organophosphate pesticides is correlated significantly to TSPO binding affinity, mitochondrial membrane potential reduction in HepG2 cells, and developmental toxicity in Caenorhabditis elegans and Danio rerio (p < 0.05). Structural analysis suggests that in some cases the Krebs cycle is a potential target of organophosphate and carbamate exposure at early life stages. The results support the hypothesis that mitochondrial effects of some organophosphate pesticides-particularly those that require enzymatic activation to the oxon form-may augment the documented effects of disruption of acetylcholine signaling. This study provides a proof of concept for applying new approach methodologies to interrogate mechanisms of action for cumulative risk assessment.
Collapse
Affiliation(s)
- Maxwell C K Leung
- Department of Environmental Toxicology, University of California, Davis, CA, United States; Nicholas School of the Environment, Duke University, Durham, NC, United States.
| | - Joel N Meyer
- Nicholas School of the Environment, Duke University, Durham, NC, United States
| |
Collapse
|
18
|
Noyes PD, Friedman KP, Browne P, Haselman JT, Gilbert ME, Hornung MW, Barone S, Crofton KM, Laws SC, Stoker TE, Simmons SO, Tietge JE, Degitz SJ. Evaluating Chemicals for Thyroid Disruption: Opportunities and Challenges with in Vitro Testing and Adverse Outcome Pathway Approaches. ENVIRONMENTAL HEALTH PERSPECTIVES 2019; 127:95001. [PMID: 31487205 PMCID: PMC6791490 DOI: 10.1289/ehp5297] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/01/2019] [Accepted: 08/13/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Extensive clinical and experimental research documents the potential for chemical disruption of thyroid hormone (TH) signaling through multiple molecular targets. Perturbation of TH signaling can lead to abnormal brain development, cognitive impairments, and other adverse outcomes in humans and wildlife. To increase chemical safety screening efficiency and reduce vertebrate animal testing, in vitro assays that identify chemical interactions with molecular targets of the thyroid system have been developed and implemented. OBJECTIVES We present an adverse outcome pathway (AOP) network to link data derived from in vitro assays that measure chemical interactions with thyroid molecular targets to downstream events and adverse outcomes traditionally derived from in vivo testing. We examine the role of new in vitro technologies, in the context of the AOP network, in facilitating consideration of several important regulatory and biological challenges in characterizing chemicals that exert effects through a thyroid mechanism. DISCUSSION There is a substantial body of knowledge describing chemical effects on molecular and physiological regulation of TH signaling and associated adverse outcomes. Until recently, few alternative nonanimal assays were available to interrogate chemical effects on TH signaling. With the development of these new tools, screening large libraries of chemicals for interactions with molecular targets of the thyroid is now possible. Measuring early chemical interactions with targets in the thyroid pathway provides a means of linking adverse outcomes, which may be influenced by many biological processes, to a thyroid mechanism. However, the use of in vitro assays beyond chemical screening is complicated by continuing limits in our knowledge of TH signaling in important life stages and tissues, such as during fetal brain development. Nonetheless, the thyroid AOP network provides an ideal tool for defining causal linkages of a chemical exerting thyroid-dependent effects and identifying research needs to quantify these effects in support of regulatory decision making. https://doi.org/10.1289/EHP5297.
Collapse
Affiliation(s)
- Pamela D Noyes
- National Center for Environmental Assessment, Office of Research and Development (ORD), U.S. Environmental Protection Agency (EPA), Washington, DC, USA
| | - Katie Paul Friedman
- National Center for Computational Toxicology, ORD, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Patience Browne
- Environment Health and Safety Division, Environment Directorate, Organisation for Economic Co-operation and Development (OECD), Paris, France
| | - Jonathan T Haselman
- Mid-Continent Ecology Division, National Health and Environmental Effects Research Laboratory (NHEERL), ORD, U.S. EPA, Duluth, Minnesota, USA
| | - Mary E Gilbert
- Toxicity Assessment Division, NHEERL, ORD, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Michael W Hornung
- Mid-Continent Ecology Division, National Health and Environmental Effects Research Laboratory (NHEERL), ORD, U.S. EPA, Duluth, Minnesota, USA
| | - Stan Barone
- Office of Pollution Prevention and Toxics, Office of Chemical Safety and Pollution Prevention, U.S. EPA, Washington, DC, USA
| | - Kevin M Crofton
- National Center for Computational Toxicology, ORD, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Susan C Laws
- Toxicity Assessment Division, NHEERL, ORD, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Tammy E Stoker
- Toxicity Assessment Division, NHEERL, ORD, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Steven O Simmons
- National Center for Computational Toxicology, ORD, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Joseph E Tietge
- Mid-Continent Ecology Division, National Health and Environmental Effects Research Laboratory (NHEERL), ORD, U.S. EPA, Duluth, Minnesota, USA
| | - Sigmund J Degitz
- Mid-Continent Ecology Division, National Health and Environmental Effects Research Laboratory (NHEERL), ORD, U.S. EPA, Duluth, Minnesota, USA
| |
Collapse
|
19
|
Abstract
The more than 80,000 chemicals in commerce present a challenge for hazard assessments that toxicity testing in the 21st century strives to address through high-throughput screening (HTS) assays. Assessing chemical effects on human development adds an additional layer of complexity to the screening, with a need to capture complex and dynamic events essential for proper embryo-fetal development. HTS data from ToxCast/Tox21 informs systems toxicology models, which incorporate molecular targets and biological pathways into mechanistic models describing the effects of chemicals on human cells, 3D organotypic culture models, and small model organisms. Adverse Outcome Pathways (AOPs) provide a useful framework for integrating the evidence derived from these in silico and in vitro systems to inform chemical hazard characterization. To illustrate this formulation, we have built an AOP for developmental toxicity through a mode of action linked to embryonic vascular disruption (Aop43). Here, we review the model for quantitative prediction of developmental vascular toxicity from ToxCast HTS data and compare the HTS results to functional vascular development assays in complex cell systems, virtual tissues, and small model organisms. ToxCast HTS predictions from several published and unpublished assays covering different aspects of the angiogenic cycle were generated for a test set of 38 chemicals representing a range of putative vascular disrupting compounds (pVDCs). Results boost confidence in the capacity to predict adverse developmental outcomes from HTS in vitro data and model computational dynamics for in silico reconstruction of developmental systems biology. Finally, we demonstrate the integration of the AOP and developmental systems toxicology to investigate the unique modes of action of two angiogenesis inhibitors.
Collapse
|
20
|
Fay KA, Villeneuve DL, Swintek J, Edwards SW, Nelms MD, Blackwell BR, Ankley GT. Differentiating Pathway-Specific From Nonspecific Effects in High-Throughput Toxicity Data: A Foundation for Prioritizing Adverse Outcome Pathway Development. Toxicol Sci 2019. [PMID: 29529260 DOI: 10.1093/toxsci/kfy049] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The U.S. Environmental Protection Agency's ToxCast program has screened thousands of chemicals for biological activity, primarily using high-throughput in vitro bioassays. Adverse outcome pathways (AOPs) offer a means to link pathway-specific biological activities with potential apical effects relevant to risk assessors. Thus, efforts are underway to develop AOPs relevant to pathway-specific perturbations detected in ToxCast assays. Previous work identified a "cytotoxic burst" (CTB) phenomenon wherein large numbers of the ToxCast assays begin to respond at or near test chemical concentrations that elicit cytotoxicity, and a statistical approach to defining the bounds of the CTB was developed. To focus AOP development on the molecular targets corresponding to ToxCast assays indicating pathway-specific effects, we conducted a meta-analysis to identify which assays most frequently respond at concentrations below the CTB. A preliminary list of potentially important, target-specific assays was determined by ranking assays by the fraction of chemical hits below the CTB compared with the number of chemicals tested. Additional priority assays were identified using a diagnostic-odds-ratio approach which gives greater ranking to assays with high specificity but low responsivity. Combined, the two prioritization methods identified several novel targets (e.g., peripheral benzodiazepine and progesterone receptors) to prioritize for AOP development, and affirmed the importance of a number of existing AOPs aligned with ToxCast targets (e.g., thyroperoxidase, estrogen receptor, aromatase). The prioritization approaches did not appear to be influenced by inter-assay differences in chemical bioavailability. Furthermore, the outcomes were robust based on a variety of different parameters used to define the CTB.
