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Đukić-Ćosić D. Toxicogenomics: opportunities and challenges of application in drug development, toxicity prediction and human health risk assessment. MAKEDONSKO FARMACEVTSKI BILTEN 2022. [DOI: 10.33320/maced.pharm.bull.2022.68.03.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Danijela Đukić-Ćosić
- University of Belgrade – Faculty of Pharmacy, Department of Toxicology “Akademik Danilo Soldatović“, Vojvode Stepe 450, 11000 Belgrade, Serbia
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Lin Z, Huang Y, Jiang H, Zhang D, Yang Y, Geng X, Li B. Functional differences and similarities in activated peripheral blood mononuclear cells by lipopolysaccharide or phytohemagglutinin stimulation between human and cynomolgus monkeys. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:257. [PMID: 33708884 PMCID: PMC7940909 DOI: 10.21037/atm-20-4548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background The monkey is a primary species used in toxicological research. However, the failures of preclinical studies to predict a life-threatening “cytokine storm”, which, for instance, rapidly occurred in six healthy volunteers with the CD28 superagonist monoclonal antibody (mAb) TGN1412 in the first-in-human phase I clinical trial, have emphasized a need to clarify the differences between human and monkey immune systems. Methods In the present study, we analyzed and compared the lymphocyte proliferation, cytokine secretion, and gene expression profiles after phytohemagglutinin (PHA) and lipopolysaccharide (LPS) stimulation of peripheral blood mononuclear cells (PBMCs) from three healthy humans and cynomolgus monkeys (Macaca fascicularis). Results The results derived from comparison with the corresponding control groups showed that PHA in humans induced a stronger proliferation and wider range of cytokine secretion, along with a greater number of differently expressed genes (DEGs), than when PHA was applied in cynomolgus monkeys. The significant upregulation of genes involved in the mitotic cell cycle, including cyclin B2, TOP2A, TYMS, and CEP55, was observed in human PBMCs with PHA stimulation, while only infrequent or slight upregulation occurred in cynomolgus monkey PBMCs, which may be one of the reasons for a stronger response to PHA in humans. In contrast to PHA, LPS in both species induced a similar proliferation ratio, cytokine profile, and DEG count, suggesting that human and cynomolgus monkeys have a similar response intensity for innate immune responses. Furthermore, 38 and 20 overlapped genes under PHA and LPS stimulation, respectively, were found in both species. These overlapped DEGs were associated with the same biological functions, including DNA replication, mitosis, immune response, chemotaxis, and inflammatory response. Thus, these results might reflect the highly conserved signatures of immune responses to PHA/LPS stimulation across the primates. Moreover, there were some differences in antigen processing and presentation, and the interferon gamma (INF-γ)–mediated signaling pathway in these species detected by gene expression profile study. Conclusions In conclusion, this is the first study to compare data on the responses of PBMCs to PHA and LPS in humans versus cynomolgus monkeys, and these findings may provide crucial insights into translating non-human primate (NHP) studies into human trials.
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Affiliation(s)
- Zhi Lin
- National Institute for Food and Drug Control, National Center for Safety Evaluation of Drugs, Beijing Key Lab for Preclinical Safety Evaluation of Drugs, Beijing, China
| | - Ying Huang
- National Institute for Food and Drug Control, National Center for Safety Evaluation of Drugs, Beijing Key Lab for Preclinical Safety Evaluation of Drugs, Beijing, China
| | - Hua Jiang
- National Institute for Food and Drug Control, National Center for Safety Evaluation of Drugs, Beijing Key Lab for Preclinical Safety Evaluation of Drugs, Beijing, China
| | - Di Zhang
- National Institute for Food and Drug Control, National Center for Safety Evaluation of Drugs, Beijing Key Lab for Preclinical Safety Evaluation of Drugs, Beijing, China
| | - Yanwei Yang
- National Institute for Food and Drug Control, National Center for Safety Evaluation of Drugs, Beijing Key Lab for Preclinical Safety Evaluation of Drugs, Beijing, China
| | - Xingchao Geng
- National Institute for Food and Drug Control, National Center for Safety Evaluation of Drugs, Beijing Key Lab for Preclinical Safety Evaluation of Drugs, Beijing, China
| | - Bo Li
- National Institute for Food and Drug Control, National Center for Safety Evaluation of Drugs, Beijing Key Lab for Preclinical Safety Evaluation of Drugs, Beijing, China
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Almeida TS, Arantes MR, Lopes Neto JJ, Souza TM, Pessoa IP, Medeiros JL, Tabosa PMS, Moreira TB, Farias DF, Carvalho AFU. Evaluation of seeds ethanolic extracts of Triplaris gardneriana Wedd. using in vitro and in vivo toxicological methods. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2020; 83:135-152. [PMID: 32114934 DOI: 10.1080/15287394.2020.1731035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Triplaris gardneriana Wedd. is a tree used in folk medicine to treat venereal diseases and inflammation as well as a source of biological compounds with antioxidant capacity. In order to assess the safety of these bioactive compounds, the present study aimed to determine the toxicity of an ethanolic extract of T. gardneriana, (EETg). Toxicological tests included hemolytic activity, toxicity toward the brine shrimp Artemia, cytotoxicity against breast cancer cells (MCF7) and acute oral toxicity in rodents. In addition, toxicogenomics techniques were used to determine genome expression in MCF7 cells exposed to EETg. The results showed that the extract exhibits approximately 60% of hemolytic activity at the highest tested concentration (64 µg/ml) and toxicity against nauplii of Artemia sp. (LC50 of 67.85 µg/ml). Further, EETg appears to be cytotoxic to MCF7 (cell viability reduced to 40% at 250 µg/ml after 24 hr). Genomic data demonstrated differential expression of 14 genes. Data analysis indicated possible altered pathways (e.g., xenobiotic metabolism), possible adverse health risks (e.g., hepatotoxicity), and drugs with similar gene expression profile (e.g., antimicrobials). The investigation provides important information on potentially adverse aspects of EETg, which need to be considered prior to the therapeutic utilization of this plant.Abbreviations: EETg: ethanolic extract of T. gardneriana seeds; MCF7: michigan cancer foundation-7 which refers to a human breast cell line (adenocarcinoma); NGS: next-generation sequencing; edgeR: empirical analysis of digital gene expression data in R; Consensus: consensus path database; FDR: false discovery rate; NCBI: national center for biotechnology information; KEGG: kyoto encyclopedia of genes and genomes; Ingenuity: ingenuity pathway analysis software; CMAP: connectivity map; OECD: organization for economic co-operation and development; HL-60: human promyelocytic leukemia cells; PC3: prostate cancer cells.
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Affiliation(s)
- Thiago S Almeida
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Mariana R Arantes
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - José J Lopes Neto
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Terezinha M Souza
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Igor P Pessoa
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Jackeline L Medeiros
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Pedro M S Tabosa
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Thais B Moreira
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Davi F Farias
- Department of Molecular Biology, Federal University of Paraíba, João Pessoa, Brazil
| | - Ana F U Carvalho
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
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Abstract
Next generation sequencing (NGS) represents several powerful platforms that have revolutionized RNA and DNA analysis. The parallel sequencing of millions of DNA molecules can provide mechanistic insights into toxicology and provide new avenues for biomarker discovery with growing relevance for risk assessment. The evolution of NGS technologies has improved over the last decade with increased sensitivity and accuracy to foster new biomarker assays from tissue, blood and other biofluids. NGS sequencing technologies can identify transcriptional changes and genomic targets with base pair precision in response to chemical exposure. Further, there are several exciting movements within the toxicology community that incorporate NGS platforms into new strategies for more rapid toxicological characterizations. These include the Tox21 in vitro high throughput transcriptomic screening program, development of organotypic spheroids, alternative animal models, mining archival tissues, liquid biopsy and epigenomics. This review will describe NGS-based technologies, demonstrate how they can be used as tools for target discovery in tissue and blood, and suggest how they might be applied for risk assessment.
