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Tsai HHD, Ford LC, Burnett SD, Dickey AN, Wright FA, Chiu WA, Rusyn I. Informing Hazard Identification and Risk Characterization of Environmental Chemicals by Combining Transcriptomic and Functional Data from Human-Induced Pluripotent Stem-Cell-Derived Cardiomyocytes. Chem Res Toxicol 2024; 37:1428-1444. [PMID: 39046974 DOI: 10.1021/acs.chemrestox.4c00193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Environmental chemicals may contribute to the global burden of cardiovascular disease, but experimental data are lacking to determine which substances pose the greatest risk. Human-induced pluripotent stem cell (iPSC)-derived cardiomyocytes are a high-throughput cardiotoxicity model that is widely used to test drugs and chemicals; however, most studies focus on exploring electro-physiological readouts. Gene expression data may provide additional molecular insights to be used for both mechanistic interpretation and dose-response analyses. Therefore, we hypothesized that both transcriptomic and functional data in human iPSC-derived cardiomyocytes may be used as a comprehensive screening tool to identify potential cardiotoxicity hazards and risks of the chemicals. To test this hypothesis, we performed concentration-response analysis of 464 chemicals from 12 classes, including both pharmaceuticals and nonpharmaceutical substances. Functional effects (beat frequency, QT prolongation, and asystole), cytotoxicity, and whole transcriptome response were evaluated. Points of departure were derived from phenotypic and transcriptomic data, and risk characterization was performed. Overall, 244 (53%) substances were active in at least one phenotype; as expected, pharmaceuticals with known cardiac liabilities were the most active. Positive chronotropy was the functional phenotype activated by the largest number of tested chemicals. No chemical class was particularly prone to pose a potential hazard to cardiomyocytes; a varying proportion (10-44%) of substances in each class had effects on cardiomyocytes. Transcriptomic data showed that 69 (15%) substances elicited significant gene expression changes; most perturbed pathways were highly relevant to known key characteristics of human cardiotoxicants. The bioactivity-to-exposure ratios showed that phenotypic- and transcriptomic-based POD led to similar results for risk characterization. Overall, our findings demonstrate how the integrative use of in vitro transcriptomic and phenotypic data from iPSC-derived cardiomyocytes not only offers a complementary approach for hazard and risk prioritization, but also enables mechanistic interpretation of the in vitro test results to increase confidence in decision-making.
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Affiliation(s)
- Han-Hsuan D Tsai
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Lucie C Ford
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Sarah D Burnett
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Allison N Dickey
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, United States
| | - Fred A Wright
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, United States
- Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, United States
| | - Weihsueh A Chiu
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, Texas A&M University, College Station, Texas 77843, United States
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, United States
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Sharapova T, Talaty N, Buck WR, Fossey S, Liguori MJ, Van Vleet TR. Reduced hepatic global hydroxymethylation in mice treated with non-genotoxic carcinogens is transiently reversible with a methyl supplemented diet. Toxicol Appl Pharmacol 2021; 415:115439. [PMID: 33549593 DOI: 10.1016/j.taap.2021.115439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/20/2021] [Accepted: 01/31/2021] [Indexed: 01/05/2023]
Abstract
Non-genotoxic carcinogens (NGCs) are known to cause perturbations in DNA methylation, which can be an early event leading to changes in gene expression and the onset of carcinogenicity. Phenobarbital (PB) has been shown to alter liver DNA methylation and hydroxymethylation patterns in mice in a time dependent manner. The goals of this study were to assess if clofibrate (CFB), a well-studied rodent NGC, would produce epigenetic changes in mice similar to PB, and if a methyl donor supplementation (MDS) would modulate epigenetic and gene expression changes induced by phenobarbital. CByB6F1 mice were treated with 0.5% clofibrate or 0.14% phenobarbital for 7 and 28 days. A subgroup of PB treated and control mice were also fed MDS diet. Liquid Chromatography-Ionization Mass Spectrometry (LC-MS) was used to quantify global liver 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) levels. Gene expression analysis was conducted using Affymetrix microarrays. A decrease in liver 5hmC but not 5mC levels was observed upon treatment with both CFB and PB with varying time of onset. We observed moderate increases in 5hmC levels in PB-treated mice when exposed to MDS diet and lower expression levels of several phenobarbital induced genes involved in cell proliferation, growth, and invasion, suggesting an early modulating effect of methyl donor supplementation. Overall, epigenetic profiling can aid in identifying early mechanism-based biomarkers of non-genotoxic carcinogenicity and increases the quality of cancer risk assessment for candidate drugs. Global DNA methylation assessment by LC-MS is an informative first step toward understanding the risk of carcinogenicity.
