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Gi M, Suzuki S, Kanki M, Yokohira M, Tsukamoto T, Fujioka M, Vachiraarunwong A, Qiu G, Guo R, Wanibuchi H. A novel support vector machine-based 1-day, single-dose prediction model of genotoxic hepatocarcinogenicity in rats. Arch Toxicol 2024:10.1007/s00204-024-03755-w. [PMID: 38762666 DOI: 10.1007/s00204-024-03755-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/27/2024] [Indexed: 05/20/2024]
Abstract
The development of a rapid and accurate model for determining the genotoxicity and carcinogenicity of chemicals is crucial for effective cancer risk assessment. This study aims to develop a 1-day, single-dose model for identifying genotoxic hepatocarcinogens (GHCs) in rats. Microarray gene expression data from the livers of rats administered a single dose of 58 compounds, including 5 GHCs, was obtained from the Open TG-GATEs database and used for the identification of marker genes and the construction of a predictive classifier to identify GHCs in rats. We identified 10 gene markers commonly responsive to all 5 GHCs and used them to construct a support vector machine-based predictive classifier. In the silico validation using the expression data of the Open TG-GATEs database indicates that this classifier distinguishes GHCs from other compounds with high accuracy. To further assess the model's effectiveness and reliability, we conducted multi-institutional 1-day single oral administration studies on rats. These studies examined 64 compounds, including 23 GHCs, with gene expression data of the marker genes obtained via quantitative PCR 24 h after a single oral administration. Our results demonstrate that qPCR analysis is an effective alternative to microarray analysis. The GHC predictive model showed high accuracy and reliability, achieving a sensitivity of 91% (21/23) and a specificity of 93% (38/41) across multiple validation studies in three institutions. In conclusion, the present 1-day single oral administration model proves to be a reliable and highly sensitive tool for identifying GHCs and is anticipated to be a valuable tool in identifying and screening potential GHCs.
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Affiliation(s)
- Min Gi
- Department of Environmental Risk Assessment, Graduate School of Medicine, Osaka Metropolitan University, Osaka, 545-8585, Japan
- Department of Molecular Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, 545-8585, Japan
| | - Shugo Suzuki
- Department of Molecular Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, 545-8585, Japan
| | - Masayuki Kanki
- Department of Molecular Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, 545-8585, Japan
| | - Masanao Yokohira
- Department of Medical Education, Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
- Department of Pathology and Host-Defense, Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Tetsuya Tsukamoto
- Department of Diagnostic Pathology, Graduate School of Medicine, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Masaki Fujioka
- Department of Molecular Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, 545-8585, Japan
| | - Arpamas Vachiraarunwong
- Department of Environmental Risk Assessment, Graduate School of Medicine, Osaka Metropolitan University, Osaka, 545-8585, Japan
| | - Guiyu Qiu
- Department of Molecular Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, 545-8585, Japan
| | - Runjie Guo
- Department of Environmental Risk Assessment, Graduate School of Medicine, Osaka Metropolitan University, Osaka, 545-8585, Japan
| | - Hideki Wanibuchi
- Department of Molecular Pathology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, 545-8585, Japan.
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2
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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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3
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Assessment of genotoxic chemicals using chemogenomic profiling based on gene-knockout library in Saccharomyces cerevisiae. Toxicol In Vitro 2021; 79:105278. [PMID: 34843885 DOI: 10.1016/j.tiv.2021.105278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/19/2021] [Accepted: 11/23/2021] [Indexed: 02/07/2023]
Abstract
Understanding the adverse effects of genotoxic chemicals and identifying them effectively from non-genotoxic chemicals are of great worldwide concerns. Here, Saccharomyces cerevisiae (yeast) genome-wide single-gene knockout screening approach was conducted to assess two genotoxic chemicals (4-nitroquinoline-1-oxide (4-NQO) and formaldehyde (FA)) and environmental pollutant dichloroacetic acid (DCA, genotoxicity is controversial). DNA repair was significant enriched in the gene ontology (GO) biology process (BP) terms and KEGG pathways when exposed to low concentrations of 4-NQO and FA. Higher concentrations of 4-NQO and FA influenced some RNA metabolic and biosynthesis pathways. Moreover, replication and repair associated pathways were top ranked KEGG pathways with high fold-change for low concentrations of 4-NQO and FA. The similar gene profiles perturbed by DCA with three test concentrations identified, the common GO BP terms associated with aromatic amino acid family biosynthetic process and ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway. DCA has no obvious genotoxicity as there was no enriched DNA damage and repair pathways and fold-change of replication and repair KEGG pathways were very low. Five genes (RAD18, RAD59, MUS81, MMS4, and BEM4) could serve as candidate genes for genotoxic chemicals. Overall, the yeast functional genomic profiling showed great performance for assessing the signatures and potential molecular mechanisms of genotoxic chemicals.
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4
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Zhao Y, Hasse S, Bourgoin SG. Phosphatidylserine-specific phospholipase A1: A friend or the devil in disguise. Prog Lipid Res 2021; 83:101112. [PMID: 34166709 DOI: 10.1016/j.plipres.2021.101112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/30/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
Abstract
Various human tissues and cells express phospholipase A1 member A (PLA1A), including the liver, lung, prostate gland, and immune cells. The enzyme belongs to the pancreatic lipase family. PLA1A specifically hydrolyzes sn-1 fatty acid of phosphatidylserine (PS) or 1-acyl-lysophosphatidylserine (1-acyl-lysoPS). PS externalized by activated cells or apoptotic cells or extracellular vesicles is a potential source of substrate for the production of unsaturated lysoPS species by PLA1A. Maturation and functions of many immune cells, such as T cells, dendritic cells, macrophages, and mast cells, can be regulated by PLA1A and lysoPS. Several lysoPS receptors, including GPR34, GPR174 and P2Y10, have been identified. High serum levels and high PLA1A expression are associated with autoimmune disorders such as Graves' disease and systemic lupus erythematosus. Increased expression of PLA1A is associated with metastatic melanomas. PLA1A may contribute to cardiometabolic disorders through mediating cholesterol transportation and producing lysoPS. Furthermore, PLA1A is necessary for hepatitis C virus assembly and can play a role in the antivirus innate immune response. This review summarizes recent findings on PLA1A expression, lysoPS and lysoPS receptors in autoimmune disorders, cancers, cardiometabolic disorders, antivirus immune responses, as well as regulations of immune cells.
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Affiliation(s)
- Yang Zhao
- Centre de recherche du CHU de Québec-Université Laval, Centre ARThrite de l'Université Laval, Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, G1V 4G2, Canada
| | - Stephan Hasse
- Centre de recherche du CHU de Québec-Université Laval, Centre ARThrite de l'Université Laval, Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, G1V 4G2, Canada
| | - Sylvain G Bourgoin
- Centre de recherche du CHU de Québec-Université Laval, Centre ARThrite de l'Université Laval, Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec, G1V 4G2, Canada.