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Affiliation(s)
- B Alex Merrick
- Molecular and Genomic Toxicology Group, Biomolecular Screening Branch, Division National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, Ph: 919-541-1531,
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5
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The use of evidence from high-throughput screening and transcriptomic data in human health risk assessments. Toxicol Appl Pharmacol 2019; 380:114706. [DOI: 10.1016/j.taap.2019.114706] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 12/23/2022]
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6
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Transcriptional study after Beauvericin and Enniatin B combined exposure in Jurkat T cells. Food Chem Toxicol 2019; 130:122-129. [DOI: 10.1016/j.fct.2019.05.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/09/2019] [Accepted: 05/11/2019] [Indexed: 12/12/2022]
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Chain FJJ, Finlayson S, Crease T, Cristescu M. Variation in transcriptional responses to copper exposure across Daphnia pulex lineages. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 210:85-97. [PMID: 30836324 DOI: 10.1016/j.aquatox.2019.02.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
Copper pollution is pervasive in aquatic habitats and is particularly harmful to invertebrates sensitive to environmental changes such as Daphnia pulex. Mechanisms of toxicity and tolerance to copper are not well understood. We used RNA-sequencing to investigate these mechanisms in three genetically distinct D. pulex clonal lineages with different histories of copper exposure. Upregulated genes after copper exposure were enriched with Gene Ontology (GO) categories involved in digestion, molting and growth, whereas downregulated genes after copper exposure were enriched in the metal-regulatory system, immune response and epigenetic modifications. The three D. pulex clones in our study show largely similar transcriptional patterns in response to copper, with only a total of twenty genes differentially expressed in a single clonal lineages. We also detected lower relative expression of some genes known to be important for copper tolerance, metallothionein and glutathione-S-transferase, in a sensitive lineage sampled from an uncontaminated habitat. Daphnia-specific genes (without orthologs outside the genus) and Daphnia-specific duplications (genes duplicated in the Daphnia lineage) were overrepresented in differentially expressed genes, highlighting an important role for newly emerged genes in tolerating environmental stressors. The results indicate that the D. pulex lineages tested in this study generally respond to copper stress using the same major pathways, but that the more resistant clone with previous copper exposure might be better able to regulate key genes. This finding highlights the important nuances in gene expression among clones, shaped by historical exposure and influencing copper tolerance.
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Affiliation(s)
- Frédéric J J Chain
- Department of Biology, McGill University, QC, H3A 1B1, Canada; Department of Biological Sciences, University of Massachusetts Lowell, MA, 01854, USA
| | - Sarah Finlayson
- Department of Biology, McGill University, QC, H3A 1B1, Canada
| | - Teresa Crease
- Department of Integrative Biology, University of Guelph, ON, N1G 2W1, Canada
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Van Vleet TR, Liguori MJ, Lynch JJ, Rao M, Warder S. Screening Strategies and Methods for Better Off-Target Liability Prediction and Identification of Small-Molecule Pharmaceuticals. SLAS DISCOVERY 2018; 24:1-24. [PMID: 30196745 DOI: 10.1177/2472555218799713] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pharmaceutical discovery and development is a long and expensive process that, unfortunately, still results in a low success rate, with drug safety continuing to be a major impedance. Improved safety screening strategies and methods are needed to more effectively fill this critical gap. Recent advances in informatics are now making it possible to manage bigger data sets and integrate multiple sources of screening data in a manner that can potentially improve the selection of higher-quality drug candidates. Integrated screening paradigms have become the norm in Pharma, both in discovery screening and in the identification of off-target toxicity mechanisms during later-stage development. Furthermore, advances in computational methods are making in silico screens more relevant and suggest that they may represent a feasible option for augmenting the current screening paradigm. This paper outlines several fundamental methods of the current drug screening processes across Pharma and emerging techniques/technologies that promise to improve molecule selection. In addition, the authors discuss integrated screening strategies and provide examples of advanced screening paradigms.
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Affiliation(s)
- Terry R Van Vleet
- 1 Department of Investigative Toxicology and Pathology, AbbVie, N Chicago, IL, USA
| | - Michael J Liguori
- 1 Department of Investigative Toxicology and Pathology, AbbVie, N Chicago, IL, USA
| | - James J Lynch
- 2 Department of Integrated Science and Technology, AbbVie, N Chicago, IL, USA
| | - Mohan Rao
- 1 Department of Investigative Toxicology and Pathology, AbbVie, N Chicago, IL, USA
| | - Scott Warder
- 3 Department of Target Enabling Science and Technology, AbbVie, N Chicago, IL, USA
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Vachon J, Pagé-Larivière F, Sirard MA, Rodriguez MJ, Levallois P, Campagna C. Availability, Quality, and Relevance of Toxicogenomics Data for Human Health Risk Assessment: A Scoping Review of the Literature on Trihalomethanes. Toxicol Sci 2018. [DOI: 10.1093/toxsci/kfy050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Julien Vachon
- Direction de la Santé Environnementale et de la Toxicologie, Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada G1V 5B3
| | - Florence Pagé-Larivière
- Département des Sciences Animales, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec, Québec, Canada G1V 0A6
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Québec, Québec, Canada G1V 0A6
| | - Marc-André Sirard
- Département des Sciences Animales, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec, Québec, Canada G1V 0A6
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Québec, Québec, Canada G1V 0A6
| | - Manuel J Rodriguez
- École Supérieure d’Aménagement du Territoire et de Développement Régional, Université Laval, Québec, Québec, Canada G1V 0A6
- Chaire de Recherche CRSNG en Eau Potable, Université Laval, Québec, Québec, Canada G1V 0A6
| | - Patrick Levallois
- Direction de la Santé Environnementale et de la Toxicologie, Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada G1V 5B3
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, Québec, Canada G1V 0A6
- Axe Santé des Populations et Pratiques Optimales en Santé, Centre de Recherche du Centre Hospitalier Universitaire de Québec (CRCHUQ), Québec, Québec, Canada G1S 4L8
| | - Céline Campagna
- Direction de la Santé Environnementale et de la Toxicologie, Institut National de Santé Publique du Québec (INSPQ), Québec, Québec, Canada G1V 5B3
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, Québec, Québec, Canada G1V 0A6
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Escrivá L, Jennen D, Caiment F, Manyes L. Transcriptomic study of the toxic mechanism triggered by beauvericin in Jurkat cells. Toxicol Lett 2017; 284:213-221. [PMID: 29203277 DOI: 10.1016/j.toxlet.2017.11.035] [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: 09/20/2017] [Revised: 11/10/2017] [Accepted: 11/27/2017] [Indexed: 01/28/2023]
Abstract
Beauvericin (BEA), an ionophoric cyclic hexadepsipeptide mycotoxin, is able to increase oxidative stress by altering membrane ion permeability and uncoupling oxidative phosphorylation. A toxicogenomic study was performed to investigate gene expression changes triggered by BEA exposure (1.5, 3 and 5 μM; 24 h) in Jurkat cells through RNA-sequencing and differential gene expression analysis. Perturbed gene expression was observed in a concentration dependent manner, with 43 differentially expressed genes (DEGs) overlapped in the three studied concentrations. Gene ontology (GO) analysis showed several biological processes related to electron transport chain, oxidative phosphorylation, and cellular respiration significantly altered. Molecular functions linked to mitochondrial respiratory chain and oxidoreductase activity were over-represented (q-value < 0.01). Pathway analysis revealed oxidative phosphorylation and electron transport chain as the most significantly altered pathways in all studied doses (z-score > 1.96; adj p-value < 0.05). 77 genes involved in the respiratory chain were significantly down-regulated at least at one dose. Moreover, 21 genes related to apoptosis and programmed cell death, and 12 genes related to caspase activity were significantly altered, mainly affecting initiator caspases 8, 9 and 10. The results demonstrated BEA-induced mitochondrial damage affecting the respiratory chain, and pointing to apoptosis through the caspase cascade in human lymphoblastic T cells.
