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Sostare E, Bowen TJ, Lawson TN, Freier A, Li X, Lloyd GR, Najdekr L, Jankevics A, Smith T, Varshavi D, Ludwig C, Colbourne JK, Weber RJM, Crizer DM, Auerbach SS, Bucher JR, Viant MR. Metabolomics Simultaneously Derives Benchmark Dose Estimates and Discovers Metabolic Biotransformations in a Rat Bioassay. Chem Res Toxicol 2024. [PMID: 38842447 DOI: 10.1021/acs.chemrestox.4c00002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Benchmark dose (BMD) modeling estimates the dose of a chemical that causes a perturbation from baseline. Transcriptional BMDs have been shown to be relatively consistent with apical end point BMDs, opening the door to using molecular BMDs to derive human health-based guidance values for chemical exposure. Metabolomics measures the responses of small-molecule endogenous metabolites to chemical exposure, complementing transcriptomics by characterizing downstream molecular phenotypes that are more closely associated with apical end points. The aim of this study was to apply BMD modeling to in vivo metabolomics data, to compare metabolic BMDs to both transcriptional and apical end point BMDs. This builds upon our previous application of transcriptomics and BMD modeling to a 5-day rat study of triphenyl phosphate (TPhP), applying metabolomics to the same archived tissues. Specifically, liver from rats exposed to five doses of TPhP was investigated using liquid chromatography-mass spectrometry and 1H nuclear magnetic resonance spectroscopy-based metabolomics. Following the application of BMDExpress2 software, 2903 endogenous metabolic features yielded viable dose-response models, confirming a perturbation to the liver metabolome. Metabolic BMD estimates were similarly sensitive to transcriptional BMDs, and more sensitive than both clinical chemistry and apical end point BMDs. Pathway analysis of the multiomics data sets revealed a major effect of TPhP exposure on cholesterol (and downstream) pathways, consistent with clinical chemistry measurements. Additionally, the transcriptomics data indicated that TPhP activated xenobiotic metabolism pathways, which was confirmed by using the underexploited capability of metabolomics to detect xenobiotic-related compounds. Eleven biotransformation products of TPhP were discovered, and their levels were highly correlated with multiple xenobiotic metabolism genes. This work provides a case study showing how metabolomics and transcriptomics can estimate mechanistically anchored points-of-departure. Furthermore, the study demonstrates how metabolomics can also discover biotransformation products, which could be of value within a regulatory setting, for example, as an enhancement of OECD Test Guideline 417 (toxicokinetics).
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Affiliation(s)
- Elena Sostare
- Michabo Health Science Ltd., Union House, 111 New Union Street, Coventry CV1 2NT, U.K
| | - Tara J Bowen
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Thomas N Lawson
- Michabo Health Science Ltd., Union House, 111 New Union Street, Coventry CV1 2NT, U.K
| | - Anne Freier
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Xiaojing Li
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Gavin R Lloyd
- Phenome Centre Birmingham, University of Birmingham, Birmingham B15 2TT, U.K
| | - Lukáš Najdekr
- Phenome Centre Birmingham, University of Birmingham, Birmingham B15 2TT, U.K
| | - Andris Jankevics
- Phenome Centre Birmingham, University of Birmingham, Birmingham B15 2TT, U.K
| | - Thomas Smith
- Phenome Centre Birmingham, University of Birmingham, Birmingham B15 2TT, U.K
| | - Dorsa Varshavi
- Phenome Centre Birmingham, University of Birmingham, Birmingham B15 2TT, U.K
| | - Christian Ludwig
- Phenome Centre Birmingham, University of Birmingham, Birmingham B15 2TT, U.K
| | - John K Colbourne
- Michabo Health Science Ltd., Union House, 111 New Union Street, Coventry CV1 2NT, U.K
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Ralf J M Weber
- Michabo Health Science Ltd., Union House, 111 New Union Street, Coventry CV1 2NT, U.K
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
- Phenome Centre Birmingham, University of Birmingham, Birmingham B15 2TT, U.K
| | - David M Crizer
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park NC 27709, North Carolina, United States
| | - Scott S Auerbach
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park NC 27709, North Carolina, United States
| | - John R Bucher
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park NC 27709, North Carolina, United States
| | - Mark R Viant
- Michabo Health Science Ltd., Union House, 111 New Union Street, Coventry CV1 2NT, U.K
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, U.K
- Phenome Centre Birmingham, University of Birmingham, Birmingham B15 2TT, U.K
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2
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Gao X, Johnson WE, Yourick MR, Campasino K, Sprando RL, Yourick JJ. Hepatotoxicity of Silver Nanoparticles: Benchmark Concentration Modeling of an In Vitro Transcriptomics Study in Human iPSC-derived Hepatocytes. Regul Toxicol Pharmacol 2024:105653. [PMID: 38825064 DOI: 10.1016/j.yrtph.2024.105653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/21/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
Despite two decades of research on silver nanoparticle (AgNP) toxicity, a safe threshold for exposure has not yet been established, albeit being critically needed for risk assessment and regulatory decision-making. Traditionally, a point-of-departure (PoD) value is derived from dose response of apical endpoints in animal studies using either the no-observed-adverse-effect level (NOAEL) approach, or benchmark dose (BMD) modeling. To develop new approach methodologies (NAMs) to inform human risk assessment of AgNPs, we conducted a concentration response modeling of the transcriptomic changes in hepatocytes derived from human induced pluripotent stem cells (iPSCs) after being exposed to a wide range concentration (0.01-25 μg/ml) of AgNPs for 24 h. A plausible transcriptomic PoD of 0.21 μg/ml was derived for a pathway related to the mode-of-action (MOA) of AgNPs, and a more conservative PoD of 0.10 μg/ml for a gene ontology (GO) term not apparently associated with the MOA of AgNPs. A reference dose (RfD) could be calculated from either of the PoDs as a safe threshold for AgNP exposure. The current study illustrates the usefulness of in vitro transcriptomic concentration response study using human cells as a NAM for toxicity study of chemicals that lack adequate toxicity data to inform human risk assessment.
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Affiliation(s)
- Xiugong Gao
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
| | - W Evan Johnson
- Division of Infectious Disease, Center for Data Science, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Miranda R Yourick
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Kayla Campasino
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Robert L Sprando
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Jeffrey J Yourick
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
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3
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Costa E, Johnson KJ, Walker CA, O’Brien JM. Transcriptomic point of departure determination: a comparison of distribution-based and gene set-based approaches. Front Genet 2024; 15:1374791. [PMID: 38784034 PMCID: PMC11112360 DOI: 10.3389/fgene.2024.1374791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
A key step in assessing the potential human and environmental health risks of industrial and agricultural chemicals is to determine the toxicity point of departure (POD), which is the highest dose level that causes no adverse effect. Transcriptomic POD (tPOD) values have been suggested to accurately estimate toxicity POD values. One step in the most common approach for tPOD determination involves mapping genes to annotated gene sets, a process that might lead to substantial information loss particularly in species with poor gene annotation. Alternatively, methods that calculate tPOD values directly from the distribution of individual gene POD values omit this mapping step. Using rat transcriptome data for 79 molecules obtained from Open TG-GATEs (Toxicogenomics Project Genomics Assisted Toxicity Evaluation System), the hypothesis was tested that methods based on the distribution of all individual gene POD values will give a similar tPOD value to that obtained via the gene set-based method. Gene set-based tPOD values using four different gene set structures were compared to tPOD values from five different individual gene distribution methods. Results revealed a high tPOD concordance for all methods tested, especially for molecules with at least 300 dose-responsive probesets: for 90% of those molecules, the tPOD values from all methods were within 4-fold of each other. In addition, random gene sets based upon the structure of biological knowledge-derived gene sets produced tPOD values with a median absolute fold change of 1.3-1.4 when compared to the original biological knowledge-derived gene set counterparts, suggesting that little biological information is used in the gene set-based tPOD generation approach. These findings indicate using individual gene distributions to calculate a tPOD is a viable and parsimonious alternative to using gene sets. Importantly, individual gene distribution-based tPOD methods do not require knowledge of biological organization and can be applied to any species including those with poorly annotated gene sets.
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Affiliation(s)
| | | | | | - Jason M. O’Brien
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Ottawa, ON, Canada
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Schmeisser S, Miccoli A, von Bergen M, Berggren E, Braeuning A, Busch W, Desaintes C, Gourmelon A, Grafström R, Harrill J, Hartung T, Herzler M, Kass GEN, Kleinstreuer N, Leist M, Luijten M, Marx-Stoelting P, Poetz O, van Ravenzwaay B, Roggeband R, Rogiers V, Roth A, Sanders P, Thomas RS, Marie Vinggaard A, Vinken M, van de Water B, Luch A, Tralau T. New approach methodologies in human regulatory toxicology - Not if, but how and when! ENVIRONMENT INTERNATIONAL 2023; 178:108082. [PMID: 37422975 PMCID: PMC10858683 DOI: 10.1016/j.envint.2023.108082] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
The predominantly animal-centric approach of chemical safety assessment has increasingly come under pressure. Society is questioning overall performance, sustainability, continued relevance for human health risk assessment and ethics of this system, demanding a change of paradigm. At the same time, the scientific toolbox used for risk assessment is continuously enriched by the development of "New Approach Methodologies" (NAMs). While this term does not define the age or the state of readiness of the innovation, it covers a wide range of methods, including quantitative structure-activity relationship (QSAR) predictions, high-throughput screening (HTS) bioassays, omics applications, cell cultures, organoids, microphysiological systems (MPS), machine learning models and artificial intelligence (AI). In addition to promising faster and more efficient toxicity testing, NAMs have the potential to fundamentally transform today's regulatory work by allowing more human-relevant decision-making in terms of both hazard and exposure assessment. Yet, several obstacles hamper a broader application of NAMs in current regulatory risk assessment. Constraints in addressing repeated-dose toxicity, with particular reference to the chronic toxicity, and hesitance from relevant stakeholders, are major challenges for the implementation of NAMs in a broader context. Moreover, issues regarding predictivity, reproducibility and quantification need to be addressed and regulatory and legislative frameworks need to be adapted to NAMs. The conceptual perspective presented here has its focus on hazard assessment and is grounded on the main findings and conclusions from a symposium and workshop held in Berlin in November 2021. It intends to provide further insights into how NAMs can be gradually integrated into chemical risk assessment aimed at protection of human health, until eventually the current paradigm is replaced by an animal-free "Next Generation Risk Assessment" (NGRA).
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Affiliation(s)
| | - Andrea Miccoli
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany; National Research Council, Ancona, Italy
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany; University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Leipzig, Germany
| | | | - Albert Braeuning
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Wibke Busch
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Christian Desaintes
- European Commission (EC), Directorate General for Research and Innovation (RTD), Brussels, Belgium
| | - Anne Gourmelon
- Organisation for Economic Cooperation and Development (OECD), Environment Directorate, Paris, France
| | | | - Joshua Harrill
- Center for Computational Toxicology and Exposure (CCTE), United States Environmental Protection Agency (US EPA), Durham, USA
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Johns Hopkins Bloomberg School of Public Health Baltimore MD USA, CAAT-Europe, University of Konstanz, Konstanz, Germany
| | - Matthias Herzler
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | | | - Nicole Kleinstreuer
- NTP Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), National Institute of Environmental Health Sciences (NIEHS), Durham, USA
| | - Marcel Leist
- CAAT‑Europe and Department of Biology, University of Konstanz, Konstanz, Germany
| | - Mirjam Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Oliver Poetz
- NMI Natural and Medical Science Institute at the University of Tuebingen, Reutlingen, Germany; SIGNATOPE GmbH, Reutlingen, Germany
| | | | - Rob Roggeband
- European Partnership for Alternative Approaches to Animal Testing (EPAA), Procter and Gamble Services Company NV/SA, Strombeek-Bever, Belgium
| | - Vera Rogiers
- Scientific Committee on Consumer Safety (SCCS), Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Adrian Roth
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Pascal Sanders
- Fougeres Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Fougères, France France
| | - Russell S Thomas
- Center for Computational Toxicology and Exposure (CCTE), United States Environmental Protection Agency (US EPA), Durham, USA
| | | | | | | | - Andreas Luch
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Tewes Tralau
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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5
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Nault R, Cave MC, Ludewig G, Moseley HN, Pennell KG, Zacharewski T. A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:65001. [PMID: 37352010 PMCID: PMC10289218 DOI: 10.1289/ehp11484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023]
Abstract
BACKGROUND Funding agencies, publishers, and other stakeholders are pushing environmental health science investigators to improve data sharing; to promote the findable, accessible, interoperable, and reusable (FAIR) principles; and to increase the rigor and reproducibility of the data collected. Accomplishing these goals will require significant cultural shifts surrounding data management and strategies to develop robust and reliable resources that bridge the technical challenges and gaps in expertise. OBJECTIVE In this commentary, we examine the current state of managing data and metadata-referred to collectively as (meta)data-in the experimental environmental health sciences. We introduce new tools and resources based on in vivo experiments to serve as examples for the broader field. METHODS We discuss previous and ongoing efforts to improve (meta)data collection and curation. These include global efforts by the Functional Genomics Data Society to develop metadata collection tools such as the Investigation, Study, Assay (ISA) framework, and the Center for Expanded Data Annotation and Retrieval. We also conduct a case study of in vivo data deposited in the Gene Expression Omnibus that demonstrates the current state of in vivo environmental health data and highlights the value of using the tools we propose to support data deposition. DISCUSSION The environmental health science community has played a key role in efforts to achieve the goals of the FAIR guiding principles and is well positioned to advance them further. We present a proposed framework to further promote these objectives and minimize the obstacles between data producers and data scientists to maximize the return on research investments. https://doi.org/10.1289/EHP11484.