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5
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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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6
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Huang SH, Lin YC, Tung CW. Identification of Time-Invariant Biomarkers for Non-Genotoxic Hepatocarcinogen Assessment. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17124298. [PMID: 32560183 PMCID: PMC7345770 DOI: 10.3390/ijerph17124298] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 12/12/2022]
Abstract
Non-genotoxic hepatocarcinogens (NGHCs) can only be confirmed by 2-year rodent studies. Toxicogenomics (TGx) approaches using gene expression profiles from short-term animal studies could enable early assessment of NGHCs. However, high variance in the modulation of the genes had been noted among exposure styles and datasets. Expanding from our previous strategy in identifying consensus biomarkers in multiple experiments, we aimed to identify time-invariant biomarkers for NGHCs in short-term exposure styles and validate their applicability to long-term exposure styles. In this study, nine time-invariant biomarkers, namely A2m, Akr7a3, Aqp7, Ca3, Cdc2a, Cdkn3, Cyp2c11, Ntf3, and Sds, were identified from four large-scale microarray datasets. Machine learning techniques were subsequently employed to assess the prediction performance of the biomarkers. The biomarker set along with the Random Forest models gave the highest median area under the receiver operating characteristic curve (AUC) of 0.824 and a low interquartile range (IQR) variance of 0.036 based on a leave-one-out cross-validation. The application of the models to the external validation datasets achieved high AUC values of greater than or equal to 0.857. Enrichment analysis of the biomarkers inferred the involvement of chronic inflammatory diseases such as liver cirrhosis, fibrosis, and hepatocellular carcinoma in NGHCs. The time-invariant biomarkers provided a robust alternative for NGHC prediction.
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Affiliation(s)
- Shan-Han Huang
- Ph. D. Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (S.-H.H.); (Y.-C.L.)
| | - Ying-Chi Lin
- Ph. D. Program in Toxicology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (S.-H.H.); (Y.-C.L.)
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chun-Wei Tung
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei 11031, Taiwan
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli County 35053, Taiwan
- Correspondence:
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Nicolaidou V, Koufaris C. Application of transcriptomic and microRNA profiling in the evaluation of potential liver carcinogens. Toxicol Ind Health 2020; 36:386-397. [PMID: 32419640 DOI: 10.1177/0748233720922710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hepatocarcinogens are agents that increase the incidence of liver cancer in exposed animals or humans. It is now established that carcinogenic exposures have a widespread impact on the transcriptome, inducing both adaptive and adverse changes in the activities of genes and pathways. Chemical hepatocarcinogens have also been shown to affect expression of microRNA (miRNA), the evolutionarily conserved noncoding RNA that regulates gene expression posttranscriptionally. Considerable effort has been invested into examining the involvement of mRNA in chemical hepatocarcinogenesis and their potential usage for the classification and prediction of new chemical entities. For miRNA, there has been an increasing number of studies reported over the past decade, although not to the same degree as for transcriptomic studies. Current data suggest that it is unlikely that any gene or miRNA signature associated with short-term carcinogen exposure can replace the rodent bioassay. In this review, we discuss the application of transcriptomic and miRNA profiles to increase mechanistic understanding of chemical carcinogens and to aid in their classification.
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Affiliation(s)
- Vicky Nicolaidou
- Department of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus
| | - Costas Koufaris
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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8
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Pouché L, Vitobello A, Römer M, Glogovac M, MacLeod AK, Ellinger-Ziegelbauer H, Westphal M, Dubost V, Stiehl DP, Dumotier B, Fekete A, Moulin P, Zell A, Schwarz M, Moreno R, Huang JTJ, Elcombe CR, Henderson CJ, Roland Wolf C, Moggs JG, Terranova R. Xenobiotic CAR Activators Induce Dlk1-Dio3 Locus Noncoding RNA Expression in Mouse Liver. Toxicol Sci 2018; 158:367-378. [PMID: 28541575 DOI: 10.1093/toxsci/kfx104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Derisking xenobiotic-induced nongenotoxic carcinogenesis (NGC) represents a significant challenge during the safety assessment of chemicals and therapeutic drugs. The identification of robust mechanism-based NGC biomarkers has the potential to enhance cancer hazard identification. We previously demonstrated Constitutive Androstane Receptor (CAR) and WNT signaling-dependent up-regulation of the pluripotency associated Dlk1-Dio3 imprinted gene cluster noncoding RNAs (ncRNAs) in the liver of mice treated with tumor-promoting doses of phenobarbital (PB). Here, we have compared phenotypic, transcriptional ,and proteomic data from wild-type, CAR/PXR double knock-out and CAR/PXR double humanized mice treated with either PB or chlordane, and show that hepatic Dlk1-Dio3 locus long ncRNAs are upregulated in a CAR/PXR-dependent manner by two structurally distinct CAR activators. We further explored the specificity of Dlk1-Dio3 locus ncRNAs as hepatic NGC biomarkers in mice treated with additional compounds working through distinct NGC modes of action. We propose that up-regulation of Dlk1-Dio3 cluster ncRNAs can serve as an early biomarker for CAR activator-induced nongenotoxic hepatocarcinogenesis and thus may contribute to mechanism-based assessments of carcinogenicity risk for chemicals and novel therapeutics.
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Affiliation(s)
- Lucie Pouché
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, CH-4057 Basel, Switzerland
| | - Antonio Vitobello
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, CH-4057 Basel, Switzerland
| | - Michael Römer
- Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
| | - Milica Glogovac
- Novartis Business Services, Novartis Pharma, CH-4057 Basel, Switzerland
| | - A Kenneth MacLeod
- Division of Cancer Research, Jacqui Wood Cancer Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, UK
| | | | - Magdalena Westphal
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, CH-4057 Basel, Switzerland
| | - Valérie Dubost
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, CH-4057 Basel, Switzerland
| | - Daniel Philipp Stiehl
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, CH-4057 Basel, Switzerland
| | - Bérengère Dumotier
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, CH-4057 Basel, Switzerland
| | - Alexander Fekete
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139
| | - Pierre Moulin
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, CH-4057 Basel, Switzerland
| | - Andreas Zell
- Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Schwarz
- Department of Toxicology, University of Tübingen, 72074 Tübingen, Germany
| | - Rita Moreno
- Division of Cancer Research, Jacqui Wood Cancer Centre, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Jeffrey T J Huang
- Biomarker and Drug Analysis Core Facility, School of Medicine, Jacqui Wood Cancer Centre, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | | | - Colin J Henderson
- Division of Cancer Research, Jacqui Wood Cancer Centre, Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - C Roland Wolf
- Division of Cancer Research, Jacqui Wood Cancer Centre, Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Jonathan G Moggs
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, CH-4057 Basel, Switzerland
| | - Rémi Terranova
- Preclinical Safety, Translational Medicine, Novartis Institutes for Biomedical Research, CH-4057 Basel, Switzerland
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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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10
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Modernizing Human Cancer Risk Assessment of Therapeutics. Trends Pharmacol Sci 2017; 39:232-247. [PMID: 29242029 DOI: 10.1016/j.tips.2017.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/17/2017] [Accepted: 11/17/2017] [Indexed: 12/14/2022]
Abstract
Cancer risk assessment of therapeutics is plagued by poor translatability of rodent models of carcinogenesis. In order to overcome this fundamental limitation, new approaches are needed that enable us to evaluate cancer risk directly in humans and human-based cellular models. Our enhanced understanding of the mechanisms of carcinogenesis and the influence of human genome sequence variation on cancer risk motivates us to re-evaluate how we assess the carcinogenic risk of therapeutics. This review will highlight new opportunities for applying this knowledge to the development of a battery of human-based in vitro models and biomarkers for assessing cancer risk of novel therapeutics.
