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Short-term in vivo testing to discriminate genotoxic carcinogens from non-genotoxic carcinogens and non-carcinogens using next-generation RNA sequencing, DNA microarray, and qPCR. Genes Environ 2023; 45:7. [PMID: 36755350 PMCID: PMC9909887 DOI: 10.1186/s41021-023-00262-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/05/2023] [Indexed: 02/10/2023] Open
Abstract
Next-generation RNA sequencing (RNA-Seq) has identified more differentially expressed protein-coding genes (DEGs) and provided a wider quantitative range of expression level changes than conventional DNA microarrays. JEMS·MMS·Toxicogenomics group studied DEGs with targeted RNA-Seq on freshly frozen rat liver tissues and on formalin-fixed paraffin-embedded (FFPE) rat liver tissues after 28 days of treatment with chemicals and quantitative real-time PCR (qPCR) on rat and mouse liver tissues after 4 to 48 h treatment with chemicals and analyzed by principal component analysis (PCA) as statics. Analysis of rat public DNA microarray data (Open TG-GATEs) was also performed. In total, 35 chemicals were analyzed [15 genotoxic hepatocarcinogens (GTHCs), 9 non-genotoxic hepatocarcinogens (NGTHCs), and 11 non-genotoxic non-hepatocarcinogens (NGTNHCs)]. As a result, 12 marker genes (Aen, Bax, Btg2, Ccnf, Ccng1, Cdkn1a, Gdf15, Lrp1, Mbd1, Phlda3, Plk2, and Tubb4b) were proposed to discriminate GTHCs from NGTHCs and NGTNHCs. U.S. Environmental Protection Agency studied DEGs induced by 4 known GTHCs in rat liver using DNA microarray and proposed 7 biomarker genes, Bax, Bcmp1, Btg2, Ccng1, Cdkn1a, Cgr19, and Mgmt for GTHCs. Studies involving the use of whole-transcriptome RNA-Seq upon exposure to chemical carcinogens in vivo have also been performed in rodent liver, kidney, lung, colon, and other organs, although discrimination of GTHCs from NGTHCs was not examined. Candidate genes published using RNA-Seq, qPCR, and DNA microarray will be useful for the future development of short-term in vivo studies of environmental carcinogens using RNA-Seq.
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Harris KL, Myers MB, McKim KL, Elespuru RK, Parsons BL. Rationale and Roadmap for Developing Panels of Hotspot Cancer Driver Gene Mutations as Biomarkers of Cancer Risk. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:152-175. [PMID: 31469467 PMCID: PMC6973253 DOI: 10.1002/em.22326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 05/24/2023]
Abstract
Cancer driver mutations (CDMs) are necessary and causal for carcinogenesis and have advantages as reporters of carcinogenic risk. However, little progress has been made toward developing measurements of CDMs as biomarkers for use in cancer risk assessment. Impediments for using a CDM-based metric to inform cancer risk include the complexity and stochastic nature of carcinogenesis, technical difficulty in quantifying low-frequency CDMs, and lack of established relationships between cancer driver mutant fractions and tumor incidence. Through literature review and database analyses, this review identifies the most promising targets to investigate as biomarkers of cancer risk. Mutational hotspots were discerned within the 20 most mutated genes across the 10 deadliest cancers. Forty genes were identified that encompass 108 mutational hotspot codons overrepresented in the COSMIC database; 424 different mutations within these hotspot codons account for approximately 63,000 tumors and their prevalence across tumor types is described. The review summarizes literature on the prevalence of CDMs in normal tissues and suggests such mutations are direct and indirect substrates for chemical carcinogenesis, which occurs in a spatially stochastic manner. Evidence that hotspot CDMs (hCDMs) frequently occur as tumor subpopulations is presented, indicating COSMIC data may underestimate mutation prevalence. Analyses of online databases show that genes containing hCDMs are enriched in functions related to intercellular communication. In its totality, the review provides a roadmap for the development of tissue-specific, CDM-based biomarkers of carcinogenic potential, comprised of batteries of hCDMs and can be measured by error-correct next-generation sequencing. Environ. Mol. Mutagen. 61:152-175, 2020. Published 2019. This article is a U.S. Government work and is in the public domain in the USA. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Kelly L. Harris
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
| | - Meagan B. Myers
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
| | - Karen L. McKim
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
| | - Rosalie K. Elespuru
- Division of Biology, Chemistry and Materials ScienceCDRH/OSEL, US Food and Drug AdministrationSilver SpringMaryland
| | - Barbara L. Parsons