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Affiliation(s)
- L Escrivá
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain.
| | - D Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, The Netherlands
| | - F Caiment
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, The Netherlands
| | - L Manyes
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain
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11
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Costa PM, Gosens I, Williams A, Farcal L, Pantano D, Brown DM, Stone V, Cassee FR, Halappanavar S, Fadeel B. Transcriptional profiling reveals gene expression changes associated with inflammation and cell proliferation following short-term inhalation exposure to copper oxide nanoparticles. J Appl Toxicol 2017; 38:385-397. [PMID: 29094763 DOI: 10.1002/jat.3548] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/20/2017] [Accepted: 09/05/2017] [Indexed: 01/09/2023]
Abstract
Our recent studies revealed a dose-dependent proinflammatory response to copper oxide nanoparticles (CuO NPs) in rats following short-term inhalation exposure for five consecutive days. Here transcriptomics approaches were applied using the same model to assess global gene expression in lung tissues obtained 1 day post-exposure and after a recovery period of 22 days from rats exposed to clean air or 6 hour equivalent doses of 3.3 mg m-3 (low dose) and 13.2 mg m-3 (high dose). Microarray analyses yielded about 1000 differentially expressed genes in the high-dose group and 200 in low-dose compared to the clean air control group, and less than 20 after the recovery period. Pathway analysis indicated cell proliferation/survival and inflammation as the main processes triggered by exposure to CuO NPs. We did not find significant perturbations of pathways related to oxidative stress. Upregulation of epithelial cell transforming protein 2 (Ect2), a known oncogene, was noted and ECT2 protein was upregulated in the lungs of exposed animals. Proliferation of alveolar epithelial cells was demonstrated based on Ki67 expression. The gene encoding monocyte chemoattractant protein 1 (or CCL2) was also upregulated and this was confirmed by immunohistochemistry. However, no aberrant DNA methylation of inflammation-associated genes was observed. In conclusion, we have found that inhalation of CuO NPs in rats causes upregulation of the oncoprotein ECT2 and the chemokine CCL2 and other proinflammatory markers as well as proliferation in bronchoalveolar epithelium after a short-term inhalation exposure. Thus, pathways known to be associated with neoplastic processes and inflammation were affected in this model.
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Affiliation(s)
- Pedro M Costa
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ilse Gosens
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Lucian Farcal
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniele Pantano
- School of Life Sciences, Heriot-Watt University, Edinburgh, UK
| | - David M Brown
- School of Life Sciences, Heriot-Watt University, Edinburgh, UK
| | - Vicki Stone
- School of Life Sciences, Heriot-Watt University, Edinburgh, UK
| | - Flemming R Cassee
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands.,Institute for Risk Assessment Studies, Utrecht University, Utrecht, The Netherlands
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Bengt Fadeel
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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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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Vachon J, Campagna C, Rodriguez MJ, Sirard MA, Levallois P. Barriers to the use of toxicogenomics data in human health risk assessment: A survey of Canadian risk assessors. Regul Toxicol Pharmacol 2017; 85:119-123. [PMID: 28137640 DOI: 10.1016/j.yrtph.2017.01.008] [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: 08/25/2016] [Revised: 11/24/2016] [Accepted: 01/25/2017] [Indexed: 02/06/2023]
Abstract
Regulatory agencies worldwide need to modernize human health risk assessment (HHRA) to meet challenges of the 21st century. Toxicogenomics is at the core of this improvement. Today, however, the use of toxicogenomics data in HHRA is very limited. The purpose of this survey was to identify barriers to the application of toxicogenomics data in HHRA by human health risk assessors. An online survey targeting Canadian risk assessors gathered information on their knowledge and perception of toxicogenomics, their current and future inclusion of toxicogenomics data in HHRA, and barriers to the use of such data. Twenty-nine (29) participants completed a questionnaire after 2 months of solicitation. The results show that the application of toxicogenomics data in Canada is marginal, with 85% of respondents reporting that they never or rarely used such data. Knowledge of toxicogenomics by Canadian risk assessors is also limited: about two-thirds of respondents (68%) were not at all or only slightly familiar with the concept. Lack of guidelines for toxicogenomics data interpretation, data quality assessment and on their use in HHRA, were found to be major barriers. In conclusion, there is a need for interventions aimed at facilitating the use of toxicogenomics data in HHRA, when available.
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Affiliation(s)
- Julien Vachon
- Département de médecine sociale et préventive, Faculté de médecine, Université Laval, Québec, QC, Canada; Direction de la santé environnementale et de la toxicologie, Institut national de santé publique du Québec (INSPQ), Québec, QC, Canada; Axe Santé des populations et pratiques optimales en santé, Centre de recherche du Centre hospitalier universitaire de Québec, Québec, QC, Canada.
| | - Céline Campagna
- Département de médecine sociale et préventive, Faculté de médecine, Université Laval, Québec, QC, Canada; Direction de la santé environnementale et de la toxicologie, Institut national de santé publique du Québec (INSPQ), Québec, QC, Canada.
| | - Manuel J Rodriguez
- École supérieure d'aménagement du territoire et de développement régional, Faculté d'aménagement, d'architecture, d'art et de design, Université Laval, Québec, QC, Canada; Chaire de recherche industrielle CRSNG, Gestion et surveillance de la qualité de l'eau potable, Université Laval, Québec, QC, Canada.
| | - Marc-André Sirard
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada; Centre de recherche en reproduction, développement et santé intergénérationnelle, Centre de recherche du Centre hospitalier de Québec, Québec, QC, Canada.
| | - Patrick Levallois
- Département de médecine sociale et préventive, Faculté de médecine, Université Laval, Québec, QC, Canada; Direction de la santé environnementale et de la toxicologie, Institut national de santé publique du Québec (INSPQ), Québec, QC, Canada; Axe Santé des populations et pratiques optimales en santé, Centre de recherche du Centre hospitalier universitaire de Québec, Québec, QC, Canada.