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11
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Beger R, Yu LR, Daniels J, Mattes W. Exploratory biomarkers: Analytical approaches and their implications. CURRENT OPINION IN TOXICOLOGY 2017. [DOI: 10.1016/j.cotox.2017.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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12
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Terranova R, Vitobello A, Del Rio Espinola A, Wolf CR, Schwarz M, Thomson J, Meehan R, Moggs J. Progress in identifying epigenetic mechanisms of xenobiotic-induced non-genotoxic carcinogenesis. CURRENT OPINION IN TOXICOLOGY 2017. [DOI: 10.1016/j.cotox.2017.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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13
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Identification of consensus biomarkers for predicting non-genotoxic hepatocarcinogens. Sci Rep 2017; 7:41176. [PMID: 28117354 PMCID: PMC5259716 DOI: 10.1038/srep41176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/16/2016] [Indexed: 12/31/2022] Open
Abstract
The assessment of non-genotoxic hepatocarcinogens (NGHCs) is currently relying on two-year rodent bioassays. Toxicogenomics biomarkers provide a potential alternative method for the prioritization of NGHCs that could be useful for risk assessment. However, previous studies using inconsistently classified chemicals as the training set and a single microarray dataset concluded no consensus biomarkers. In this study, 4 consensus biomarkers of A2m, Ca3, Cxcl1, and Cyp8b1 were identified from four large-scale microarray datasets of the one-day single maximum tolerated dose and a large set of chemicals without inconsistent classifications. Machine learning techniques were subsequently applied to develop prediction models for NGHCs. The final bagging decision tree models were constructed with an average AUC performance of 0.803 for an independent test. A set of 16 chemicals with controversial classifications were reclassified according to the consensus biomarkers. The developed prediction models and identified consensus biomarkers are expected to be potential alternative methods for prioritization of NGHCs for further experimental validation.
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14
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Derisking Drug-Induced Carcinogenicity for Novel Therapeutics. Trends Cancer 2016; 2:398-408. [DOI: 10.1016/j.trecan.2016.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 12/21/2022]
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15
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Rieswijk L, Brauers KJJ, Coonen MLJ, Jennen DGJ, van Breda SGJ, Kleinjans JCS. Exploiting microRNA and mRNA profiles generated in vitro from carcinogen-exposed primary mouse hepatocytes for predicting in vivo genotoxicity and carcinogenicity. Mutagenesis 2016; 31:603-15. [PMID: 27338304 DOI: 10.1093/mutage/gew027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The well-defined battery of in vitro systems applied within chemical cancer risk assessment is often characterised by a high false-positive rate, thus repeatedly failing to correctly predict the in vivo genotoxic and carcinogenic properties of test compounds. Toxicogenomics, i.e. mRNA-profiling, has been proven successful in improving the prediction of genotoxicity in vivo and the understanding of underlying mechanisms. Recently, microRNAs have been discovered as post-transcriptional regulators of mRNAs. It is thus hypothesised that using microRNA response-patterns may further improve current prediction methods. This study aimed at predicting genotoxicity and non-genotoxic carcinogenicity in vivo, by comparing microRNA- and mRNA-based profiles, using a frequently applied in vitro liver model and exposing this to a range of well-chosen prototypical carcinogens. Primary mouse hepatocytes (PMH) were treated for 24 and 48h with 21 chemical compounds [genotoxins (GTX) vs. non-genotoxins (NGTX) and non-genotoxic carcinogens (NGTX-C) versus non-carcinogens (NC)]. MicroRNA and mRNA expression changes were analysed by means of Exiqon and Affymetrix microarray-platforms, respectively. Classification was performed by using Prediction Analysis for Microarrays (PAM). Compounds were randomly assigned to training and validation sets (repeated 10 times). Before prediction analysis, pre-selection of microRNAs and mRNAs was performed by using a leave-one-out t-test. No microRNAs could be identified that accurately predicted genotoxicity or non-genotoxic carcinogenicity in vivo. However, mRNAs could be detected which appeared reliable in predicting genotoxicity in vivo after 24h (7 genes) and 48h (2 genes) of exposure (accuracy: 90% and 93%, sensitivity: 65% and 75%, specificity: 100% and 100%). Tributylinoxide and para-Cresidine were misclassified. Also, mRNAs were identified capable of classifying NGTX-C after 24h (5 genes) as well as after 48h (3 genes) of treatment (accuracy: 78% and 88%, sensitivity: 83% and 83%, specificity: 75% and 93%). Wy-14,643, phenobarbital and ampicillin trihydrate were misclassified. We conclude that genotoxicity and non-genotoxic carcinogenicity probably cannot be accurately predicted based on microRNA profiles. Overall, transcript-based prediction analyses appeared to clearly outperform microRNA-based analyses.
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Affiliation(s)
- Linda Rieswijk
- Department of Toxicogenomics, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 40, 6229ER Maastricht, Netherlands and Netherlands Toxicogenomics Centre (NTC), Universiteitssingel 40, 6229ER Maastricht, Netherlands
| | - Karen J J Brauers
- Department of Toxicogenomics, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 40, 6229ER Maastricht, Netherlands and
| | - Maarten L J Coonen
- Department of Toxicogenomics, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 40, 6229ER Maastricht, Netherlands and Netherlands Toxicogenomics Centre (NTC), Universiteitssingel 40, 6229ER Maastricht, Netherlands
| | - Danyel G J Jennen
- Department of Toxicogenomics, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 40, 6229ER Maastricht, Netherlands and Netherlands Toxicogenomics Centre (NTC), Universiteitssingel 40, 6229ER Maastricht, Netherlands
| | - Simone G J van Breda
- Department of Toxicogenomics, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 40, 6229ER Maastricht, Netherlands and
| | - Jos C S Kleinjans
- Department of Toxicogenomics, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 40, 6229ER Maastricht, Netherlands and Netherlands Toxicogenomics Centre (NTC), Universiteitssingel 40, 6229ER Maastricht, Netherlands
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Luijten M, Olthof ED, Hakkert BC, Rorije E, van der Laan JW, Woutersen RA, van Benthem J. An integrative test strategy for cancer hazard identification. Crit Rev Toxicol 2016; 46:615-39. [PMID: 27142259 DOI: 10.3109/10408444.2016.1171294] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Assessment of genotoxic and carcinogenic potential is considered one of the basic requirements when evaluating possible human health risks associated with exposure to chemicals. Test strategies currently in place focus primarily on identifying genotoxic potential due to the strong association between the accumulation of genetic damage and cancer. Using genotoxicity assays to predict carcinogenic potential has the significant drawback that risks from non-genotoxic carcinogens remain largely undetected unless carcinogenicity studies are performed. Furthermore, test systems already developed to reduce animal use are not easily accepted and implemented by either industries or regulators. This manuscript reviews the test methods for cancer hazard identification that have been adopted by the regulatory authorities, and discusses the most promising alternative methods that have been developed to date. Based on these findings, a generally applicable tiered test strategy is proposed that can be considered capable of detecting both genotoxic as well as non-genotoxic carcinogens and will improve understanding of the underlying mode of action. Finally, strengths and weaknesses of this new integrative test strategy for cancer hazard identification are presented.