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
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Auerbach SS. In vivo Signatures of Genotoxic and Non-genotoxic Chemicals. TOXICOGENOMICS IN PREDICTIVE CARCINOGENICITY 2016. [DOI: 10.1039/9781782624059-00113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This chapter reviews the findings from a broad array of in vivo genomic studies with the goal of identifying a general signature of genotoxicity (GSG) that is indicative of exposure to genotoxic agents (i.e. agents that are active in either the bacterial mutagenesis and/or the in vivo micronucleus test). While the GSG has largely emerged from systematic studies of rat and mouse liver, its response is evident across a broad collection of genotoxic treatments that cover a variety of tissues and species. Pathway-based characterization of the GSG indicates that it is enriched with genes that are regulated by p53. In addition to the GSG, another pan-tissue signature related to bone marrow suppression (a common effect of genotoxic agent exposure) is reviewed. Overall, these signatures are quite effective in identifying genotoxic agents; however, there are situations where false positive findings can occur, for example when necrotizing doses of non-genotoxic soft electrophiles (e.g. thioacetamide) are used. For this reason specific suggestions for best practices for generating for use in the creation and application of in vivo genomic signatures are reviewed.
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Affiliation(s)
- Scott S. Auerbach
- Toxicoinformatic Group, Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences PO Box 12233 MD K2-17 Research Triangle Park NC 27709 USA
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Kimura M, Mizukami S, Watanabe Y, Onda N, Yoshida T, Shibutani M. Aberrant cell cycle regulation in rat liver cells induced by post-initiation treatment with hepatocarcinogens/hepatocarcinogenic tumor promoters. ACTA ACUST UNITED AC 2016; 68:399-408. [PMID: 27402199 DOI: 10.1016/j.etp.2016.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/22/2016] [Accepted: 06/07/2016] [Indexed: 01/23/2023]
Abstract
The present study aimed to determine the onset time of hepatocarcinogen/hepatocarcinogenic tumor promoter-specific cell proliferation, apoptosis and aberrant cell cycle regulation after post-initiation treatment. Six-week-old rats were treated with the genotoxic hepatocarcinogen, carbadox (CRB), the marginally hepatocarcinogenic leucomalachite green (LMG), the tumor promoter, β-naphthoflavone (BNF) or the non-carcinogenic hepatotoxicant, acetaminophen, for 2, 4 or 6 weeks during the post-initiation phase using a medium-term liver bioassay. Cell proliferation activity, expression of G2 to M phase- and spindle checkpoint-related molecules, and apoptosis were immunohistochemically analyzed at week 2 and 4, and tumor promotion activity was assessed at week 6. At week 2, hepatocarcinogen/tumor promoter-specific aberrant cell cycle regulation was not observed. At week 4, BNF and LMG increased cell proliferation together with hepatotoxicity, while CRB did not. Additionally, BNF and CRB reduced the number of cells expressing phosphorylated-histone H3 in both ubiquitin D (UBD)(+) cells and Ki-67(+) proliferating cells, suggesting development of spindle checkpoint dysfunction, regardless of cell proliferation activity. At week 6, examined hepatocarcinogens/tumor promoters increased preneoplastic hepatic foci expressing glutathione S-transferase placental form. These results suggest that some hepatocarcinogens/tumor promoters increase their toxicity after post-initiation treatment, causing regenerative cell proliferation. In contrast, some genotoxic hepatocarcinogens may disrupt the spindle checkpoint without facilitating cell proliferation at the early stage of tumor promotion. This suggests that facilitation of cell proliferation and disruption of spindle checkpoint function are induced by different mechanisms during hepatocarcinogenesis. Four weeks of post-initiation treatment may be sufficient to induce hepatocarcinogen/tumor promoter-specific cellular responses.
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Affiliation(s)
- Masayuki Kimura
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan; Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193, Japan
| | - Sayaka Mizukami
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan; Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193, Japan
| | - Yousuke Watanabe
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan; Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193, Japan
| | - Nobuhiko Onda
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Toshinori Yoshida
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Makoto Shibutani
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan.