Collapse
Affiliation(s)
- Kellie A Fay
- University of Minnesota-Duluth, Biology Department; 1035 Kirby Drive, Swenson Science Building 207, Duluth, MN 55812.,CSRA Inc, Science and Engineering, 6201 Congdon Blvd, Duluth, MN 55804
| | - Daniel L Villeneuve
- U.S. EPA National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804
| | - Joe Swintek
- Badger Technical Services, 6201 Congdon Blvd, Duluth, MN 55804
| | - Stephen W Edwards
- U.S. EPA National Health and Environmental Effects Research Laboratory, Integrated Systems Toxicology Division, 109 TW Alexander Dr. (MD B105-03), RTP, NC 27711.,RTI International, Research Computing Division, 3040 E Cornwallis Rd, Durham, NC 27709
| | - Mark D Nelms
- U.S. EPA National Health and Environmental Effects Research Laboratory, Integrated Systems Toxicology Division, 109 TW Alexander Dr. (MD B105-03), RTP, NC 27711
| | - Brett R Blackwell
- U.S. EPA National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804
| | - Gerald T Ankley
- U.S. EPA National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN 55804
| |
Collapse
|
21
|
Olsvik P, Berntssen M, Søfteland L, Sanden M. Transcriptional effects of dietary chlorpyrifos‑methyl exposure in Atlantic salmon (Salmo salar) brain and liver. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:43-54. [DOI: 10.1016/j.cbd.2018.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/30/2018] [Accepted: 11/04/2018] [Indexed: 01/20/2023]
|
22
|
Watt ED, Judson RS. Uncertainty quantification in ToxCast high throughput screening. PLoS One 2018; 13:e0196963. [PMID: 30044784 PMCID: PMC6059398 DOI: 10.1371/journal.pone.0196963] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/24/2018] [Indexed: 01/04/2023] Open
Abstract
High throughput screening (HTS) projects like the U.S. Environmental Protection Agency's ToxCast program are required to address the large and rapidly increasing number of chemicals for which we have little to no toxicity measurements. Concentration-response parameters such as potency and efficacy are extracted from HTS data using nonlinear regression, and models and analyses built from these parameters are used to predict in vivo and in vitro toxicity of thousands of chemicals. How these predictions are impacted by uncertainties that stem from parameter estimation and propagated through the models and analyses has not been well explored. While data size and complexity makes uncertainty quantification computationally expensive for HTS datasets, continued advancements in computational resources have allowed these computational challenges to be met. This study uses nonparametric bootstrap resampling to calculate uncertainties in concentration-response parameters from a variety of HTS assays. Using the ToxCast estrogen receptor model for bioactivity as a case study, we highlight how these uncertainties can be propagated through models to quantify the uncertainty in model outputs. Uncertainty quantification in model outputs is used to identify potential false positives and false negatives and to determine the distribution of model values around semi-arbitrary activity cutoffs, increasing confidence in model predictions. At the individual chemical-assay level, curves with high variability are flagged for manual inspection or retesting, focusing subject-matter-expert time on results that need further input. This work improves the confidence of predictions made using HTS data, increasing the ability to use this data in risk assessment.
Collapse
Affiliation(s)
- Eric D. Watt
- U.S. Environmental Protection Agency, National Center for Computational Toxicology, Research Triangle Park, North Carolina, United States of America
- Oak Ridge Institute for Science Education Postdoctoral Fellow, Oak Ridge, Tennessee, United States of America
| | - Richard S. Judson
- U.S. Environmental Protection Agency, National Center for Computational Toxicology, Research Triangle Park, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
23
|
Mansouri K, Grulke CM, Judson RS, Williams AJ. OPERA models for predicting physicochemical properties and environmental fate endpoints. J Cheminform 2018. [PMID: 29520515 PMCID: PMC5843579 DOI: 10.1186/s13321-018-0263-1] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The collection of chemical structure information and associated experimental data for quantitative structure–activity/property relationship (QSAR/QSPR) modeling is facilitated by an increasing number of public databases containing large amounts of useful data. However, the performance of QSAR models highly depends on the quality of the data and modeling methodology used. This study aims to develop robust QSAR/QSPR models for chemical properties of environmental interest that can be used for regulatory purposes. This study primarily uses data from the publicly available PHYSPROP database consisting of a set of 13 common physicochemical and environmental fate properties. These datasets have undergone extensive curation using an automated workflow to select only high-quality data, and the chemical structures were standardized prior to calculation of the molecular descriptors. The modeling procedure was developed based on the five Organization for Economic Cooperation and Development (OECD) principles for QSAR models. A weighted k-nearest neighbor approach was adopted using a minimum number of required descriptors calculated using PaDEL, an open-source software. The genetic algorithms selected only the most pertinent and mechanistically interpretable descriptors (2–15, with an average of 11 descriptors). The sizes of the modeled datasets varied from 150 chemicals for biodegradability half-life to 14,050 chemicals for logP, with an average of 3222 chemicals across all endpoints. The optimal models were built on randomly selected training sets (75%) and validated using fivefold cross-validation (CV) and test sets (25%). The CV Q2 of the models varied from 0.72 to 0.95, with an average of 0.86 and an R2 test value from 0.71 to 0.96, with an average of 0.82. Modeling and performance details are described in QSAR model reporting format and were validated by the European Commission’s Joint Research Center to be OECD compliant. All models are freely available as an open-source, command-line application called OPEn structure–activity/property Relationship App (OPERA). OPERA models were applied to more than 750,000 chemicals to produce freely available predicted data on the U.S. Environmental Protection Agency’s CompTox Chemistry Dashboard.![]()
Collapse
Affiliation(s)
- Kamel Mansouri
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA. .,Oak Ridge Institute for Science and Education, 1299 Bethel Valley Road, Oak Ridge, TN, 37830, USA. .,ScitoVation LLC, 6 Davis Drive, Research Triangle Park, NC, 27709, USA.
| | - Chris M Grulke
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Richard S Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| | - Antony J Williams
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711, USA
| |
Collapse
|
24
|
Scialli AR, Daston G, Chen C, Coder PS, Euling SY, Foreman J, Hoberman AM, Hui J, Knudsen T, Makris SL, Morford L, Piersma AH, Stanislaus D, Thompson KE. Rethinking developmental toxicity testing: Evolution or revolution? Birth Defects Res 2018; 110:840-850. [PMID: 29436169 DOI: 10.1002/bdr2.1212] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/18/2017] [Accepted: 01/29/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND Current developmental toxicity testing adheres largely to protocols suggested in 1966 involving the administration of test compound to pregnant laboratory animals. After more than 50 years of embryo-fetal development testing, are we ready to consider a different approach to human developmental toxicity testing? METHODS A workshop was held under the auspices of the Developmental and Reproductive Toxicology Technical Committee of the ILSI Health and Environmental Sciences Institute to consider how we might design developmental toxicity testing if we started over with 21st century knowledge and techniques (revolution). We first consider what changes to the current protocols might be recommended to make them more predictive for human risk (evolution). RESULTS The evolutionary approach includes modifications of existing protocols and can include humanized models, disease models, more accurate assessment and testing of metabolites, and informed approaches to dose selection. The revolution could start with hypothesis-driven testing where we take what we know about a compound or close analog and answer specific questions using targeted experimental techniques rather than a one-protocol-fits-all approach. Central to the idea of hypothesis-driven testing is the concept that testing can be done at the level of mode of action. It might be feasible to identify a small number of key events at a molecular or cellular level that predict an adverse outcome and for which testing could be performed in vitro or in silico or, rarely, using limited in vivo models. Techniques for evaluating these key events exist today or are in development. DISCUSSION Opportunities exist for refining and then replacing current developmental toxicity testing protocols using techniques that have already been developed or are within reach.