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Riebeling C, Jungnickel H, Luch A, Haase A. Systems Biology to Support Nanomaterial Grouping. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 947:143-171. [PMID: 28168668 DOI: 10.1007/978-3-319-47754-1_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The assessment of potential health risks of engineered nanomaterials (ENMs) is a challenging task due to the high number and great variety of already existing and newly emerging ENMs. Reliable grouping or categorization of ENMs with respect to hazards could help to facilitate prioritization and decision making for regulatory purposes. The development of grouping criteria, however, requires a broad and comprehensive data basis. A promising platform addressing this challenge is the systems biology approach. The different areas of systems biology, most prominently transcriptomics, proteomics and metabolomics, each of which provide a wealth of data that can be used to reveal novel biomarkers and biological pathways involved in the mode-of-action of ENMs. Combining such data with classical toxicological data would enable a more comprehensive understanding and hence might lead to more powerful and reliable prediction models. Physico-chemical data provide crucial information on the ENMs and need to be integrated, too. Overall statistical analysis should reveal robust grouping and categorization criteria and may ultimately help to identify meaningful biomarkers and biological pathways that sufficiently characterize the corresponding ENM subgroups. This chapter aims to give an overview on the different systems biology technologies and their current applications in the field of nanotoxicology, as well as to identify the existing challenges.
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Affiliation(s)
- Christian Riebeling
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Harald Jungnickel
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Andreas Luch
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Andrea Haase
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany.
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Thompson CM, Rager JE, Suh M, Ring CL, Proctor DM, Haws LC, Fry RC, Harris MA. Transcriptomic responses in the oral cavity of F344 rats and B6C3F1 mice following exposure to Cr(VI): Implications for risk assessment. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:706-716. [PMID: 27859739 PMCID: PMC5215477 DOI: 10.1002/em.22064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/27/2016] [Indexed: 05/13/2023]
Abstract
Exposure to hexavalent chromium [Cr(VI)] in drinking water was previously reported to increase oral tumor incidence in F344 rats. To investigate the mode of action for these tumors, transcriptomic profiles in oral mucosa samples of F344 rats and B6C3F1 mice were analyzed following exposure to 0.1-180 ppm Cr(VI) for 7 or 90 days. In rats, genome-wide microarray analyses identified no significantly differentially expressed genes (DEGs) at either time point. In mice, 14 and 1 DEGs were respectively identified after 7 and 90 days of exposure. Therefore, relaxed statistical criteria were employed to identify potential DEGs (pDEGs), followed by high-throughput benchmark dose modeling to identify responsive pDEGs for pathway enrichment analysis. This identified 288 and 168 pDEGs in the rat oral mucosa, of which only 20 and 7 showed evidence of dose-response. No significant pathway enrichment was obtained with either pDEG or dose-responsive pDEG lists. Similar results were obtained in mice. These analyses indicate a negligible transcriptional response in the oral mucosa of both species. Comparison of the total number of gene changes in the oral mucosa of rats and mice with responses in the duodenum of animals from the same study demonstrated remarkable dose-response concordance across tissues and species as a function of tissue chromium concentration. The low chromium levels in the oral mucosa and negligible transcript response are consistent with an absence of tissue lesions. These findings are used to compare the merits of linear and nonlinear approaches for deriving toxicity criteria based on the oral tumors in rats. Environ. Mol. Mutagen. 57:706-716, 2016. © 2016 The Authors. Environmental and Molecular Mutagenesis Published by Wiley Periodicals, Inc.
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Affiliation(s)
| | | | - Mina Suh
- ToxStrategies, IncMission ViejoCalifornia
| | | | | | | | - Rebecca C. Fry
- Department of Environmental Sciences and EngineeringGillings School of Global Public HealthChapel HillNorth Carolina
- Curriculum in Toxicology, University of North Carolina at Chapel HillChapel HillNorth Carolina
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Habas K, Anderson D, Brinkworth M. Detection of phase specificity of in vivo germ cell mutagens in an in vitro germ cell system. Toxicology 2016; 353-354:1-10. [PMID: 27059372 DOI: 10.1016/j.tox.2016.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/24/2016] [Accepted: 04/04/2016] [Indexed: 10/22/2022]
Abstract
In vivo tests for male reproductive genotoxicity are time consuming, resource-intensive and their use should be minimised according to the principles of the 3Rs. Accordingly, we investigated the effects in vitro, of a variety of known, phase-specific germ cell mutagens, i.e., pre-meiotic, meiotic, and post-meiotic genotoxins, on rat spermatogenic cell types separated using Staput unit-gravity velocity sedimentation, evaluating DNA damage using the Comet assay. N-ethyl-N-nitrosourea (ENU), N-methyl-N-nitrosourea (MNU) (spermatogenic phase), 6-mercaptopurine (6-MP) and 5-bromo-2'-deoxy-uridine (5-BrdU) (meiotic phase), methyl methanesulphonate (MMS) and ethyl methanesulphonate (EMS) (post-meiotic phase) were selected for use as they are potent male rodent, germ cell mutagens in vivo. DNA damage was detected directly using the Comet assay and indirectly using the TUNEL assay. Treatment of the isolated cells with ENU and MNU produced the greatest concentration-related increase in DNA damage in spermatogonia. Spermatocytes were most sensitive to 6-MP and 5-BrdU while spermatids were particularly susceptible to MMS and EMS. Increases were found when measuring both Olive tail moment (OTM) and% tail DNA, but the greatest changes were in OTM. Parallel results were found with the TUNEL assay, which showed highly significant, concentration dependent effects of all these genotoxins on spermatogonia, spermatocytes and spermatids in the same way as for DNA damage. The specific effects of these chemicals on different germ cell types matches those produced in vivo. This approach therefore shows potential for use in the detection of male germ cell genotoxicity and could contribute to the reduction of the use of animals in such toxicity assays.
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Affiliation(s)
- Khaled Habas
- Division of Medical Sciences, Faculty of Life Sciences, University of Bradford, Bradford, Richmond Road, West Yorkshire BD7 1DP, UK
| | - Diana Anderson
- Division of Medical Sciences, Faculty of Life Sciences, University of Bradford, Bradford, Richmond Road, West Yorkshire BD7 1DP, UK
| | - Martin Brinkworth
- Division of Medical Sciences, Faculty of Life Sciences, University of Bradford, Bradford, Richmond Road, West Yorkshire BD7 1DP, UK.