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Affiliation(s)
- Rance Nault
- Biochemistry & Molecular Biology Department, Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Matthew C. Cave
- Division of Gastroenterology, Hepatology, and Nutrition, University of Louisville, Louisville, Kentucky, USA
| | - Gabriele Ludewig
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa, USA
| | - Hunter N.B. Moseley
- Molecular and Cellular Biochemistry Department, University of Kentucky, Lexington, Kentucky, USA
| | - Kelly G. Pennell
- Department of Civil Engineering, University of Kentucky, Lexington, Kentucky, USA
| | - Tim Zacharewski
- Biochemistry & Molecular Biology Department, Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan, USA
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6
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Tsai HHD, House JS, Wright FA, Chiu WA, Rusyn I. A tiered testing strategy based on in vitro phenotypic and transcriptomic data for selecting representative petroleum UVCBs for toxicity evaluation in vivo. Toxicol Sci 2023; 193:219-233. [PMID: 37079747 PMCID: PMC10230285 DOI: 10.1093/toxsci/kfad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Hazard evaluation of substances of "unknown or variable composition, complex reaction products and biological materials" (UVCBs) remains a major challenge in regulatory science because their chemical composition is difficult to ascertain. Petroleum substances are representative UVCBs and human cell-based data have been previously used to substantiate their groupings for regulatory submissions. We hypothesized that a combination of phenotypic and transcriptomic data could be integrated to make decisions as to selection of group-representative worst-case petroleum UVCBs for subsequent toxicity evaluation in vivo. We used data obtained from 141 substances from 16 manufacturing categories previously tested in 6 human cell types (induced pluripotent stem cell [iPSC]-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, and MCF7 and A375 cell lines). Benchmark doses for gene-substance combinations were calculated, and both transcriptomic and phenotype-derived points of departure (PODs) were obtained. Correlation analysis and machine learning were used to assess associations between phenotypic and transcriptional PODs and to determine the most informative cell types and assays, thus representing a cost-effective integrated testing strategy. We found that 2 cell types-iPSC-derived-hepatocytes and -cardiomyocytes-contributed the most informative and protective PODs and may be used to inform selection of representative petroleum UVCBs for further toxicity evaluation in vivo. Overall, although the use of new approach methodologies to prioritize UVCBs has not been widely adopted, our study proposes a tiered testing strategy based on iPSC-derived hepatocytes and cardiomyocytes to inform selection of representative worst-case petroleum UVCBs from each manufacturing category for further toxicity evaluation in vivo.
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Affiliation(s)
- Han-Hsuan Doris Tsai
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - John S House
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Fred A Wright
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, USA
- Department of Biological Sciences and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, USA
| | - Weihsueh A Chiu
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
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Li J, Zagorski JW, Kaminski NE. Establishment of a point of departure for CBD hepatotoxicity employing human HepaRG spheroids. Toxicology 2023; 488:153469. [PMID: 36863504 DOI: 10.1016/j.tox.2023.153469] [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: 01/27/2023] [Revised: 02/17/2023] [Accepted: 02/26/2023] [Indexed: 03/04/2023]
Abstract
The United States Food and Drug Administration recently approved the use of Cannabis sativa derived cannabidiol (CBD) in the treatment of Dravet Syndrome and Lennox-Gastaut Syndrome, under the trade name, Epidiolex. In double-blinded, placebo-controlled clinical trials, elevated ALT levels were observed in some patients, but these findings could not be uncoupled from the confounds of potential drug-drug interactions with co-administration of valproate and clobazam. Given the uncertainty of the potential hepatatoxic effects of CBD, the objective of the present study was to determine a point of departure for CBD, using human HepaRG spheroid cultures, followed by transcriptomic benchmark dose analysis. Treatment of HepaRG spheroids with CBD for 24 and 72 h, resulted in EC50 concentrations for cytotoxicity of 86.27 µM and 58.04 µM, respectively. Subsequent transcriptomic analysis at these timepoints demonstrated little alteration of gene and pathway data sets at a CBD concentration at or below 10 µM. Although this current analysis was conducted using liver cells, interestingly the findings at 72 h post CBD treatment showed suppression of many genes more commonly associated with immune regulation. Indeed, the immune system is a well-established target for CBD based on immune function assays. Collectively, in the present studies a point of departure was derived using transcriptomic changes produced by CBD in a human cell-based model system, which has been shown to accurately translate to human hepatotoxicity modeling.
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Affiliation(s)
- Jinpeng Li
- Center for Research on Ingredient Safety, Michigan State University, East Lansing, MI 48824, United States; Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, United States
| | - Joseph W Zagorski
- Center for Research on Ingredient Safety, Michigan State University, East Lansing, MI 48824, United States; Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, United States
| | - Norbert E Kaminski
- Center for Research on Ingredient Safety, Michigan State University, East Lansing, MI 48824, United States; Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, United States; Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, United States.
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8
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Fortin AMV, Long AS, Williams A, Meier MJ, Cox J, Pinsonnault C, Yauk CL, White PA. Application of a new approach methodology (NAM)-based strategy for genotoxicity assessment of data-poor compounds. FRONTIERS IN TOXICOLOGY 2023; 5:1098432. [PMID: 36756349 PMCID: PMC9899896 DOI: 10.3389/ftox.2023.1098432] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/02/2023] [Indexed: 01/24/2023] Open
Abstract
The conventional battery for genotoxicity testing is not well suited to assessing the large number of chemicals needing evaluation. Traditional in vitro tests lack throughput, provide little mechanistic information, and have poor specificity in predicting in vivo genotoxicity. New Approach Methodologies (NAMs) aim to accelerate the pace of hazard assessment and reduce reliance on in vivo tests that are time-consuming and resource-intensive. As such, high-throughput transcriptomic and flow cytometry-based assays have been developed for modernized in vitro genotoxicity assessment. This includes: the TGx-DDI transcriptomic biomarker (i.e., 64-gene expression signature to identify DNA damage-inducing (DDI) substances), the MicroFlow® assay (i.e., a flow cytometry-based micronucleus (MN) test), and the MultiFlow® assay (i.e., a multiplexed flow cytometry-based reporter assay that yields mode of action (MoA) information). The objective of this study was to investigate the utility of the TGx-DDI transcriptomic biomarker, multiplexed with the MicroFlow® and MultiFlow® assays, as an integrated NAM-based testing strategy for screening data-poor compounds prioritized by Health Canada's New Substances Assessment and Control Bureau. Human lymphoblastoid TK6 cells were exposed to 3 control and 10 data-poor substances, using a 6-point concentration range. Gene expression profiling was conducted using the targeted TempO-Seq™ assay, and the TGx-DDI classifier was applied to the dataset. Classifications were compared with those based on the MicroFlow® and MultiFlow® assays. Benchmark Concentration (BMC) modeling was used for potency ranking. The results of the integrated hazard calls indicate that five of the data-poor compounds were genotoxic in vitro, causing DNA damage via a clastogenic MoA, and one via a pan-genotoxic MoA. Two compounds were likely irrelevant positives in the MN test; two are considered possibly genotoxic causing DNA damage via an ambiguous MoA. BMC modeling revealed nearly identical potency rankings for each assay. This ranking was maintained when all endpoint BMCs were converted into a single score using the Toxicological Prioritization (ToxPi) approach. Overall, this study contributes to the establishment of a modernized approach for effective genotoxicity assessment and chemical prioritization for further regulatory scrutiny. We conclude that the integration of TGx-DDI, MicroFlow®, and MultiFlow® endpoints is an effective NAM-based strategy for genotoxicity assessment of data-poor compounds.
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Affiliation(s)
- Anne-Marie V. Fortin
- Department of Biology, University of Ottawa, Ottawa, ON, Canada,Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Alexandra S. Long
- Existing Substances Risk Assessment Bureau, Health Canada, Ottawa, ON, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Matthew J. Meier
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Julie Cox
- Bureau of Gastroenterology, Infection and Viral Diseases, Health Canada, Ottawa, ON, Canada
| | - Claire Pinsonnault
- New Substances Assessment and Control Bureau, Health Canada, Ottawa, ON, Canada
| | - Carole L. Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, Canada,*Correspondence: Carole L. Yauk, ; Paul A. White,
| | - Paul A. White
- Department of Biology, University of Ottawa, Ottawa, ON, Canada,Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada,*Correspondence: Carole L. Yauk, ; Paul A. White,
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9
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Pouillot R, Santillana Farakos S, Van Doren JM. Modeling the risk of low bone mass and osteoporosis as a function of urinary cadmium in U.S adults aged 50-79 years. ENVIRONMENTAL RESEARCH 2022; 212:113315. [PMID: 35436451 DOI: 10.1016/j.envres.2022.113315] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/03/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
We developed an association model to estimate the risk of femoral neck low bone mass and osteoporosis from exposure to cadmium for women and men aged 50-79 in the U.S, as a function of the urinary cadmium (U-Cd) levels. We analyzed data from the NHANES 2005-2014 surveys and evaluated the relationship between U-Cd and femoral neck bone mineral density (BMD) using univariate and multivariate regression models with a combination of NHANES cycle, gender, age, smoking, race/ethnicity, height, body weight, body mass index, lean body mass, diabetes, kidney disease, physical activity, menopausal status, hormone replacement therapy, urinary lead, and prednisone intake as confounding variables. The regression coefficient between U-Cd and femoral neck BMD obtained with the best multivariate regression was used to develop an association model that can estimate the additional risk of low bone mass or osteoporosis in the population given a certain level of U-Cd. Results showed a linear relationship between U-Cd and BMD, conditional to body weight, where individuals with higher U-Cd had decreased BMD values. Our results do not support the hypothesis of a threshold for the effect of Cd on bone. Our model estimates that exposure to Cd results in an increase of 0.51 percentage points (CI95% 0.00, 0.92) of the population diagnosed with osteoporosis, compared to a theoretical absence of exposure. We estimate that 16% (CI95%: 0.00, 40%) of osteoporosis cases in the U.S. 50-79 aged population are a result of Cd exposure. This study presents the first continuous model estimating low bone mass and osteoporosis risk in the U.S. population given actual or potential changes in U-Cd levels. Our model will provide information to inform FDA's Closer to Zero initiative goal to reduce exposure to toxic elements.
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Affiliation(s)
- Régis Pouillot
- Division of Risk and Decision Analysis, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
| | - Sofia Santillana Farakos
- Division of Risk and Decision Analysis, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States.
| | - Jane M Van Doren
- Division of Risk and Decision Analysis, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States
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10
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Kim S, White SM, Radke EG, Dean JL. Harmonization of transcriptomic and methylomic analysis in environmental epidemiology studies for potential application in chemical risk assessment. ENVIRONMENT INTERNATIONAL 2022; 164:107278. [PMID: 35537365 DOI: 10.1016/j.envint.2022.107278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Recent efforts have posited the utility of transcriptomic-based approaches to understand chemical-related perturbations in the context of human health risk assessment. Epigenetic modification (e.g., DNA methylation) can influence gene expression changes and is known to occur as a molecular response to some chemical exposures. Characterization of these methylation events is critical to understand the molecular consequences of chemical exposures. In this context, a novel workflow was developed to interrogate publicly available epidemiological transcriptomic and methylomic data to identify relevant pathway level changes in response to chemical exposure, using inorganic arsenic as a case study. Gene Set Enrichment Analysis (GSEA) was used to identify causal methylation events that result in concomitant downstream transcriptional deregulation. This analysis demonstrated an unequal distribution of differentially methylated regions across the human genome. After mapping these events to known genes, significant enrichment of a subset of these pathways suggested that arsenic-mediated methylation may be both specific and non-specific. Parallel GSEA performed on matched transcriptomic samples determined that a substantially reduced subset of these pathways are enriched and that not all chemically-induced methylation results in a downstream alteration in gene expression. The resulting pathways were found to be representative of well-established molecular events known to occur in response to arsenic exposure. The harmonization of enriched transcriptional patterns with those identified from the methylomic platform promoted the characterization of plausibly causal molecular signaling events. The workflow described here enables significant gene and methylation-specific pathways to be identified from whole blood samples of individuals exposed to environmentally relevant chemical levels. As future efforts solidify specific causal relationships between these molecular events and relevant apical endpoints, this novel workflow could aid risk assessments by identifying molecular targets serving as biomarkers of hazard, informing mechanistic understanding, and characterizing dose ranges that promote relevant molecular/epigenetic signaling events occuring in response to chemical exposures.