Collapse
Affiliation(s)
- Anthony R Scialli
- Reproductive Toxicology Center and Scialli Consulting LLC, Washington, DC
| | | | - Connie Chen
- ILSI Health and Environmental Sciences Institute, Washington, DC
| | | | - Susan Y Euling
- Office of Children's Health Protection, U.S. Environmental Protection Agency, Washington, DC
| | | | | | - Julia Hui
- Celgene Corporation, Summit, New Jersey
| | - Thomas Knudsen
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Susan L Makris
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Washington, DC
| | | | - Aldert H Piersma
- Center for Health Protection, National Institute for Public Health and the Environment RIVM, Bilthoven and Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | | | - Kary E Thompson
- Drug Safety Evaluation, Bristol-Myers Squibb, New Brunswick, New Jersey
| |
Collapse
|
25
|
Strickland JD, Martin MT, Richard AM, Houck KA, Shafer TJ. Screening the ToxCast phase II libraries for alterations in network function using cortical neurons grown on multi-well microelectrode array (mwMEA) plates. Arch Toxicol 2018; 92:487-500. [PMID: 28766123 PMCID: PMC6438628 DOI: 10.1007/s00204-017-2035-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022]
Abstract
Methods are needed for rapid screening of environmental compounds for neurotoxicity, particularly ones that assess function. To demonstrate the utility of microelectrode array (MEA)-based approaches as a rapid neurotoxicity screening tool, 1055 chemicals from EPA's phase II ToxCast library were evaluated for effects on neural function and cell health. Primary cortical networks were grown on multi-well microelectrode array (mwMEA) plates. On day in vitro 13, baseline activity (40 min) was recorded prior to exposure to each compound (40 µM). Changes in spontaneous network activity [mean firing rate (MFR)] and cell viability (lactate dehydrogenase and CellTiter Blue) were assessed within the same well following compound exposure. Following exposure, 326 compounds altered (increased or decreased) normalized MFR beyond hit thresholds based on 2× the median absolute deviation of DMSO-treated wells. Pharmaceuticals, pesticides, fungicides, chemical intermediates, and herbicides accounted for 86% of the hits. Further, changes in MFR occurred in the absence of cytotoxicity, as only eight compounds decreased cell viability. ToxPrint chemotype analysis identified several structural domains (e.g., biphenyls and alkyl phenols) significantly enriched with MEA actives relative to the total test set. The top 5 enriched ToxPrint chemotypes were represented in 26% of the MEA hits, whereas the top 11 ToxPrints were represented in 34% of MEA hits. These results demonstrate that large-scale functional screening using neural networks on MEAs can fill a critical gap in assessment of neurotoxicity potential in ToxCast assay results. Further, a data-mining approach identified ToxPrint chemotypes enriched in the MEA-hit subset, which define initial structure-activity relationship inferences, establish potential mechanistic associations to other ToxCast assay endpoints, and provide working hypotheses for future studies.
Collapse
Affiliation(s)
- Jenna D Strickland
- Axion Biosystems, Atlanta, GA, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
| | - Matthew T Martin
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, MD D143-02, Research Triangle Park, NC, 27711, USA
- Pfizer Inc, Groton, CT, USA
| | - Ann M Richard
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, MD D143-02, Research Triangle Park, NC, 27711, USA
| | - Keith A Houck
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, MD D143-02, Research Triangle Park, NC, 27711, USA
| | - Timothy J Shafer
- Integrated Systems Toxicology Division, U.S. Environmental Protection Agency, MD105-05, Research Triangle Park, NC, 27711, USA.
| |
Collapse
|
26
|
Arini A, Mittal K, Dornbos P, Head J, Rutkiewicz J, Basu N. A cell-free testing platform to screen chemicals of potential neurotoxic concern across twenty vertebrate species. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2017; 36:3081-3090. [PMID: 28594109 DOI: 10.1002/etc.3880] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/09/2017] [Accepted: 06/05/2017] [Indexed: 05/20/2023]
Abstract
There is global demand for new in vitro testing tools for ecological risk assessment. The objective of the present study was to apply a set of cell-free neurochemical assays to screen many chemicals across many species in a relatively high-throughput manner. The platform assessed 7 receptors and enzymes that mediate neurotransmission of γ-aminobutyric acid, dopamine, glutamate, and acetylcholine. Each assay was optimized to work across 20 vertebrate species (5 fish, 5 birds, 7 mammalian wildlife, 3 biomedical species including humans). We tested the screening assay platform against 80 chemicals (23 pharmaceuticals and personal care products, 20 metal[loid]s, 22 polycyclic aromatic hydrocarbons and halogenated organic compounds, 15 pesticides). In total, 10 800 species-chemical-assay combinations were tested, and significant differences were found in 4041 cases. All 7 assays were significantly affected by at least one chemical in each species tested. Among the 80 chemicals tested, nearly all resulted in a significant impact on at least one species and one assay. The 5 most active chemicals were prochloraz, HgCl2 , Sn, benzo[a]pyrene, and vinclozolin. Clustering analyses revealed groupings according to chemicals, species, and chemical-assay combinations. The results show that cell-free assays can screen a large number of samples in a short period of time in a cost-effective manner in a range of animals not easily studied using traditional approaches. Strengths and limitations of this approach are discussed, as well as next steps. Environ Toxicol Chem 2017;36:3081-3090. © 2017 SETAC.
Collapse
Affiliation(s)
- Adeline Arini
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Krittika Mittal
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Peter Dornbos
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Jessica Head
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Jennifer Rutkiewicz
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
- ToxServices, Ann Arbor, Michigan, USA
| | - Niladri Basu
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
27
|
Liu J, Patlewicz G, Williams AJ, Thomas RS, Shah I. Predicting Organ Toxicity Using in Vitro Bioactivity Data and Chemical Structure. Chem Res Toxicol 2017; 30:2046-2059. [PMID: 28768096 DOI: 10.1021/acs.chemrestox.7b00084] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Animal testing alone cannot practically evaluate the health hazard posed by tens of thousands of environmental chemicals. Computational approaches making use of high-throughput experimental data may provide more efficient means to predict chemical toxicity. Here, we use a supervised machine learning strategy to systematically investigate the relative importance of study type, machine learning algorithm, and type of descriptor on predicting in vivo repeat-dose toxicity at the organ-level. A total of 985 compounds were represented using chemical structural descriptors, ToxPrint chemotype descriptors, and bioactivity descriptors from ToxCast in vitro high-throughput screening assays. Using ToxRefDB, a total of 35 target organ outcomes were identified that contained at least 100 chemicals (50 positive and 50 negative). Supervised machine learning was performed using Naïve Bayes, k-nearest neighbor, random forest, classification and regression trees, and support vector classification approaches. Model performance was assessed based on F1 scores using 5-fold cross-validation with balanced bootstrap replicates. Fixed effects modeling showed the variance in F1 scores was explained mostly by target organ outcome, followed by descriptor type, machine learning algorithm, and interactions between these three factors. A combination of bioactivity and chemical structure or chemotype descriptors were the most predictive. Model performance improved with more chemicals (up to a maximum of 24%), and these gains were correlated (ρ = 0.92) with the number of chemicals. Overall, the results demonstrate that a combination of bioactivity and chemical descriptors can accurately predict a range of target organ toxicity outcomes in repeat-dose studies, but specific experimental and methodologic improvements may increase predictivity.