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5
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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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Kimura M, Mizukami S, Watanabe Y, Hasegawa-Baba Y, Onda N, Yoshida T, Shibutani M. Disruption of spindle checkpoint function in rats following 28 days of repeated administration of renal carcinogens. J Toxicol Sci 2016; 41:91-104. [PMID: 26763396 DOI: 10.2131/jts.41.91] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We previously reported that 28-day exposure to hepatocarcinogens that facilitate cell proliferation specifically alters the expression of G1/S checkpoint-related genes and proteins, induces aberrant early expression of ubiquitin D (UBD) at the G2 phase, and increases apoptosis in the rat liver, indicating G1/S and spindle checkpoint dysfunction. The present study aimed to determine the time of onset of carcinogen-specific cell-cycle disruption after repeated administration of renal carcinogens for up to 28 days. Rats were orally administered the renal carcinogens nitrofurantoin (NFT), 1-amino-2,4-dibromoantraquinone (ADAQ), and 1,2,3-trichloropropane (TCP) or the non-carcinogenic renal toxicants 1-chloro-2-propanol, triamterene, and carboxin for 3, 7 or 28 days. Both immunohistochemical single-molecule analysis and real-time RT-PCR analysis revealed that carcinogen-specific expression changes were not observed after 28 days of administration. However, the renal carcinogens ADAQ and TCP specifically reduced the number of cells expressing phosphorylated-histone H3 at Ser10 in both UBD(+) cells and proliferating cells, suggestive of insufficient UBD expression at the M phase and early transition of proliferating cells from the M phase, without increasing apoptosis, after 28 days of administration. In contrast, NFT, which has marginal carcinogenic potential, did not induce such cellular responses. These results suggest that it may take 28 days to induce spindle checkpoint dysfunction by renal carcinogens; however, induction of apoptosis may not be essential. Thus, induction of spindle checkpoint dysfunction may be dependent on carcinogenic potential of carcinogen examined, and marginal carcinogens may not exert sufficient responses even after 28 days of administration.
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Affiliation(s)
- Masayuki Kimura
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
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7
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Henderson CJ, Cameron AR, Chatham L, Stanley LA, Wolf CR. Evidence that the capacity of nongenotoxic carcinogens to induce oxidative stress is subject to marked variability. Toxicol Sci 2015; 145:138-48. [PMID: 25690736 PMCID: PMC4833039 DOI: 10.1093/toxsci/kfv039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Many drugs and environmental chemicals which are not directly mutagenic have the capacity to increase the incidence of tumors in the liver and other tissues. For this reason, such compounds are known as nongenotoxic carcinogens. The mechanisms underlying their effects remain unclear; however, their capacity to induce oxidative stress is considered to be a critical step in the carcinogenic process, although the evidence that this is actually the case remains equivocal and sparse. We have exploited a novel heme oxygenase-1 reporter mouse to evaluate the capacity of nongenotoxic carcinogens with different mechanisms of action to induce oxidative stress in the liver in vivo. When these compounds were administered at doses reported to cause liver tumors, marked differences in activation of the reporter were observed. 1,4-Dichlorobenzene and nafenopin were strong inducers of oxidative stress, whereas phenobarbital, piperonyl butoxide, cyproterone acetate, and WY14,643 were, at best, only very weak inducers. In the case of phenobarbital and thioacetamide, the number of LacZ-positive hepatocytes increased with time, and for the latter also with dose. The data obtained demonstrate that although some nongenotoxic carcinogens can induce oxidative stress, it is not a dominant feature of the response to these compounds. Therefore in contrast to the current models, these data suggest that oxidative stress is not a key determinant in the mechanism of nongenotoxic carcinogenesis but may contribute to the effects in a compound-specific manner.