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Affiliation(s)
- Mirjam Luijten
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , the Netherlands
| | - Evelyn D Olthof
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , the Netherlands
| | - Betty C Hakkert
- b Centre for Safety of Substances and Products, National Institute for Public Health and the Environment (RIVM) , Bilthoven , the Netherlands
| | - Emiel Rorije
- b Centre for Safety of Substances and Products, National Institute for Public Health and the Environment (RIVM) , Bilthoven , the Netherlands
| | | | - Ruud A Woutersen
- d Netherlands Organization for Applied Scientific Research (TNO) , Zeist , the Netherlands
| | - Jan van Benthem
- a Centre for Health Protection, National Institute for Public Health and the Environment (RIVM) , Bilthoven , the Netherlands
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17
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Qin C, Tanis KQ, Podtelezhnikov AA, Glaab WE, Sistare FD, DeGeorge JJ. Toxicogenomics in drug development: a match made in heaven? Expert Opin Drug Metab Toxicol 2016; 12:847-9. [PMID: 27050123 DOI: 10.1080/17425255.2016.1175437] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Chunhua Qin
- Safety Assessment and Laboratory Animal Resources, Merck & Co., West Point, PA, USA
| | - Keith Q. Tanis
- Genetics and Pharmacogenomics, Merck & Co., West Point, PA, USA
| | | | - Warren E. Glaab
- Safety Assessment and Laboratory Animal Resources, Merck & Co., West Point, PA, USA
| | - Frank D. Sistare
- Safety Assessment and Laboratory Animal Resources, Merck & Co., West Point, PA, USA
| | - Joseph J. DeGeorge
- Safety Assessment and Laboratory Animal Resources, Merck & Co., West Point, PA, USA
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18
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Saito F, Matsumoto H, Akahori Y, Takeyoshi M. Simpler alternative to CARCINOscreen ® based on quantitative PCR (qPCR). J Toxicol Sci 2016; 41:383-90. [DOI: 10.2131/jts.41.383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Fumiyo Saito
- Chemicals Assessment and Research Center, Chemicals Evaluation and Research Institute, Japan (CERI)
| | - Hiroshi Matsumoto
- Chemicals Assessment and Research Center, Chemicals Evaluation and Research Institute, Japan (CERI)
| | - Yumi Akahori
- Chemicals Assessment and Research Center, Chemicals Evaluation and Research Institute, Japan (CERI)
| | - Masahiro Takeyoshi
- Chemicals Assessment and Research Center, Chemicals Evaluation and Research Institute, Japan (CERI)
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19
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Deferme L, Wolters J, Claessen S, Briedé J, Kleinjans J. Oxidative Stress Mechanisms Do Not Discriminate between Genotoxic and Nongenotoxic Liver Carcinogens. Chem Res Toxicol 2015. [DOI: 10.1021/acs.chemrestox.5b00222] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Lize Deferme
- Department of Toxicogenomics,
School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Jarno Wolters
- Department of Toxicogenomics,
School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Sandra Claessen
- Department of Toxicogenomics,
School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Jacco Briedé
- Department of Toxicogenomics,
School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics,
School of Oncology and Developmental Biology (GROW), Maastricht University, 6200 MD Maastricht, The Netherlands
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Becker RA, Patlewicz G, Simon TW, Rowlands JC, Budinsky RA. The adverse outcome pathway for rodent liver tumor promotion by sustained activation of the aryl hydrocarbon receptor. Regul Toxicol Pharmacol 2015; 73:172-90. [PMID: 26145830 DOI: 10.1016/j.yrtph.2015.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 12/29/2022]
Abstract
An Adverse Outcome Pathway (AOP) represents the existing knowledge of a biological pathway leading from initial molecular interactions of a toxicant and progressing through a series of key events (KEs), culminating with an apical adverse outcome (AO) that has to be of regulatory relevance. An AOP based on the mode of action (MOA) of rodent liver tumor promotion by dioxin-like compounds (DLCs) has been developed and the weight of evidence (WoE) of key event relationships (KERs) evaluated using evolved Bradford Hill considerations. Dioxins and DLCs are potent aryl hydrocarbon receptor (AHR) ligands that cause a range of species-specific adverse outcomes. The occurrence of KEs is necessary for inducing downstream biological responses and KEs may occur at the molecular, cellular, tissue and organ levels. The common convention is that an AOP begins with the toxicant interaction with a biological response element; for this AOP, this initial event is binding of a DLC ligand to the AHR. Data from mechanistic studies, lifetime bioassays and approximately thirty initiation-promotion studies have established dioxin and DLCs as rat liver tumor promoters. Such studies clearly show that sustained AHR activation, weeks or months in duration, is necessary to induce rodent liver tumor promotion--hence, sustained AHR activation is deemed the molecular initiating event (MIE). After this MIE, subsequent KEs are 1) changes in cellular growth homeostasis likely associated with expression changes in a number of genes and observed as development of hepatic foci and decreases in apoptosis within foci; 2) extensive liver toxicity observed as the constellation of effects called toxic hepatopathy; 3) cellular proliferation and hyperplasia in several hepatic cell types. This progression of KEs culminates in the AO, the development of hepatocellular adenomas and carcinomas and cholangiolar carcinomas. A rich data set provides both qualitative and quantitative knowledge of the progression of this AOP through KEs and the KERs. Thus, the WoE for this AOP is judged to be strong. Species-specific effects of dioxins and DLCs are well known--humans are less responsive than rodents and rodent species differ in sensitivity between strains. Consequently, application of this AOP to evaluate potential human health risks must take these differences into account.
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Affiliation(s)
- Richard A Becker
- Regulatory and Technical Affairs Department, American Chemistry Council (ACC), Washington, DC 20002, USA.
| | - Grace Patlewicz
- DuPont Haskell Global Centers for Health and Environmental Sciences, Newark, DE 19711, USA
| | - Ted W Simon
- Ted Simon LLC, 4184 Johnston Road, Winston, GA 30187, USA
| | - J Craig Rowlands
- The Dow Chemical Company, Toxicology & Environmental Research & Consulting, 1803 Building Washington Street, Midland, MI 48674, USA
| | - Robert A Budinsky
- The Dow Chemical Company, Toxicology & Environmental Research & Consulting, 1803 Building Washington Street, Midland, MI 48674, USA
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21
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Sandhu KS, Veeramachaneni V, Yao X, Nie A, Lord P, Amaratunga D, McMillian MK, Verheyen GR. Release of (and lessons learned from mining) a pioneering large toxicogenomics database. Pharmacogenomics 2015; 16:779-801. [PMID: 26067483 DOI: 10.2217/pgs.15.38] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM We release the Janssen Toxicogenomics database. This rat liver gene-expression database was generated using Codelink microarrays, and has been used over the past years within Janssen to derive signatures for multiple end points and to classify proprietary compounds. MATERIALS & METHODS The release consists of gene-expression responses to 124 compounds, selected to give a broad coverage of liver-active compounds. A selection of the compounds were also analyzed on Affymetrix microarrays. RESULTS The release includes results of an in-house reannotation pipeline to Entrez gene annotations, to classify probes into different confidence classes. High confidence unambiguously annotated probes were used to create gene-level data which served as starting point for cross-platform comparisons. Connectivity map-based similarity methods show excellent agreement between Codelink and Affymetrix runs of the same samples. We also compared our dataset with the Japanese Toxicogenomics Project and observed reasonable agreement, especially for compounds with stronger gene signatures. We describe an R-package containing the gene-level data and show how it can be used for expression-based similarity searches. CONCLUSION Comparing the same biological samples run on the Affymetrix and the Codelink platform, good correspondence is observed using connectivity mapping approaches. As expected, this correspondence is smaller when the data are compared with an independent dataset such as TG-GATE. We hope that this collection of gene-expression profiles will be incorporated in toxicogenomics pipelines of users.