Collapse
Affiliation(s)
- Jie Liu
- Department of Information Science, University of Arkansas at Little Rock , Arkansas 72204, United States.,Oak Ridge Institute for Science Education, National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency , Research Triangle Park, Durham, North Carolina 27711, United States
| | - Grace Patlewicz
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency , Research Triangle Park, Durham, North Carolina 27711, United States
| | - Antony J Williams
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency , Research Triangle Park, Durham, North Carolina 27711, United States
| | - Russell S Thomas
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency , Research Triangle Park, Durham, North Carolina 27711, United States
| | - Imran Shah
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency , Research Triangle Park, Durham, North Carolina 27711, United States
| |
Collapse
|
28
|
Blackwell BR, Ankley GT, Corsi SR, DeCicco LA, Houck K, Judson R, Li S, Martin M, Murphy E, Schroeder AL, Smith ET, Swintek J, Villeneuve DL. An "EAR" on Environmental Surveillance and Monitoring: A Case Study on the Use of Exposure-Activity Ratios (EARs) to Prioritize Sites, Chemicals, and Bioactivities of Concern in Great Lakes Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:8713-8724. [PMID: 28671818 PMCID: PMC6132252 DOI: 10.1021/acs.est.7b01613] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Current environmental monitoring approaches focus primarily on chemical occurrence. However, based on concentration alone, it can be difficult to identify which compounds may be of toxicological concern and should be prioritized for further monitoring, in-depth testing, or management. This can be problematic because toxicological characterization is lacking for many emerging contaminants. New sources of high-throughput screening (HTS) data, such as the ToxCast database, which contains information for over 9000 compounds screened through up to 1100 bioassays, are now available. Integrated analysis of chemical occurrence data with HTS data offers new opportunities to prioritize chemicals, sites, or biological effects for further investigation based on concentrations detected in the environment linked to relative potencies in pathway-based bioassays. As a case study, chemical occurrence data from a 2012 study in the Great Lakes Basin along with the ToxCast effects database were used to calculate exposure-activity ratios (EARs) as a prioritization tool. Technical considerations of data processing and use of the ToxCast database are presented and discussed. EAR prioritization identified multiple sites, biological pathways, and chemicals that warrant further investigation. Prioritized bioactivities from the EAR analysis were linked to discrete adverse outcome pathways to identify potential adverse outcomes and biomarkers for use in subsequent monitoring efforts.
Collapse
Affiliation(s)
- Brett R. Blackwell
- US EPA, Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN, USA 55804
- Corresponding author: 6201 Congdon Blvd, Duluth, MN 55804; ; T: (218) 529-5078; Fax: (218) 529-5003
| | - Gerald T. Ankley
- US EPA, Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN, USA 55804
| | - Steve R. Corsi
- US Geological Survey, Wisconsin Water Science Center, 8505 Research Way, Middleton, WI, USA 53562
| | - Laura A. DeCicco
- US Geological Survey, Wisconsin Water Science Center, 8505 Research Way, Middleton, WI, USA 53562
| | - Keith Houck
- US EPA, National Center for Computational Toxicology, 109 T.W. Alexander Dr, Research Triangle Park, NC, USA 27711
| | - Richard Judson
- US EPA, National Center for Computational Toxicology, 109 T.W. Alexander Dr, Research Triangle Park, NC, USA 27711
| | - Shibin Li
- US EPA, Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN, USA 55804
- National Research Council, US EPA, 6201 Congdon Blvd, Duluth, MN, USA 55804
| | - Matt Martin
- US EPA, National Center for Computational Toxicology, 109 T.W. Alexander Dr, Research Triangle Park, NC, USA 27711
| | - Elizabeth Murphy
- US EPA, Great Lakes National Program Office, 77 West Jackson Blvd, Chicago, IL, USA 60604
| | - Anthony L. Schroeder
- University of Minnesota Crookston, Math, Science, and Technology Department, 2900 University Ave, Crookston, MN, USA 56716
| | - Edwin T. Smith
- US EPA, Great Lakes National Program Office, 77 West Jackson Blvd, Chicago, IL, USA 60604
| | - Joe Swintek
- Badger Technical Services, 6201 Congdon Blvd, Duluth, MN, USA 55804
| | - Daniel L. Villeneuve
- US EPA, Mid-Continent Ecology Division, 6201 Congdon Blvd, Duluth, MN, USA 55804
| |
Collapse
|
29
|
Abstract
The physiological relevance of Matrigel as a cell-culture substrate and in angiogenesis assays is often called into question. Here, we describe an array-based method for the identification of synthetic hydrogels that promote the formation of robust in vitro vascular networks for the detection of putative vascular disruptors, and that support human embryonic stem cell expansion and pluripotency. We identified hydrogel substrates that promoted endothelial-network formation by primary human umbilical vein endothelial cells and by endothelial cells derived from human induced pluripotent stem cells, and used the hydrogels with endothelial networks to identify angiogenesis inhibitors. The synthetic hydrogels show superior sensitivity and reproducibility over Matrigel when evaluating known inhibitors, as well as in a blinded screen of a subset of 38 chemicals, selected according to predicted vascular disruption potential, from the Toxicity ForeCaster library of the US Environmental Protection Agency. The identified synthetic hydrogels should be suitable alternatives to Matrigel for common cell-culture applications.
Collapse
|
30
|
Zang Q, Mansouri K, Williams AJ, Judson RS, Allen DG, Casey WM, Kleinstreuer NC. In Silico Prediction of Physicochemical Properties of Environmental Chemicals Using Molecular Fingerprints and Machine Learning. J Chem Inf Model 2017; 57:36-49. [PMID: 28006899 PMCID: PMC6131700 DOI: 10.1021/acs.jcim.6b00625] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There are little available toxicity data on the vast majority of chemicals in commerce. High-throughput screening (HTS) studies, such as those being carried out by the U.S. Environmental Protection Agency (EPA) ToxCast program in partnership with the federal Tox21 research program, can generate biological data to inform models for predicting potential toxicity. However, physicochemical properties are also needed to model environmental fate and transport, as well as exposure potential. The purpose of the present study was to generate an open-source quantitative structure-property relationship (QSPR) workflow to predict a variety of physicochemical properties that would have cross-platform compatibility to integrate into existing cheminformatics workflows. In this effort, decades-old experimental property data sets available within the EPA EPI Suite were reanalyzed using modern cheminformatics workflows to develop updated QSPR models capable of supplying computationally efficient, open, and transparent HTS property predictions in support of environmental modeling efforts. Models were built using updated EPI Suite data sets for the prediction of six physicochemical properties: octanol-water partition coefficient (logP), water solubility (logS), boiling point (BP), melting point (MP), vapor pressure (logVP), and bioconcentration factor (logBCF). The coefficient of determination (R2) between the estimated values and experimental data for the six predicted properties ranged from 0.826 (MP) to 0.965 (BP), with model performance for five of the six properties exceeding those from the original EPI Suite models. The newly derived models can be employed for rapid estimation of physicochemical properties within an open-source HTS workflow to inform fate and toxicity prediction models of environmental chemicals.
Collapse
Affiliation(s)
- Qingda Zang
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC 27709, USA
| | - Kamel Mansouri
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Antony J. Williams
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - Richard S. Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | - David G. Allen
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC 27709, USA
| | - Warren M. Casey
- National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Nicole C. Kleinstreuer
- National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| |
Collapse
|
31
|
Environmental Reviews and Case Studies: Biological Effects–Based Tools for Monitoring Impacted Surface Waters in the Great Lakes: A Multiagency Program in Support of the Great Lakes Restoration Initiative. ACTA ACUST UNITED AC 2017. [DOI: 10.1017/s1466046613000458] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
32
|
Janesick AS, Dimastrogiovanni G, Chamorro-Garcia R, Blumberg B. Reply to "Comment on 'On the Utility of ToxCast™ and ToxPi as Methods for Identifying New Obesogens'". ENVIRONMENTAL HEALTH PERSPECTIVES 2017; 125:A12-A14. [PMID: 28055946 PMCID: PMC5224935 DOI: 10.1289/ehp1122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Amanda S. Janesick
- Department of Otolaryngology–Head & Neck Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Giorgio Dimastrogiovanni
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA
- Department of Environmental Chemistry, IIQAB-CSIC (Superior Council of Scientific Investigations), Barcelona, Spain
| | - Raquel Chamorro-Garcia
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| |
Collapse
|
33
|
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". ENVIRONMENTAL HEALTH PERSPECTIVES 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] [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:
| |
Collapse
|
34
|
Kleinstreuer NC, Ceger P, Watt ED, Martin M, Houck K, Browne P, Thomas RS, Casey WM, Dix DJ, Allen D, Sakamuru S, Xia M, Huang R, Judson R. Development and Validation of a Computational Model for Androgen Receptor Activity. Chem Res Toxicol 2016; 30:946-964. [PMID: 27933809 PMCID: PMC5396026 DOI: 10.1021/acs.chemrestox.6b00347] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Testing thousands of chemicals to identify potential androgen receptor (AR) agonists or antagonists would cost millions of dollars and take decades to complete using current validated methods. High-throughput in vitro screening (HTS) and computational toxicology approaches can more rapidly and inexpensively identify potential androgen-active chemicals. We integrated 11 HTS ToxCast/Tox21 in vitro assays into a computational network model to distinguish true AR pathway activity from technology-specific assay interference. The in vitro HTS assays probed perturbations of the AR pathway at multiple points (receptor binding, coregulator recruitment, gene transcription, and protein production) and multiple cell types. Confirmatory in vitro antagonist assay data and cytotoxicity information were used as additional flags for potential nonspecific activity. Validating such alternative testing strategies requires high-quality reference data. We compiled 158 putative androgen-active and -inactive chemicals from a combination of international test method validation efforts and semiautomated systematic literature reviews. Detailed in vitro assay information and results were compiled into a single database using a standardized ontology. Reference chemical concentrations that activated or inhibited AR pathway activity were identified to establish a range of potencies with reproducible reference chemical results. Comparison with existing Tier 1 AR binding data from the U.S. EPA Endocrine Disruptor Screening Program revealed that the model identified binders at relevant test concentrations (<100 μM) and was more sensitive to antagonist activity. The AR pathway model based on the ToxCast/Tox21 assays had balanced accuracies of 95.2% for agonist (n = 29) and 97.5% for antagonist (n = 28) reference chemicals. Out of 1855 chemicals screened in the AR pathway model, 220 chemicals demonstrated AR agonist or antagonist activity and an additional 174 chemicals were predicted to have potential weak AR pathway activity.