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Affiliation(s)
- Colin J Henderson
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital & Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Amy R Cameron
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital & Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Lynsey Chatham
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital & Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Lesley A Stanley
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital & Medical School, University of Dundee, Dundee DD1 9SY, UK
| | - Charles Roland Wolf
- Division of Cancer Research, Medical Research Institute, Jacqui Wood Cancer Centre, Ninewells Hospital & Medical School, University of Dundee, Dundee DD1 9SY, UK
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8
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Kimura M, Mizukami S, Watanabe Y, Hasegawa-Baba Y, Onda N, Yoshida T, Shibutani M. Disruption of spindle checkpoint function ahead of facilitation of cell proliferation by repeated administration of hepatocarcinogens in rats. J Toxicol Sci 2015; 40:855-71. [DOI: 10.2131/jts.40.855] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Masayuki Kimura
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
- Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University
| | - Sayaka Mizukami
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
- Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University
| | - Yousuke Watanabe
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
- Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University
| | - Yasuko Hasegawa-Baba
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
| | - Nobuhiko Onda
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
| | - Toshinori Yoshida
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
| | - Makoto Shibutani
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
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9
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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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Distinguishing between genotoxic and non-genotoxic hepatocarcinogens by gene expression profiling and bioinformatic pathway analysis. Sci Rep 2013; 3:2783. [PMID: 24089152 PMCID: PMC6505678 DOI: 10.1038/srep02783] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 09/06/2013] [Indexed: 01/09/2023] Open
Abstract
A rapid and sensitive method to determine the characteristics of carcinogens is needed. In this study, we used a microarray-based genomics approach, with a short-term in vivo model, in combination with insights from statistical and mechanistic analyses to determine the characteristics of carcinogens. Carcinogens were evaluated based on the different mechanisms involved in the responses to genotoxic carcinogens and non-genotoxic carcinogens. Gene profiling was performed at two time points after treatment with six training and four test carcinogens. We mapped the DEG (differentially expressed gene)-related pathways to analyze cellular processes, and we discovered significant mechanisms that involve critical cellular components. Classification results were further supported by Comet and Micronucleus assays. Mechanistic studies based on gene expression profiling enhanced our understanding of the characteristics of different carcinogens. Moreover, the efficiency of this study was demonstrated by the short-term nature of the animal experiments that were conducted.
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A toxicogenomic approach for the prediction of murine hepatocarcinogenesis using ensemble feature selection. PLoS One 2013; 8:e73938. [PMID: 24040119 PMCID: PMC3769381 DOI: 10.1371/journal.pone.0073938] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 07/24/2013] [Indexed: 01/19/2023] Open
Abstract
The current strategy for identifying the carcinogenicity of drugs involves the 2-year bioassay in male and female rats and mice. As this assay is cost-intensive and time-consuming there is a high interest in developing approaches for the screening and prioritization of drug candidates in preclinical safety evaluations. Predictive models based on toxicogenomics investigations after short-term exposure have shown their potential for assessing the carcinogenic risk. In this study, we investigated a novel method for the evaluation of toxicogenomics data based on ensemble feature selection in conjunction with bootstrapping for the purpose to derive reproducible and characteristic multi-gene signatures. This method was evaluated on a microarray dataset containing global gene expression data from liver samples of both male and female mice. The dataset was generated by the IMI MARCAR consortium and included gene expression profiles of genotoxic and nongenotoxic hepatocarcinogens obtained after treatment of CD-1 mice for 3 or 14 days. We developed predictive models based on gene expression data of both sexes and the models were employed for predicting the carcinogenic class of diverse compounds. Comparing the predictivity of our multi-gene signatures against signatures from literature, we demonstrated that by incorporating our gene sets as features slightly higher accuracy is on average achieved by a representative set of state-of-the art supervised learning methods. The constructed models were also used for the classification of Cyproterone acetate (CPA), Wy-14643 (WY) and Thioacetamid (TAA), whose primary mechanism of carcinogenicity is controversially discussed. Based on the extracted mouse liver gene expression patterns, CPA would be predicted as a nongenotoxic compound. In contrast, both WY and TAA would be classified as genotoxic mouse hepatocarcinogens.