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Affiliation(s)
- Stephanie Kim
- Superfund and Emergency Management Division, Region 2, U.S. Environmental Protection Agency, NY, USA.
| | - Shana M White
- Chemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, USA.
| | - Elizabeth G Radke
- Chemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, D.C., USA.
| | - Jeffry L Dean
- Chemical and Pollutant Assessment Division, Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, USA.
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11
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Johnson KJ, Costa E, Marshall V, Sriram S, Venkatraman A, Stebbins K, LaRocca J. A microRNA or messenger RNA point of departure estimates an apical endpoint point of departure in a rat developmental toxicity model. Birth Defects Res 2022; 114:559-576. [PMID: 35596682 PMCID: PMC9324934 DOI: 10.1002/bdr2.2046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/10/2022]
Abstract
Traditional developmental toxicity testing practice examines fetal apical endpoints to identify a point of departure (POD) for risk assessment. A potential new testing paradigm involves deriving a POD from a comprehensive analysis of molecular-level change. Here, the rat ketoconazole endocrine-mediated developmental toxicity model was used to test the hypothesis that maternal epigenomic (miRNA) and transcriptomic (mRNA) PODs are similar to fetal apical endpoint PODs. Sprague-Dawley rats were exposed from gestation day (GD) 6-21 to 0, 0.063, 0.2, 0.63, 2, 6.3, 20, or 40 mg/kg/day ketoconazole. Dam systemic, liver, and placenta PODs, along with GD 21 fetal resorption, body weight, and skeletal apical PODs were derived using BMDS software. GD 21 dam liver and placenta miRNA and mRNA PODs were obtained using three methods: a novel individual molecule POD accumulation method, a first mode method, and a gene set method. Dam apical POD values ranged from 2.0 to 38.6 mg/kg/day; the lowest value was for placenta histopathology. Fetal apical POD values were 10.9-20.3 mg/kg/day; the lowest value was for fetal resorption. Dam liver miRNA and mRNA POD values were 0.34-0.69 mg/kg/day, and placenta miRNA and mRNA POD values were 2.53-6.83 mg/kg/day. Epigenomic and transcriptomic POD values were similar across liver and placenta. Deriving a molecular POD from dam liver or placenta was protective of a fetal apical POD. These data support the conclusion that a molecular POD can be used to estimate, or be protective of, a developmental toxicity apical POD.
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Affiliation(s)
| | | | - Valerie Marshall
- Labcorp Early Development Laboratories, Inc., Greenfield, Indiana, USA
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12
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Speen AM, Murray JR, Krantz QT, Davies D, Evansky P, Harrill JA, Everett LJ, Bundy JL, Dailey LA, Hill J, Zander W, Carlsten E, Monsees M, Zavala J, Higuchi MA. Benchmark Dose Modeling Approaches for Volatile Organic Chemicals using a Novel Air-Liquid Interface In Vitro Exposure System. Toxicol Sci 2022; 188:88-107. [PMID: 35426944 DOI: 10.1093/toxsci/kfac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Inhalation is the most relevant route of volatile organic chemical (VOC) exposure; however, due to unique challenges posed by their chemical properties and poor solubility in aqueous solutions, in vitro chemical safety testing is predominantly performed using direct application dosing/submerged exposures. To address the difficulties in screening toxic effects of VOCs, our cell culture exposure system permits cells to be exposed to multiple concentrations at air-liquid interface (ALI) in a 24-well format. ALI exposure methods permit direct chemical-to-cell interaction with the test article at physiological conditions. In the present study, BEAS-2B and primary normal human bronchial epithelial cells (pHBEC) are used to assess gene expression, cytotoxicity, and cell viability responses to a variety of volatile chemicals including acrolein, formaldehyde, 1,3-butadiene, acetaldehyde, 1-bromopropane, carbon tetrachloride, dichloromethane, and trichloroethylene. BEAS-2B cells were exposed to all the test agents, while pHBECs were only exposed to the latter four listed above. The VOC concentrations tested elicited only slight cell viability changes in both cell types. Gene expression changes were analyzed using benchmark dose (BMD) modeling. The BMD for the most sensitive gene set was within one order of magnitude of the threshold-limit value reported by the American Conference of Governmental Industrial Hygienists, and the most sensitive gene sets impacted by exposure correlate to known adverse health effects recorded in epidemiologic and in vivo exposure studies. Overall, our study outlines a novel in vitro approach for evaluating molecular-based points-of-departure in human airway epithelial cell exposure to volatile chemicals.
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Affiliation(s)
- Adam M Speen
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee 37830, USA
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Jessica R Murray
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Quentin Todd Krantz
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - David Davies
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Paul Evansky
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Joshua A Harrill
- CCTE, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Logan J Everett
- CCTE, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Joseph L Bundy
- CCTE, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Lisa A Dailey
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Jazzlyn Hill
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
- Oak Ridge Associated Universities (ORAU), Oak Ridge, Tennessee 37830, USA
| | - Wyatt Zander
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
- Oak Ridge Associated Universities (ORAU), Oak Ridge, Tennessee 37830, USA
| | - Elise Carlsten
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
- Oak Ridge Associated Universities (ORAU), Oak Ridge, Tennessee 37830, USA
| | - Michael Monsees
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
- Oak Ridge Associated Universities (ORAU), Oak Ridge, Tennessee 37830, USA
| | - Jose Zavala
- MedTec BioLab Inc., Hillsborough, North Carolina 27278, USA
| | - Mark A Higuchi
- CPHEA, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
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13
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Ji C, Weissmann A, Shao K. A computational system for Bayesian benchmark dose estimation of genomic data in BBMD. ENVIRONMENT INTERNATIONAL 2022; 161:107135. [PMID: 35151117 PMCID: PMC8934139 DOI: 10.1016/j.envint.2022.107135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/16/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Existing studies have revealed that the benchmark dose (BMD) estimates from short-term in vivo transcriptomics studies can approximate those from long-term guideline toxicity assessments. Existing software applications follow this trend by analyzing omics data through the maximum likelihood estimation and choosing the "best" model for BMD estimates. However, this practice ignores the model uncertainty and may result in over-confident inferences and predictions, leading to an inadequate decision. OBJECTIVE By generally following the National Toxicology Program Approach to Genomic Dose-Response Modeling, we developed a web-based dose-response modeling and BMD estimation system, Bayesian BMD (BBMD), for genomic data to quantitatively address uncertainty from various sources. The performances of BBMD are compared with BMDExpress. METHODS The system is primarily based on the previously developed BBMD system and further developed in a genomic perspective. Bayesian model averaging method is applied to BMD estimation and pathways analyses. Generally, the system is unique regarding the flexibility in preparing/storing data and in characterizing uncertainties. RESULTS This system was tested and validated versus 24 previously published in-vivo microarray dose-response datasets (GSE45892) and 64 molecules data from the Open TG-Gates database. Short term transcriptional BMD values for the median pathway in BBMD are highly correlated with the long-term apical BMD values (R = 0.78-0.91). The BMD estimates obtained by BBMD were compared to those by BMDExpress. The results indicate that BBMD provides more adequate results in terms of less extreme values and no failure in BMD and BMDL calculations. Also, the pathway analysis in BBMD provides a conservative estimate because a broader confidence interval is established. DISCUSSION Overall, this study demonstrates that dose-response modeling using genomic data can play a substantial role in support of chemical risk assessment. BBMD represents a robust and user-friendly alternative for genomic dose-response data analysis with outstanding functionalities to quantify uncertainty from various sources.
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Affiliation(s)
- Chao Ji
- Department of Environmental and Occupational Health, School of Public Health, Indiana University - Bloomington, Bloomington, IN 47405, USA
| | | | - Kan Shao
- Department of Environmental and Occupational Health, School of Public Health, Indiana University - Bloomington, Bloomington, IN 47405, USA.
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14
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Dent MP, Vaillancourt E, Thomas RS, Carmichael PL, Ouedraogo G, Kojima H, Barroso J, Ansell J, Barton-Maclaren TS, Bennekou SH, Boekelheide K, Ezendam J, Field J, Fitzpatrick S, Hatao M, Kreiling R, Lorencini M, Mahony C, Montemayor B, Mazaro-Costa R, Oliveira J, Rogiers V, Smegal D, Taalman R, Tokura Y, Verma R, Willett C, Yang C. Paving the way for application of next generation risk assessment to safety decision-making for cosmetic ingredients. Regul Toxicol Pharmacol 2021; 125:105026. [PMID: 34389358 PMCID: PMC8547713 DOI: 10.1016/j.yrtph.2021.105026] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/22/2021] [Accepted: 08/06/2021] [Indexed: 11/30/2022]
Abstract
Next generation risk assessment (NGRA) is an exposure-led, hypothesis-driven approach that has the potential to support animal-free safety decision-making. However, significant effort is needed to develop and test the in vitro and in silico (computational) approaches that underpin NGRA to enable confident application in a regulatory context. A workshop was held in Montreal in 2019 to discuss where effort needs to be focussed and to agree on the steps needed to ensure safety decisions made on cosmetic ingredients are robust and protective. Workshop participants explored whether NGRA for cosmetic ingredients can be protective of human health, and reviewed examples of NGRA for cosmetic ingredients. From the limited examples available, it is clear that NGRA is still in its infancy, and further case studies are needed to determine whether safety decisions are sufficiently protective and not overly conservative. Seven areas were identified to help progress application of NGRA, including further investments in case studies that elaborate on scenarios frequently encountered by industry and regulators, including those where a ‘high risk’ conclusion would be expected. These will provide confidence that the tools and approaches can reliably discern differing levels of risk. Furthermore, frameworks to guide performance and reporting should be developed.
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Affiliation(s)
- M P Dent
- Unilever Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, MK44 1LQ, UK.
| | - E Vaillancourt
- Health Canada, Healthy Environments and Consumer Safety Branch, 269 Laurier Ave. W., Ottawa, ON K1A 0K9, Canada.
| | - R S Thomas
- Center for Computational Toxicology and Exposure, U.S. Environmental Protection Agency, Research, Triangle Park, NC, 27711, USA.
| | - P L Carmichael
- Unilever Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, MK44 1LQ, UK.
| | - G Ouedraogo
- l'Oréal, Research and Development, Paris, France.
| | - H Kojima
- National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, 158-8501, Tokyo, Japan.
| | - J Barroso
- European Commission, Joint Research Centre (JRC), Ispra, VA, Italy.
| | - J Ansell
- US Personal Care Products Council (PCPC), 1620 L St. NW, Suite 1200, Washington, D.C, 20036, USA.
| | - T S Barton-Maclaren
- Health Canada, Healthy Environments and Consumer Safety Branch, 269 Laurier Ave. W., Ottawa, ON K1A 0K9, Canada.
| | - S H Bennekou
- National Food Institute, Technical University of Denmark (DTU), Copenhagen, Denmark.
| | - K Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - J Ezendam
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
| | - J Field
- Health Canada, Healthy Environments and Consumer Safety Branch, 269 Laurier Ave. W., Ottawa, ON K1A 0K9, Canada.
| | - S Fitzpatrick
- US Food and Drug Administration (US FDA), Center for Food Safety and Applied Nutrition (CFSAN), 5001 Campus Drive, College Park, MD, 20740, USA.
| | - M Hatao
- Japan Cosmetic Industry Association (JCIA), Metro City Kamiyacho 6F, 5-1-5, Toranomon, Minato-ku, Tokyo, 105-0001 Japan.
| | - R Kreiling
- Clariant Produkte (Deutschland) GmbH, Am Unisyspark 1, 65843, Sulzbach, Germany.
| | - M Lorencini
- Grupo Boticário, Research & Development, São José dos Pinhais, Brazil.
| | - C Mahony
- Procter & Gamble Technical Centres Ltd, Reading, RG2 0RX, UK.
| | - B Montemayor
- Cosmetics Alliance Canada, 420 Britannia Road East Suite 102, Mississauga, ON L4Z 3L5, Canada.
| | - R Mazaro-Costa
- Departament of Pharmacology, Universidade Federal de Goiás, Goiânia, GO, 74.690-900, Brazil.
| | - J Oliveira
- Brazilian Health Regulatory Agency (ANVISA), Gerência de Produtos de Higiene, Perfumes, Cosméticos e Saneantes, Setor de Indústria e Abastecimento (SIA), Trecho 5, Área Especial 57, CEP 71205-050, Brasília, DF, Brazil.
| | - V Rogiers
- Vrije Universiteit Brussel, Brussels, Belgium.
| | - D Smegal
- US Food and Drug Administration (US FDA), Center for Food Safety and Applied Nutrition (CFSAN), 5001 Campus Drive, College Park, MD, 20740, USA.
| | - R Taalman
- Cosmetics Europe, Avenue Herrmann-Debroux 40, 1160 Auderghem, Belgium.
| | - Y Tokura
- Allergic Disease Research Center, Chutoen General Medical Center, Kakegawa, Japan.
| | - R Verma
- US Food and Drug Administration (US FDA), Center for Food Safety and Applied Nutrition (CFSAN), 5001 Campus Drive, College Park, MD, 20740, USA.
| | - C Willett
- Humane Society International, Washington, DC, USA.
| | - C Yang
- Taiwan Cosmetic Industry Association (TWCIA), 8F No. 136, Bo'ai Rd., Zhongzheng Dist., Taipei City, 100, Taiwan, ROC.