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Labib S, Williams A, Yauk CL, Nikota JK, Wallin H, Vogel U, Halappanavar S. Nano-risk Science: application of toxicogenomics in an adverse outcome pathway framework for risk assessment of multi-walled carbon nanotubes. Part Fibre Toxicol 2016; 13:15. [PMID: 26979667 PMCID: PMC4792104 DOI: 10.1186/s12989-016-0125-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/01/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND A diverse class of engineered nanomaterials (ENMs) exhibiting a wide array of physical-chemical properties that are associated with toxicological effects in experimental animals is in commercial use. However, an integrated framework for human health risk assessment (HHRA) of ENMs has yet to be established. Rodent 2-year cancer bioassays, clinical chemistry, and histopathological endpoints are still considered the 'gold standard' for detecting substance-induced toxicity in animal models. However, the use of data derived from alternative toxicological tools, such as genome-wide expression profiling and in vitro high-throughput assays, are gaining acceptance by the regulatory community for hazard identification and for understanding the underlying mode-of-action. Here, we conducted a case study to evaluate the application of global gene expression data in deriving pathway-based points of departure (PODs) for multi-walled carbon nanotube (MWCNT)-induced lung fibrosis, a non-cancer endpoint of regulatory importance. METHODS Gene expression profiles from the lungs of mice exposed to three individual MWCNTs with different physical-chemical properties were used within the framework of an adverse outcome pathway (AOP) for lung fibrosis to identify key biological events linking MWCNT exposure to lung fibrosis. Significantly perturbed pathways were categorized along the key events described in the AOP. Benchmark doses (BMDs) were calculated for each perturbed pathway and were used to derive transcriptional BMDs for each MWCNT. RESULTS Similar biological pathways were perturbed by the different MWCNT types across the doses and post-exposure time points studied. The pathway BMD values showed a time-dependent trend, with lower BMDs for pathways perturbed at the earlier post-exposure time points (24 h, 3d). The transcriptional BMDs were compared to the apical BMDs derived by the National Institute for Occupational Safety and Health (NIOSH) using alveolar septal thickness and fibrotic lesions endpoints. We found that regardless of the type of MWCNT, the BMD values for pathways associated with fibrosis were 14.0-30.4 μg/mouse, which are comparable to the BMDs derived by NIOSH for MWCNT-induced lung fibrotic lesions (21.0-27.1 μg/mouse). CONCLUSIONS The results demonstrate that transcriptomic data can be used to as an effective mechanism-based method to derive acceptable levels of exposure to nanomaterials in product development when epidemiological data are unavailable.
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Affiliation(s)
- Sarah Labib
- 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
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
| | - Jake K. Nikota
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
| | - Håkan Wallin
- National Research Centre for the Working Environment, Lerso Parkallé 105, DK-2100 Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, DK-1353 Copenhagen K, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Lerso Parkallé 105, DK-2100 Copenhagen, Denmark
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
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Madden JC, Rogiers V, Vinken M. Application of in silico and in vitro methods in the development of adverse outcome pathway constructs in wildlife. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0584. [PMID: 25405971 DOI: 10.1098/rstb.2013.0584] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
There is a long history of using both in silico and in vitro methods to predict adverse effects in humans and environmental species where toxicity data are lacking. Currently, there is a great deal of interest in applying these methods to the development of so-called 'adverse outcome pathway' (AOP) constructs. The AOP approach provides a framework for organizing information at the chemical and biological level, allowing evidence from both in silico and in vitro studies to be rationally combined to fill gaps in knowledge concerning toxicological events. Fundamental to this new paradigm is a greater understanding of the mechanisms of toxicity and, in particular, where these mechanisms may be conserved across taxa, such as between model animals and related wild species. This presents an opportunity to make predictions across diverse species, where empirical data are unlikely to become available as is the case for most species of wildlife.
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Affiliation(s)
- Judith C Madden
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom St., Liverpool L3 3AF, UK
| | - Vera Rogiers
- Department of Toxicology, Center for Pharmaceutical Research, Vrije Universiteit Brussel, Laarbeeklaan 103, Brussels 1090, Belgium
| | - Mathieu Vinken
- Department of Toxicology, Center for Pharmaceutical Research, Vrije Universiteit Brussel, Laarbeeklaan 103, Brussels 1090, Belgium
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Li HH, Hyduke DR, Chen R, Heard P, Yauk CL, Aubrecht J, Fornace AJ. Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:505-19. [PMID: 25733355 PMCID: PMC4506269 DOI: 10.1002/em.21941] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/19/2015] [Indexed: 05/11/2023]
Abstract
The development of in vitro molecular biomarkers to accurately predict toxicological effects has become a priority to advance testing strategies for human health risk assessment. The application of in vitro transcriptomic biomarkers promises increased throughput as well as a reduction in animal use. However, the existing protocols for predictive transcriptional signatures do not establish appropriate guidelines for dose selection or account for the fact that toxic agents may have pleiotropic effects. Therefore, comparison of transcriptome profiles across agents and studies has been difficult. Here we present a dataset of transcriptional profiles for TK6 cells exposed to a battery of well-characterized genotoxic and nongenotoxic chemicals. The experimental conditions applied a new dose optimization protocol that was based on evaluating expression changes in several well-characterized stress-response genes using quantitative real-time PCR in preliminary dose-finding studies. The subsequent microarray-based transcriptomic analyses at the optimized dose revealed responses to the test chemicals that were typically complex, often exhibiting substantial overlap in the transcriptional responses between a variety of the agents making analysis challenging. Using the nearest shrunken centroids method we identified a panel of 65 genes that could accurately classify toxicants as genotoxic or nongenotoxic. To validate the 65-gene panel as a genomic biomarker of genotoxicity, the gene expression profiles of an additional three well-characterized model agents were analyzed and a case study demonstrating the practical application of this genomic biomarker-based approach in risk assessment was performed to demonstrate its utility in genotoxicity risk assessment.
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Affiliation(s)
- Heng-Hong Li
- Department of Biochemistry and Molecular & Cellular Biology, and Department of Oncology, Georgetown University Medical Center, Washington, DC 20057
| | - Daniel R. Hyduke
- Department of Biochemistry and Molecular & Cellular Biology, and Department of Oncology, Georgetown University Medical Center, Washington, DC 20057
- Biological Engineering Department, Utah State University, Logan, UT 84321
| | - Renxiang Chen
- Department of Biochemistry and Molecular & Cellular Biology, and Department of Oncology, Georgetown University Medical Center, Washington, DC 20057
| | - Pamela Heard
- Pfizer Global Research and Development, Drug Safety Research and Development, Eastern Point Road, Groton, CT 06340
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, K1A 0K9, Canada
| | - Jiri Aubrecht
- Pfizer Global Research and Development, Drug Safety Research and Development, Eastern Point Road, Groton, CT 06340
| | - Albert J. Fornace
- Department of Biochemistry and Molecular & Cellular Biology, and Department of Oncology, Georgetown University Medical Center, Washington, DC 20057
- To whom correspondence should be addressed at: Lombardi Comprehensive Cancer Center, 3970 Reservoir Rd. NW, Room E504, Washington, DC 20057. Fax: (202) 687-3140.,
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20
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Li Z, Long Y, Zhong L, Song G, Zhang X, Yuan L, Cui Z, Dai H. RNA sequencing provides insights into the toxicogenomic response of ZF4 cells to methyl methanesulfonate. J Appl Toxicol 2015; 36:94-104. [DOI: 10.1002/jat.3147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/10/2015] [Accepted: 02/10/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Zhouquan Li
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
- University of Chinese Academy of Sciences; Yuquan Road 19A Beijing 100039 People's Republic of China
| | - Yong Long
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Liqiao Zhong
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
- University of Chinese Academy of Sciences; Yuquan Road 19A Beijing 100039 People's Republic of China
| | - Guili Song
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Xiaohua Zhang
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Li Yuan
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Zongbin Cui
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
| | - Heping Dai
- State Key Laboratory of Fresh water Ecology and Biotechnology; Institute of Hydrobiology, Chinese Academy of Sciences; 7 Southern East Lake Road Wuhan 430072 People's Republic of China
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21
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Castiblanco Rodriguez AL. Approaches and perspectives to toxicogenetics and toxicogenomics. REVISTA DE LA FACULTAD DE MEDICINA 2015. [DOI: 10.15446/revfacmed.v62n4.45218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Toxicology is one of the scientific disciplines that has most<br />evolved in recent years due to scientific and technological<br />advances that have created a deeper understanding of the<br />genetic and molecular basis for appreciative variability in<br />toxic response from one person to another. The application<br />of this knowledge in toxicology is known as toxicogenetics<br />and toxicogenomics. The latter is the discipline that studies<br />the genomic response of organisms exposed to chemical<br />agents, including drugs, environmental pollutants, food<br />additives, and other commonly used chemical products.<br />The use of emerging omic technologies, such as genomics,<br />transcriptomics, proteomics, metabolomics and bioinformatics<br />techniques, permits the analysis of many variants of genes<br />simultaneously in an organism exposed to toxic agents in order<br />to search for genes susceptible to damage, to detect patterns<br />and mechanisms of toxicity, and determine specific profiles<br />of gene expression that give origin to biomarkers of exposure<br />and risk. This constitutes predictive toxicology.