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12
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Yafune A, Taniai E, Morita R, Akane H, Kimura M, Mitsumori K, Shibutani M. Immunohistochemical cellular distribution of proteins related to M phase regulation in early proliferative lesions induced by tumor promotion in rat two-stage carcinogenesis models. ACTA ACUST UNITED AC 2013; 66:1-11. [PMID: 23890812 DOI: 10.1016/j.etp.2013.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 06/02/2013] [Accepted: 07/01/2013] [Indexed: 10/26/2022]
Abstract
We have previously reported that 28-day treatment with hepatocarcinogens increases liver cells expressing p21(Cip1), a G1/S checkpoint protein, and M phase proteins, i.e., nuclear Cdc2, Aurora B, phosphorylated-Histone H3 (p-Histone H3) and heterochromatin protein 1α (HP1α), in rats. To examine the roles of these markers in the early stages of carcinogenesis, we investigated their cellular distribution in several carcinogenic target organs using rat two-stage carcinogenesis models. Promoting agents targeting the liver (piperonyl butoxide and methapyrilene hydrochloride), thyroid (sulfadimethoxine), urinary bladder (phenylethyl isothiocyanate), and forestomach and glandular stomach (catechol) were administered to rats after initiation treatment for the liver with N-diethylnitrosamine, thyroid with N-bis(2-hydroxypropyl)nitrosamine, urinary bladder with N-butyl-N-(4-hydroxybutyl)nitrosamine, and forestomach and glandular stomach with N-methyl-N'-nitro-N-nitrosoguanidine. Numbers of cells positive for nuclear Cdc2, Aurora B, p-Histone H3 and HP1α increased within preneoplastic lesions as determined by glutathione S-transferase placental form in the liver or phosphorylated p44/42 mitogen-activated protein kinase in the thyroid, and hyperplastic lesions having no known preneoplastic markers in the urinary bladder, forestomach and glandular stomach. Immunoreactive cells for p21(Cip1) were decreased within thyroid preneoplastic lesions; however, they were increased within liver preneoplastic lesions and hyperplastic lesions in other organs. These results suggest that M phase disruption commonly occur during the formation of preneoplastic lesions and hyperplastic lesions. Differences in the expression patterns of p21(Cip1) between thyroid preneoplastic and proliferative lesions in other organs may reflect differences in cell cycle regulation involving G1/S checkpoint function between proliferative lesions in each organ.
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Affiliation(s)
- Atsunori Yafune
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu-shi, Tokyo 183-8509, Japan; Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193, Japan
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Thompson CM, Gregory Hixon J, Proctor DM, Haws LC, Suh M, Urban JD, Harris MA. Assessment of genotoxic potential of Cr(VI) in the mouse duodenum: an in silico comparison with mutagenic and nonmutagenic carcinogens across tissues. Regul Toxicol Pharmacol 2012; 64:68-76. [PMID: 22705708 DOI: 10.1016/j.yrtph.2012.05.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 05/15/2012] [Accepted: 05/16/2012] [Indexed: 01/09/2023]
Abstract
In vitro studies on hexavalent chromium [Cr(VI)] indicate that reduced forms of this metal can interact with DNA and cause mutations. Recently, Cr(VI) was shown to induce intestinal tumors in mice; however, Cr(VI) elicited redox changes, cytotoxicity and hyperplasia - suggesting involvement of tissue injury rather than direct mutagenesis. Moreover, toxicogenomic analyses indicated limited evidence for DNA damage responses. Herein, we extend these toxicogenomic analyses by comparing the gene expression patterns elicited by Cr(VI) with those of four mutagenic and four nonmutagenic carcinogens. To date, toxicogenomic profiles for mutagenic and nonmutagenic duodenal carcinogens do not exist, thus duodenal gene changes in mice were compared to those elicited by hepatocarcinogens. Specifically, duodenal gene changes in mice following exposure to Cr(VI) in drinking water were compared to hepatic gene changes previously identified as potentially discriminating mutagenic and nonmutagenic hepatocarcinogens. Using multivariate statistical analyses (including logistic regression classification), the Cr(VI) gene responses clustered apart from mutagenic carcinogens and closely with nonmutagenic carcinogens. These findings are consistent with other intestinal data supporting a nonmutagenic mode of action (MOA). These findings may be useful as part of a full weight of evidence MOA evaluation for Cr(VI)-induced intestinal carcinogenesis. Limitations to this analysis will also be discussed.