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Affiliation(s)
- T Sharapova
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL, United States.
| | - N Talaty
- Discovery Platform Technologies, AbbVie Inc., North Chicago, IL, United States
| | - W R Buck
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL, United States
| | - S Fossey
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL, United States
| | - M J Liguori
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL, United States
| | - T R Van Vleet
- Investigative Toxicology and Pathology, AbbVie Inc., North Chicago, IL, United States
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Song J, Eghan K, Lee S, Park JS, Yoon S, Pimtong W, Kim WK. A Phenotypic and Genotypic Evaluation of Developmental Toxicity of Polyhexamethylene Guanidine Phosphate Using Zebrafish Embryo/Larvae. TOXICS 2020; 8:E33. [PMID: 32370250 PMCID: PMC7355787 DOI: 10.3390/toxics8020033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 11/16/2022]
Abstract
Polyhexamethylene guanidine-phosphate (PHMG-P), a guanidine-based cationic antimicrobial polymer, is an effective antimicrobial biocide, potent even at low concentrations. Due to its resilient bactericidal properties, it has been used extensively in consumer products. It was safely used until its use in humidifiers led to a catastrophic event in South Korea. Epidemiological studies have linked the use of PHMG-P as a humidifier disinfectant to pulmonary fibrosis. However, little is known about its harmful impacts other than pulmonary fibrosis. Thus, we applied a zebrafish embryo/larvae model to evaluate developmental and cardiotoxic effects and transcriptome changes using RNA-sequencing. Zebrafish embryos were exposed to 0.1, 0.2, 0.3, 0.4, 0.5, 1, and 2 mg/L of PHMG-P from 3 h to 96 h post fertilization. 2 mg/L of PHMG-P resulted in total mortality and an LC50 value at 96 h was determined at 1.18 mg/L. Significant developmental changes were not observed but the heart rate of zebrafish larvae was significantly altered. In transcriptome analysis, immune and inflammatory responses were significantly affected similarly to those in epidemiological studies. Our qPCR analysis (Itgb1b, TNC, Arg1, Arg2, IL-1β, Serpine-1, and Ptgs2b) also confirmed this following a 96 h exposure to 0.4 mg/L of PHMG-P. Based on our results, PHMG-P might induce lethal and cardiotoxic effects in zebrafish, and crucial transcriptome changes were linked to immune and inflammatory response.
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Affiliation(s)
- Jeongah Song
- Jeonbuk Department of Inhalation Research, Korea Institute of Toxicology, Jeongeup 56212, Korea;
| | - Kojo Eghan
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Korea; (K.E.); (S.L.); (J.-S.P.); (S.Y.)
- Human and Environmental Toxicology, University of Science and Technology, Daejeon 34113, Korea
| | - Sangwoo Lee
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Korea; (K.E.); (S.L.); (J.-S.P.); (S.Y.)
| | - Jong-Su Park
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Korea; (K.E.); (S.L.); (J.-S.P.); (S.Y.)
| | - Seokjoo Yoon
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Korea; (K.E.); (S.L.); (J.-S.P.); (S.Y.)
- Human and Environmental Toxicology, University of Science and Technology, Daejeon 34113, Korea
| | - Wittaya Pimtong
- Nano Environmental and Health Safety Research Team, National Nanotechnology Center, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | - Woo-Keun Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon 34114, Korea; (K.E.); (S.L.); (J.-S.P.); (S.Y.)