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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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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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Titz B, Elamin A, Martin F, Schneider T, Dijon S, Ivanov NV, Hoeng J, Peitsch MC. Proteomics for systems toxicology. Comput Struct Biotechnol J 2014; 11:73-90. [PMID: 25379146 PMCID: PMC4212285 DOI: 10.1016/j.csbj.2014.08.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Current toxicology studies frequently lack measurements at molecular resolution to enable a more mechanism-based and predictive toxicological assessment. Recently, a systems toxicology assessment framework has been proposed, which combines conventional toxicological assessment strategies with system-wide measurement methods and computational analysis approaches from the field of systems biology. Proteomic measurements are an integral component of this integrative strategy because protein alterations closely mirror biological effects, such as biological stress responses or global tissue alterations. Here, we provide an overview of the technical foundations and highlight select applications of proteomics for systems toxicology studies. With a focus on mass spectrometry-based proteomics, we summarize the experimental methods for quantitative proteomics and describe the computational approaches used to derive biological/mechanistic insights from these datasets. To illustrate how proteomics has been successfully employed to address mechanistic questions in toxicology, we summarized several case studies. Overall, we provide the technical and conceptual foundation for the integration of proteomic measurements in a more comprehensive systems toxicology assessment framework. We conclude that, owing to the critical importance of protein-level measurements and recent technological advances, proteomics will be an integral part of integrative systems toxicology approaches in the future.
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Kohonen P, Ceder R, Smit I, Hongisto V, Myatt G, Hardy B, Spjuth O, Grafström R. Cancer biology, toxicology and alternative methods development go hand-in-hand. Basic Clin Pharmacol Toxicol 2014; 115:50-8. [PMID: 24779563 DOI: 10.1111/bcpt.12257] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/21/2014] [Indexed: 12/13/2022]
Abstract
Toxicological research faces the challenge of integrating knowledge from diverse fields and novel technological developments generally in the biological and medical sciences. We discuss herein the fact that the multiple facets of cancer research, including discovery related to mechanisms, treatment and diagnosis, overlap many up and coming interest areas in toxicology, including the need for improved methods and analysis tools. Common to both disciplines, in vitro and in silico methods serve as alternative investigation routes to animal studies. Knowledge on cancer development helps in understanding the relevance of chemical toxicity studies in cell models, and many bioinformatics-based cancer biomarker discovery tools are also applicable to computational toxicology. Robotics-aided, cell-based, high-throughput screening, microscale immunostaining techniques and gene expression profiling analyses are common tools in cancer research, and when sequentially combined, form a tiered approach to structured safety evaluation of thousands of environmental agents, novel chemicals or engineered nanomaterials. Comprehensive tumour data collections in databases have been translated into clinically useful data, and this concept serves as template for computer-driven evaluation of toxicity data into meaningful results. Future 'cancer research-inspired knowledge management' of toxicological data will aid the translation of basic discovery results and chemicals- and materials-testing data to information relevant to human health and environmental safety.
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Affiliation(s)
- Pekka Kohonen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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Application of “Omics” Technologies to In Vitro Toxicology. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2014. [DOI: 10.1007/978-1-4939-0521-8_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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29
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Nesnow S. Integration of toxicological approaches with “omic” and related technologies to elucidate mechanisms of carcinogenic action: Propiconazole, an example. Cancer Lett 2013. [DOI: 10.1016/j.canlet.2012.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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30
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An approach for integrating toxicogenomic data in risk assessment: the dibutyl phthalate case study. Toxicol Appl Pharmacol 2013; 271:324-35. [PMID: 23537663 DOI: 10.1016/j.taap.2013.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 11/24/2022]
Abstract
An approach for evaluating and integrating genomic data in chemical risk assessment was developed based on the lessons learned from performing a case study for the chemical dibutyl phthalate. A case study prototype approach was first developed in accordance with EPA guidance and recommendations of the scientific community. Dibutyl phthalate (DBP) was selected for the case study exercise. The scoping phase of the dibutyl phthalate case study was conducted by considering the available DBP genomic data, taken together with the entire data set, for whether they could inform various risk assessment aspects, such as toxicodynamics, toxicokinetics, and dose-response. A description of weighing the available dibutyl phthalate data set for utility in risk assessment provides an example for considering genomic data for future chemical assessments. As a result of conducting the scoping process, two questions--Do the DBP toxicogenomic data inform 1) the mechanisms or modes of action?, and 2) the interspecies differences in toxicodynamics?--were selected to focus the case study exercise. Principles of the general approach include considering the genomics data in conjunction with all other data to determine their ability to inform the various qualitative and/or quantitative aspects of risk assessment, and evaluating the relationship between the available genomic and toxicity outcome data with respect to study comparability and phenotypic anchoring. Based on experience from the DBP case study, recommendations and a general approach for integrating genomic data in chemical assessment were developed to advance the broader effort to utilize 21st century data in risk assessment.