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Taniai E, Yafune A, Kimura M, Morita R, Nakane F, Suzuki K, Mitsumori K, Shibutani M. Fluctuations in cell proliferation, apoptosis, and cell cycle regulation at the early stage of tumor promotion in rat two-stage carcinogenesis models. J Toxicol Sci 2012. [DOI: 10.2131/jts.37.1113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Eriko Taniai
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
- Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University
| | - Atsunori Yafune
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
- Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University
| | - Masayuki Kimura
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
| | - Reiko Morita
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
- Pathogenetic Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University
| | - Fumiyuki Nakane
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
| | - Kazuhiko Suzuki
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
| | - Kunitoshi Mitsumori
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
| | - Makoto Shibutani
- Laboratory of Veterinary Pathology, Tokyo University of Agriculture and Technology
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Doktorova TY, Pauwels M, Vinken M, Vanhaecke T, Rogiers V. Opportunities for an alternative integrating testing strategy for carcinogen hazard assessment? Crit Rev Toxicol 2011; 42:91-106. [DOI: 10.3109/10408444.2011.623151] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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16
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Pronk TE, van der Veen JW, Ezendam J, Van Loveren H, Pennings JL. Effects of pooling RNA from samples treated with different compounds for determining class specific biomarkers and processes in toxicogenomics. Toxicol In Vitro 2011; 25:1841-7. [DOI: 10.1016/j.tiv.2011.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 05/10/2011] [Accepted: 05/13/2011] [Indexed: 12/14/2022]
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17
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Adler S, Basketter D, Creton S, Pelkonen O, van Benthem J, Zuang V, Andersen KE, Angers-Loustau A, Aptula A, Bal-Price A, Benfenati E, Bernauer U, Bessems J, Bois FY, Boobis A, Brandon E, Bremer S, Broschard T, Casati S, Coecke S, Corvi R, Cronin M, Daston G, Dekant W, Felter S, Grignard E, Gundert-Remy U, Heinonen T, Kimber I, Kleinjans J, Komulainen H, Kreiling R, Kreysa J, Leite SB, Loizou G, Maxwell G, Mazzatorta P, Munn S, Pfuhler S, Phrakonkham P, Piersma A, Poth A, Prieto P, Repetto G, Rogiers V, Schoeters G, Schwarz M, Serafimova R, Tähti H, Testai E, van Delft J, van Loveren H, Vinken M, Worth A, Zaldivar JM. Alternative (non-animal) methods for cosmetics testing: current status and future prospects-2010. Arch Toxicol 2011; 85:367-485. [PMID: 21533817 DOI: 10.1007/s00204-011-0693-2] [Citation(s) in RCA: 358] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 03/03/2011] [Indexed: 01/09/2023]
Abstract
The 7th amendment to the EU Cosmetics Directive prohibits to put animal-tested cosmetics on the market in Europe after 2013. In that context, the European Commission invited stakeholder bodies (industry, non-governmental organisations, EU Member States, and the Commission's Scientific Committee on Consumer Safety) to identify scientific experts in five toxicological areas, i.e. toxicokinetics, repeated dose toxicity, carcinogenicity, skin sensitisation, and reproductive toxicity for which the Directive foresees that the 2013 deadline could be further extended in case alternative and validated methods would not be available in time. The selected experts were asked to analyse the status and prospects of alternative methods and to provide a scientifically sound estimate of the time necessary to achieve full replacement of animal testing. In summary, the experts confirmed that it will take at least another 7-9 years for the replacement of the current in vivo animal tests used for the safety assessment of cosmetic ingredients for skin sensitisation. However, the experts were also of the opinion that alternative methods may be able to give hazard information, i.e. to differentiate between sensitisers and non-sensitisers, ahead of 2017. This would, however, not provide the complete picture of what is a safe exposure because the relative potency of a sensitiser would not be known. For toxicokinetics, the timeframe was 5-7 years to develop the models still lacking to predict lung absorption and renal/biliary excretion, and even longer to integrate the methods to fully replace the animal toxicokinetic models. For the systemic toxicological endpoints of repeated dose toxicity, carcinogenicity and reproductive toxicity, the time horizon for full replacement could not be estimated.