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15
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Luijten M, Wackers PFK, Rorije E, Pennings JLA, Heusinkveld HJ. Relevance of In Vitro Transcriptomics for In Vivo Mode of Action Assessment. Chem Res Toxicol 2020; 34:452-459. [PMID: 33378166 DOI: 10.1021/acs.chemrestox.0c00313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recently, we reported an in vitro toxicogenomics comparison approach to categorize chemical substances according to similarities in their proposed toxicological modes of action. Use of such an approach for regulatory purposes requires, among others, insight into the extent of biological concordance between in vitro and in vivo findings. To that end, we applied the comparison approach to transcriptomics data from the Open TG-GATEs database for 137 substances with diverging modes of action and evaluated the outcomes obtained for rat primary hepatocytes and for rat liver. The results showed that a relatively small number of matches observed in vitro were also observed in vivo, whereas quite a large number of matches between substances were found to be relevant solely in vivo or in vitro. The latter could not be explained by physicochemical properties, leading to insufficient bioavailability or poor water solubility. Nevertheless, pathway analyses indicated that for relevant matches the mechanisms perturbed in vitro are consistent with those perturbed in vivo. These findings support the utility of the comparison approach as tool in mechanism-based risk assessment.
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Affiliation(s)
- Mirjam Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
| | - Paul F K Wackers
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
| | - Emiel Rorije
- Centre for Safety of Substances and Products, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
| | - Jeroen L A Pennings
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
| | - Harm J Heusinkveld
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands
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16
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Bianchi E, Costa E, Yan ZJ, Murphy L, Howell J, Anderson D, Mukerji P, Venkatraman A, Terry C, Johnson KJ. A rat subchronic study transcriptional point of departure estimates a carcinogenicity study apical point of departure. Food Chem Toxicol 2020; 147:111869. [PMID: 33217531 DOI: 10.1016/j.fct.2020.111869] [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: 09/11/2020] [Revised: 10/28/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022]
Abstract
Considerations of human relevance and animal use are driving research to identify new approaches to inform risk assessment of chemicals and replace guideline-based rodent carcinogenicity tests. Here, the hypothesis was tested across four agrochemicals that 1) a rat 90-day transcriptome-based BEPOD is protective of a rat carcinogenicity study and 2) a subchronic liver or kidney BEPOD would approximate a cancer bioassay apical POD derived from other organs and a rat subchronic BEPOD would approximate a mouse cancer bioassay apical POD. Using RNA sequencing and BMDExpress software, liver and/or kidney BEPOD values were generated in male rats exposed for 90 days to either Triclopyr Acid, Pronamide, Sulfoxaflor, or Fenpicoxamid. BEPOD values were compared to benchmark dose-derived apical POD values generated from rat 90-day and rodent carcinogenicity studies. Across all four agrochemicals, findings showed that a rat 90-day study BEPOD approximated the most sensitive apical POD (within 10-fold) generated from the 90-day rat study and long-term rodent carcinogenicity studies. This study supports the conclusion that a subchronic transcriptome-based BEPOD could be utilized to estimate an apical POD within a risk-based approach of chronic toxicity and carcinogenicity agrochemical assessment, abrogating the need for time- and resource-intensive rodent carcinogenicity studies and minimizing animal testing.
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17
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Korchevskiy A. Using benchmark dose modeling for the quantitative risk assessment: Carbon nanotubes, asbestos, glyphosate. J Appl Toxicol 2020; 41:148-160. [PMID: 33040390 DOI: 10.1002/jat.4063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 11/12/2022]
Abstract
Benchmark dose method is one of the most famous quantitative approaches available for toxicological risks prediction. However, it is not fully clear how occupational health professionals can use it for specific workplace scenarios requiring carcinogen risk assessment. The paper explores the hypothesis that benchmark dose method allows to effectively approximate dose-response data on carcinogenic response, providing reasonable estimations of risks in the situations when a choice between more complex models is not warranted for practical purposes. Three case studies were analyzed for the agents with different levels of scientific confidence in human carcinogenicity: carbon nanotubes, amosite asbestos, and glyphosate. For each agent, a critical study was determined, and a dose-response slope factor was quantified, based on the weighted average lower bound benchmark dose. The linear slope factors of 0.111 lifetime excess cases of lung carcinoma per mg/m3 of MWCNT-7 (in rats exposure equivalent), 0.009 cases of mesothelioma per f/cc-years of cumulative exposure to amosite asbestos, and 0.000094 cases of malignant lymphoma per mg/kg/day of glyphosate (in mice equivalent) were determined. The correlations between the proposed linear predictive models and observed data points were R = 0.96 (R2 = 0.92) for carbon nanotubes, R = 0.97 (R2 = 0.95) for amosite asbestos, and R = 0.89 (R2 = 0.79) for glyphosate. In all three cases, the linear extrapolation yielded comparable level of risk estimations with the "best fit" nonlinear model; for nanoparticles and amosite asbestos, linear estimations were more conservative. By performing a simulation study, it was demonstrated that a weighted average benchmark dose expressed the highest correlation with multistage and quantal-linear models.
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18
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Johnson KJ, Auerbach SS, Costa E. A Rat Liver Transcriptomic Point of Departure Predicts a Prospective Liver or Non-liver Apical Point of Departure. Toxicol Sci 2020; 176:86-102. [PMID: 32384157 PMCID: PMC7357187 DOI: 10.1093/toxsci/kfaa062] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Identifying a toxicity point of departure (POD) is a required step in human health risk characterization of crop protection molecules, and this POD has historically been derived from apical endpoints across a battery of animal-based toxicology studies. Using rat transcriptome and apical data for 79 molecules obtained from Open TG-GATES (Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System) (632 datasets), the hypothesis was tested that a short-term exposure, transcriptome-based liver biological effect POD (BEPOD) could estimate a longer-term exposure "systemic" apical endpoint POD. Apical endpoints considered were body weight, clinical observation, kidney weight and histopathology and liver weight and histopathology. A BMDExpress algorithm using Gene Ontology Biological Process gene sets was optimized to derive a liver BEPOD most predictive of a systemic apical POD. Liver BEPODs were stable from 3 h to 29 days of exposure; the median fold difference of the 29-day BEPOD to BEPODs from earlier time points was approximately 1 (range: 0.7-1.1). Strong positive correlation (Pearson R = 0.86) and predictive accuracy (root mean square difference = 0.41) were observed between a concurrent (29 days) liver BEPOD and the systemic apical POD. Similar Pearson R and root mean square difference values were observed for comparisons between a 29-day systemic apical POD and liver BEPODs derived from 3 h to 15 days of exposure. These data across 79 molecules suggest that a longer-term exposure study apical POD from liver and non-liver compartments can be estimated using a liver BEPOD derived from an acute or subacute exposure study.
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Affiliation(s)
- Kamin J Johnson
- Predictive Safety Center, Corteva Agriscience, Indianapolis, Indiana
| | - Scott S Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Eduardo Costa
- Data Science and Informatics, Corteva Agriscience, Mogi Mirim, Sao Paulo, Brazil
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19
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Hartwig A, Arand M, Epe B, Guth S, Jahnke G, Lampen A, Martus HJ, Monien B, Rietjens IMCM, Schmitz-Spanke S, Schriever-Schwemmer G, Steinberg P, Eisenbrand G. Mode of action-based risk assessment of genotoxic carcinogens. Arch Toxicol 2020; 94:1787-1877. [PMID: 32542409 PMCID: PMC7303094 DOI: 10.1007/s00204-020-02733-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/16/2022]
Abstract
The risk assessment of chemical carcinogens is one major task in toxicology. Even though exposure has been mitigated effectively during the last decades, low levels of carcinogenic substances in food and at the workplace are still present and often not completely avoidable. The distinction between genotoxic and non-genotoxic carcinogens has traditionally been regarded as particularly relevant for risk assessment, with the assumption of the existence of no-effect concentrations (threshold levels) in case of the latter group. In contrast, genotoxic carcinogens, their metabolic precursors and DNA reactive metabolites are considered to represent risk factors at all concentrations since even one or a few DNA lesions may in principle result in mutations and, thus, increase tumour risk. Within the current document, an updated risk evaluation for genotoxic carcinogens is proposed, based on mechanistic knowledge regarding the substance (group) under investigation, and taking into account recent improvements in analytical techniques used to quantify DNA lesions and mutations as well as "omics" approaches. Furthermore, wherever possible and appropriate, special attention is given to the integration of background levels of the same or comparable DNA lesions. Within part A, fundamental considerations highlight the terms hazard and risk with respect to DNA reactivity of genotoxic agents, as compared to non-genotoxic agents. Also, current methodologies used in genetic toxicology as well as in dosimetry of exposure are described. Special focus is given on the elucidation of modes of action (MOA) and on the relation between DNA damage and cancer risk. Part B addresses specific examples of genotoxic carcinogens, including those humans are exposed to exogenously and endogenously, such as formaldehyde, acetaldehyde and the corresponding alcohols as well as some alkylating agents, ethylene oxide, and acrylamide, but also examples resulting from exogenous sources like aflatoxin B1, allylalkoxybenzenes, 2-amino-3,8-dimethylimidazo[4,5-f] quinoxaline (MeIQx), benzo[a]pyrene and pyrrolizidine alkaloids. Additionally, special attention is given to some carcinogenic metal compounds, which are considered indirect genotoxins, by accelerating mutagenicity via interactions with the cellular response to DNA damage even at low exposure conditions. Part C finally encompasses conclusions and perspectives, suggesting a refined strategy for the assessment of the carcinogenic risk associated with an exposure to genotoxic compounds and addressing research needs.
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Affiliation(s)
- Andrea Hartwig
- Department of Food Chemistry and Toxicology, Institute of Applied Biosciences (IAB), Karlsruhe Institute of Technology (KIT), Adenauerring 20a, 76131, Karlsruhe, Germany.
| | - Michael Arand
- Institute of Pharmacology and Toxicology, University of Zurich, 8057, Zurich, Switzerland
| | - Bernd Epe
- Institute of Pharmacy and Biochemistry, University of Mainz, 55099, Mainz, Germany
| | - Sabine Guth
- Department of Toxicology, IfADo-Leibniz Research Centre for Working Environment and Human Factors, TU Dortmund, Ardeystr. 67, 44139, Dortmund, Germany
| | - Gunnar Jahnke
- Department of Food Chemistry and Toxicology, Institute of Applied Biosciences (IAB), Karlsruhe Institute of Technology (KIT), Adenauerring 20a, 76131, Karlsruhe, Germany
| | - Alfonso Lampen
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Hans-Jörg Martus
- Novartis Institutes for BioMedical Research, 4002, Basel, Switzerland
| | - Bernhard Monien
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Simone Schmitz-Spanke
- Institute and Outpatient Clinic of Occupational, Social and Environmental Medicine, University of Erlangen-Nuremberg, Henkestr. 9-11, 91054, Erlangen, Germany
| | - Gerlinde Schriever-Schwemmer
- Department of Food Chemistry and Toxicology, Institute of Applied Biosciences (IAB), Karlsruhe Institute of Technology (KIT), Adenauerring 20a, 76131, Karlsruhe, Germany
| | - Pablo Steinberg
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Str. 9, 76131, Karlsruhe, Germany
| | - Gerhard Eisenbrand
- Retired Senior Professor for Food Chemistry and Toxicology, Kühler Grund 48/1, 69126, Heidelberg, Germany.
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Mezencev R, Auerbach SS. The sensitivity of transcriptomics BMD modeling to the methods used for microarray data normalization. PLoS One 2020; 15:e0232955. [PMID: 32413060 PMCID: PMC7228135 DOI: 10.1371/journal.pone.0232955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 04/25/2020] [Indexed: 11/25/2022] Open
Abstract
Whole-genome expression data generated by microarray studies have shown promise for quantitative human health risk assessment. While numerous approaches have been developed to determine benchmark doses (BMDs) from probeset-level dose responses, sensitivity of the results to methods used for normalization of the data has not yet been systematically investigated. Normalization of microarray data converts raw hybridization signals to expression estimates that are expected to be proportional to the amounts of transcripts in the profiled specimens. Different approaches to normalization have been shown to greatly influence the results of some downstream analyses, including biological interpretation. In this study we evaluate the influence of microarray normalization methods on the transcriptomic BMDs. We demonstrate using in vivo data that the use of alternative pipelines for normalization of Affymetrix microarray data can have a considerable impact on the number of detected differentially expressed genes and pathways (processes) determined to be treatment responsive, which may lead to alternative interpretations of the data. In addition, we found that normalization can have a considerable effect (as much as ~30-fold in this study) on estimation of the minimum biological potency (transcriptomic point of departure). We argue for consideration of alternative normalization methods and their data-informed selection to most effectively interpret microarray data for use in human health risk assessment.