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Key Words
- 3 beta-hydroxysteroid dehydrogenase/delta-5–delta-4 isomerase type II
- ADME
- AGD
- ALDH2
- AR
- BBDR model
- CNPs
- CYP2D6
- Cyp11a1/P450scc
- Cyp17a1
- Cyp2b1
- Cyp3a1
- DBP
- DEG
- DEHP
- D–R
- EDC
- Endocrine disrupting chemical
- GO
- Hsd3b
- IRIS
- Insl3
- Integrated Risk Information System
- MBP
- MOA
- Male development
- NIEHS
- NOAEL
- National Institute of Environmental Health Sciences
- PBPK modeling
- Phthalates
- RT-PCR
- Risk assessment
- SD
- STAR
- Scarb1
- Science to Achieve Results
- Sprague–Dawley
- Star
- T
- TD
- TDS
- TGx
- TK
- Testosterone
- Toxicogenomic
- U.S. Environmental Protection Agency
- UDP glucuronosyltransferase 2B1
- UF(H)
- US EPA
- Ugt2b1
- WOE
- absorption, distribution, metabolism, and excretion
- aldehyde dehydrogenase-2
- androgen receptor
- anogenital distance
- biologically based dose–response model
- copy number polymorphisms
- cytochrome P450 2D6
- cytochrome P450, family 11, subfamily a, polypeptide 1
- cytochrome P450, family 17, subfamily a, polypeptide 1
- cytochrome P450, family 2, subfamily b, polypeptide 1
- cytochrome P450, family 3, subfamily a, polypeptide 1
- di-(2-ethylhexyl) phthalate
- dibutyl phthalate
- differentially-expressed gene
- dose–response
- endocrine disrupting chemical
- gene ontology
- insulin-like 3
- mode of action
- monobutyl phthalate
- no observed adverse effect level
- physiologically based pharmacokinetic modeling
- reverse transcription-polymerase chain reaction
- scavenger receptor class B, member 1
- steroidogenic acute regulatory protein
- testicular dysgenesis syndrome
- testosterone
- toxicodynamics
- toxicogenomic
- toxicokinetics
- uncertainty factor for uncertainty in extrapolating animal data to humans (i.e., interspecies uncertainty) (http://www.epa.gov/IRIS/)
- weight-of-evidence
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Thompson CM, Proctor DM, Suh M, Haws LC, Kirman CR, Harris MA. Assessment of the mode of action underlying development of rodent small intestinal tumors following oral exposure to hexavalent chromium and relevance to humans. Crit Rev Toxicol 2013; 43:244-74. [PMID: 23445218 PMCID: PMC3604738 DOI: 10.3109/10408444.2013.768596] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 01/16/2013] [Accepted: 01/17/2013] [Indexed: 12/13/2022]
Abstract
Abstract Chronic exposure to high concentrations of hexavalent chromium (Cr(VI)) in drinking water causes intestinal adenomas and carcinomas in mice, but not in rats. Cr(VI) causes damage to intestinal villi and crypt hyperplasia in mice after only one week of exposure. After two years of exposure, intestinal damage and crypt hyperplasia are evident in mice (but not rats), as are intestinal tumors. Although Cr(VI) has genotoxic properties, these findings suggest that intestinal tumors in mice arise as a result of chronic mucosal injury. To better understand the mode of action (MOA) of Cr(VI) in the intestine, a 90-day drinking water study was conducted to collect histological, biochemical, toxicogenomic and pharmacokinetic data in intestinal tissues. Using MOA analyses and human relevance frameworks proposed by national and international regulatory agencies, the weight of evidence supports a cytotoxic MOA with the following key events: (a) absorption of Cr(VI) from the intestinal lumen, (b) toxicity to intestinal villi, (c) crypt regenerative hyperplasia and (d) clonal expansion of mutations within the crypt stem cells, resulting in late onset tumorigenesis. This article summarizes the data supporting each key event in the MOA, as well as data that argue against a mutagenic MOA for Cr(VI)-induced intestinal tumors.
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Shukla SJ, Huang R, Simmons SO, Tice RR, Witt KL, Vanleer D, Ramabhadran R, Austin CP, Xia M. Profiling environmental chemicals for activity in the antioxidant response element signaling pathway using a high throughput screening approach. ENVIRONMENTAL HEALTH PERSPECTIVES 2012; 120:1150-6. [PMID: 22551509 PMCID: PMC3440086 DOI: 10.1289/ehp.1104709] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 05/02/2012] [Indexed: 05/24/2023]
Abstract
BACKGROUND Oxidative stress has been implicated in the pathogenesis of a variety of diseases ranging from cancer to neurodegeneration, highlighting the need to identify chemicals that can induce this effect. The antioxidant response element (ARE) signaling pathway plays an important role in the amelioration of oxidative stress. Thus, assays that detect the up-regulation of this pathway could be useful for identifying chemicals that induce oxidative stress. OBJECTIVES We used cell-based reporter methods and informatics tools to efficiently screen a large collection of environmental chemicals and identify compounds that induce oxidative stress. METHODS We utilized two cell-based ARE assay reporters, β-lactamase and luciferase, to screen a U.S. National Toxicology Program 1,408-compound library (NTP 1408, which contains 1,340 unique compounds) for their ability to induce oxidative stress in HepG2 cells using quantitative high throughput screening (qHTS). RESULTS Roughly 3% (34 of 1,340) of the unique compounds demonstrated activity across both cell-based assays. Based on biological activity and structure-activity relationship profiles, we selected 50 compounds for retesting in the two ARE assays and in an additional follow-up assay that employed a mutated ARE linked to β-lactamase. Using this strategy, we identified 30 compounds that demonstrated activity in the ARE-bla and ARE-luc assays and were able to determine structural features conferring compound activity across assays. CONCLUSIONS Our results support the robustness of using two different cell-based approaches for identifying compounds that induce ARE signaling. Together, these methods are useful for prioritizing chemicals for further in-depth mechanism-based toxicity testing.
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Affiliation(s)
- Sunita J Shukla
- NIH Chemical Genomics Center, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland, USA
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Ouedraogo M, Baudoux T, Stévigny C, Nortier J, Colet JM, Efferth T, Qu F, Zhou J, Chan K, Shaw D, Pelkonen O, Duez P. Review of current and "omics" methods for assessing the toxicity (genotoxicity, teratogenicity and nephrotoxicity) of herbal medicines and mushrooms. JOURNAL OF ETHNOPHARMACOLOGY 2012; 140:492-512. [PMID: 22386524 DOI: 10.1016/j.jep.2012.01.059] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/31/2012] [Accepted: 01/31/2012] [Indexed: 05/31/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The increasing use of traditional herbal medicines around the world requires more scientific evidence for their putative harmlessness. To this end, a plethora of methods exist, more or less satisfying. In this post-genome era, recent reviews are however scarce, not only on the use of new "omics" methods (transcriptomics, proteomics, metabonomics) for genotoxicity, teratogenicity, and nephrotoxicity assessment, but also on conventional ones. METHODS The present work aims (i) to review conventional methods used to assess genotoxicity, teratogenicity and nephrotoxicity of medicinal plants and mushrooms; (ii) to report recent progress in the use of "omics" technologies in this field; (iii) to underline advantages and limitations of promising methods; and lastly (iv) to suggest ways whereby the genotoxicity, teratogenicity, and nephrotoxicity assessment of traditional herbal medicines could be more predictive. RESULTS Literature and safety reports show that structural alerts, in silico and classical in vitro and in vivo predictive methods are often used. The current trend to develop "omics" technologies to assess genotoxicity, teratogenicity and nephrotoxicity is promising but most often relies on methods that are still not standardized and validated. CONCLUSION Hence, it is critical that toxicologists in industry, regulatory agencies and academic institutions develop a consensus, based on rigorous methods, about the reliability and interpretation of endpoints. It will also be important to regulate the integration of conventional methods for toxicity assessments with new "omics" technologies.