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Affiliation(s)
- Sarah Adler
- Centre for Documentation and Evaluation of Alternatives to Animal Experiments (ZEBET), Federal Institute for Risk Assessment (BfR), Berlin, Germany
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18
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Hakvoort TBM, Moerland PD, Frijters R, Sokolović A, Labruyère WT, Vermeulen JLM, Ver Loren van Themaat E, Breit TM, Wittink FRA, van Kampen AHC, Verhoeven AJ, Lamers WH, Sokolović M. Interorgan coordination of the murine adaptive response to fasting. J Biol Chem 2011; 286:16332-43. [PMID: 21393243 DOI: 10.1074/jbc.m110.216986] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Starvation elicits a complex adaptive response in an organism. No information on transcriptional regulation of metabolic adaptations is available. We, therefore, studied the gene expression profiles of brain, small intestine, kidney, liver, and skeletal muscle in mice that were subjected to 0-72 h of fasting. Functional-category enrichment, text mining, and network analyses were employed to scrutinize the overall adaptation, aiming to identify responsive pathways, processes, and networks, and their regulation. The observed transcriptomics response did not follow the accepted "carbohydrate-lipid-protein" succession of expenditure of energy substrates. Instead, these processes were activated simultaneously in different organs during the entire period. The most prominent changes occurred in lipid and steroid metabolism, especially in the liver and kidney. They were accompanied by suppression of the immune response and cell turnover, particularly in the small intestine, and by increased proteolysis in the muscle. The brain was extremely well protected from the sequels of starvation. 60% of the identified overconnected transcription factors were organ-specific, 6% were common for 4 organs, with nuclear receptors as protagonists, accounting for almost 40% of all transcriptional regulators during fasting. The common transcription factors were PPARα, HNF4α, GCRα, AR (androgen receptor), SREBP1 and -2, FOXOs, EGR1, c-JUN, c-MYC, SP1, YY1, and ETS1. Our data strongly suggest that the control of metabolism in four metabolically active organs is exerted by transcription factors that are activated by nutrient signals and serves, at least partly, to prevent irreversible brain damage.
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Affiliation(s)
- Theodorus B M Hakvoort
- Tytgat Institute for Liver and Intestinal Research (formerly AMC Liver Center), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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19
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Bruning O, Yuan X, Rodenburg W, Bruins W, van Oostrom CT, Rauwerda H, Wittink FR, Jonker MJ, de Vries A, Breit TM. Serious complications in gene-expression studies with stress perturbation: An example of UV-exposed p53-mutant mouse embryonic fibroblasts. Transcription 2011; 1:159-164. [PMID: 21326892 DOI: 10.4161/trns.1.3.13487] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/30/2010] [Accepted: 08/30/2010] [Indexed: 01/06/2023] Open
Abstract
Reanalysis of our UV study of p53-mutant mouse embryonic fibroblasts revealed an intriguing orchestration of massive transcriptome responses. However, close scrutiny of the data uncovered an affected mRNA/rRNA ratio, effectively inhibiting valid data analysis. UV-dose range-finding showed low-dose UV specific- and high-dose stress-related responses, which represent a plea for UV dose range-finding in experimental design.
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Affiliation(s)
- Oskar Bruning
- MicroArray Department and Integrative Bioinformatics Unit (MAD-IBU); Swammerdam Institute for Life Sciences; Faculty of Science; University of Amsterdam (UvA); Amsterdam, The Netherlands
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20
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van Dartel DAM, Pennings JLA, de la Fonteyne LJJ, Brauers KJJ, Claessen S, van Delft JH, Kleinjans JCS, Piersma AH. Concentration-dependent gene expression responses to flusilazole in embryonic stem cell differentiation cultures. Toxicol Appl Pharmacol 2010; 251:110-8. [PMID: 21192963 DOI: 10.1016/j.taap.2010.12.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 12/15/2010] [Accepted: 12/17/2010] [Indexed: 01/09/2023]
Abstract
The murine embryonic stem cell test (EST) is designed to evaluate developmental toxicity based on compound-induced inhibition of embryonic stem cell (ESC) differentiation into cardiomyocytes. The addition of transcriptomic evaluation within the EST may result in enhanced predictability and improved characterization of the applicability domain, therefore improving usage of the EST for regulatory testing strategies. Transcriptomic analyses assessing factors critical for risk assessment (i.e. dose) are needed to determine the value of transcriptomic evaluation in the EST. Here, using the developmentally toxic compound, flusilazole, we investigated the effect of compound concentration on gene expression regulation and toxicity prediction in ESC differentiation cultures. Cultures were exposed for 24 h to multiple concentrations of flusilazole (0.54-54 μM) and RNA was isolated. In addition, we sampled control cultures 0, 24, and 48 h to evaluate the transcriptomic status of the cultures across differentiation. Transcriptomic profiling identified a higher sensitivity of development-related processes as compared to cell division-related processes in flusilazole-exposed differentiation cultures. Furthermore, the sterol synthesis-related mode of action of flusilazole toxicity was detected. Principal component analysis using gene sets related to normal ESC differentiation was used to describe the dynamics of ESC differentiation, defined as the 'differentiation track'. The concentration-dependent effects on development were reflected in the significance of deviation of flusilazole-exposed cultures from this transcriptomic-based differentiation track. Thus, the detection of developmental toxicity in EST using transcriptomics was shown to be compound concentration-dependent. This study provides further insight into the possible application of transcriptomics in the EST as an improved alternative model system for developmental toxicity testing.