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Affiliation(s)
- Roman Mezencev
- Center for Public Health and Environmental Assessment, Office of Research and Development, US EPA, Washington DC, United States of America
| | - Scott S. Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, NC, United States of America
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21
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LaRocca J, Costa E, Sriram S, Hannas BR, Johnson KJ. Short-term toxicogenomics as an alternative approach to chronic in vivo studies for derivation of points of departure: A case study in the rat with a triazole fungicide. Regul Toxicol Pharmacol 2020; 113:104655. [PMID: 32268158 DOI: 10.1016/j.yrtph.2020.104655] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 01/17/2023]
Abstract
The derivation of an apical endpoint point of departure (POD) from animal-intensive testing programs has been the traditional cornerstone of human health risk assessment. Replacement of in vivo chronic studies with novel approaches, such as toxicogenomics, holds promise for future alternative testing paradigms that significantly reduce animal testing. We hypothesized that a toxicogenomic POD following a 14 day exposure in the rat would approximate the most sensitive apical endpoint POD derived from a battery of chronic, carcinogenicity, reproduction and endocrine guideline toxicity studies. To test this hypothesis, we utilized myclobutanil, a triazole fungicide, as a model compound. In the 14 day study, male rats were administered 0 (vehicle), 30, 150, or 400 mg/kg/day myclobutanil via oral gavage. Endpoints evaluated included traditional apical, hormone, and liver and testis transcriptomic (whole genome RNA sequencing) data. From the transcriptomic data, liver and testis biological effect POD (BEPOD) values were derived. Myclobutanil exposure for 14 days resulted in increased liver weight, altered serum hormones, liver histopathology, and differential gene expression in liver and testis. The liver and testis BEPODs from the short-term study were 22.2 and 25.4 mg/kg/day, respectively. These BEPODs were approximately an order of magnitude higher than the most sensitive apical POD identified from the two year cancer bioassay based on testis atrophy (1.4 mg/kg/day). This study demonstrates the promise of using a short-term study BEPOD to derive a POD for human health risk assessment while substantially reducing animal testing.
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22
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Rogiers V, Benfenati E, Bernauer U, Bodin L, Carmichael P, Chaudhry Q, Coenraads PJ, Cronin MT, Dent M, Dusinska M, Ellison C, Ezendam J, Gaffet E, Galli CL, Goebel C, Granum B, Hollnagel HM, Kern PS, Kosemund-Meynen K, Ouédraogo G, Panteri E, Rousselle C, Stepnik M, Vanhaecke T, von Goetz N, Worth A. The way forward for assessing the human health safety of cosmetics in the EU - Workshop proceedings. Toxicology 2020; 436:152421. [DOI: 10.1016/j.tox.2020.152421] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 12/20/2022]
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23
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Nault R, Bals B, Teymouri F, Black MB, Andersen ME, McMullen PD, Krishnan S, Kuravadi N, Paul N, Kumar S, Kannan K, Jayachandra KC, Alagappan L, Patel BD, Bogen KT, Gollapudi BB, Klaunig JE, Zacharewski TR, Bringi V. A toxicogenomic approach for the risk assessment of the food contaminant acetamide. Toxicol Appl Pharmacol 2020; 388:114872. [PMID: 31881176 PMCID: PMC7014822 DOI: 10.1016/j.taap.2019.114872] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/10/2019] [Accepted: 12/20/2019] [Indexed: 12/26/2022]
Abstract
Acetamide (CAS 60-35-5) is detected in common foods. Chronic rodent bioassays led to its classification as a group 2B possible human carcinogen due to the induction of liver tumors in rats. We used a toxicogenomics approach in Wistar rats gavaged daily for 7 or 28 days at doses of 300 to 1500 mg/kg/day (mkd) to determine a point of departure (POD) and investigate its mode of action (MoA). Ki67 labeling was increased at doses ≥750 mkd up to 3.3-fold representing the most sensitive apical endpoint. Differential gene expression analysis by RNA-Seq identified 1110 and 1814 differentially expressed genes in male and female rats, respectively, following 28 days of treatment. Down-regulated genes were associated with lipid metabolism while up-regulated genes included cell signaling, immune response, and cell cycle functions. Benchmark dose (BMD) modeling of the Ki67 labeling index determined the BMD10 lower confidence limit (BMDL10) as 190 mkd. Transcriptional BMD modeling revealed excellent concordance between transcriptional POD and apical endpoints. Collectively, these results indicate that acetamide is most likely acting through a mitogenic MoA, though specific key initiating molecular events could not be elucidated. A POD value of 190 mkd determined for cell proliferation is suggested for risk assessment purposes.
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Affiliation(s)
- Rance Nault
- Institute for Integrative Toxicology, Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States of America
| | - Bryan Bals
- Michigan Biotechnology Institute, Lansing, MI, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tim R Zacharewski
- Institute for Integrative Toxicology, Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States of America
| | - Venkataraman Bringi
- Chemical Engineering & Materials Science, Michigan State University, East Lansing, MI, USA.
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24
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Jensen SM, Kluxen FM, Ritz C. A Review of Recent Advances in Benchmark Dose Methodology. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2019; 39:2295-2315. [PMID: 31046141 DOI: 10.1111/risa.13324] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 02/01/2019] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
In this review, recent methodological developments for the benchmark dose (BMD) methodology are summarized. Specifically, we introduce the advances for the main steps in BMD derivation: selecting the procedure for defining a BMD from a predefined benchmark response (BMR), setting a BMR, selecting a dose-response model, and estimating the corresponding BMD lower limit (BMDL). Although the last decade has shown major progress in the development of BMD methodology, there is still room for improvement. Remaining challenges are the implementation of new statistical methods in user-friendly software and the lack of consensus about how to derive the BMDL.
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Affiliation(s)
- Signe M Jensen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Christian Ritz
- Department of Nutrition, Sports and Exercise, University of Copenhagen, Copenhagen, Denmark
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25
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Abassi S, Wang H, Ponmani T, Ki JS. Small heat shock protein genes of the green algae Closterium ehrenbergii: Cloning and differential expression under heat and heavy metal stresses. ENVIRONMENTAL TOXICOLOGY 2019; 34:1013-1024. [PMID: 31095847 DOI: 10.1002/tox.22772] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/24/2019] [Accepted: 04/28/2019] [Indexed: 06/09/2023]
Abstract
The freshwater green algae Closterium ehrenbergii has been considered as a model for eco-toxicological assessment in aquatic systems. Heat shock proteins (HSPs) are a class of highly conserved proteins produced in all living organisms, which participate in environmental stress responses. In the present study, we determined the cDNA sequences of small heat shock protein 10 (sHSP10) and sHSP17.1 from C. ehrenbergii, and examined the physiological changes and transcriptional responses of the genes after exposure to thermal shock and toxicants treatments. The open reading frame (ORF) of CeHSP10 was 300 bp long, encoding 99 amino acid (aa) residues (10.53 kDa) with a GroES chaperonin conserved site of 22 aa. The CeHSP17.1 had a 468 bp ORF, encoding 155 aa with a conserved C-terminal α-crystallin domain. For heat stress, cells presented pigment loss and possible chloroplast damage, with an up-regulation in the expression of both sHSP10 and sHSP17.1 genes. As for the heavy metal stressors, an increase in the production of reactive oxygen species was registered in a dose dependent manner, with a significant up-regulation of both sHSP10 and sHSP17.1 genes. These results suggest that sHSP genes in C. ehrenbergii may play a role in responses to stress environments, and they could be used as an early detection parameter as biomarker genes in molecular toxicity assessments.
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Affiliation(s)
- Sofia Abassi
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
| | - Hui Wang
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
| | - Thangaraj Ponmani
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul, South Korea
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26
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Malinowska JM, Viant MR. Confidence in metabolite identification dictates the applicability of metabolomics to regulatory toxicology. CURRENT OPINION IN TOXICOLOGY 2019. [DOI: 10.1016/j.cotox.2019.03.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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27
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Harrill J, Shah I, Setzer RW, Haggard D, Auerbach S, Judson R, Thomas RS. Considerations for Strategic Use of High-Throughput Transcriptomics Chemical Screening Data in Regulatory Decisions. CURRENT OPINION IN TOXICOLOGY 2019; 15:64-75. [PMID: 31501805 DOI: 10.1016/j.cotox.2019.05.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, numerous organizations, including governmental regulatory agencies in the U.S. and abroad, have proposed using data from New Approach Methodologies (NAMs) for augmenting and increasing the pace of chemical assessments. NAMs are broadly defined as any technology, methodology, approach or combination thereof that can be used to provide information on chemical hazard and risk assessment that avoids the use of intact animals. High-throughput transcriptomics (HTTr) is a type of NAM that uses gene expression profiling as an endpoint for rapidly evaluating the effects of large numbers of chemicals on in vitro cell culture systems. As compared to targeted high-throughput screening (HTS) approaches that measure the effect of chemical X on target Y, HTTr is a non-targeted approach that allows researchers to more broadly characterize the integrated response of an intact biological system to chemicals that may affect a specific biological target or many biological targets under a defined set of treatment conditions (time, concentration, etc.). HTTr screening performed in concentration-response mode can provide potency estimates for the concentrations of chemicals that produce perturbations in cellular response pathways. Here, we discuss study design considerations for HTTr concentration-response screening and present a framework for the use of HTTr-based biological pathway-altering concentrations (BPACs) in a screening-level, risk-based chemical prioritization approach. The framework involves concentration-response modeling of HTTr data, mapping gene level responses to biological pathways, determination of BPACs, in vitro-to-in vivo extrapolation (IVIVE) and comparison to human exposure predictions.
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Affiliation(s)
- Joshua Harrill
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Imran Shah
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - R Woodrow Setzer
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Derik Haggard
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, USA
| | - Scott Auerbach
- National Toxicology Program, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC, USA
| | - Richard Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Russell S Thomas
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
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28
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Thomas RS, Bahadori T, Buckley TJ, Cowden J, Deisenroth C, Dionisio KL, Frithsen JB, Grulke CM, Gwinn MR, Harrill JA, Higuchi M, Houck KA, Hughes MF, Hunter ES, Isaacs KK, Judson RS, Knudsen TB, Lambert JC, Linnenbrink M, Martin TM, Newton SR, Padilla S, Patlewicz G, Paul-Friedman K, Phillips KA, Richard AM, Sams R, Shafer TJ, Setzer RW, Shah I, Simmons JE, Simmons SO, Singh A, Sobus JR, Strynar M, Swank A, Tornero-Valez R, Ulrich EM, Villeneuve DL, Wambaugh JF, Wetmore BA, Williams AJ. The Next Generation Blueprint of Computational Toxicology at the U.S. Environmental Protection Agency. Toxicol Sci 2019; 169:317-332. [PMID: 30835285 PMCID: PMC6542711 DOI: 10.1093/toxsci/kfz058] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The U.S. Environmental Protection Agency (EPA) is faced with the challenge of efficiently and credibly evaluating chemical safety often with limited or no available toxicity data. The expanding number of chemicals found in commerce and the environment, coupled with time and resource requirements for traditional toxicity testing and exposure characterization, continue to underscore the need for new approaches. In 2005, EPA charted a new course to address this challenge by embracing computational toxicology (CompTox) and investing in the technologies and capabilities to push the field forward. The return on this investment has been demonstrated through results and applications across a range of human and environmental health problems, as well as initial application to regulatory decision-making within programs such as the EPA's Endocrine Disruptor Screening Program. The CompTox initiative at EPA is more than a decade old. This manuscript presents a blueprint to guide the strategic and operational direction over the next 5 years. The primary goal is to obtain broader acceptance of the CompTox approaches for application to higher tier regulatory decisions, such as chemical assessments. To achieve this goal, the blueprint expands and refines the use of high-throughput and computational modeling approaches to transform the components in chemical risk assessment, while systematically addressing key challenges that have hindered progress. In addition, the blueprint outlines additional investments in cross-cutting efforts to characterize uncertainty and variability, develop software and information technology tools, provide outreach and training, and establish scientific confidence for application to different public health and environmental regulatory decisions.