- Human and Environmental Toxicology, University of Science and Technology, Daejeon 34113, Korea
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Vahle JL, Anderson U, Blomme EA, Hoflack JC, Stiehl DP. Use of toxicogenomics in drug safety evaluation: Current status and an industry perspective. Regul Toxicol Pharmacol 2018; 96:18-29. [DOI: 10.1016/j.yrtph.2018.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 10/17/2022]
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Attoff K, Gliga A, Lundqvist J, Norinder U, Forsby A. Whole genome microarray analysis of neural progenitor C17.2 cells during differentiation and validation of 30 neural mRNA biomarkers for estimation of developmental neurotoxicity. PLoS One 2017; 12:e0190066. [PMID: 29261810 PMCID: PMC5738075 DOI: 10.1371/journal.pone.0190066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/07/2017] [Indexed: 01/01/2023] Open
Abstract
Despite its high relevance, developmental neurotoxicity (DNT) is one of the least studied forms of toxicity. Current guidelines for DNT testing are based on in vivo testing and they require extensive resources. Transcriptomic approaches using relevant in vitro models have been suggested as a useful tool for identifying possible DNT-generating compounds. In this study, we performed whole genome microarray analysis on the murine progenitor cell line C17.2 following 5 and 10 days of differentiation. We identified 30 genes that are strongly associated with neural differentiation. The C17.2 cell line can be differentiated into a co-culture of both neurons and neuroglial cells, giving a more relevant picture of the brain than using neuronal cells alone. Among the most highly upregulated genes were genes involved in neurogenesis (CHRDL1), axonal guidance (BMP4), neuronal connectivity (PLXDC2), axonogenesis (RTN4R) and astrocyte differentiation (S100B). The 30 biomarkers were further validated by exposure to non-cytotoxic concentrations of two DNT-inducing compounds (valproic acid and methylmercury) and one neurotoxic chemical possessing a possible DNT activity (acrylamide). Twenty-eight of the 30 biomarkers were altered by at least one of the neurotoxic substances, proving the importance of these biomarkers during differentiation. These results suggest that gene expression profiling using a predefined set of biomarkers could be used as a sensitive tool for initial DNT screening of chemicals. Using a predefined set of mRNA biomarkers, instead of the whole genome, makes this model affordable and high-throughput. The use of such models could help speed up the initial screening of substances, possibly indicating alerts that need to be further studied in more sophisticated models.
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Affiliation(s)
- Kristina Attoff
- Department of Neurochemistry, Stockholm University, Stockholm, Sweden
- * E-mail:
| | - Anda Gliga
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jessica Lundqvist
- Department of Neurochemistry, Stockholm University, Stockholm, Sweden
- Swetox, Karolinska Institutet, Unit of Toxicology Sciences, Södertälje, Sweden
| | - Ulf Norinder
- Swetox, Karolinska Institutet, Unit of Toxicology Sciences, Södertälje, Sweden
| | - Anna Forsby
- Department of Neurochemistry, Stockholm University, Stockholm, Sweden
- Swetox, Karolinska Institutet, Unit of Toxicology Sciences, Södertälje, Sweden
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Lievano F, Scarazzini L, Shen F, Duhig J, Jokinen J. The future of safety science is happening now: The modernization of the benefit-risk paradigm. Pharmacoepidemiol Drug Saf 2017; 26:869-874. [DOI: 10.1002/pds.4241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/28/2017] [Accepted: 05/07/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Fabio Lievano
- Pharmacovigilance and Patient Safety; AbbVie Inc.; North Chicago IL USA
| | - Linda Scarazzini
- Pharmacovigilance and Patient Safety; AbbVie Inc.; North Chicago IL USA
| | - Frank Shen
- Pharmacovigilance and Patient Safety; AbbVie Inc.; North Chicago IL USA
| | - James Duhig
- Pharmacovigilance and Patient Safety; AbbVie Inc.; North Chicago IL USA
| | - Jeremy Jokinen
- Pharmacovigilance and Patient Safety; AbbVie Inc.; North Chicago IL USA
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Yeakley JM, Shepard PJ, Goyena DE, VanSteenhouse HC, McComb JD, Seligmann BE. A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling. PLoS One 2017; 12:e0178302. [PMID: 28542535 PMCID: PMC5444820 DOI: 10.1371/journal.pone.0178302] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/10/2017] [Indexed: 11/18/2022] Open
Abstract
The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0.9) for 20,629 targets. Unlike many expression assays, TempO-Seq does not require RNA purification, cDNA synthesis, or capture of targeted RNA, and lacks a 3' end bias. To investigate the sensitivity of the TempO-Seq assay to identify significantly modulated compound-responsive genes, we derived whole transcriptome profiles from MCF-7 cells treated with the histone deacetylase inhibitor Trichostatin A (TSA) and identified more than 9,000 differentially expressed genes. The TSA profile for MCF-7 cells overlapped those for HL-60 and PC-3 cells in the Connectivity Map (cMAP) database, suggesting a common TSA-specific expression profile independent of baseline gene expression. A 43-gene cell-independent TSA signature was extracted from cMAP and confirmed in TempO-Seq MCF-7 data. Additional genes that were not previously reported to be TSA responsive in the cMAP database were also identified. TSA treatment of 5 cell types revealed 1,136 differentially expressed genes in common, including 785 genes not previously reported to be TSA responsive. We conclude that TSA induces a specific expression signature that is consistent across widely different cell types, that this signature contains genes not previously associated with TSA responses, and that TempO-Seq provides the sensitive differential expression detection needed to define such compound-specific, cell-independent, changes in expression.
