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Mennen R, Hallmark N, Pallardy M, Bars R, Tinwell H, Piersma A. Genome-wide expression screening in the cardiac embryonic stem cell test shows additional differentiation routes that are regulated by morpholines and piperidines. Curr Res Toxicol 2022; 3:100086. [PMID: 36157598 PMCID: PMC9489494 DOI: 10.1016/j.crtox.2022.100086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 08/08/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
The cardiac embryonic stem cell test showed additional differentiation routes. Morpholines and piperidines regulated the alternative differentiation routes. The gene expression levels help in understanding the applicability domain.
The cardiac embryonic stem cell test (ESTc) is a well-studied non-animal alternative test method based on cardiac cell differentiation inhibition as a measure for developmental toxicity of tested chemicals. In the ESTc, a heterogenic cell population is generated besides cardiomyocytes. Using the full biological domain of ESTc may improve the sensitivity of the test system, possibly broadening the range of chemicals for which developmental effects can be detected in the test. In order to improve our knowledge of the biological and chemical applicability domains of the ESTc, we applied a hypothesis-generating data-driven approach on control samples as follows. A genome-wide expression screening was performed, using Next Generation Sequencing (NGS), to map the range of developmental pathways in the ESTc and to search for a predictive embryotoxicity biomarker profile, instead of the conventional read-out of beating cardiomyocytes. The detected developmental pathways included circulatory system development, skeletal system development, heart development, muscle and organ tissue development, and nervous system and cell development. Two pesticidal chemical classes, the morpholines and piperidines, were assessed for perturbation of differentiation in the ESTc using NGS. In addition to the anticipated impact on cardiomyocyte differentiation, the other developmental pathways were also regulated, in a concentration–response fashion. Despite the structural differences between the morpholine and piperidine pairs, their gene expression effect patterns were largely comparable. In addition, some chemical-specific gene regulation was also observed, which may help with future mechanistic understanding of specific effects with individual test compounds. These similar and unique regulations of gene expression profiles by the test compounds, adds to our knowledge of the chemical applicability domain, specificity and sensitivity of the ESTc. Knowledge of both the biological and chemical applicability domain contributes to the optimal placement of ESTc in test batteries and in Integrated Approaches to Testing and Assessment (IATA).
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Affiliation(s)
- R.H. Mennen
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Corresponding author at: National Institute for Public Health and Environment (RIVM), Centre for Health Protection (GZB), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands.
| | - N. Hallmark
- Bayer AG Crop Science Division, Monheim, Germany
| | - M. Pallardy
- Inflammation, Microbiome and Immunosurveillance, Université Paris-Saclay, INSERM UMR996, Châtenay-Malabry 92296, France
| | - R. Bars
- Bayer Crop Science, Sophia-Antipolis, France
| | - H. Tinwell
- Bayer Crop Science, Sophia-Antipolis, France
| | - A.H. Piersma
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, the Netherlands
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Amini A, Chien S, Bayat M. Impact of Ultrasound Therapy on Stem Cell Differentiation - A Systematic Review. Curr Stem Cell Res Ther 2020; 15:462-472. [PMID: 32096749 DOI: 10.2174/1574888x15666200225124934] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 01/08/2020] [Accepted: 01/10/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE This is a systematic review of the effects of low-intensity pulsed ultrasound (LIPUS) on stem cell differentiation. BACKGROUND DATA Recent studies have investigated several types of stem cells from different sources in the body. These stem cells should strictly be certified and promoted for cell therapies before being used in medical applications. LIPUS has been used extensively in treatment centers and in research to promote stem cell differentiation, function, and proliferation. MATERIALS AND METHODS The databases of PubMed, Google Scholar, and Scopus were searched for abstracts and full-text scientific papers published from 1989-2019 that reported the application of LIPUS on stem cell differentiation. Related English language articles were found using the following defined keywords: low-intensity pulsed ultrasound, stem cell, differentiation. Criteria for inclusion in the review were: LIPUS with frequencies of 1-3 MHz and pulsed ultrasound intensity of <500 mW/cm2. Duration, exposure time, and cell sources were taken into consideration. RESULTS Fifty-two articles were selected based on the inclusion criteria. Most articles demonstrated that the application of LIPUS had positive effects on stem cell differentiation. However, some authors recommended that LIPUS combined with other physical therapy aides was more effective in stem cell differentiation. CONCLUSION LIPUS significantly increases the level of stem cell differentiation in cells derived mainly from bone marrow mesenchymal stem cells. There is a need for further studies to analyze the effect of LIPUS on cells derived from other sources, particularly adipose tissue-derived mesenchymal stem cells, for treating hard diseases, such as osteoporosis and diabetic foot ulcer. Due to a lack of reporting on standard LIPUS parameters in the field, more experiments comparing the protocols for standardization of LIPUS parameters are needed to establish the best protocol, which would allow for the best results.