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Affiliation(s)
- Russell S. Thomas
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Tina Bahadori
- National Center for Environmental Assessment, Office of Research and Development, US Environmental Protection Agency
| | - Timothy J. Buckley
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - John Cowden
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Chad Deisenroth
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Kathie L. Dionisio
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Jeffrey B. Frithsen
- Chemical Safety for Sustainability National Research Program, Office of Research and Development, US Environmental Protection Agency
| | - Christopher M. Grulke
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Maureen R. Gwinn
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Joshua A. Harrill
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Mark Higuchi
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Keith A. Houck
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Michael F. Hughes
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - E. Sidney Hunter
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Kristin K. Isaacs
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Richard S. Judson
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Thomas B. Knudsen
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Jason C. Lambert
- National Center for Environmental Assessment, Office of Research and Development, US Environmental Protection Agency
| | - Monica Linnenbrink
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Todd M. Martin
- National Risk Management Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Seth R. Newton
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Stephanie Padilla
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Grace Patlewicz
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Katie Paul-Friedman
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Katherine A. Phillips
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Ann M. Richard
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Reeder Sams
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Timothy J. Shafer
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - R. Woodrow Setzer
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Imran Shah
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Jane E. Simmons
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Steven O. Simmons
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Amar Singh
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Jon R. Sobus
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Mark Strynar
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Adam Swank
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Rogelio Tornero-Valez
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Elin M. Ulrich
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Daniel L Villeneuve
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - John F. Wambaugh
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
| | - Barbara A. Wetmore
- National Exposure Research Laboratory, Office of Research and Development, US Environmental Protection Agency
| | - Antony J. Williams
- National Center for Computational Toxicology, Office of Research and Development, US Environmental Protection Agency
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29
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Schmitz-Spanke S. Toxicogenomics - What added Value Do These Approaches Provide for Carcinogen Risk Assessment? ENVIRONMENTAL RESEARCH 2019; 173:157-164. [PMID: 30909101 DOI: 10.1016/j.envres.2019.03.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 06/09/2023]
Abstract
It is still a major challenge to protect humans at workplaces and in the environment. To cope with this task, it is a prerequisite to obtain detailed information on the extent of chemical perturbations of biological pathways, in particular, adaptive vs. adverse effects and the dose-response relationships. This knowledge serves as the basis for the classification of non-carcinogens and carcinogens and for further distinguishing carcinogens in genotoxic (DNA damaging) or non-genotoxic compounds. Basing on quantitative dose-response relationships, points of departures can be derived for chemical risk assessment. In recent years, new methods have shown their capability to support the established rodent models of carcinogenicity testing. In vitro high throughput screening assays assess more comprehensively cell response. In addition, omics technologies were applied to study the mode of action of chemicals whereby the term "toxicogenomics" comprises various technologies such as transcriptomics, epigenomics, or metabolomics. This review aims to summarize the current state of toxicogenomic approaches in risk science and to compare them with established ones. For example, measurement of global transcriptional changes generates meaningful information for toxicological risk assessment such as accurate classification of genotoxic/non-genotoxic carcinogens. Alteration in mRNA expression offers previously unknown insights in the mode of action and enables the definition of key events. Based on these, benchmark doses can be calculated for the transition from an adaptive to an adverse state. In short, this review assesses the potential and challenges of transcriptomics and addresses the impact of other omics technologies on risk assessment in terms of hazard identification and dose-response assessment.
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Affiliation(s)
- Simone Schmitz-Spanke
- Institute and Outpatient Clinic of Occupational, Social and Environmental Medicine, University of Erlangen-Nuremberg, Henkestr. 9-11, 91054, Erlangen, Germany.
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30
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Dose-dependence of chemical carcinogenicity: Biological mechanisms for thresholds and implications for risk assessment. Chem Biol Interact 2019; 301:112-127. [DOI: 10.1016/j.cbi.2019.01.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/11/2019] [Accepted: 01/25/2019] [Indexed: 12/19/2022]
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31
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Farmahin R, Gannon AM, Gagné R, Rowan-Carroll A, Kuo B, Williams A, Curran I, Yauk CL. Hepatic transcriptional dose-response analysis of male and female Fischer rats exposed to hexabromocyclododecane. Food Chem Toxicol 2018; 133:110262. [PMID: 30594549 DOI: 10.1016/j.fct.2018.12.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/13/2018] [Accepted: 12/20/2018] [Indexed: 12/14/2022]
Abstract
Hexabromocyclododecane (HBCD) is a brominated flame retardant found in the environment and human tissues. The toxicological effects of HBCD exposure are not clearly understood. We employed whole-genome RNA-sequencing on liver samples from male and female Fischer rats exposed to 0, 250, 1250, and 5000 mg technical mixture of HBCD/kg diet for 28 days to gain further insight into HBCD toxicity. HBCD altered 428 and 250 gene transcripts in males and females, respectively, which were involved in metabolism of xenobiotics, oxidative stress, immune response, metabolism of glucose and lipids, circadian regulation, cell cycle, fibrotic activity, and hormonal balance. Signature analysis supported that HBCD operates through the constitutive androstane and pregnane X receptors. The median transcriptomic benchmark dose (BMD) for the lowest statistically significant pathway was within 1.5-fold of the BMD for increased liver weight, while the BMD for the lowest pathway with at least three modeled genes (minimum 5% of pathway) was similar to the lowest apical endpoint BMD. The results show how transcriptional analyses can inform mechanisms underlying chemical toxicity and the doses at which potentially adverse effects occur. This experiment is part of a larger study exploring the use of toxicogenomics and high-throughput screening for human health risk assessment.
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Affiliation(s)
- Reza Farmahin
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Anne Marie Gannon
- Regulatory Toxicology Research Division, Health Products and Food Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Rémi Gagné
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Ivan Curran
- Regulatory Toxicology Research Division, Health Products and Food Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada.
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Guo X, Mei N. Benchmark Dose Modeling of In Vitro Genotoxicity Data: a Reanalysis. Toxicol Res 2018; 34:303-310. [PMID: 30370005 PMCID: PMC6195882 DOI: 10.5487/tr.2018.34.4.303] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 08/16/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023] Open
Abstract
The methods of applied genetic toxicology are changing from qualitative hazard identification to quantitative risk assessment. Recently, quantitative analysis with point of departure (PoD) metrics and benchmark dose (BMD) modeling have been applied to in vitro genotoxicity data. Two software packages are commonly used for BMD analysis. In previous studies, we performed quantitative dose-response analysis by using the PROAST software to quantitatively evaluate the mutagenicity of four piperidine nitroxides with various substituent groups on the 4-position of the piperidine ring and six cigarette whole smoke solutions (WSSs) prepared by bubbling machine-generated whole smoke. In the present study, we reanalyzed the obtained genotoxicity data by using the EPA's BMD software (BMDS) to evaluate the inter-platform quantitative agreement of the estimates of genotoxic potency. We calculated the BMDs for 10%, 50%, and 100% (i.e., a two-fold increase), and 200% increases over the concurrent vehicle controls to achieve better discrimination of the dose-responses, along with their BMDLs (the lower 95% confidence interval of the BMD) and BMDUs (the upper 95% confidence interval of the BMD). The BMD values and rankings estimated in this study by using the EPA's BMDS were reasonably similar to those calculated in our previous studies by using PROAST. These results indicated that both software packages were suitable for dose-response analysis using the mouse lymphoma assay and that the BMD modeling results from these software packages produced comparable rank orders of the mutagenic potency.
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Affiliation(s)
- Xiaoqing Guo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
| | - Nan Mei
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Jefferson, AR, USA
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33
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Auerbach SS, Paules RS. Genomic dose response: Successes, challenges, and next steps. CURRENT OPINION IN TOXICOLOGY 2018. [DOI: 10.1016/j.cotox.2019.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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34
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Metabolomics Discovers Early-Response Metabolic Biomarkers that Can Predict Chronic Reproductive Fitness in Individual Daphnia magna. Metabolites 2018; 8:metabo8030042. [PMID: 30041468 PMCID: PMC6160912 DOI: 10.3390/metabo8030042] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/09/2018] [Accepted: 07/18/2018] [Indexed: 12/11/2022] Open
Abstract
Chemical risk assessment remains entrenched in chronic toxicity tests that set safety thresholds based on animal pathology or fitness. Chronic tests are resource expensive and lack mechanistic insight. Discovering a chemical's mode-of-action can in principle provide predictive molecular biomarkers for a toxicity endpoint. Furthermore, since molecular perturbations precede pathology, early-response molecular biomarkers may enable shorter, more resource efficient testing that can predict chronic animal fitness. This study applied untargeted metabolomics to attempt to discover early-response metabolic biomarkers that can predict reproductive fitness of Daphnia magna, an internationally-recognized test species. First, we measured the reproductive toxicities of cadmium, 2,4-dinitrophenol and propranolol to individual Daphnia in 21-day OECD toxicity tests, then measured the metabolic profiles of these animals using mass spectrometry. Multivariate regression successfully discovered putative metabolic biomarkers that strongly predict reproductive impairment by each chemical, and for all chemicals combined. The non-chemical-specific metabolic biomarkers were then applied to metabolite data from Daphnia 24-h acute toxicity tests and correctly predicted that significant decreases in reproductive fitness would occur if these animals were exposed to cadmium, 2,4-dinitrophenol or propranolol for 21 days. While the applicability of these findings is limited to three chemicals, they provide proof-of-principle that early-response metabolic biomarkers of chronic animal fitness can be discovered for regulatory toxicity testing.
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Chepelev NL, Gagné R, Maynor T, Kuo B, Hobbs CA, Recio L, Yauk CL. Transcriptional profiling of male CD-1 mouse lungs and Harderian glands supports the involvement of calcium signaling in acrylamide-induced tumors. Regul Toxicol Pharmacol 2018; 95:75-90. [DOI: 10.1016/j.yrtph.2018.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 02/06/2018] [Accepted: 02/09/2018] [Indexed: 12/18/2022]
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36
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Dean JL, Zhao QJ, Lambert JC, Hawkins BS, Thomas RS, Wesselkamper SC. Editor's Highlight: Application of Gene Set Enrichment Analysis for Identification of Chemically Induced, Biologically Relevant Transcriptomic Networks and Potential Utilization in Human Health Risk Assessment. Toxicol Sci 2018; 157:85-99. [PMID: 28123101 DOI: 10.1093/toxsci/kfx021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The rate of new chemical development in commerce combined with a paucity of toxicity data for legacy chemicals presents a unique challenge for human health risk assessment. There is a clear need to develop new technologies and incorporate novel data streams to more efficiently inform derivation of toxicity values. One avenue of exploitation lies in the field of transcriptomics and the application of gene expression analysis to characterize biological responses to chemical exposures. In this context, gene set enrichment analysis (GSEA) was employed to evaluate tissue-specific, dose-response gene expression data generated following exposure to multiple chemicals for various durations. Patterns of transcriptional enrichment were evident across time and with increasing dose, and coordinated enrichment plausibly linked to the etiology of the biological responses was observed. GSEA was able to capture both transient and sustained transcriptional enrichment events facilitating differentiation between adaptive versus longer term molecular responses. When combined with benchmark dose (BMD) modeling of gene expression data from key drivers of biological enrichment, GSEA facilitated characterization of dose ranges required for enrichment of biologically relevant molecular signaling pathways, and promoted comparison of the activation dose ranges required for individual pathways. Median transcriptional BMD values were calculated for the most sensitive enriched pathway as well as the overall median BMD value for key gene members of significantly enriched pathways, and both were observed to be good estimates of the most sensitive apical endpoint BMD value. Together, these efforts support the application of GSEA to qualitative and quantitative human health risk assessment.
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Affiliation(s)
- Jeffry L Dean
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Q Jay Zhao
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Jason C Lambert
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Belinda S Hawkins
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
| | - Russell S Thomas
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Scott C Wesselkamper
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Cincinnati, Ohio, USA
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37
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Venkatratnam A, House JS, Konganti K, McKenney C, Threadgill DW, Chiu WA, Aylor DL, Wright FA, Rusyn I. Population-based dose-response analysis of liver transcriptional response to trichloroethylene in mouse. Mamm Genome 2018; 29:168-181. [PMID: 29353386 DOI: 10.1007/s00335-018-9734-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/17/2018] [Indexed: 12/23/2022]
Abstract
Studies of gene expression are common in toxicology and provide important clues to mechanistic understanding of adverse effects of chemicals. Most prior studies have been performed in a single strain or cell line; however, gene expression is heavily influenced by the genetic background, and these genotype-expression differences may be key drivers of inter-individual variation in response to chemical toxicity. In this study, we hypothesized that the genetically diverse Collaborative Cross mouse population can be used to gain insight and suggest mechanistic hypotheses for the dose- and genetic background-dependent effects of chemical exposure. This hypothesis was tested using a model liver toxicant trichloroethylene (TCE). Liver transcriptional responses to TCE exposure were evaluated 24 h after dosing. Transcriptomic dose-responses were examined for both TCE and its major oxidative metabolite trichloroacetic acid (TCA). As expected, peroxisome- and fatty acid metabolism-related pathways were among the most dose-responsive enriched pathways in all strains. However, nearly half of the TCE-induced liver transcriptional perturbation was strain-dependent, with abundant evidence of strain/dose interaction, including in the peroxisomal signaling-associated pathways. These effects were highly concordant between the administered TCE dose and liver levels of TCA. Dose-response analysis of gene expression at the pathway level yielded points of departure similar to those derived from the traditional toxicology studies for both non-cancer and cancer effects. Mapping of expression-genotype-dose relationships revealed some significant associations; however, the effects of TCE on gene expression in liver appear to be highly polygenic traits that are challenging to positionally map. This study highlights the usefulness of mouse population-based studies in assessing inter-individual variation in toxicological responses, but cautions that genetic mapping may be challenging because of the complexity in gene exposure-dose relationships.