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Affiliation(s)
- Joanne M. Yeakley
- BioSpyder Technologies, Incorporated, Carlsbad, California, United States of America
- * E-mail:
| | - Peter J. Shepard
- BioSpyder Technologies, Incorporated, Carlsbad, California, United States of America
| | - Diana E. Goyena
- BioSpyder Technologies, Incorporated, Carlsbad, California, United States of America
| | | | - Joel D. McComb
- BioSpyder Technologies, Incorporated, Carlsbad, California, United States of America
| | - Bruce E. Seligmann
- BioSpyder Technologies, Incorporated, Carlsbad, California, United States of America
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Sutherland JJ, Webster YW, Willy JA, Searfoss GH, Goldstein KM, Irizarry AR, Hall DG, Stevens JL. Toxicogenomic module associations with pathogenesis: a network-based approach to understanding drug toxicity. THE PHARMACOGENOMICS JOURNAL 2017; 18:377-390. [DOI: 10.1038/tpj.2017.17] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/19/2017] [Accepted: 02/28/2017] [Indexed: 12/11/2022]
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Cornet C, Calzolari S, Miñana-Prieto R, Dyballa S, van Doornmalen E, Rutjes H, Savy T, D'Amico D, Terriente J. ZeGlobalTox: An Innovative Approach to Address Organ Drug Toxicity Using Zebrafish. Int J Mol Sci 2017; 18:E864. [PMID: 28422076 PMCID: PMC5412445 DOI: 10.3390/ijms18040864] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/07/2017] [Accepted: 04/14/2017] [Indexed: 02/06/2023] Open
Abstract
Toxicity is one of the major attrition causes during the drug development process. In that line, cardio-, neuro-, and hepatotoxicities are among the main reasons behind the retirement of drugs in clinical phases and post market withdrawal. Zebrafish exploitation in high-throughput drug screening is becoming an important tool to assess the toxicity and efficacy of novel drugs. This animal model has, from early developmental stages, fully functional organs from a physiological point of view. Thus, drug-induced organ-toxicity can be detected in larval stages, allowing a high predictive power on possible human drug-induced liabilities. Hence, zebrafish can bridge the gap between preclinical in vitro safety assays and rodent models in a fast and cost-effective manner. ZeGlobalTox is an innovative assay that sequentially integrates in vivo cardio-, neuro-, and hepatotoxicity assessment in the same animal, thus impacting strongly in the 3Rs principles. It Reduces, by up to a third, the number of animals required to assess toxicity in those organs. It Refines the drug toxicity evaluation through novel physiological parameters. Finally, it might allow the Replacement of classical species, such as rodents and larger mammals, thanks to its high predictivity (Specificity: 89%, Sensitivity: 68% and Accuracy: 78%).
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Affiliation(s)
- Carles Cornet
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
| | - Simone Calzolari
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
| | - Rafael Miñana-Prieto
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
| | - Sylvia Dyballa
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
| | - Els van Doornmalen
- Pivot Park Screening Centre (PPSC), Kloosterstraat 9, 5349AB OSS, The Netherland.
| | - Helma Rutjes
- Pivot Park Screening Centre (PPSC), Kloosterstraat 9, 5349AB OSS, The Netherland.
| | - Thierry Savy
- Multilevel Dynamics in Morphogenesis Unit, USR3695 CNRS, 91190 Gif sur Yvette, France.
| | - Davide D'Amico
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
| | - Javier Terriente
- ZeClinics SL, PRBB (Barcelona Biomedical Research Park), 08003 Barcelona, Spain.