Collapse
Affiliation(s)
- Nicole C Kleinstreuer
- NIH/NIEHS/DNTP/The NTP Interagency Center for the Evaluation of Alternative Toxicological Methods , Research Triangle Park, North Carolina 27713, United States
| | - Patricia Ceger
- Integrated Laboratory Systems, Inc. , Research Triangle Park, North Carolina 27560, United States
| | - Eric D Watt
- EPA/ORD/National Center for Computational Toxicology , Research Triangle Park, North Carolina 27711, United States
| | - Matthew Martin
- EPA/ORD/National Center for Computational Toxicology , Research Triangle Park, North Carolina 27711, United States
| | - Keith Houck
- EPA/ORD/National Center for Computational Toxicology , Research Triangle Park, North Carolina 27711, United States
| | - Patience Browne
- OECD Environment Directorate, Environment Health and Safety Division , Paris 75775, France
| | - Russell S Thomas
- EPA/ORD/National Center for Computational Toxicology , Research Triangle Park, North Carolina 27711, United States
| | - Warren M Casey
- NIH/NIEHS/DNTP/The NTP Interagency Center for the Evaluation of Alternative Toxicological Methods , Research Triangle Park, North Carolina 27713, United States
| | - David J Dix
- EPA/OCSPP/Office of Science Coordination and Policy , Washington, DC, 20460, United States
| | - David Allen
- Integrated Laboratory Systems, Inc. , Research Triangle Park, North Carolina 27560, United States
| | - Srilatha Sakamuru
- NIH/National Center for Advancing Translational Sciences , Bethesda, Maryland 20892, United States
| | - Menghang Xia
- NIH/National Center for Advancing Translational Sciences , Bethesda, Maryland 20892, United States
| | - Ruili Huang
- NIH/National Center for Advancing Translational Sciences , Bethesda, Maryland 20892, United States
| | - Richard Judson
- EPA/ORD/National Center for Computational Toxicology , Research Triangle Park, North Carolina 27711, United States
| |
Collapse
|
35
|
Miller MM, Alyea RA, LeSommer C, Doheny DL, Rowley SM, Childs KM, Balbuena P, Ross SM, Dong J, Sun B, Andersen MA, Clewell RA. Editor's Highlight: Development of an In vitro Assay Measuring Uterine-Specific Estrogenic Responses for Use in Chemical Safety Assessment. Toxicol Sci 2016; 154:162-173. [PMID: 27503385 PMCID: PMC5091368 DOI: 10.1093/toxsci/kfw152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A toxicity pathway approach was taken to develop an in vitro assay using human uterine epithelial adenocarcinoma (Ishikawa) cells as a replacement for measuring an in vivo uterotrophic response to estrogens. The Ishikawa cell was determined to be fit for the purpose of recapitulating in vivo uterine response by verifying fidelity of the biological pathway components and the dose-response predictions to women of child-bearing age. Expression of the suite of estrogen receptors that control uterine proliferation (ERα66, ERα46, ERα36, ERβ, G-protein coupled estrogen receptor (GPER)) were confirmed across passages and treatment conditions. Phenotypic responses to ethinyl estradiol (EE) from transcriptional activation of ER-mediated genes, to ALP enzyme induction and cellular proliferation occurred at concentrations consistent with estrogenic activity in adult women (low picomolar). To confirm utility of this model to predict concentration-response for uterine proliferation with xenobiotics, we tested the concentration-response for compounds with known uterine estrogenic activity in humans and compared the results to assays from the ToxCast and Tox21 suite of estrogen assays. The Ishikawa proliferation assay was consistent with in vivo responses and was a more sensitive measure of uterine response. Because this assay was constructed by first mapping the key molecular events for cellular response, and then ensuring that the assay incorporated these events, the resulting cellular assay should be a reliable tool for identifying estrogenic compounds and may provide improved quantitation of chemical concentration response for in vitro-based safety assessments.
Collapse
Affiliation(s)
- Michelle M Miller
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
- ScitoVation, Research Triangle Park, North Carolina
| | - Rebecca A Alyea
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
| | - Caroline LeSommer
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
| | - Daniel L Doheny
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
- ScitoVation, Research Triangle Park, North Carolina
| | - Sean M Rowley
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
- ScitoVation, Research Triangle Park, North Carolina
| | - Kristin M Childs
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
| | - Pergentino Balbuena
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
- ScitoVation, Research Triangle Park, North Carolina
| | - Susan M Ross
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
- ScitoVation, Research Triangle Park, North Carolina
| | - Jian Dong
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
| | - Bin Sun
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
| | - Melvin A Andersen
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
- ScitoVation, Research Triangle Park, North Carolina
| | - Rebecca A Clewell
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina;
- ScitoVation, Research Triangle Park, North Carolina
- *The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina
| |
Collapse
|
36
|
Davis JM, Ekman DR, Teng Q, Ankley GT, Berninger JP, Cavallin JE, Jensen KM, Kahl MD, Schroeder AL, Villeneuve DL, Jorgenson ZG, Lee KE, Collette TW. Linking field-based metabolomics and chemical analyses to prioritize contaminants of emerging concern in the Great Lakes basin. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2016; 35:2493-2502. [PMID: 27027868 DOI: 10.1002/etc.3409] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/18/2016] [Accepted: 02/22/2016] [Indexed: 05/02/2023]
Abstract
The ability to focus on the most biologically relevant contaminants affecting aquatic ecosystems can be challenging because toxicity-assessment programs have not kept pace with the growing number of contaminants requiring testing. Because it has proven effective at assessing the biological impacts of potentially toxic contaminants, profiling of endogenous metabolites (metabolomics) may help screen out contaminants with a lower likelihood of eliciting biological impacts, thereby prioritizing the most biologically important contaminants. The authors present results from a study that utilized cage-deployed fathead minnows (Pimephales promelas) at 18 sites across the Great Lakes basin. They measured water temperature and contaminant concentrations in water samples (132 contaminants targeted, 86 detected) and used 1 H-nuclear magnetic resonance spectroscopy to measure endogenous metabolites in polar extracts of livers. They used partial least-squares regression to compare relative abundances of endogenous metabolites with contaminant concentrations and temperature. The results indicated that profiles of endogenous polar metabolites covaried with at most 49 contaminants. The authors identified up to 52% of detected contaminants as not significantly covarying with changes in endogenous metabolites, suggesting they likely were not eliciting measurable impacts at these sites. This represents a first step in screening for the biological relevance of detected contaminants by shortening lists of contaminants potentially affecting these sites. Such information may allow risk assessors to prioritize contaminants and focus toxicity testing on the most biologically relevant contaminants. Environ Toxicol Chem 2016;35:2493-2502. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.