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Affiliation(s)
- Dorien A M van Dartel
- Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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21
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Yuan X, Jonker MJ, de Wilde J, Verhoef A, Wittink FR, van Benthem J, Bessems JG, Hakkert BC, Kuiper RV, van Steeg H, Breit TM, Luijten M. Finding maximal transcriptome differences between reprotoxic and non-reprotoxic phthalate responses in rat testis. J Appl Toxicol 2010; 31:421-30. [DOI: 10.1002/jat.1601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 08/30/2010] [Accepted: 08/31/2010] [Indexed: 11/07/2022]
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22
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van Dartel DAM, Pennings JLA, de la Fonteyne LJJ, van Herwijnen MH, van Delft JH, van Schooten FJ, Piersma AH. Monitoring developmental toxicity in the embryonic stem cell test using differential gene expression of differentiation-related genes. Toxicol Sci 2010; 116:130-9. [PMID: 20421339 DOI: 10.1093/toxsci/kfq127] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The embryonic stem cell test (EST) has been designed to predict developmental toxicity based upon compound-induced inhibition of embryonic stem cell (ESC) differentiation. The end point scoring, the test duration, and the definition of the predictivity and the applicability domain require improvements to facilitate implementation of the EST into regulatory testing strategies. The use of transcriptomics to study compound-induced differentiation modulation may improve the EST in each of these aspects. ESC differentiation was induced, and cell samples were collected after 0, 24, and 48 h of differentiation. Additionally, samples were collected that were 24 h exposed to one of five developmentally toxic compounds or a nondevelopmentally toxic compound. All samples were hybridized to Affymetrix GeneChips, and analyses revealed that 26 genes were significantly regulated both during ESC differentiation and by exposure to each of the developmentally toxic compounds tested. Using principal component analysis, we defined a "differentiation track" on the basis of this gene list, which represents ESC differentiation. We showed that significant deviation from the differentiation track was in line with the developmental toxic properties of the compounds. The significance of deviation was analyzed using the leave-one-out cross-validation, which showed a favorable prediction of toxicity in the system. Our findings show that gene expression signatures can be used to identify developmental toxicant-induced differentiation modulation. In addition, studying compound-induced effects at an early stage of differentiation combined with transcriptomics leads to increased objectivity in determining differentiation inhibition and to a reduction of the test duration. Furthermore, this approach may improve the predictivity and applicability domain of the EST.
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Affiliation(s)
- Dorien A M van Dartel
- Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands.
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Impact of the circadian clock on in vitro genotoxic risk assessment assays. Mutat Res 2009; 680:87-94. [PMID: 19751845 DOI: 10.1016/j.mrgentox.2009.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 09/04/2009] [Indexed: 01/10/2023]
Abstract
Our society expects safety assessment for drugs, chemicals, cosmetics, and foods, which to date cannot be achieved without the use of laboratory animals. At the same time, society aims at refining, reducing, and (ultimately) replacing animal testing. As a consequence, much effort is taken to establish alternatives, such as toxicogenomics-based risk assessment assays on cultured cells and tissues. Evidently, the properties of cells in vitro will considerably differ from the in vivo situation. This review will discuss the impact of the circadian clock, an internal time keeping system that drives 24-h rhythms in metabolism, physiology and behavior, on in vitro genotoxic risk assessment. Our recent observation that DNA damaging agents can synchronize the circadian clock of individual cells in culture (and as a consequence the cyclic expression of clock-controlled genes, comprising up to 10% of the transcriptome) implies that the circadian clock should not be neglected when developing cell or tissue-based alternatives for chronic rodent toxicity assays.
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