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Ihlaseh-Catalano SM, Bailey KA, Cardoso APF, Ren H, Fry RC, Camargo JLV, Wolf DC. Dose and temporal effects on gene expression profiles of urothelial cells from rats exposed to diuron. Toxicology 2014; 325:21-30. [DOI: 10.1016/j.tox.2014.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/14/2014] [Accepted: 08/19/2014] [Indexed: 01/08/2023]
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11
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Integrated systems toxicology approaches identified the possible involvement of ABC transporters pathway in erythromycin estolate-induced liver injury in rat. Food Chem Toxicol 2014; 65:343-55. [DOI: 10.1016/j.fct.2013.12.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/30/2013] [Accepted: 12/31/2013] [Indexed: 02/08/2023]
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12
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Schneider CK. First-in-human trials with therapeutic proteins: regulatory rethink? Expert Rev Clin Pharmacol 2014; 1:327-31. [PMID: 24422687 DOI: 10.1586/17512433.1.3.327] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christian K Schneider
- Paul-Ehrlich-Institut, Federal Agency for Sera and Vaccines, Paul-Ehrlich-Straße 51-59, D-63225 Langen, Germany.
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13
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Application of “Omics” Technologies to In Vitro Toxicology. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2014. [DOI: 10.1007/978-1-4939-0521-8_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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14
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Sasseville VG, Mansfield KG, Brees DJ. Safety biomarkers in preclinical development: translational potential. Vet Pathol 2013; 51:281-91. [PMID: 24091814 DOI: 10.1177/0300985813505117] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The identification, application, and qualification of safety biomarkers are becoming increasingly critical to successful drug discovery and development as companies are striving to develop drugs for difficult targets and for novel disease indications in a risk-adverse environment. Translational safety biomarkers that are minimally invasive and monitor drug-induced toxicity during human clinical trials are urgently needed to assess whether toxicities observed in preclinical toxicology studies are relevant to humans at therapeutic doses. The interpretation of data during the biomarker qualification phase should include careful consideration of the analytic method used, the biology, pharmacokinetic and pharmacodynamic properties of the biomarker, and the pathophysiology of the process studied. The purpose of this review is to summarize commonly employed technologies in the development of fluid- and tissue-based safety biomarkers in drug discovery and development and to highlight areas of ongoing novel assay development.
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Affiliation(s)
- V G Sasseville
- Discovery and Investigative Safety, Preclinical Safety, Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA.
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Rodrigues RM, De Kock J, Branson S, Vinken M, Meganathan K, Chaudhari U, Sachinidis A, Govaere O, Roskams T, De Boe V, Vanhaecke T, Rogiers V. Human skin-derived stem cells as a novel cell source for in vitro hepatotoxicity screening of pharmaceuticals. Stem Cells Dev 2013; 23:44-55. [PMID: 23952781 DOI: 10.1089/scd.2013.0157] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human skin-derived precursors (hSKP) are postnatal stem cells with neural crest properties that reside in the dermis of human skin. These cells can be easily isolated from small (fore) skin segments and have the capacity to differentiate into multiple cell types. In this study, we show that upon exposure to hepatogenic growth factors and cytokines, hSKP acquire sufficient hepatic features that could make these cells suitable in vitro tools for hepatotoxicity screening of new chemical entities and already existing pharmaceutical compounds. Indeed, hepatic differentiated hSKP [hSKP-derived hepatic progenitor cells (hSKP-HPC)] express hepatic progenitor cell markers (EPCAM, NCAM2, PROM1) and adult hepatocyte markers (ALB), as well as key biotransformation enzymes (CYP1B1, FMO1, GSTA4, GSTM3) and influx and efflux drug transporters (ABCC4, ABCA1, SLC2A5). Using a toxicogenomics approach, we could demonstrate that hSKP-HPC respond to acetaminophen exposure in a comparable way to primary human hepatocytes in culture. The toxicological responses "liver damage", "liver proliferation", "liver necrosis" and "liver steatosis" were found to be significantly enriched in both in vitro models. Also genes associated with either cytotoxic responses or induction of apoptosis (BCL2L11, FOS, HMOX1, TIMP3, and AHR) were commonly upregulated and might represent future molecular biomarkers for hepatotoxicity. In conclusion, our data gives a first indication that hSKP-HPC might represent a suitable preclinical model for in vitro screening of hepatotoxicity. To the best of our knowledge, this is the first report in which human postnatal stem cells derived from skin are described as a potentially relevant cell source for in vitro hepatotoxicity testing of pharmaceutical compounds.