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Affiliation(s)
- Abdollah Amini
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sufan Chien
- Price Institute of Surgical Research, University of Louisville, Louisville, KY, United States
| | - Mohammad Bayat
- Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Price Institute of Surgical Research, University of Louisville, Louisville, KY, United States
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3
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In vitro prenatal developmental toxicity induced by some petroleum substances is mediated by their 3- to 7-ring PAH constituent with a potential role for the aryl hydrocarbon receptor (AhR). Toxicol Lett 2019; 315:64-76. [DOI: 10.1016/j.toxlet.2019.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 07/05/2019] [Accepted: 08/03/2019] [Indexed: 12/31/2022]
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4
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Kamelia L, Louisse J, de Haan L, Rietjens IM, Boogaard PJ. Prenatal developmental toxicity testing of petroleum substances: Application of the mouse embryonic stem cell test (EST) to compare in vitro potencies with potencies observed in vivo. Toxicol In Vitro 2017; 44:303-312. [DOI: 10.1016/j.tiv.2017.07.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 07/19/2017] [Indexed: 11/16/2022]
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5
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Zhang YY, Tang LL, Zheng B, Ge RS, Zhu DY. Protein profiles of cardiomyocyte differentiation in murine embryonic stem cells exposed to perfluorooctane sulfonate. J Appl Toxicol 2016; 36:726-40. [PMID: 26178269 DOI: 10.1002/jat.3207] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 06/03/2015] [Accepted: 06/03/2015] [Indexed: 12/30/2022]
Abstract
Perfluorooctane sulfonate (PFOS) is a persistent organic contaminant that may affect diverse systems in animals and humans, including the cardiovascular system. However, little is known about the mechanism by which it affects the biological systems. Herein, we used embryonic stem cell test procedure as a tool to assess the developmental cardiotoxicity of PFOS. The differentially expressed proteins were identified by quantitative proteomics that combines the stable isotope labeling of amino acids with high-performance liquid chromatography-electrospray ionization tandem mass spectrometry. Results of the embryonic stem cell test procedure suggested that PFOS was a weak embryotoxic chemical. Nevertheless, a few marker proteins related to cardiovascular development (Brachyury, GATA4, MEF2C, α-actinin) were significantly reduced by exposure to PFOS. In total, 176 differential proteins were identified by proteomics analysis, of which 67 were upregulated and 109 were downregulated. Gene ontology annotation classified these proteins into 13 groups by molecular functions, 12 groups by cellular locations and 10 groups by biological processes. Most proteins were mainly relevant to either catalytic activity (25.6%), nucleus localization (28.9%) or to cellular component organization (19.8%). Pathway analysis revealed that 32 signaling pathways were affected, particularly these involved in metabolism. Changes in five proteins, including L-threonine dehydrogenase, X-ray repair cross-complementing 5, superoxide dismutase 2, and DNA methyltransferase 3b and 3a were confirmed by Western blotting, suggesting the reliability of the technique. These results revealed potential new targets of PFOS on the developmental cardiovascular system.