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Affiliation(s)
| | | | - Xiang Yao
- Data Sciences, R&D IT, Janssen Pharmaceutical Research & Development, LLC, 3120 Merryfield Row, San Diego, CA 92121, USA
| | - Alex Nie
- Special Counsel, Patent Atterney, Sheppard, Mullin, Richter & Hampton LLP, 379 Lytton Ave, Palo Alto, CA 94301, USA
| | - Peter Lord
- Discotox Ltd, Hebden Bridge, West Yorkshire, UK
| | | | | | - Geert R Verheyen
- Radius Group, Thomas More University College, Kleinhoefstraat 4, 2440 Geel, Belgium
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22
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Rieswijk L, Brauers KJJ, Coonen MLJ, van Breda SGJ, Jennen DGJ, Kleinjans JCS. Evaluating microRNA profiles reveals discriminative responses following genotoxic or non-genotoxic carcinogen exposure in primary mouse hepatocytes. Mutagenesis 2015; 30:771-84. [DOI: 10.1093/mutage/gev036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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23
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Bourdon-Lacombe JA, Moffat ID, Deveau M, Husain M, Auerbach S, Krewski D, Thomas RS, Bushel PR, Williams A, Yauk CL. Technical guide for applications of gene expression profiling in human health risk assessment of environmental chemicals. Regul Toxicol Pharmacol 2015; 72:292-309. [PMID: 25944780 DOI: 10.1016/j.yrtph.2015.04.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 01/14/2023]
Abstract
Toxicogenomics promises to be an important part of future human health risk assessment of environmental chemicals. The application of gene expression profiles (e.g., for hazard identification, chemical prioritization, chemical grouping, mode of action discovery, and quantitative analysis of response) is growing in the literature, but their use in formal risk assessment by regulatory agencies is relatively infrequent. Although additional validations for specific applications are required, gene expression data can be of immediate use for increasing confidence in chemical evaluations. We believe that a primary reason for the current lack of integration is the limited practical guidance available for risk assessment specialists with limited experience in genomics. The present manuscript provides basic information on gene expression profiling, along with guidance on evaluating the quality of genomic experiments and data, and interpretation of results presented in the form of heat maps, pathway analyses and other common approaches. Moreover, potential ways to integrate information from gene expression experiments into current risk assessment are presented using published studies as examples. The primary objective of this work is to facilitate integration of gene expression data into human health risk assessments of environmental chemicals.
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Affiliation(s)
| | - Ivy D Moffat
- Water and Air Quality Bureau, Health Canada, Ottawa, ON, Canada.
| | - Michelle Deveau
- Water and Air Quality Bureau, Health Canada, Ottawa, ON, Canada
| | - Mainul Husain
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Scott Auerbach
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - Daniel Krewski
- McLaughlin Centre for Population Health Risk Assessment, University of Ottawa, Ottawa, ON, Canada
| | - Russell S Thomas
- National Centre for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Pierre R Bushel
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
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Biales AD, Fritsch EB, Connon RE. In response: integration of 'omics to larger-scale watershed assessments: a mixed government/academic perspective. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2015; 34:700-702. [PMID: 25809101 DOI: 10.1002/etc.2841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Adam D Biales
- National Exposure Research Laboratory US Environmental Protection Agency Cincinnati, Ohio, USA
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25
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Groh KJ, Carvalho RN, Chipman JK, Denslow ND, Halder M, Murphy CA, Roelofs D, Rolaki A, Schirmer K, Watanabe KH. Development and application of the adverse outcome pathway framework for understanding and predicting chronic toxicity: I. Challenges and research needs in ecotoxicology. CHEMOSPHERE 2015; 120:764-77. [PMID: 25439131 DOI: 10.1016/j.chemosphere.2014.09.068] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/11/2014] [Accepted: 09/19/2014] [Indexed: 05/02/2023]
Abstract
To elucidate the effects of chemicals on populations of different species in the environment, efficient testing and modeling approaches are needed that consider multiple stressors and allow reliable extrapolation of responses across species. An adverse outcome pathway (AOP) is a concept that provides a framework for organizing knowledge about the progression of toxicity events across scales of biological organization that lead to adverse outcomes relevant for risk assessment. In this paper, we focus on exploring how the AOP concept can be used to guide research aimed at improving both our understanding of chronic toxicity, including delayed toxicity as well as epigenetic and transgenerational effects of chemicals, and our ability to predict adverse outcomes. A better understanding of the influence of subtle toxicity on individual and population fitness would support a broader integration of sublethal endpoints into risk assessment frameworks. Detailed mechanistic knowledge would facilitate the development of alternative testing methods as well as help prioritize higher tier toxicity testing. We argue that targeted development of AOPs supports both of these aspects by promoting the elucidation of molecular mechanisms and their contribution to relevant toxicity outcomes across biological scales. We further discuss information requirements and challenges in application of AOPs for chemical- and site-specific risk assessment and for extrapolation across species. We provide recommendations for potential extension of the AOP framework to incorporate information on exposure, toxicokinetics and situation-specific ecological contexts, and discuss common interfaces that can be employed to couple AOPs with computational modeling approaches and with evolutionary life history theory. The extended AOP framework can serve as a venue for integration of knowledge derived from various sources, including empirical data as well as molecular, quantitative and evolutionary-based models describing species responses to toxicants. This will allow a more efficient application of AOP knowledge for quantitative chemical- and site-specific risk assessment as well as for extrapolation across species in the future.