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Affiliation(s)
- Robim M Rodrigues
- 1 Department of Toxicology, Center for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB) , Brussels, Belgium
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Abstract
Adverse toxicologic effects are categorized as chemical-based, on-target, or off-target effects. Chemical-based toxicity is defined as toxicity that is related to the physicochemical characteristics of a compound and its effects on cellular organelles, membranes, and/or metabolic pathways. On-target refers to exaggerated and adverse pharmacologic effects at the target of interest in the test system. Off-target refers to adverse effects as a result of modulation of other targets; these may be related biologically or totally unrelated to the target of interest. Both the risk assessment and development strategies used for xenobiotics are influenced by the understanding of the mechanism of toxicity. It is imperative that the toxicologic pathologist use the toxicologic and biologic data at hand and literature information on the target to form testable hypotheses related to whether a toxicity is chemical-based, on-target, or off-target. The objective of this session at the 2012 Society of Toxicologic Pathologists Symposium in Boston, Massachusetts, was to discuss chemical-based, on-target, and off-target-based effects and the scientific approaches used to aid in their human risk assessment.
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Affiliation(s)
- Daniel G. Rudmann
- Eli Lilly and Company, Lilly Research Laboratories, Indianapolis, Indiana, USA
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17
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Chen M, Zhang M, Borlak J, Tong W. A Decade of Toxicogenomic Research and Its Contribution to Toxicological Science. Toxicol Sci 2012; 130:217-28. [DOI: 10.1093/toxsci/kfs223] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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McBurney RN, Hines WM, VonTungeln LS, Schnackenberg LK, Beger RD, Moland CL, Han T, Fuscoe JC, Chang CW, Chen JJ, Su Z, Fan XH, Tong W, Booth SA, Balasubramanian R, Courchesne PL, Campbell JM, Graber A, Guo Y, Juhasz P, Li TY, Lynch MD, Morel NM, Plasterer TN, Takach EJ, Zeng C, Beland FA. The liver toxicity biomarker study phase I: markers for the effects of tolcapone or entacapone. Toxicol Pathol 2012; 40:951-64. [PMID: 22573522 DOI: 10.1177/0192623312444026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Liver Toxicity Biomarker Study is a systems toxicology approach to discover biomarkers that are indicative of a drug's potential to cause human idiosyncratic drug-induced liver injury. In phase I, the molecular effects in rat liver and blood plasma induced by tolcapone (a "toxic" drug) were compared with the molecular effects in the same tissues by dosing with entacapone (a "clean" drug, similar to tolcapone in chemical structure and primary pharmacological mechanism). Two durations of drug exposure, 3 and 28 days, were employed. Comprehensive molecular analysis of rat liver and plasma samples yielded marker analytes for various drug-vehicle or drug-drug comparisons. An important finding was that the marker analytes associated with tolcapone only partially overlapped with marker analytes associated with entacapone, despite the fact that both drugs have similar chemical structures and the same primary pharmacological mechanism of action. This result indicates that the molecular analyses employed in the study are detecting substantial "off-target" markers for the two drugs. An additional interesting finding was the modest overlap of the marker data sets for 3-day exposure and 28-day exposure, indicating that the molecular changes in liver and plasma caused by short- and long-term drug treatments do not share common characteristics.