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Affiliation(s)
- Ying-Ying Zhang
- Institute of Pharmacology, Toxicology, and Biochemical Pharmaceutics, Zhejiang University, Hangzhou, China
| | - Lei-Lei Tang
- Institute of Pharmacology, Toxicology, and Biochemical Pharmaceutics, Zhejiang University, Hangzhou, China
| | - Bei Zheng
- Institute of Pharmacology, Toxicology, and Biochemical Pharmaceutics, Zhejiang University, Hangzhou, China
| | - Ren-Shan Ge
- Institute of Reproductive Biomedicine and the 2nd Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dan-Yan Zhu
- Institute of Pharmacology, Toxicology, and Biochemical Pharmaceutics, Zhejiang University, Hangzhou, China
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6
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Schulpen SH, Theunissen PT, Pennings JL, Piersma AH. Comparison of gene expression regulation in mouse- and human embryonic stem cell assays during neural differentiation and in response to valproic acid exposure. Reprod Toxicol 2015; 56:77-86. [DOI: 10.1016/j.reprotox.2015.06.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 12/15/2022]
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7
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Schulpen SHW, Pennings JLA, Piersma AH. Gene Expression Regulation and Pathway Analysis After Valproic Acid and Carbamazepine Exposure in a Human Embryonic Stem Cell-Based Neurodevelopmental Toxicity Assay. Toxicol Sci 2015; 146:311-20. [PMID: 25979313 DOI: 10.1093/toxsci/kfv094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Differentiating pluripotent stem cells in vitro have proven useful for the study of developmental toxicity. Here, we studied the effects of anticonvulsant drug exposure in a human embryonic stem cell (hESC)-based neurodevelopmental toxicity test (hESTn). During neural differentiation the cells were exposed, for either 1 or 7 days, to noncytotoxic concentration ranges of valproic acid (VPA) or carbamazepine (CBZ), antiepileptic drugs known to cause neurodevelopmental toxicity. The effects observed on gene expression and correlated processes and pathways were in line with processes associated with neural development and pharmaceutical mode of action. In general, VPA showed a higher number of genes and molecular pathways affected than CBZ. The response kinetics differed between both compounds, with CBZ showing higher response magnitudes at day 1, versus VPA at day 7. With this study, we demonstrated the potential and biological relevance of the application of this hESC-based differentiation assay in combination with transcriptomics, as a tool to study neurodevelopmental toxicity.
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Affiliation(s)
- Sjors H W Schulpen
- *Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands and Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jeroen L A Pennings
- *Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands and
| | - Aldert H Piersma
- *Laboratory for Health Protection Research, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands and Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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8
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Kroese ED, Bosgra S, Buist HE, Lewin G, van der Linden SC, Man HY, Piersma AH, Rorije E, Schulpen SHW, Schwarz M, Uibel F, van Vugt-Lussenburg BMA, Wolterbeek APM, van der Burg B. Evaluation of an alternative in vitro test battery for detecting reproductive toxicants in a grouping context. Reprod Toxicol 2014; 55:11-9. [PMID: 25461900 DOI: 10.1016/j.reprotox.2014.10.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 09/17/2014] [Accepted: 10/01/2014] [Indexed: 01/17/2023]
Abstract
Previously we showed a battery consisting of CALUX transcriptional activation assays, the ReProGlo assay, and the embryonic stem cell test, and zebrafish embryotoxicity assay as 'apical' tests to correctly predict developmental toxicity for 11 out of 12 compounds, and to explain the one false negative [7]. Here we report on applying this battery within the context of grouping and read across, put forward as a potential tool to fill data gaps and avoid animal testing, to distinguish in vivo non- or weak developmental toxicants from potent developmental toxicants within groups of structural analogs. The battery correctly distinguished 2-methylhexanoic acid, monomethyl phthalate, and monobutyltin trichloride as non- or weak developmental toxicants from structurally related developmental toxicants valproic acid, mono-ethylhexyl phthalate, and tributyltin chloride, respectively, and, therefore, holds promise as a biological verification model in grouping and read across approaches. The relevance of toxicokinetic information is indicated.