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Affiliation(s)
- Moustapha Ouedraogo
- Laboratory of Pharmacology and Toxicology, Health Sciences Faculty, University of Ouagadougou, 03 BP 7021 Ouagadougou 03, Burkina Faso. mustapha
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Doktorova TY, Ellinger-Ziegelbauer H, Vinken M, Vanhaecke T, van Delft J, Kleinjans J, Ahr HJ, Rogiers V. Comparison of hepatocarcinogen-induced gene expression profiles in conventional primary rat hepatocytes with in vivo rat liver. Arch Toxicol 2012; 86:1399-411. [PMID: 22484513 DOI: 10.1007/s00204-012-0847-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 03/22/2012] [Indexed: 01/07/2023]
Abstract
At present, substantial efforts are focused on the development of in vitro assays coupled with "omics" technologies for the identification of carcinogenic substances as an alternative to the classical 2-year rodent carcinogenicity bioassay. A prerequisite for the eventual regulatory acceptance of such assays, however, is the in vivo relevance of the observed in vitro findings. In the current study, hepatocarcinogen-induced gene expression profiles generated after the exposure of conventional cultures of primary rat hepatocytes to three non-genotoxic carcinogens (methapyrilene hydrochloride, piperonyl butoxide, and Wy-14643), three genotoxic carcinogens (aflatoxin B1, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, and 2-nitrofluorene), and two non-carcinogens (nifedipine and clonidine) are compared with previously obtained in vivo data after oral administration for up to 14 days of the same hepatocarcinogens to rats. In addition to the comparison of deregulated genes and functions per compound between in vivo and in vitro models, the major discriminating cellular pathways found in vivo in livers of exposed rats were examined for deregulation in vitro. Further, in vivo-derived gene signatures for the identification of genotoxic versus non-genotoxic carcinogens are used to classify in vitro-tested hepatocarcinogens and non-carcinogens. In the primary hepatocyte cultures, two out of the three tested genotoxic carcinogens mimicked the in vivo-relevant DNA damage response and were correctly assessed. Exposure to the non-genotoxic hepatocarcinogens, however, triggered a relatively weak response in the in vitro system, with no clear similarities to in vivo. This study contributes to the further optimization of toxicogenomics predictive tools when applied in in vitro settings.
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Affiliation(s)
- Tatyana Y Doktorova
- Department of Toxicology, Center for Pharmaceutical Research, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
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McHale CM, Zhang L, Smith MT. Current understanding of the mechanism of benzene-induced leukemia in humans: implications for risk assessment. Carcinogenesis 2012; 33:240-52. [PMID: 22166497 PMCID: PMC3271273 DOI: 10.1093/carcin/bgr297] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 11/21/2011] [Accepted: 12/07/2011] [Indexed: 01/01/2023] Open
Abstract
Benzene causes acute myeloid leukemia and probably other hematological malignancies. As benzene also causes hematotoxicity even in workers exposed to levels below the US permissible occupational exposure limit of 1 part per million, further assessment of the health risks associated with its exposure, particularly at low levels, is needed. Here, we describe the probable mechanism by which benzene induces leukemia involving the targeting of critical genes and pathways through the induction of genetic, chromosomal or epigenetic abnormalities and genomic instability, in a hematopoietic stem cell (HSC); stromal cell dysregulation; apoptosis of HSCs and stromal cells and altered proliferation and differentiation of HSCs. These effects modulated by benzene-induced oxidative stress, aryl hydrocarbon receptor dysregulation and reduced immunosurveillance, lead to the generation of leukemic stem cells and subsequent clonal evolution to leukemia. A mode of action (MOA) approach to the risk assessment of benzene was recently proposed. This approach is limited, however, by the challenges of defining a simple stochastic MOA of benzene-induced leukemogenesis and of identifying relevant and quantifiable parameters associated with potential key events. An alternative risk assessment approach is the application of toxicogenomics and systems biology in human populations, animals and in vitro models of the HSC stem cell niche, exposed to a range of levels of benzene. These approaches will inform our understanding of the mechanisms of benzene toxicity and identify additional biomarkers of exposure, early effect and susceptibility useful for risk assessment.
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Affiliation(s)
| | | | - Martyn T. Smith
- Division of Environmental Health Sciences, Genes and Environment Laboratory, School of Public Health, University of California, Berkeley, CA 94720-7356, USA
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Euling SY, White LD, Kim AS, Sen B, Wilson VS, Keshava C, Keshava N, Hester S, Ovacik MA, Ierapetritou MG, Androulakis IP, Gaido KW. Use of genomic data in risk assessment case study: II. Evaluation of the dibutyl phthalate toxicogenomic data set. Toxicol Appl Pharmacol 2011; 271:349-62. [PMID: 21745491 DOI: 10.1016/j.taap.2011.06.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 06/03/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
Abstract
An evaluation of the toxicogenomic data set for dibutyl phthalate (DBP) and male reproductive developmental effects was performed as part of a larger case study to test an approach for incorporating genomic data in risk assessment. The DBP toxicogenomic data set is composed of nine in vivo studies from the published literature that exposed rats to DBP during gestation and evaluated gene expression changes in testes or Wolffian ducts of male fetuses. The exercise focused on qualitative evaluation, based on a lack of available dose-response data, of the DBP toxicogenomic data set to postulate modes and mechanisms of action for the male reproductive developmental outcomes, which occur in the lower dose range. A weight-of-evidence evaluation was performed on the eight DBP toxicogenomic studies of the rat testis at the gene and pathway levels. The results showed relatively strong evidence of DBP-induced downregulation of genes in the steroidogenesis pathway and lipid/sterol/cholesterol transport pathway as well as effects on immediate early gene/growth/differentiation, transcription, peroxisome proliferator-activated receptor signaling and apoptosis pathways in the testis. Since two established modes of action (MOAs), reduced fetal testicular testosterone production and Insl3 gene expression, explain some but not all of the testis effects observed in rats after in utero DBP exposure, other MOAs are likely to be operative. A reanalysis of one DBP microarray study identified additional pathways within cell signaling, metabolism, hormone, disease, and cell adhesion biological processes. These putative new pathways may be associated with DBP effects on the testes that are currently unexplained. This case study on DBP identified data gaps and research needs for the use of toxicogenomic data in risk assessment. Furthermore, this study demonstrated an approach for evaluating toxicogenomic data in human health risk assessment that could be applied to future chemicals.
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Affiliation(s)
- Susan Y Euling
- National Center for Environmental Assessment, U.S. Environmental Protection Agency, Washington, DC, USA.
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Makris SL, Euling SY, Gray LE, Benson R, Foster P. Use of genomic data in risk assessment case study: I. Evaluation of the dibutyl phthalate male reproductive development toxicity data set. Toxicol Appl Pharmacol 2010; 271:336-48. [PMID: 20849870 DOI: 10.1016/j.taap.2010.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2010] [Revised: 09/03/2010] [Accepted: 09/07/2010] [Indexed: 10/19/2022]
Abstract
A case study was conducted, using dibutyl phthalate (DBP), to explore an approach to using toxicogenomic data in risk assessment. The toxicity and toxicogenomic data sets relative to DBP-related male reproductive developmental outcomes were considered conjointly to derive information about mode and mechanism of action. In this manuscript, we describe the case study evaluation of the toxicological database for DBP, focusing on identifying the full spectrum of male reproductive developmental effects. The data were assessed to 1) evaluate low dose and low incidence findings and 2) identify male reproductive toxicity endpoints without well-established modes of action (MOAs). These efforts led to the characterization of data gaps and research needs for the toxicity and toxicogenomic studies in a risk assessment context. Further, the identification of endpoints with unexplained MOAs in the toxicity data set was useful in the subsequent evaluation of the mechanistic information that the toxicogenomic data set evaluation could provide. The extensive analysis of the toxicology data set within the MOA context provided a resource of information for DBP in attempts to hypothesize MOAs (for endpoints without a well-established MOA) and to phenotypically anchor toxicogenomic and other mechanistic data both to toxicity endpoints and to available toxicogenomic data. This case study serves as an example of the steps that can be taken to develop a toxicological data source for a risk assessment, both in general and especially for risk assessments that include toxicogenomic data.
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Affiliation(s)
- Susan L Makris
- U.S. Environmental Protection Agency, National Center for Environmental Assessment, Office of Research and Development, (Mail code 8623P), 1200 Pennsylvania Ave., NW, Washington, DC 20460, USA.
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