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Affiliation(s)
- Ksenia J Groh
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Department of Chemistry and Applied Biosciences, 8093 Zürich, Switzerland.
| | - Raquel N Carvalho
- European Commission, Joint Research Centre, Institute for Environment and Sustainability, Water Resources Unit, 21027 Ispra, Italy
| | | | - Nancy D Denslow
- University of Florida, Department of Physiological Sciences, Center for Environmental and Human Toxicology and Genetics Institute, 32611 Gainesville, FL, USA
| | - Marlies Halder
- European Commission, Joint Research Centre, Institute for Health and Consumer Protection, Systems Toxicology Unit, 21027 Ispra, Italy
| | - Cheryl A Murphy
- Michigan State University, Fisheries and Wildlife, Lyman Briggs College, 48824 East Lansing, MI, USA
| | - Dick Roelofs
- VU University, Institute of Ecological Science, 1081 HV Amsterdam, The Netherlands
| | - Alexandra Rolaki
- European Commission, Joint Research Centre, Institute for Health and Consumer Protection, Systems Toxicology Unit, 21027 Ispra, Italy
| | - Kristin Schirmer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Department of Environmental Systems Science, 8092 Zürich, Switzerland; EPF Lausanne, School of Architecture, Civil and Environmental Engineering, 1015 Lausanne, Switzerland
| | - Karen H Watanabe
- Oregon Health & Science University, Institute of Environmental Health, Division of Environmental and Biomolecular Systems, 97239-3098 Portland, OR, USA
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Liang RY, Tu HF, Tan X, Yeh YS, Chueh PJ, Chuang SM. A gene signature for gold nanoparticle-exposed human cell lines. Toxicol Res (Camb) 2015. [DOI: 10.1039/c4tx00181h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A unique four-gene signature for AuNP exposure was identified using the cDNA microarray and evaluated by qPCR and biological assays in mammalian cell lines.
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Affiliation(s)
- Ruei-Yue Liang
- Institute of Biomedical Sciences
- National Chung Hsing University
- Taichung
- Taiwan
| | - Hsin-Fang Tu
- Bachelor Program of Biotechnology
- National Chung Hsing University
- Taichung
- Taiwan
| | - Xiaotong Tan
- Institute of Biomedical Sciences
- National Chung Hsing University
- Taichung
- Taiwan
| | - Yu-Shan Yeh
- Center for Measurement Standards (CMS)
- Industrial Technology Research Institute (ITRI)
- Hsinchu
- Taiwan
| | - Pin Ju Chueh
- Institute of Biomedical Sciences
- National Chung Hsing University
- Taichung
- Taiwan
| | - Show-Mei Chuang
- Institute of Biomedical Sciences
- National Chung Hsing University
- Taichung
- Taiwan
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27
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A novel toxicogenomics-based approach to categorize (non-)genotoxic carcinogens. Arch Toxicol 2014; 89:2413-27. [DOI: 10.1007/s00204-014-1368-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/04/2014] [Indexed: 10/24/2022]
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28
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Cox LA(T, Popken D, Marty MS, Rowlands JC, Patlewicz G, Goyak KO, Becker RA. Developing scientific confidence in HTS-derived prediction models: Lessons learned from an endocrine case study. Regul Toxicol Pharmacol 2014; 69:443-50. [DOI: 10.1016/j.yrtph.2014.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 04/28/2014] [Accepted: 05/07/2014] [Indexed: 11/16/2022]
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Gusenleitner D, Auerbach SS, Melia T, Gómez HF, Sherr DH, Monti S. Genomic models of short-term exposure accurately predict long-term chemical carcinogenicity and identify putative mechanisms of action. PLoS One 2014; 9:e102579. [PMID: 25058030 PMCID: PMC4109923 DOI: 10.1371/journal.pone.0102579] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 06/20/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Despite an overall decrease in incidence of and mortality from cancer, about 40% of Americans will be diagnosed with the disease in their lifetime, and around 20% will die of it. Current approaches to test carcinogenic chemicals adopt the 2-year rodent bioassay, which is costly and time-consuming. As a result, fewer than 2% of the chemicals on the market have actually been tested. However, evidence accumulated to date suggests that gene expression profiles from model organisms exposed to chemical compounds reflect underlying mechanisms of action, and that these toxicogenomic models could be used in the prediction of chemical carcinogenicity. RESULTS In this study, we used a rat-based microarray dataset from the NTP DrugMatrix Database to test the ability of toxicogenomics to model carcinogenicity. We analyzed 1,221 gene-expression profiles obtained from rats treated with 127 well-characterized compounds, including genotoxic and non-genotoxic carcinogens. We built a classifier that predicts a chemical's carcinogenic potential with an AUC of 0.78, and validated it on an independent dataset from the Japanese Toxicogenomics Project consisting of 2,065 profiles from 72 compounds. Finally, we identified differentially expressed genes associated with chemical carcinogenesis, and developed novel data-driven approaches for the molecular characterization of the response to chemical stressors. CONCLUSION Here, we validate a toxicogenomic approach to predict carcinogenicity and provide strong evidence that, with a larger set of compounds, we should be able to improve the sensitivity and specificity of the predictions. We found that the prediction of carcinogenicity is tissue-dependent and that the results also confirm and expand upon previous studies implicating DNA damage, the peroxisome proliferator-activated receptor, the aryl hydrocarbon receptor, and regenerative pathology in the response to carcinogen exposure.
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Affiliation(s)
- Daniel Gusenleitner
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Computational Biomedicine, Boston University Medical Campus, Boston, Massachusetts, United States of America
| | - Scott S. Auerbach
- Biomolecular Screening Branch, Division of the National Toxicology Program at the National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, North Carolina, United States of America
| | - Tisha Melia
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Harold F. Gómez
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - David H. Sherr
- Department of Environmental Health, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Stefano Monti
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- Department of Computational Biomedicine, Boston University Medical Campus, Boston, Massachusetts, United States of America
- * E-mail:
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30
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Gooderham N, Koufaris C. Using microRNA profiles to predict and evaluate hepatic carcinogenic potential. Toxicol Lett 2014; 228:127-32. [DOI: 10.1016/j.toxlet.2014.04.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/17/2014] [Accepted: 04/20/2014] [Indexed: 01/17/2023]
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Melis JPM, Derks KWJ, Pronk TE, Wackers P, Schaap MM, Zwart E, van Ijcken WFJ, Jonker MJ, Breit TM, Pothof J, van Steeg H, Luijten M. In vivo murine hepatic microRNA and mRNA expression signatures predicting the (non-)genotoxic carcinogenic potential of chemicals. Arch Toxicol 2014; 88:1023-34. [PMID: 24390151 DOI: 10.1007/s00204-013-1189-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/18/2013] [Indexed: 01/06/2023]
Abstract
There is a high need to improve the assessment of, especially non-genotoxic, carcinogenic features of chemicals. We therefore explored a toxicogenomics-based approach using genome-wide microRNA and mRNA expression profiles upon short-term exposure in mice. For this, wild-type mice were exposed for seven days to three different classes of chemicals, i.e., four genotoxic carcinogens (GTXC), seven non-genotoxic carcinogens (NGTXC), and five toxic non-carcinogens. Hepatic expression patterns of mRNA and microRNA transcripts were determined after exposure and used to assess the discriminative power of the in vivo transcriptome for GTXC and NGTXC. A final classifier set, discriminative for GTXC and NGTXC, was generated from the transcriptomic data using a tiered approach. This appeared to be a valid approach, since the predictive power of the final classifier set in three different classifier algorithms was very high for the original training set of chemicals. Subsequent validation in an additional set of chemicals revealed that the predictive power for GTXC remained high, in contrast to NGTXC, which appeared to be more troublesome. Our study demonstrated that the in vivo microRNA-ome has less discriminative power to correctly identify (non-)genotoxic carcinogen classes. The results generally indicate that single mRNA transcripts do have the potential to be applied in risk assessment, but that additional (genomic) strategies are necessary to correctly predict the non-genotoxic carcinogenic potential of a chemical.