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Affiliation(s)
| | | | | | - Geertje Lewin
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), Hannover, Germany
| | | | - Hai-yen Man
- BioDetection Systems BV, Amsterdam, The Netherlands
| | - Aldert H Piersma
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands; Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Emiel Rorije
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sjors H W Schulpen
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Michael Schwarz
- Institute of Experimental and Clinical Pharmacology and Toxicology, Department of Toxicology, University of Tübingen, Tübingen, Germany
| | - Frederik Uibel
- Institute of Experimental and Clinical Pharmacology and Toxicology, Department of Toxicology, University of Tübingen, Tübingen, Germany
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9
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van Dartel DA, Schulpen SH, Theunissen PT, Bunschoten A, Piersma AH, Keijer J. Dynamic changes in energy metabolism upon embryonic stem cell differentiation support developmental toxicant identification. Toxicology 2014; 324:76-87. [DOI: 10.1016/j.tox.2014.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 02/06/2023]
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10
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Using Pluripotent Stem Cells and Their Progeny as an In VitroModel to Assess (Developmental) Neurotoxicity. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1002/9783527674183.ch13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Balmer NV, Klima S, Rempel E, Ivanova VN, Kolde R, Weng MK, Meganathan K, Henry M, Sachinidis A, Berthold MR, Hengstler JG, Rahnenführer J, Waldmann T, Leist M. From transient transcriptome responses to disturbed neurodevelopment: role of histone acetylation and methylation as epigenetic switch between reversible and irreversible drug effects. Arch Toxicol 2014; 88:1451-68. [PMID: 24935251 PMCID: PMC4067541 DOI: 10.1007/s00204-014-1279-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 05/19/2014] [Indexed: 01/17/2023]
Abstract
The superordinate principles governing the transcriptome response of differentiating cells exposed to drugs are still unclear. Often, it is assumed that toxicogenomics data reflect the immediate mode of action (MoA) of drugs. Alternatively, transcriptome changes could describe altered differentiation states as indirect consequence of drug exposure. We used here the developmental toxicants valproate and trichostatin A to address this question. Neurally differentiating human embryonic stem cells were treated for 6 days. Histone acetylation (primary MoA) increased quickly and returned to baseline after 48 h. Histone H3 lysine methylation at the promoter of the neurodevelopmental regulators PAX6 or OTX2 was increasingly altered over time. Methylation changes remained persistent and correlated with neurodevelopmental defects and with effects on PAX6 gene expression, also when the drug was washed out after 3-4 days. We hypothesized that drug exposures altering only acetylation would lead to reversible transcriptome changes (indicating MoA), and challenges that altered methylation would lead to irreversible developmental disturbances. Data from pulse-chase experiments corroborated this assumption. Short drug treatment triggered reversible transcriptome changes; longer exposure disrupted neurodevelopment. The disturbed differentiation was reflected by an altered transcriptome pattern, and the observed changes were similar when the drug was washed out during the last 48 h. We conclude that transcriptome data after prolonged chemical stress of differentiating cells mainly reflect the altered developmental stage of the model system and not the drug MoA. We suggest that brief exposures, followed by immediate analysis, are more suitable for information on immediate drug responses and the toxicity MoA.
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Affiliation(s)
- Nina V. Balmer
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Stefanie Klima
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Eugen Rempel
- Department of Statistics, TU Dortmund, Dortmund, Germany
| | - Violeta N. Ivanova
- Chair for Bioinformatics and Information Mining, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | | | - Matthias K. Weng
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Kesavan Meganathan
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Margit Henry
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Agapios Sachinidis
- Institute of Neurophysiology, University of Cologne, 50931 Cologne, Germany
| | - Michael R. Berthold
- Chair for Bioinformatics and Information Mining, University of Konstanz, Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
| | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), 44139 Dortmund, Germany
| | | | - Tanja Waldmann
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
| | - Marcel Leist
- Doerenkamp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, Box 657, 78457 Constance, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Constance, Germany
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12
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A statistical approach towards the derivation of predictive gene sets for potency ranking of chemicals in the mouse embryonic stem cell test. Toxicol Lett 2014; 225:342-9. [DOI: 10.1016/j.toxlet.2014.01.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/15/2014] [Accepted: 01/17/2014] [Indexed: 11/24/2022]
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13
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Evaluation of an alternative in vitro test battery for detecting reproductive toxicants. Reprod Toxicol 2013; 38:53-64. [PMID: 23511061 DOI: 10.1016/j.reprotox.2013.03.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/06/2013] [Accepted: 03/09/2013] [Indexed: 01/01/2023]
Abstract
The application of alternative methods in developmental and reproductive toxicology is challenging in view of the complexity of mechanisms involved. A battery of complementary test systems may provide a better prediction of developmental and reproductive toxicity than single assays. We tested twelve compounds with varying mechanisms of toxic action in an assay battery including 24 CALUX transcriptional activation assays, mouse cardiac embryonic stem cell test, ReProGlo assay, zebrafish embryotoxicity assay, and two CYP17 and two CYP19 activity assays. The battery correctly detected 11/12 compounds tested, with one false negative occurring, which could be explained by the absence of the specific mechanism of action of this compound in the battery. Toxicokinetic modeling revealed that toxic concentrations were in the range expected from in vivo reproductive toxicity data. This study illustrates added value of combining assays that contain complementary biological processes and mechanisms, increasing predictive value of the battery over individual assays.