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Affiliation(s)
- Abhishek Venkatratnam
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, Texas, 77843, USA.,Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina, 27599, USA
| | - John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, 27695, USA
| | - Kranti Konganti
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, Texas, 77843, USA
| | - Connor McKenney
- NCSU Undergraduate program in Genetics, North Carolina State University, Raleigh, North Carolina, 27695, USA
| | - David W Threadgill
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, Texas, 77843, USA
| | - Weihsueh A Chiu
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, Texas, 77843, USA
| | - David L Aylor
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, 27695, USA.,Department of Statistics, North Carolina State University, Raleigh, North Carolina, 27695, USA
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, 4458 TAMU, College Station, Texas, 77843, USA.
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38
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The challenge of the application of 'omics technologies in chemicals risk assessment: Background and outlook. Regul Toxicol Pharmacol 2017; 91 Suppl 1:S14-S26. [DOI: 10.1016/j.yrtph.2017.09.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 11/21/2022]
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39
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House JS, Grimm FA, Jima DD, Zhou YH, Rusyn I, Wright FA. A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics. Front Genet 2017; 8:168. [PMID: 29163636 PMCID: PMC5672545 DOI: 10.3389/fgene.2017.00168] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/18/2017] [Indexed: 12/21/2022] Open
Abstract
Cell-based assays are an attractive option to measure gene expression response to exposure, but the cost of whole-transcriptome RNA sequencing has been a barrier to the use of gene expression profiling for in vitro toxicity screening. In addition, standard RNA sequencing adds variability due to variable transcript length and amplification. Targeted probe-sequencing technologies such as TempO-Seq, with transcriptomic representation that can vary from hundreds of genes to the entire transcriptome, may reduce some components of variation. Analyses of high-throughput toxicogenomics data require renewed attention to read-calling algorithms and simplified dose–response modeling for datasets with relatively few samples. Using data from induced pluripotent stem cell-derived cardiomyocytes treated with chemicals at varying concentrations, we describe here and make available a pipeline for handling expression data generated by TempO-Seq to align reads, clean and normalize raw count data, identify differentially expressed genes, and calculate transcriptomic concentration–response points of departure. The methods are extensible to other forms of concentration–response gene-expression data, and we discuss the utility of the methods for assessing variation in susceptibility and the diseased cellular state.
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Affiliation(s)
- John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
| | - Fabian A Grimm
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Dereje D Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, United States
| | - Yi-Hui Zhou
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States.,Department of Statistics, North Carolina State University, Raleigh, NC, United States
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40
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Zhou YH, Cichocki JA, Soldatow VY, Scholl EH, Gallins PJ, Jima D, Yoo HS, Chiu WA, Wright FA, Rusyn I. Editor's Highlight: Comparative Dose-Response Analysis of Liver and Kidney Transcriptomic Effects of Trichloroethylene and Tetrachloroethylene in B6C3F1 Mouse. Toxicol Sci 2017; 160:95-110. [PMID: 28973375 PMCID: PMC5837274 DOI: 10.1093/toxsci/kfx165] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Trichloroethylene (TCE) and tetrachloroethylene (PCE) are ubiquitous environmental contaminants and occupational health hazards. Recent health assessments of these agents identified several critical data gaps, including lack of comparative analysis of their effects. This study examined liver and kidney effects of TCE and PCE in a dose-response study design. Equimolar doses of TCE (24, 80, 240, and 800 mg/kg) or PCE (30, 100, 300, and 1000 mg/kg) were administered by gavage in aqueous vehicle to male B6C3F1/J mice. Tissues were collected 24 h after exposure. Trichloroacetic acid (TCA), a major oxidative metabolite of both compounds, was measured and RNA sequencing was performed. PCE had a stronger effect on liver and kidney transcriptomes, as well as greater concentrations of TCA. Most dose-responsive pathways were common among chemicals/tissues, with the strongest effect on peroxisomal β-oxidation. Effects on liver and kidney mitochondria-related pathways were notably unique to PCE. We performed dose-response modeling of the transcriptomic data and compared the resulting points of departure (PODs) to those for apical endpoints derived from long-term studies with these chemicals in rats, mice, and humans, converting to human equivalent doses using tissue-specific dosimetry models. Tissue-specific acute transcriptional effects of TCE and PCE occurred at human equivalent doses comparable to those for apical effects. These data are relevant for human health assessments of TCE and PCE as they provide data for dose-response analysis of the toxicity mechanisms. Additionally, they provide further evidence that transcriptomic data can be useful surrogates for in vivo PODs, especially when toxicokinetic differences are taken into account.
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Affiliation(s)
- Yi-Hui Zhou
- Department of Biological Sciences
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
| | - Joseph A. Cichocki
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas
| | - Valerie Y. Soldatow
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina
| | - Elizabeth H. Scholl
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
| | - Paul J. Gallins
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
| | - Dereje Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
| | - Hong-Sik Yoo
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina
| | - Weihsueh A. Chiu
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas
| | - Fred A. Wright
- Department of Biological Sciences
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
- Department of Statistics, North Carolina State University, Raleigh, North Carolina
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas
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41
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LaRocca J, Johnson KJ, LeBaron MJ, Rasoulpour RJ. The interface of epigenetics and toxicology in product safety assessment. CURRENT OPINION IN TOXICOLOGY 2017. [DOI: 10.1016/j.cotox.2017.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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42
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Integration of the TGx-28.65 genomic biomarker with the flow cytometry micronucleus test to assess the genotoxicity of disperse orange and 1,2,4-benzenetriol in human TK6 cells. Mutat Res 2017; 806:51-62. [PMID: 29017062 DOI: 10.1016/j.mrfmmm.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/21/2017] [Accepted: 09/10/2017] [Indexed: 12/13/2022]
Abstract
In vitro gene expression signatures to predict toxicological responses can provide mechanistic context for regulatory testing. We previously developed the TGx-28.65 genomic biomarker from a database of gene expression profiles derived from human TK6 cells exposed to 28 well-known compounds. The biomarker comprises 65 genes that can classify chemicals as DNA damaging or non-DNA damaging. In this study, we applied the TGx-28.65 genomic biomarker in parallel with the in vitro micronucleus (MN) assay to determine if two chemicals of regulatory interest at Health Canada, disperse orange (DO: the orange azo dye 3-[[4-[(4-Nitrophenyl)azo]phenyl] benzylamino]propanenitrile) and 1,2,4-benzenetriol (BT: a metabolite of benzene) are genotoxic or non-genotoxic. Both chemicals caused dose-dependent declines in relative survival and increases in apoptosis. A strong significant increase in MN induction was observed for all concentrations of BT; the top two concentrations of DO also caused a statistically significant increase in MN, but these increases were <2-fold above controls. TGx-28.65 analysis classified BT as genotoxic at all three concentrations and DO as genotoxic at the mid and high concentrations. Thus, although DO only caused a small increase in MN, this response was sufficient to induce a cellular DNA damage response. Benchmark dose modeling confirmed that BT is much more potent than DO. The results strongly suggest that follow-up work is required to assess whether DO and BT are also genotoxic in vivo. This is particularly important for DO, which may require metabolic activation by bacterial gut flora to fully induce its genotoxic potential. Our previously published data and this proof of concept study suggest that the TGx-28.65 genomic biomarker has the potential to add significant value to existing approaches used to assess genotoxicity.
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43
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Transcriptional profiling of male F344 rats suggests the involvement of calcium signaling in the mode of action of acrylamide-induced thyroid cancer. Food Chem Toxicol 2017; 107:186-200. [DOI: 10.1016/j.fct.2017.06.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 12/21/2022]
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Recio L, Friedman M, Marroni D, Maynor T, Chepelev NL. Impact of Acrylamide on Calcium Signaling and Cytoskeletal Filaments in Testes From F344 Rat. Int J Toxicol 2017; 36:124-132. [PMID: 28403741 DOI: 10.1177/1091581817697696] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acrylamide (AA) at high exposure levels is neurotoxic, induces testicular toxicity, and increases dominant lethal mutations in rats. RNA-sequencing in testes was used to identify differentially expressed genes (DEG), explore AA-induced pathway perturbations that could contribute to AA-induced testicular toxicity and then used to derive a benchmark dose (BMD). Male F344/DuCrl rats were administered 0.0, 0.5, 1.5, 3.0, 6.0, or 12.0 mg AA/kg bw/d in drinking water for 5, 15, or 31 days. The experimental design used exposure levels that spanned and exceeded the exposure levels used in the rat dominant lethal, 2-generation reproductive toxicology, and cancer bioassays. The time of sample collection was based on previous studies that developed gene expression-based BMD. At 12.0 mg/kg, there were 38, 33, and 65 DEG ( P value <.005; fold change >1.5) in the testes after 5, 15, or 31 days of exposure, respectively. At 31 days, there was a dose-dependent increase in the number of DEG, and at 12.0 mg/kg/d the top three functional clusters affected by AA exposure were actin filament organization, response to calcium ion, and regulation of cell proliferation. The BMD lower 95% confidence limit using DEG ranged from 1.8 to 6.8 mg/kg compared to a no-observed-adverse-effect-level of 2.0 mg/kg/d for male reproductive toxicity. These results are consistent with the known effects of AA on calcium signaling and cytoskeletal actin filaments leading to neurotoxicity and suggest that AA can cause rat dominant lethal mutations by these same mechanisms leading to impaired chromosome segregation during cell division.
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Affiliation(s)
- Leslie Recio
- 1 Integrated Laboratory Systems Inc, Research Triangle Park, NC, USA
| | - Marvin Friedman
- 2 SNF SAS, rue Adrienne Bolland, ZAC de Milieux, Andrézieux, Rhône-Alpes, France
| | - Dennis Marroni
- 2 SNF SAS, rue Adrienne Bolland, ZAC de Milieux, Andrézieux, Rhône-Alpes, France
| | - Timothy Maynor
- 1 Integrated Laboratory Systems Inc, Research Triangle Park, NC, USA
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45
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Waldmann T, Grinberg M, König A, Rempel E, Schildknecht S, Henry M, Holzer AK, Dreser N, Shinde V, Sachinidis A, Rahnenführer J, Hengstler JG, Leist M. Stem Cell Transcriptome Responses and Corresponding Biomarkers That Indicate the Transition from Adaptive Responses to Cytotoxicity. Chem Res Toxicol 2016; 30:905-922. [PMID: 28001369 DOI: 10.1021/acs.chemrestox.6b00259] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Analysis of transcriptome changes has become an established method to characterize the reaction of cells to toxicants. Such experiments are mostly performed at compound concentrations close to the cytotoxicity threshold. At present, little information is available on concentration-dependent features of transcriptome changes, in particular, at the transition from noncytotoxic concentrations to conditions that are associated with cell death. Thus, it is unclear in how far cell death confounds the results of transcriptome studies. To explore this gap of knowledge, we treated pluripotent stem cells differentiating to human neuroepithelial cells (UKN1 assay) for short periods (48 h) with increasing concentrations of valproic acid (VPA) and methyl mercury (MeHg), two compounds with vastly different modes of action. We developed various visualization tools to describe cellular responses, and the overall response was classified as "tolerance" (minor transcriptome changes), "functional adaptation" (moderate/strong transcriptome responses, but no cytotoxicity), and "degeneration". The latter two conditions were compared, using various statistical approaches. We identified (i) genes regulated at cytotoxic, but not at noncytotoxic, concentrations and (ii) KEGG pathways, gene ontology term groups, and superordinate biological processes that were only regulated at cytotoxic concentrations. The consensus markers and processes found after 48 h treatment were then overlaid with those found after prolonged (6 days) treatment. The study highlights the importance of careful concentration selection and of controlling viability for transcriptome studies. Moreover, it allowed identification of 39 candidate "biomarkers of cytotoxicity". These could serve to provide alerts that data sets of interest may have been affected by cell death in the model system studied.