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Affiliation(s)
- Joost P M Melis
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
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Schmeits PCJ, Katika MR, Peijnenburg AACM, van Loveren H, Hendriksen PJM. DON shares a similar mode of action as the ribotoxic stress inducer anisomycin while TBTO shares ER stress patterns with the ER stress inducer thapsigargin based on comparative gene expression profiling in Jurkat T cells. Toxicol Lett 2013; 224:395-406. [PMID: 24247028 DOI: 10.1016/j.toxlet.2013.11.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 11/06/2013] [Accepted: 11/06/2013] [Indexed: 11/17/2022]
Abstract
Previously, we studied the effects of deoxynivalenol (DON) and tributyltin oxide (TBTO) on whole genome mRNA expression profiles of human T lymphocyte Jurkat cells. These studies indicated that DON induces ribotoxic stress and both DON and TBTO induced ER stress which resulted into T-cell activation and apoptosis. The first goal of the present study was to provide final proof for these mode of actions by comparing the effects of 6 h exposure to DON and TBTO on mRNA expression to those of positive controls of ribotoxic stress (anisomycin), ER stress (thapsigargin) and T cell activation (ionomycin). Genes affected by anisomycin and the majority of genes affected by thapsigargin were affected in the same direction by DON and TBTO, respectively, confirming the expected modes of action. Pathway analysis further sustained that DON induces ribotoxic stress and both DON and TBTO induce unfolded protein response (UPR), ER stress, T cell activation and apoptosis. The second goal was to assess whether DON and/or TBTO affect other pathways above those detected before. TBTO induced groups of genes that are involved in DNA packaging and heat shock response that were not affected by thapsigargin. DON did not affect other genes than anisomycin indicating the effect of DON to be restricted to ribotoxic stress. This study also demonstrates that comparative gene expression analysis is a very promising tool for the identification of modes of action of immunotoxic compounds.
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Affiliation(s)
- Peter C J Schmeits
- RIKILT-Institute of Food Safety, Wageningen University and Research Centre, P.O. Box 230, 6700 AE Wageningen, The Netherlands; Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
| | - Madhumohan R Katika
- RIKILT-Institute of Food Safety, Wageningen University and Research Centre, P.O. Box 230, 6700 AE Wageningen, The Netherlands; Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
| | - Ad A C M Peijnenburg
- RIKILT-Institute of Food Safety, Wageningen University and Research Centre, P.O. Box 230, 6700 AE Wageningen, The Netherlands.
| | - Henk van Loveren
- Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD Maastricht, The Netherlands; National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
| | - Peter J M Hendriksen
- RIKILT-Institute of Food Safety, Wageningen University and Research Centre, P.O. Box 230, 6700 AE Wageningen, The Netherlands.
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Bhat VS, Hester SD, Nesnow S, Eastmond DA. Concordance of Transcriptional and Apical Benchmark Dose Levels for Conazole-Induced Liver Effects in Mice. Toxicol Sci 2013; 136:205-15. [DOI: 10.1093/toxsci/kft182] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Dunnick JK, Nyska A. The toxicity and pathology of selected dietary herbal medicines. Toxicol Pathol 2012; 41:374-86. [PMID: 23262639 DOI: 10.1177/0192623312466451] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Toxicity studies were conducted by the National Toxicology Program (NTP) to provide information on the potential for toxicity from long-term use of commonly used herbal medicines. Here, we review the findings from these NTP toxicology/carcinogenesis 2-year rodent studies of 7 commonly used herbs. In these studies, the individual herb or herbal product was administered to F344/N rats and B6C3F1 mice by oral administration for up to 2 years. The spectrum of carcinogenic responses ranged from no or equivocal evidence for carcinogenic activity (ginseng, milk thistle, and turmeric oleoresin) to a liver tumor response (ginkgo, goldenseal, kava), thyroid tumor response (ginkgo), or an intestinal tumor response (Aloe vera whole leaf nondecolorized extract). Different mechanisms may be involved in the occurrence of liver (ginkgo, goldenseal, and kava kava) and gastrointestinal toxicity (turmeric oleoresin and Aloe vera whole leaf nondecolorized extract), while the toxic lesion is the same. The results from these hazard identification toxicity/carcinogenesis studies along with those from ongoing National Institute of Health clinical trials of herbal medicines provide more complete information on the risks and benefits from herbal medicine use in the general population.
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Affiliation(s)
- June K Dunnick
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA.
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Godoy P, Bolt HM. Toxicogenomic-based approaches predicting liver toxicity in vitro. Arch Toxicol 2012; 86:1163-4. [PMID: 22707156 DOI: 10.1007/s00204-012-0892-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Gene expression profiling to identify potentially relevant disease outcomes and support human health risk assessment for carbon black nanoparticle exposure. Toxicology 2012; 303:83-93. [PMID: 23146762 PMCID: PMC7125805 DOI: 10.1016/j.tox.2012.10.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 10/11/2012] [Accepted: 10/16/2012] [Indexed: 11/21/2022]
Abstract
New approaches are urgently needed to evaluate potential hazards posed by exposure to nanomaterials. Gene expression profiling provides information on potential modes of action and human relevance, and tools have recently become available for pathway-based quantitative risk assessment. The objective of this study was to use toxicogenomics in the context of human health risk assessment. We explore the utility of toxicogenomics in risk assessment, using published gene expression data from C57BL/6 mice exposed to 18, 54 and 162 μg Printex 90 carbon black nanoparticles (CBNP). Analysis of CBNP-perturbed pathways, networks and transcription factors revealed concomitant changes in predicted phenotypes (e.g., pulmonary inflammation and genotoxicity), that correlated with dose and time. Benchmark doses (BMDs) for apical endpoints were comparable to minimum BMDs for relevant pathway-specific expression changes. Comparison to inflammatory lung disease models (i.e., allergic airway inflammation, bacterial infection and tissue injury and fibrosis) and human disease profiles revealed that induced gene expression changes in Printex 90 exposed mice were similar to those typical for pulmonary injury and fibrosis. Very similar fibrotic pathways were perturbed in CBNP-exposed mice and human fibrosis disease models. Our synthesis demonstrates how toxicogenomic profiles may be used in human health risk assessment of nanoparticles and constitutes an important step forward in the ultimate recognition of toxicogenomic endpoints in human health risk. As our knowledge of molecular pathways, dose-response characteristics and relevance to human disease continues to grow, we anticipate that toxicogenomics will become increasingly useful in assessing chemical toxicities and in human health risk assessment.
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Tralau T, Riebeling C, Pirow R, Oelgeschläger M, Seiler A, Liebsch M, Luch A. Wind of change challenges toxicological regulators. ENVIRONMENTAL HEALTH PERSPECTIVES 2012; 120:1489-94. [PMID: 22871563 PMCID: PMC3556610 DOI: 10.1289/ehp.1104782] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 08/07/2012] [Indexed: 05/09/2023]
Abstract
BACKGROUND In biomedical research, the past two decades have seen the advent of in vitro model systems based on stem cells, humanized cell lines, and engineered organotypic tissues, as well as numerous cellular assays based on primarily established tumor-derived cell lines and their genetically modified derivatives. OBJECTIVE There are high hopes that these systems might replace the need for animal testing in regulatory toxicology. However, despite increasing pressure in recent years to reduce animal testing, regulators are still reluctant to adopt in vitro approaches on a large scale. It thus seems appropriate to consider how we could realistically perform regulatory toxicity testing using in vitro assays only. DISCUSSION AND CONCLUSION Here, we suggest an in vitro-only approach for regulatory testing that will benefit consumers, industry, and regulators alike.