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14
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Dose response analysis of monophthalates in the murine embryonic stem cell test assessed by cardiomyocyte differentiation and gene expression. Reprod Toxicol 2012; 35:81-8. [PMID: 22813628 DOI: 10.1016/j.reprotox.2012.07.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 06/12/2012] [Accepted: 07/03/2012] [Indexed: 11/20/2022]
Abstract
The embryonic stem cell test (EST) is based on compound-induced inhibition of cardiomyocyte differentiation of pluripotent stem cells. We examined the use of transcriptomics to assess concentration-effect relationships and performed potency ranking within a chemical class. Three embryotoxic phthalate monoesters, monobutyl phthalate (MBuP), monobenzyl phthalate (MBzP) and mono-(2-ethylhexyl) phthalate (MEHP) and the non-embryotoxic monomethyl phthalate (MMP) were studied for their effects on gene expression. Effects on gene expression were observed at concentrations that did not inhibit cardiomyocyte differentiation or induce cytotoxicity. The embryotoxic phthalate monoesters altered the expression of 668 commonly expressed genes in a concentration-dependent fashion. The same potency ranking was observed for morphology and gene expression (MEHP>MBzP>MBuP>MMP). These results indicate that integrating transcriptomics provides a sensitive method to measure the dose-dependent effects of phthalate monoester exposure and enables potency ranking based on a common mode of action within a class of compounds. Transcriptomic approaches may improve the applicability of the EST, in terms of sensitivity and specificity.
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15
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Sison-Young RLC, Kia R, Heslop J, Kelly L, Rowe C, Cross MJ, Kitteringham NR, Hanley N, Park BK, Goldring CEP. Human pluripotent stem cells for modeling toxicity. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2012; 63:207-256. [PMID: 22776643 DOI: 10.1016/b978-0-12-398339-8.00006-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The development of xenobiotics, driven by the demand for therapeutic, domestic and industrial uses continues to grow. However, along with this increasing demand is the risk of xenobiotic-induced toxicity. Currently, safety screening of xenobiotics uses a plethora of animal and in vitro model systems which have over the decades proven useful during compound development and for application in mechanistic studies of xenobiotic-induced toxicity. However, these assessments have proven to be animal-intensive and costly. More importantly, the prevalence of xenobiotic-induced toxicity is still significantly high, causing patient morbidity and mortality, and a costly impediment during drug development. This suggests that the current models for drug safety screening are not reliable in toxicity prediction, and the results not easily translatable to the clinic due to insensitive assays that do not recapitulate fully the complex phenotype of a functional cell type in vivo. Recent advances in the field of stem cell research have potentially allowed for a readily available source of metabolically competent cells for toxicity studies, derived using human pluripotent stem cells harnessed from embryos or reprogrammed from mature somatic cells. Pluripotent stem cell-derived cell types also allow for potential disease modeling in vitro for the purposes of drug toxicology and safety pharmacology, making this model possibly more predictive of drug toxicity compared with existing models. This article will review the advances and challenges of using human pluripotent stem cells for modeling metabolism and toxicity, and offer some perspectives as to where its future may lie.