Collapse
Affiliation(s)
- John M Davis
- National Exposure Research Laboratory, US Environmental Protection Agency, Athens, Georgia.
| | - Drew R Ekman
- National Exposure Research Laboratory, US Environmental Protection Agency, Athens, Georgia
| | - Quincy Teng
- National Exposure Research Laboratory, US Environmental Protection Agency, Athens, Georgia
| | - Gerald T Ankley
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Duluth, Minnesota
| | - Jason P Berninger
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Duluth, Minnesota
| | - Jenna E Cavallin
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Duluth, Minnesota
| | - Kathleen M Jensen
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Duluth, Minnesota
| | - Michael D Kahl
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Duluth, Minnesota
| | - Anthony L Schroeder
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Duluth, Minnesota
| | - Daniel L Villeneuve
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Duluth, Minnesota
| | | | - Kathy E Lee
- Minnesota Water Science Center, US Geological Survey, Grand Rapids, Minnesota
| | - Timothy W Collette
- National Exposure Research Laboratory, US Environmental Protection Agency, Athens, Georgia.
| |
Collapse
|
37
|
Hill T, Nelms MD, Edwards SW, Martin M, Judson R, Corton JC, Wood CE. Editor’s Highlight: Negative Predictors of Carcinogenicity for Environmental Chemicals. Toxicol Sci 2016; 155:157-169. [DOI: 10.1093/toxsci/kfw195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
|
38
|
Janesick AS, Dimastrogiovanni G, Vanek L, Boulos C, Chamorro-García R, Tang W, Blumberg B. On the Utility of ToxCast™ and ToxPi as Methods for Identifying New Obesogens. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:1214-26. [PMID: 26757984 PMCID: PMC4977052 DOI: 10.1289/ehp.1510352] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/07/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND In ToxCast™ Phase I, the U.S. EPA commissioned screening of 320 pesticides, herbicides, fungicides, and other chemicals in a series of high-throughput assays. The agency also developed a toxicological prioritization tool, ToxPi, to facilitate using ToxCast™ assays to predict biological function. OBJECTIVES We asked whether top-scoring PPARγ activators identified in ToxCast™ Phase I were genuine PPARγ activators and inducers of adipogenesis. Next, we identified ToxCast™ assays that should predict adipogenesis, developed an adipogenesis ToxPi, and asked how well the ToxPi predicted adipogenic activity. METHODS We used transient transfection to test the ability of ToxCast™ chemicals to modulate PPARγ and RXRα, and differentiation assays employing 3T3-L1 preadipocytes and mouse bone marrow-derived mesenchymal stem cells (mBMSCs) to evaluate the adipogenic capacity of ToxCast™ chemicals. RESULTS Only 5/21 of the top scoring ToxCast™ PPARγ activators were activators in our assays, 3 were PPARγ antagonists, the remainder were inactive. The bona fide PPARγ activators we identified induced adipogenesis in 3T3-L1 cells and mBMSCs. Only 7 of the 17 chemicals predicted to be active by the ToxPi promoted adipogenesis, 1 inhibited adipogenesis, and 2 of the 7 predicted negatives were also adipogenic. Of these 9 adipogenic chemicals, 3 activated PPARγ, and 1 activated RXRα. CONCLUSIONS ToxCast™ PPARγ and RXRα assays do not correlate well with laboratory measurements of PPARγ and RXRα activity. The adipogenesis ToxPi performed poorly, perhaps due to the performance of ToxCast™ assays. We observed a modest predictive value of ToxCast™ for PPARγ and RXRα activation and adipogenesis and it is likely that many obesogenic chemicals remain to be identified. CITATION Janesick AS, Dimastrogiovanni G, Vanek L, Boulos C, Chamorro-García R, Tang W, Blumberg B. 2016. On the utility of ToxCast™ and ToxPi as methods for identifying new obesogens. Environ Health Perspect 124:1214-1226; http://dx.doi.org/10.1289/ehp.1510352.
Collapse
Affiliation(s)
- Amanda Shaine Janesick
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA
| | - Giorgio Dimastrogiovanni
- Department of Environmental Chemistry, IIQAB-CSIC (Superior Council of Scientific Investigations), Barcelona, Spain
| | - Lenka Vanek
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA
| | - Christy Boulos
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA
| | - Raquel Chamorro-García
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA
| | - Weiyi Tang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
- Address correspondence to B. Blumberg, Developmental and Cell Biology, U.C. Irvine, 2011 BioSci 3, Irvine, CA 92697-2300 USA. Telephone: (949) 824-8573. E-mail:
| |
Collapse
|
39
|
Webster AF, Lambert IB, Yauk CL. Toxicogenomics Case Study: Furan. TOXICOGENOMICS IN PREDICTIVE CARCINOGENICITY 2016. [DOI: 10.1039/9781782624059-00390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Development of pragmatic methodologies for human health risk assessment is required to address current regulatory challenges. We applied three toxicogenomic approaches—quantitative, predictive, and mechanistic—to a case study in mice exposed for 3 weeks to the hepatocarcinogen furan. We modeled the dose response of a variety of transcriptional endpoints and found that they produced benchmark doses similar to the furan-dependent cancer benchmark doses. Meta-analyses showed strong similarity between furan-dependent gene expression changes and those associated with several hepatic pathologies. Molecular pathways facilitated the development of a molecular mode of action for furan-induced hepatocellular carcinogenicity. Finally, we compared transcriptomic profiles derived from formalin-fixed and paraffin-embedded (FFPE) samples with those from high-quality frozen samples to evaluate whether archival samples are a viable option for toxicogenomic studies. The advantage of using FFPE tissues is that they are very well characterized (phenotypically); the disadvantage is that formalin degrades biomacromolecules, including RNA. We found that FFPE samples can be used for toxicogenomics using a ribo-depletion RNA-seq protocol. Our case study demonstrates the utility of toxicogenomics data to human health risk assessment, the potential of archival FFPE tissue samples, and identifies viable strategies toward the reduction of animal usage in chemical testing.
Collapse
Affiliation(s)
- A. Francina Webster
- Department of Biology, Carleton University 1125 Colonel By Drive Ottawa ON Canada
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture 50 Colombine Driveway Ottawa ON Canada
| | - Iain B. Lambert
- Department of Biology, Carleton University 1125 Colonel By Drive Ottawa ON Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture 50 Colombine Driveway Ottawa ON Canada
| |
Collapse
|
40
|
Richard AM, Judson RS, Houck KA, Grulke CM, Volarath P, Thillainadarajah I, Yang C, Rathman J, Martin MT, Wambaugh JF, Knudsen TB, Kancherla J, Mansouri K, Patlewicz G, Williams AJ, Little SB, Crofton KM, Thomas RS. ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology. Chem Res Toxicol 2016; 29:1225-51. [PMID: 27367298 DOI: 10.1021/acs.chemrestox.6b00135] [Citation(s) in RCA: 381] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The U.S. Environmental Protection Agency's (EPA) ToxCast program is testing a large library of Agency-relevant chemicals using in vitro high-throughput screening (HTS) approaches to support the development of improved toxicity prediction models. Launched in 2007, Phase I of the program screened 310 chemicals, mostly pesticides, across hundreds of ToxCast assay end points. In Phase II, the ToxCast library was expanded to 1878 chemicals, culminating in the public release of screening data at the end of 2013. Subsequent expansion in Phase III has resulted in more than 3800 chemicals actively undergoing ToxCast screening, 96% of which are also being screened in the multi-Agency Tox21 project. The chemical library unpinning these efforts plays a central role in defining the scope and potential application of ToxCast HTS results. The history of the phased construction of EPA's ToxCast library is reviewed, followed by a survey of the library contents from several different vantage points. CAS Registry Numbers are used to assess ToxCast library coverage of important toxicity, regulatory, and exposure inventories. Structure-based representations of ToxCast chemicals are then used to compute physicochemical properties, substructural features, and structural alerts for toxicity and biotransformation. Cheminformatics approaches using these varied representations are applied to defining the boundaries of HTS testability, evaluating chemical diversity, and comparing the ToxCast library to potential target application inventories, such as used in EPA's Endocrine Disruption Screening Program (EDSP). Through several examples, the ToxCast chemical library is demonstrated to provide comprehensive coverage of the knowledge domains and target inventories of potential interest to EPA. Furthermore, the varied representations and approaches presented here define local chemistry domains potentially worthy of further investigation (e.g., not currently covered in the testing library or defined by toxicity "alerts") to strategically support data mining and predictive toxicology modeling moving forward.