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Affiliation(s)
- Tanja Waldmann
- In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Chair Foundation, University of Konstanz , 78457 Konstanz, Germany
| | - Marianna Grinberg
- Department of Statistics, Technical University of Dortmund , D-44221 Dortmund, Germany
| | - André König
- Department of Statistics, Technical University of Dortmund , D-44221 Dortmund, Germany
| | - Eugen Rempel
- Department of Statistics, Technical University of Dortmund , D-44221 Dortmund, Germany
| | - Stefan Schildknecht
- In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Chair Foundation, University of Konstanz , 78457 Konstanz, Germany
| | - Margit Henry
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne (UKK) , D-50931 Cologne, Germany
| | - Anna-Katharina Holzer
- In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Chair Foundation, University of Konstanz , 78457 Konstanz, Germany
| | - Nadine Dreser
- In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Chair Foundation, University of Konstanz , 78457 Konstanz, Germany
| | - Vaibhav Shinde
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne (UKK) , D-50931 Cologne, Germany
| | - Agapios Sachinidis
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, University of Cologne (UKK) , D-50931 Cologne, Germany
| | - Jörg Rahnenführer
- Department of Statistics, Technical University of Dortmund , D-44221 Dortmund, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Technical University of Dortmund , D-44139 Dortmund, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, Department inaugurated by the Doerenkamp-Zbinden Chair Foundation, University of Konstanz , 78457 Konstanz, Germany
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46
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Farmahin R, Williams A, Kuo B, Chepelev NL, Thomas RS, Barton-Maclaren TS, Curran IH, Nong A, Wade MG, Yauk CL. Recommended approaches in the application of toxicogenomics to derive points of departure for chemical risk assessment. Arch Toxicol 2016; 91:2045-2065. [PMID: 27928627 PMCID: PMC5399047 DOI: 10.1007/s00204-016-1886-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/02/2016] [Indexed: 12/15/2022]
Abstract
There is increasing interest in the use of quantitative transcriptomic data to determine benchmark dose (BMD) and estimate a point of departure (POD) for human health risk assessment. Although studies have shown that transcriptional PODs correlate with those derived from apical endpoint changes, there is no consensus on the process used to derive a transcriptional POD. Specifically, the subsets of informative genes that produce BMDs that best approximate the doses at which adverse apical effects occur have not been defined. To determine the best way to select predictive groups of genes, we used published microarray data from dose–response studies on six chemicals in rats exposed orally for 5, 14, 28, and 90 days. We evaluated eight approaches for selecting genes for POD derivation and three previously proposed approaches (the lowest pathway BMD, and the mean and median BMD of all genes). The relationship between transcriptional BMDs derived using these 11 approaches and PODs derived from apical data that might be used in chemical risk assessment was examined. Transcriptional BMD values for all 11 approaches were remarkably aligned with corresponding apical PODs, with the vast majority of toxicogenomics PODs being within tenfold of those derived from apical endpoints. We identified at least four approaches that produce BMDs that are effective estimates of apical PODs across multiple sampling time points. Our results support that a variety of approaches can be used to derive reproducible transcriptional PODs that are consistent with PODs produced from traditional methods for chemical risk assessment.
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Affiliation(s)
- Reza Farmahin
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Nikolai L Chepelev
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Russell S Thomas
- National Center for Computational Toxicology, United States Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Tara S Barton-Maclaren
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Ivan H Curran
- Toxicology Research Division, Health Products and Food Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Andy Nong
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Michael G Wade
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada.
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Co-exposure to low doses of the food contaminants deoxynivalenol and nivalenol has a synergistic inflammatory effect on intestinal explants. Arch Toxicol 2016; 91:2677-2687. [DOI: 10.1007/s00204-016-1902-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 11/24/2016] [Indexed: 01/24/2023]
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Cote I, Andersen ME, Ankley GT, Barone S, Birnbaum LS, Boekelheide K, Bois FY, Burgoon LD, Chiu WA, Crawford-Brown D, Crofton KM, DeVito M, Devlin RB, Edwards SW, Guyton KZ, Hattis D, Judson RS, Knight D, Krewski D, Lambert J, Maull EA, Mendrick D, Paoli GM, Patel CJ, Perkins EJ, Poje G, Portier CJ, Rusyn I, Schulte PA, Simeonov A, Smith MT, Thayer KA, Thomas RS, Thomas R, Tice RR, Vandenberg JJ, Villeneuve DL, Wesselkamper S, Whelan M, Whittaker C, White R, Xia M, Yauk C, Zeise L, Zhao J, DeWoskin RS. The Next Generation of Risk Assessment Multi-Year Study-Highlights of Findings, Applications to Risk Assessment, and Future Directions. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:1671-1682. [PMID: 27091369 PMCID: PMC5089888 DOI: 10.1289/ehp233] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/30/2015] [Accepted: 03/29/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Next Generation (NexGen) of Risk Assessment effort is a multi-year collaboration among several organizations evaluating new, potentially more efficient molecular, computational, and systems biology approaches to risk assessment. This article summarizes our findings, suggests applications to risk assessment, and identifies strategic research directions. OBJECTIVE Our specific objectives were to test whether advanced biological data and methods could better inform our understanding of public health risks posed by environmental exposures. METHODS New data and methods were applied and evaluated for use in hazard identification and dose-response assessment. Biomarkers of exposure and effect, and risk characterization were also examined. Consideration was given to various decision contexts with increasing regulatory and public health impacts. Data types included transcriptomics, genomics, and proteomics. Methods included molecular epidemiology and clinical studies, bioinformatic knowledge mining, pathway and network analyses, short-duration in vivo and in vitro bioassays, and quantitative structure activity relationship modeling. DISCUSSION NexGen has advanced our ability to apply new science by more rapidly identifying chemicals and exposures of potential concern, helping characterize mechanisms of action that influence conclusions about causality, exposure-response relationships, susceptibility and cumulative risk, and by elucidating new biomarkers of exposure and effects. Additionally, NexGen has fostered extensive discussion among risk scientists and managers and improved confidence in interpreting and applying new data streams. CONCLUSIONS While considerable uncertainties remain, thoughtful application of new knowledge to risk assessment appears reasonable for augmenting major scope assessments, forming the basis for or augmenting limited scope assessments, and for prioritization and screening of very data limited chemicals. Citation: Cote I, Andersen ME, Ankley GT, Barone S, Birnbaum LS, Boekelheide K, Bois FY, Burgoon LD, Chiu WA, Crawford-Brown D, Crofton KM, DeVito M, Devlin RB, Edwards SW, Guyton KZ, Hattis D, Judson RS, Knight D, Krewski D, Lambert J, Maull EA, Mendrick D, Paoli GM, Patel CJ, Perkins EJ, Poje G, Portier CJ, Rusyn I, Schulte PA, Simeonov A, Smith MT, Thayer KA, Thomas RS, Thomas R, Tice RR, Vandenberg JJ, Villeneuve DL, Wesselkamper S, Whelan M, Whittaker C, White R, Xia M, Yauk C, Zeise L, Zhao J, DeWoskin RS. 2016. The Next Generation of Risk Assessment multiyear study-highlights of findings, applications to risk assessment, and future directions. Environ Health Perspect 124:1671-1682; http://dx.doi.org/10.1289/EHP233.
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Affiliation(s)
- Ila Cote
- National Center for Environmental Assessment, U.S. Environmental Protection Agency (EPA), Washington, District of Columbia, USA
- Address correspondence to I. Cote, U.S. Environmental Protection Agency, Region 8, Room 8152, 1595 Wynkoop St., Denver, CO 80202-1129 USA. Telephone: (202) 288-9539. E-mail:
| | | | - Gerald T. Ankley
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Duluth, Minnesota, USA
| | - Stanley Barone
- Office of Chemical Safety and Pollution Prevention, U.S. EPA, Washington, District of Columbia, USA
| | - Linda S. Birnbaum
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Kim Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Frederic Y. Bois
- Unité Modèles pour l’Écotoxicologie et la Toxicologie, Institut National de l’Environnement Industriel et des Risques, Verneuil en Halatte, France
| | - Lyle D. Burgoon
- U.S. Army Engineer Research and Development Center, Research Triangle Park, North Carolina, USA
| | - Weihsueh A. Chiu
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | | | | | - Michael DeVito
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Robert B. Devlin
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Research Triangle Park, North Carolina, USA
| | - Stephen W. Edwards
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Research Triangle Park, North Carolina, USA
| | | | - Dale Hattis
- George Perkins Marsh Institute, Clark University, Worcester, Massachusetts, USA
| | | | - Derek Knight
- European Chemicals Agency, Annankatu, Helsinki, Finland
| | - Daniel Krewski
- McLaughlin Centre for Population Health Risk Assessment, University of Ottawa, Ottawa, Ontario, Canada
| | - Jason Lambert
- National Center for Environmental Assessment, U.S. EPA, Cincinnati, Ohio, USA
| | - Elizabeth Anne Maull
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Donna Mendrick
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
| | | | - Chirag Jagdish Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Edward J. Perkins
- U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi, USA
| | - Gerald Poje
- Grant Consulting Group, Washington, District of Columbia, USA
| | | | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Paul A. Schulte
- Education and Information Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, NIH, DHHS, Bethesda, Maryland, USA
| | - Martyn T. Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Kristina A. Thayer
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | | | - Reuben Thomas
- Gladstone Institutes, University of California, San Francisco, San Francisco, California, USA
| | - Raymond R. Tice
- National Institute of Environmental Health Sciences, and
- National Toxicology Program, National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - John J. Vandenberg
- National Center for Environmental Assessment, U.S. Environmental Protection Agency (EPA), Washington, District of Columbia, USA
| | - Daniel L. Villeneuve
- National Health and Environmental Effects Research Laboratory, U.S. EPA, Duluth, Minnesota, USA
| | - Scott Wesselkamper
- National Center for Environmental Assessment, U.S. EPA, Cincinnati, Ohio, USA
| | - Maurice Whelan
- Systems Toxicology Unit, European Commission Joint Research Centre, Ispra, Italy
| | - Christine Whittaker
- Education and Information Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio, USA
| | - Ronald White
- Center for Effective Government, Washington, District of Columbia, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, NIH, DHHS, Bethesda, Maryland, USA
| | - Carole Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Lauren Zeise
- Office of Environmental Health Hazard Assessment, California EPA, Oakland, California, USA
| | - Jay Zhao
- National Center for Environmental Assessment, U.S. EPA, Cincinnati, Ohio, USA
| | - Robert S. DeWoskin
- National Center for Environmental Assessment, U.S. Environmental Protection Agency (EPA), Washington, District of Columbia, USA
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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
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Dunnick JK, Shockley KR, Morgan DL, Brix A, Travlos GS, Gerrish K, Michael Sanders J, Ton TV, Pandiri AR. Hepatic transcriptomic alterations for N,N-dimethyl-p-toluidine (DMPT) and p-toluidine after 5-day exposure in rats. Arch Toxicol 2016; 91:1685-1696. [PMID: 27638505 DOI: 10.1007/s00204-016-1831-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/24/2016] [Indexed: 12/17/2022]
Abstract
N,N-dimethyl-p-toluidine (DMPT), an accelerant for methyl methacrylate monomers in medical devices, was a liver carcinogen in male and female F344/N rats and B6C3F1 mice in a 2-year oral exposure study. p-Toluidine, a structurally related chemical, was a liver carcinogen in mice but not in rats in an 18-month feed exposure study. In this current study, liver transcriptomic data were used to characterize mechanisms in DMPT and p-toluidine liver toxicity and for conducting benchmark dose (BMD) analysis. Male F344/N rats were exposed orally to DMPT or p-toluidine (0, 1, 6, 20, 60 or 120 mg/kg/day) for 5 days. The liver was examined for lesions and transcriptomic alterations. Both chemicals caused mild hepatic toxicity at 60 and 120 mg/kg and dose-related transcriptomic alterations in the liver. There were 511 liver transcripts differentially expressed for DMPT and 354 for p-toluidine at 120 mg/kg/day (false discovery rate threshold of 5 %). The liver transcriptomic alterations were characteristic of an anti-oxidative damage response (activation of the Nrf2 pathway) and hepatic toxicity. The top cellular processes in gene ontology (GO) categories altered in livers exposed to DMPT or p-toluidine were used for BMD calculations. The lower confidence bound benchmark doses for these chemicals were 2 mg/kg/day for DMPT and 7 mg/kg/day for p-toluidine. These studies show the promise of using 5-day target organ transcriptomic data to identify chemical-induced molecular changes that can serve as markers for preliminary toxicity risk assessment.
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Affiliation(s)
- June K Dunnick
- Toxicology Branch, National Institute of Environmental Health Sciences, P. O. Box 12233, Research Triangle Park, NC, 27709, USA.
| | - Keith R Shockley
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, P. O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Daniel L Morgan
- NTP Laboratory, National Institute of Environmental Health Sciences, P. O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Amy Brix
- Experimental Pathology Laboratories, Inc., National Institute of Environmental Health Sciences, P. O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Gregory S Travlos
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, P. O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Kevin Gerrish
- Molecular Genomics Core, National Institute of Environmental Health Sciences, P. O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - J Michael Sanders
- National Cancer Institute at NIEHS, National Institute of Environmental Health Sciences, P. O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - T V Ton
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, P. O. Box 12233, Research Triangle Park, NC, 27709, USA
| | - Arun R Pandiri
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, P. O. Box 12233, Research Triangle Park, NC, 27709, USA
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