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Affiliation(s)
- R L C Sison-Young
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom
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16
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Robinson JF, Pennings JLA, Piersma AH. A review of toxicogenomic approaches in developmental toxicology. Methods Mol Biol 2012; 889:347-371. [PMID: 22669676 DOI: 10.1007/978-1-61779-867-2_22] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Over the past decade, the use of gene expression profiling (i.e., toxicogenomics or transcriptomics) has been established as the vanguard "omics" technology to investigate exposure-induced molecular changes that underlie the development of disease. As this technology quickly advances, researchers are striving to keep pace in grasping the complexity of toxicogenomic response while at the same time determine its applicability for the field of developmental toxicology. Initial studies suggest toxicogenomics to be a promising tool for multiple types of study designs, including exposure-response investigations (dose and duration), chemical classification, and model comparisons. In this review, we examine the use of toxicogenomics in developmental toxicology, discussing biological and technical factors that influence response and interpretation. Additionally, we provide a framework to guide toxicogenomic investigations in the field of developmental toxicology.
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Affiliation(s)
- Joshua F Robinson
- National Institute for Public Health and the Environment-RIVM, Bilthoven, The Netherlands
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Suzuki N, Ando S, Yamashita N, Horie N, Saito K. Evaluation of Novel High-Throughput Embryonic Stem Cell Tests with New Molecular Markers for Screening Embryotoxic Chemicals In Vitro. Toxicol Sci 2011; 124:460-71. [DOI: 10.1093/toxsci/kfr250] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Seiler AEM, Spielmann H. The validated embryonic stem cell test to predict embryotoxicity in vitro. Nat Protoc 2011; 6:961-78. [DOI: 10.1038/nprot.2011.348] [Citation(s) in RCA: 198] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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van Dartel DAM, Piersma AH. The embryonic stem cell test combined with toxicogenomics as an alternative testing model for the assessment of developmental toxicity. Reprod Toxicol 2011; 32:235-44. [PMID: 21575713 DOI: 10.1016/j.reprotox.2011.04.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 04/20/2011] [Accepted: 04/29/2011] [Indexed: 01/15/2023]
Abstract
One of the most studied in vitro alternative testing methods for identification of developmental toxicity is the embryonic stem cell test (EST). Although the EST has been formally validated, the applicability domain as well as the predictability of the model needs further study to allow successful implementation of the EST as an alternative testing method in regulatory toxicity testing. Genomics technologies have already provided a proof of principle of their value in identification of toxicants such as carcinogenic compounds. Also within the EST, gene expression profiling has shown its value in the identification of developmental toxicity and in the evaluation of factors critical for risk assessment, such as dose and time responses. It is expected that the implementation of genomics into the EST will provide a more detailed end point evaluation as compared to the classical morphological scoring of differentiation cultures. Therefore, genomics may contribute to improvement of the EST, both in terms of definition of its applicability domain as well as its predictive capacity. In the present review, we present the progress that has been made with regard to the prediction of developmental toxicity using the EST combined with transcriptomics. Furthermore, we discuss the developments of additional aspects required for further optimization of the EST, including kinetics, the use of human embryonic stem cells (ESC) and computational toxicology. Finally, the current and future use of the EST model for prediction of developmental toxicity in testing strategies and in regulatory toxicity evaluations is discussed.
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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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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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van Dartel DAM, Pennings JLA, de la Fonteyne LJJ, Brauers KJJ, Claessen S, van Delft JH, Kleinjans JCS, Piersma AH. Evaluation of developmental toxicant identification using gene expression profiling in embryonic stem cell differentiation cultures. Toxicol Sci 2010; 119:126-34. [PMID: 20935163 DOI: 10.1093/toxsci/kfq291] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The murine embryonic stem cell test (EST) is an alternative testing method designed to assess potential developmental toxicity of compounds. The implementation of transcriptomics in the EST has been shown to reduce the culture duration and improve endpoint evaluation and is expected to result in an enhanced predictability and definition of the applicability domain. We evaluated the identification of developmental toxicity in the EST using two gene sets ("Van_Dartel_heartdiff_24h" and "EST biomarker genes") defined in our earlier studies. Nonexposed embryonic stem cells (ESC) differentiation cultures were sampled 0, 24, and 48 h after initiation of differentiation. Additionally, cultures exposed to 12 diverse well-characterized positive and negative developmental toxicants were isolated 24 h after the onset of exposure. Inhibition of ESC differentiation was evaluated in parallel by morphological scoring on culture day 10. Transcriptomics analysis was conducted using the Affymetrix Gene Chips platform. We applied principal component analysis on the basis of the two predefined gene sets to define the "differentiation track" that represents ESC differentiation. The significance of derivations in the gene expression-based differentiation track because of compound exposures were evaluated to determine developmental toxicity of tested compounds. We successfully predicted developmental toxicity using transcriptomics for 83% (10/12) and 67% (8/12) of the compounds, respectively, using the two predefined gene sets ("Van_Dartel_heartdiff_24h" and "EST biomarker genes"). Our study suggests that the application of transcriptomics may improve the applicability of the EST for the prediction of the developmental toxicity of chemicals.