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Affiliation(s)
- Tewes Tralau
- German Federal Institute for Risk Assessment (BfR), Center for Alternative Methods to Animal Experiments (ZEBET), Berlin, Germany
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Abstract
The ICH initiated talks in June 2012 to revise regulatory guidance for carcinogenicity assessment of pharmaceutical products, stimulated in part by a proposal called Negative for Endocrine, Genotoxicity, and Chronic Study Associated Histopathologic Risk Factors for Carcinogenicity in the Rat (NEGCARC) from the Pharmaceutical Research and Manufacturing Association (PhRMA). The 2012 STP Town Hall Meeting focused on the need for change in carcinogenicity assessment strategies for pharmaceuticals. Dr. Todd Bourcier from the Division of Endocrine and Metabolic Products, U.S. FDA and a member of the FDA’s Alternative Carcinogenicity Assessment Committee, was the guest speaker and a panelist. Dr. Bourcier is also one of FDA’s representatives to the ICH S1 Expert Working Group that is discussing changes to regulatory guidelines for carcinogenicity assessment. Drs. Carl Alden and Dan Morton also participated in the panel discussion.
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Affiliation(s)
| | - Todd Bourcier
- Division of Metabolic and Endocrine Products, CDER, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Carl L. Alden
- Millennium Pharmaceuticals, Inc., Cambridge, Massachusetts, USA
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Dissecting modes of action of non-genotoxic carcinogens in primary mouse hepatocytes. Arch Toxicol 2012; 86:1717-27. [PMID: 22710402 DOI: 10.1007/s00204-012-0883-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 05/29/2012] [Indexed: 10/28/2022]
Abstract
Under REACH, the European Community Regulation on chemicals, the testing strategy for carcinogenicity is based on in vitro and in vivo genotoxicity assays. Given that non-genotoxic carcinogens are negative for genotoxicity and chronic bioassays are no longer regularly performed, this class of carcinogens will go undetected. Therefore, test systems detecting non-genotoxic carcinogens, or even better their modes of action, are required. Here, we investigated whether gene expression profiling in primary hepatocytes can be used to distinguish different modes of action of non-genotoxic carcinogens. For this, primary mouse hepatocytes were exposed to 16 non-genotoxic carcinogens with diverse modes of action. Upon profiling, pathway analysis was performed to obtain insight into the biological relevance of the observed changes in gene expression. Subsequently, both a supervised and an unsupervised comparison approach were applied to recognize the modes of action at the transcriptomic level. These analyses resulted in the detection of three of eight compound classes, that is, peroxisome proliferators, metalloids and skin tumor promotors. In conclusion, gene expression profiles in primary hepatocytes, at least in rodent hepatocytes, appear to be useful to detect some, certainly not all, modes of action of non-genotoxic carcinogens.
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Merrick BA, Auerbach SS, Stockton PS, Foley JF, Malarkey DE, Sills RC, Irwin RD, Tice RR. Testing an aflatoxin B1 gene signature in rat archival tissues. Chem Res Toxicol 2012; 25:1132-44. [PMID: 22545673 DOI: 10.1021/tx3000945] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Archival tissues from laboratory studies represent a unique opportunity to explore the relationship between genomic changes and agent-induced disease. In this study, we evaluated the applicability of qPCR for detecting genomic changes in formalin-fixed, paraffin-embedded (FFPE) tissues by determining if a subset of 14 genes from a 90-gene signature derived from microarray data and associated with eventual tumor development could be detected in archival liver, kidney, and lung of rats exposed to aflatoxin B1 (AFB1) for 90 days in feed at 1 ppm. These tissues originated from the same rats used in the microarray study. The 14 genes evaluated were Adam8, Cdh13, Ddit4l, Mybl2, Akr7a3, Akr7a2, Fhit, Wwox, Abcb1b, Abcc3, Cxcl1, Gsta5, Grin2c, and the C8orf46 homologue. The qPCR FFPE liver results were compared to the original liver microarray data and to qPCR results using RNA from fresh frozen liver. Archival liver paraffin blocks yielded 30 to 50 μg of degraded RNA that ranged in size from 0.1 to 4 kB. qPCR results from FFPE and fresh frozen liver samples were positively correlated (p ≤ 0.05) by regression analysis and showed good agreement in direction and proportion of change with microarray data for 11 of 14 genes. All 14 transcripts could be amplified from FFPE kidney RNA except the glutamate receptor gene Grin2c; however, only Abcb1b was significantly upregulated from control. Abundant constitutive transcripts, S18 and β-actin, could be amplified from lung FFPE samples, but the narrow RNA size range (25-500 bp length) prevented consistent detection of target transcripts. Overall, a discrete gene signature derived from prior transcript profiling and representing cell cycle progression, DNA damage response, and xenosensor and detoxication pathways was successfully applied to archival liver and kidney by qPCR and indicated that gene expression changes in response to subchronic AFB1 exposure occurred predominantly in the liver, the primary target for AFB1-induced tumors. We conclude that an evaluation of gene signatures in archival tissues can be an important toxicological tool for evaluating critical molecular events associated with chemical exposures.
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Affiliation(s)
- B Alex Merrick
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences , Research Triangle Park, NC 27709, United States.
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Rusyn I, Sedykh A, Low Y, Guyton KZ, Tropsha A. Predictive modeling of chemical hazard by integrating numerical descriptors of chemical structures and short-term toxicity assay data. Toxicol Sci 2012; 127:1-9. [PMID: 22387746 DOI: 10.1093/toxsci/kfs095] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Quantitative structure-activity relationship (QSAR) models are widely used for in silico prediction of in vivo toxicity of drug candidates or environmental chemicals, adding value to candidate selection in drug development or in a search for less hazardous and more sustainable alternatives for chemicals in commerce. The development of traditional QSAR models is enabled by numerical descriptors representing the inherent chemical properties that can be easily defined for any number of molecules; however, traditional QSAR models often have limited predictive power due to the lack of data and complexity of in vivo endpoints. Although it has been indeed difficult to obtain experimentally derived toxicity data on a large number of chemicals in the past, the results of quantitative in vitro screening of thousands of environmental chemicals in hundreds of experimental systems are now available and continue to accumulate. In addition, publicly accessible toxicogenomics data collected on hundreds of chemicals provide another dimension of molecular information that is potentially useful for predictive toxicity modeling. These new characteristics of molecular bioactivity arising from short-term biological assays, i.e., in vitro screening and/or in vivo toxicogenomics data can now be exploited in combination with chemical structural information to generate hybrid QSAR-like quantitative models to predict human toxicity and carcinogenicity. Using several case studies, we illustrate the benefits of a hybrid modeling approach, namely improvements in the accuracy of models, enhanced interpretation of the most predictive features, and expanded applicability domain for wider chemical space coverage.
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Affiliation(s)
- Ivan Rusyn
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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