Collapse
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
| |
Collapse
|
41
|
Belair DG, Schwartz MP, Knudsen T, Murphy WL. Human iPSC-derived endothelial cell sprouting assay in synthetic hydrogel arrays. Acta Biomater 2016; 39:12-24. [PMID: 27181878 PMCID: PMC5228278 DOI: 10.1016/j.actbio.2016.05.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 01/09/2023]
Abstract
UNLABELLED Activation of vascular endothelial cells (ECs) by growth factors initiates a cascade of events during angiogenesis in vivo consisting of EC tip cell selection, sprout formation, EC stalk cell proliferation, and ultimately vascular stabilization by support cells. Although EC functional assays can recapitulate one or more aspects of angiogenesis in vitro, they are often limited by undefined substrates and lack of dependence on key angiogenic signaling axes. Here, we designed and characterized a chemically-defined model of endothelial sprouting behavior in vitro using human induced pluripotent stem cell-derived endothelial cells (iPSC-ECs). We rapidly encapsulated iPSC-ECs at high density in poly(ethylene glycol) (PEG) hydrogel spheres using thiol-ene chemistry and subsequently encapsulated cell-dense hydrogel spheres in a cell-free hydrogel layer. The hydrogel sprouting array supported pro-angiogenic phenotype of iPSC-ECs and supported growth factor-dependent proliferation and sprouting behavior. iPSC-ECs in the sprouting model responded appropriately to several reference pharmacological angiogenesis inhibitors of vascular endothelial growth factor, NF-κB, matrix metalloproteinase-2/9, protein kinase activity, and β-tubulin, which confirms their functional role in endothelial sprouting. A blinded screen of 38 putative vascular disrupting compounds from the US Environmental Protection Agency's ToxCast library identified six compounds that inhibited iPSC-EC sprouting and five compounds that were overtly cytotoxic to iPSC-ECs at a single concentration. The chemically-defined iPSC-EC sprouting model (iSM) is thus amenable to enhanced-throughput screening of small molecular libraries for effects on angiogenic sprouting and iPSC-EC toxicity assessment. STATEMENT OF SIGNIFICANCE Angiogenesis assays that are commonly used for drug screening and toxicity assessment applications typically utilize natural substrates like Matrigel(TM) that are difficult to spatially pattern, costly, ill-defined, and may exhibit lot-to-lot variability. Herein, we describe a novel angiogenic sprouting assay using chemically-defined, bioinert poly(ethylene glycol) hydrogels functionalized with biomimetic peptides to promote cell attachment and degradation in a reproducible format that may mitigate the need for natural substrates. The quantitative assay of angiogenic sprouting here enables precise control over the initial conditions and can be formulated into arrays for screening. The sprouting assay here was dependent on key angiogenic signaling axes in a screen of angiogenesis inhibitors and a blinded screen of putative vascular disrupting compounds from the US-EPA.
Collapse
Affiliation(s)
- David G Belair
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael P Schwartz
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas Knudsen
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, NC, USA
| | - William L Murphy
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA; Material Science Program, University of Wisconsin-Madison, Madison, WI, USA; Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
42
|
Leonard JA, Sobel Leonard A, Chang DT, Edwards S, Lu J, Scholle S, Key P, Winter M, Isaacs K, Tan YM. Evaluating the Impact of Uncertainties in Clearance and Exposure When Prioritizing Chemicals Screened in High-Throughput Assays. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:5961-5971. [PMID: 27124219 PMCID: PMC5783724 DOI: 10.1021/acs.est.6b00374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The toxicity-testing paradigm has evolved to include high-throughput (HT) methods for addressing the increasing need to screen hundreds to thousands of chemicals rapidly. Approaches that involve in vitro screening assays, in silico predictions of exposure concentrations, and pharmacokinetic (PK) characteristics provide the foundation for HT risk prioritization. Underlying uncertainties in predicted exposure concentrations or PK behaviors can significantly influence the prioritization of chemicals, though the impact of such influences is unclear. In the current study, a framework was developed to incorporate absorbed doses, PK properties, and in vitro dose-response data into a PK/pharmacodynamic (PD) model to allow for placement of chemicals into discrete priority bins. Literature-reported or predicted values for clearance rates and absorbed doses were used in the PK/PD model to evaluate the impact of their uncertainties on chemical prioritization. Scenarios using predicted absorbed doses resulted in a larger number of bin misassignments than those scenarios using predicted clearance rates, when comparing to bin placement using literature-reported values. Sensitivity of parameters on the model output of toxicological activity was examined across possible ranges for those parameters to provide insight into how uncertainty in their predicted values might impact uncertainty in activity.
Collapse
Affiliation(s)
- Jeremy A. Leonard
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee 37831, United States
| | - Ashley Sobel Leonard
- Department of Biological Sciences, Duke University, Durham, North Carolina 27708, United States
| | | | - Stephen Edwards
- National Health and Environmental Effects Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, United States
| | - Jingtao Lu
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee 37831, United States
| | - Steven Scholle
- National Exposure Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, United States
| | - Phillip Key
- National Exposure Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, United States
| | - Maxwell Winter
- National Exposure Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, United States
| | - Kristin Isaacs
- National Exposure Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, United States
| | - Yu-Mei Tan
- National Exposure Research Laboratory, United States Environmental Protection Agency, Research Triangle Park, North Carolina 27709, United States
| |
Collapse
|
43
|
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] [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.
Collapse
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
| |
Collapse
|
44
|
Norinder U, Boyer S. Conformal Prediction Classification of a Large Data Set of Environmental Chemicals from ToxCast and Tox21 Estrogen Receptor Assays. Chem Res Toxicol 2016; 29:1003-10. [DOI: 10.1021/acs.chemrestox.6b00037] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ulf Norinder
- Swedish Toxicology Sciences Research Center, SE-151
36 Södertälje, Sweden
| | - Scott Boyer
- Swedish Toxicology Sciences Research Center, SE-151
36 Södertälje, Sweden
| |
Collapse
|
45
|
De Abrew KN, Kainkaryam RM, Shan YK, Overmann GJ, Settivari RS, Wang X, Xu J, Adams RL, Tiesman JP, Carney EW, Naciff JM, Daston GP. Grouping 34 Chemicals Based on Mode of Action Using Connectivity Mapping. Toxicol Sci 2016; 151:447-61. [DOI: 10.1093/toxsci/kfw058] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
46
|
Harlow PH, Perry SJ, Widdison S, Daniels S, Bondo E, Lamberth C, Currie RA, Flemming AJ. The nematode Caenorhabditis elegans as a tool to predict chemical activity on mammalian development and identify mechanisms influencing toxicological outcome. Sci Rep 2016; 6:22965. [PMID: 26987796 PMCID: PMC4796825 DOI: 10.1038/srep22965] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/19/2016] [Indexed: 01/08/2023] Open
Abstract
To determine whether a C. elegans bioassay could predict mammalian developmental activity, we selected diverse compounds known and known not to elicit such activity and measured their effect on C. elegans egg viability. 89% of compounds that reduced C. elegans egg viability also had mammalian developmental activity. Conversely only 25% of compounds found not to reduce egg viability in C. elegans were also inactive in mammals. We conclude that the C. elegans egg viability assay is an accurate positive predictor, but an inaccurate negative predictor, of mammalian developmental activity. We then evaluated C. elegans as a tool to identify mechanisms affecting toxicological outcomes among related compounds. The difference in developmental activity of structurally related fungicides in C. elegans correlated with their rate of metabolism. Knockdown of the cytochrome P450s cyp-35A3 and cyp-35A4 increased the toxicity to C. elegans of the least developmentally active compounds to the level of the most developmentally active. This indicated that these P450s were involved in the greater rate of metabolism of the less toxic of these compounds. We conclude that C. elegans based approaches can predict mammalian developmental activity and can yield plausible hypotheses for factors affecting the biological potency of compounds in mammals.