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Affiliation(s)
- Dorien A M van Dartel
- Laboratory for Health Protection Research, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands.
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Coordinated waves of gene expression during neuronal differentiation of embryonic stem cells as basis for novel approaches to developmental neurotoxicity testing. Cell Death Differ 2010; 18:383-95. [PMID: 20865013 DOI: 10.1038/cdd.2010.109] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
As neuronal differentiation of embryonic stem cells (ESCs) recapitulates embryonic neurogenesis, disturbances of this process may model developmental neurotoxicity (DNT). To identify the relevant steps of in vitro neurodevelopment, we implemented a differentiation protocol yielding neurons with desired electrophysiological properties. Results from focussed transcriptional profiling suggested that detection of non-cytotoxic developmental disturbances triggered by toxicants such as retinoic acid (RA) or cyclopamine was possible. Therefore, a broad transcriptional profile of the 20-day differentiation process was obtained. Cluster analysis of expression kinetics, and bioinformatic identification of overrepresented gene ontologies revealed waves of regulation relevant for DNT testing. We further explored the concept of superimposed waves as descriptor of ordered, but overlapping biological processes. The initial wave of transcripts indicated reorganization of chromatin and epigenetic changes. Then, a transient upregulation of genes involved in the formation and patterning of neuronal precursors followed. Simultaneously, a long wave of ongoing neuronal differentiation started. This was again superseded towards the end of the process by shorter waves of neuronal maturation that yielded information on specification, extracellular matrix formation, disease-associated genes and the generation of glia. Short exposure to lead during the final differentiation phase, disturbed neuronal maturation. Thus, the wave kinetics and the patterns of neuronal specification define the time windows and end points for examination of DNT.
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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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An abbreviated protocol for multilineage neural differentiation of murine embryonic stem cells and its perturbation by methyl mercury. Reprod Toxicol 2010; 29:383-92. [PMID: 20412851 DOI: 10.1016/j.reprotox.2010.04.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 04/08/2010] [Accepted: 04/09/2010] [Indexed: 12/19/2022]
Abstract
Alternative assays are highly desirable to reduce the extensive experimental animal use in developmental toxicity testing. In the present study, we developed an improved test system for assessing neurodevelopmental toxicity using differentiating embryonic stem cells. We advanced previously established methods by merging, modifying and abbreviating the original 20-day protocol into a more efficient 13-day neural differentiation protocol. Using morphological observation, immunocytochemistry, gene expression and flow cytometry, it was shown predominantly multiple lineages of neuroectodermal cells were formed in our protocol and to a lower extent, endodermal and mesodermal differentiated cell types. This abbreviated protocol should lead to an advanced screening method using morphology in combination with selected differentiation markers aimed at predicting neurodevelopmental toxicity. Finally, the assay was shown to express differential sensitivity to a model developmental neurotoxicant, methyl mercury.
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van Dartel DA, Pennings JL, van Schooten FJ, Piersma AH. Transcriptomics-based identification of developmental toxicants through their interference with cardiomyocyte differentiation of embryonic stem cells. Toxicol Appl Pharmacol 2010; 243:420-8. [DOI: 10.1016/j.taap.2009.12.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 12/15/2009] [Indexed: 11/16/2022]
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