Collapse
Affiliation(s)
- Philippa H Harlow
- Syngenta Ltd., Jealott's Hill Research Station, Bracknell, Berkshire, RG42 6EY, UK
| | - Simon J Perry
- Syngenta Ltd., Jealott's Hill Research Station, Bracknell, Berkshire, RG42 6EY, UK
| | - Stephanie Widdison
- General Bioinformatics, Jealott's Hill Research Station, Bracknell, Berkshire, RG42 6EY, UK
| | - Shannon Daniels
- Syngenta, 3054 East Cornwallis Road, Research Triangle Park, NC 27709-2257, USA
| | - Eddie Bondo
- Syngenta, 3054 East Cornwallis Road, Research Triangle Park, NC 27709-2257, USA
| | - Clemens Lamberth
- Syngenta Crop Protection AG, Chemical Research, Schaffhauserstrasse 101, 4332 Stein, Switzerland
| | - Richard A Currie
- Syngenta Ltd., Jealott's Hill Research Station, Bracknell, Berkshire, RG42 6EY, UK
| | - Anthony J Flemming
- Syngenta Ltd., Jealott's Hill Research Station, Bracknell, Berkshire, RG42 6EY, UK
| |
Collapse
|
47
|
Pham N, Iyer S, Hackett E, Lock BH, Sandy M, Zeise L, Solomon G, Marty M. Using ToxCast to Explore Chemical Activities and Hazard Traits: A Case Study WithOrtho-Phthalates. Toxicol Sci 2016; 151:286-301. [DOI: 10.1093/toxsci/kfw049] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
|
48
|
Yoon M, Clewell HJ. Addressing Early Life Sensitivity Using Physiologically Based Pharmacokinetic Modeling and In Vitro to In Vivo Extrapolation. Toxicol Res 2016; 32:15-20. [PMID: 26977255 PMCID: PMC4780231 DOI: 10.5487/tr.2016.32.1.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 12/24/2015] [Accepted: 01/05/2016] [Indexed: 01/10/2023] Open
Abstract
Physiologically based pharmacokinetic (PBPK) modeling can provide an effective way to utilize in vitro and in silico based information in modern risk assessment for children and other potentially sensitive populations. In this review, we describe the process of in vitro to in vivo extrapolation (IVIVE) to develop PBPK models for a chemical in different ages in order to predict the target tissue exposure at the age of concern in humans. We present our on-going studies on pyrethroids as a proof of concept to guide the readers through the IVIVE steps using the metabolism data collected either from age-specific liver donors or expressed enzymes in conjunction with enzyme ontogeny information to provide age-appropriate metabolism parameters in the PBPK model in the rat and human, respectively. The approach we present here is readily applicable to not just to other pyrethroids, but also to other environmental chemicals and drugs. Establishment of an in vitro and in silico-based evaluation strategy in conjunction with relevant exposure information in humans is of great importance in risk assessment for potentially vulnerable populations like early ages where the necessary information for decision making is limited.
Collapse
|
49
|
Phillips MB, Leonard JA, Grulke CM, Chang DT, Edwards SW, Brooks R, Goldsmith MR, El-Masri H, Tan YM. A Workflow to Investigate Exposure and Pharmacokinetic Influences on High-Throughput in Vitro Chemical Screening Based on Adverse Outcome Pathways. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:53-60. [PMID: 25978103 PMCID: PMC4710605 DOI: 10.1289/ehp.1409450] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 05/13/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND Adverse outcome pathways (AOPs) link adverse effects in individuals or populations to a molecular initiating event (MIE) that can be quantified using in vitro methods. Practical application of AOPs in chemical-specific risk assessment requires incorporation of knowledge on exposure, along with absorption, distribution, metabolism, and excretion (ADME) properties of chemicals. OBJECTIVES We developed a conceptual workflow to examine exposure and ADME properties in relation to an MIE. The utility of this workflow was evaluated using a previously established AOP, acetylcholinesterase (AChE) inhibition. METHODS Thirty chemicals found to inhibit human AChE in the ToxCast™ assay were examined with respect to their exposure, absorption potential, and ability to cross the blood-brain barrier (BBB). Structures of active chemicals were compared against structures of 1,029 inactive chemicals to detect possible parent compounds that might have active metabolites. RESULTS Application of the workflow screened 10 "low-priority" chemicals of 30 active chemicals. Fifty-two of the 1,029 inactive chemicals exhibited a similarity threshold of ≥ 75% with their nearest active neighbors. Of these 52 compounds, 30 were excluded due to poor absorption or distribution. The remaining 22 compounds may inhibit AChE in vivo either directly or as a result of metabolic activation. CONCLUSIONS The incorporation of exposure and ADME properties into the conceptual workflow eliminated 10 "low-priority" chemicals that may otherwise have undergone additional, resource-consuming analyses. Our workflow also increased confidence in interpretation of in vitro results by identifying possible "false negatives." CITATION Phillips MB, Leonard JA, Grulke CM, Chang DT, Edwards SW, Brooks R, Goldsmith MR, El-Masri H, Tan YM. 2016. A workflow to investigate exposure and pharmacokinetic influences on high-throughput in vitro chemical screening based on adverse outcome pathways. Environ Health Perspect 124:53-60; http://dx.doi.org/10.1289/ehp.1409450.
Collapse
Affiliation(s)
- Martin B. Phillips
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Jeremy A. Leonard
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | | | | | - Stephen W. Edwards
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Raina Brooks
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Hisham El-Masri
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Yu-Mei Tan
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| |
Collapse
|
50
|
Hu B, Gifford E, Wang H, Bailey W, Johnson T. Analysis of the ToxCast Chemical-Assay Space Using the Comparative Toxicogenomics Database. Chem Res Toxicol 2015; 28:2210-23. [PMID: 26505644 DOI: 10.1021/acs.chemrestox.5b00369] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Many studies have attempted to predict in vivo hazards based on the ToxCast in vitro assay results with the goal of using these predictions to prioritize compounds for conventional toxicity testing. Most of these conventional studies rely on in vivo end points observed using preclinical species (e.g., mice and rats). Although the preclinical animal studies provide valuable insights, there can often be significant disconnects between these studies and safety concerns in humans. One way to address these concerns, for an admittedly more limited set of compounds, is to explore relationships between the in vitro data from human cell lines and observations from human related studies. The Comparative Toxicogenomics Database (CTD; http://ctdbase.org ) is a rich source of data linking chemicals to human diseases/adverse events and pathways. In this study we explored the relationships between ToxCast chemicals, their ToxCast in vitro test results, and their annotations of human disease/adverse event end points as captured in the CTD database. We mined these associations to identify potentially interesting, statistically significant in vitro assay and in vivo toxicity correlations. To the best of our knowledge, this is one of the first studies analyzing the relationships between the ToxCast in vitro assays results and the CTD disease/adverse event end point annotations. The in vitro profiles identified in this analysis may prove useful for prioritizing compounds for toxicity testing, suggesting mechanisms of toxicity, and forecasting potential in vivo human drug induced injury.
Collapse
Affiliation(s)
- Bingjie Hu
- Structural Chemistry, Merck Research Laboratories, Merck & Co. , West Point, Pennsylvania 19486, United States
| | - Eric Gifford
- Structural Chemistry, Merck Research Laboratories, Merck & Co. , West Point, Pennsylvania 19486, United States
| | - Huijun Wang
- Structural Chemistry, Merck Research Laboratories, Merck & Co. , Kenilworth, New Jersey 07033, United States
| | - Wendy Bailey
- Safety Assessment and Laboratory Animal Resources, Merck Research Laboratories, Merck & Co. , West Point, Pennsylvania 19486, United States
| | - Timothy Johnson
- Safety Assessment and Laboratory Animal Resources, Merck Research Laboratories, Merck & Co. , West Point, Pennsylvania 19486, United States
| |
Collapse
|