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Sellamuthu R, Umbright C, Roberts JR, Cumpston A, McKinney W, Chen BT, Frazer D, Li S, Kashon M, Joseph P. Molecular insights into the progression of crystalline silica-induced pulmonary toxicity in rats. J Appl Toxicol 2012; 33:301-12. [PMID: 22431001 DOI: 10.1002/jat.2733] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 01/11/2012] [Accepted: 01/11/2012] [Indexed: 01/28/2023]
Abstract
Identification of molecular target(s) and mechanism(s) of silica-induced pulmonary toxicity is important for the intervention and/or prevention of diseases associated with exposure to silica. Rats were exposed to crystalline silica by inhalation (15 mg m(-3), 6 h per day, 5 days) and global gene expression profile was determined in the lungs by microarray analysis at 1, 2, 4, 8 and 16 weeks following termination of silica exposure. The number of significantly differentially expressed genes (>1.5-fold change and <0.01 false discovery rate P-value) detected in the lungs during the post-exposure time intervals analyzed exhibited a steady increase in parallel with the progression of silica-induced pulmonary toxicity noticed in the rats. Quantitative real-time PCR analysis of a representative set of 10 genes confirmed the microarray findings. The number of biological functions, canonical pathways and molecular networks significantly affected by silica exposure, as identified by the bioinformatics analysis of the significantly differentially expressed genes detected during the post-exposure time intervals, also exhibited a steady increase similar to the silica-induced pulmonary toxicity. Genes involved in oxidative stress, inflammation, respiratory diseases, cancer, and tissue remodeling and fibrosis were significantly differentially expressed in the rat lungs; however, unresolved inflammation was the single most significant biological response to pulmonary exposure to silica. Excessive mucus production, as implicated by significant overexpression of the pendrin coding gene, SLC26A4, was identified as a potential novel mechanism for silica-induced pulmonary toxicity. Collectively, the findings of our study provided insights into the molecular mechanisms underlying the progression of crystalline silica-induced pulmonary toxicity in the rat. Published 2012. This article is a US Government work and is in the public domain in the USA.
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Affiliation(s)
- Rajendran Sellamuthu
- Toxicology and Molecular Biology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
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Shichor I, Shomron N, Lawlor MW, Bae SA, Zoldan J, Langer R, Kohane DS. Toxicogenomic analysis of a sustained release local anesthetic delivery system. Biomaterials 2012; 33:3586-93. [PMID: 22341215 DOI: 10.1016/j.biomaterials.2012.01.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 01/23/2012] [Indexed: 01/24/2023]
Abstract
Concerns over neurotoxicity have impeded the development of sustained release formulations providing prolonged duration local anesthesia (PDLA) from a single injection, for which there is an urgent clinical need. Here, we have used toxicogenomics to investigate whether nerve injury occurred during week-long continuous sciatic nerve blockade by microspheres containing bupivacaine, tetrodotoxin, and dexamethasone (TBD). Animals treated with amitriptyline solution (our positive control for local anesthetic-associated nerve injury) developed irreversible nerve blockade, had severely abnormal nerve histology, and the expression of hundreds of genes was altered in the dorsal root ganglia at 4 and 7 days after injection. In marked contrast, TBD-treated nerves reverted to normal function, were normal histologically and there were changes in the expression of a small number of genes. Toxicogenomic studies have great potential in delineating patterns of gene expression associated with specific patterns of tissue injury (e.g. amitriptyline neurotoxicity), and in identifying related changes in gene expression upon exposure to a drug, biomaterial, or drug delivery system.
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Affiliation(s)
- Iris Shichor
- Laboratory for Biomaterials and Drug Delivery, Department of Anesthesiology, Division of Critical Care Medicine, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Um SY, Park JH, Chung MW, Kim KB, Kim SH, Choi KH, Lee HJ. Nuclear magnetic resonance-based metabolomics for prediction of gastric damage induced by indomethacin in rats. Anal Chim Acta 2012; 722:87-94. [PMID: 22444538 DOI: 10.1016/j.aca.2012.01.062] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 12/30/2022]
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) have side effects including gastric erosions, ulceration and bleeding. In this study, pattern recognition analysis of the (1)H-nuclear magnetic resonance (NMR) spectra of urine was performed to develop surrogate biomarkers related to the gastrointestinal (GI) damage induced by indomethacin in rats. Urine was collected for 5 h after oral administration of indomethacin (25 mg kg(-1)) or co-administration with cimetidine (100 mg kg(-1)), which protects against GI damage. The (1)H-NMR urine spectra were divided into spectral bins (0.04 ppm) for global profiling, and 36 endogenous metabolites were assigned for targeted profiling. The level of gastric damage in each animal was also determined. Indomethacin caused severe gastric damage; however, indomethacin administered with cimetidine did not. Simultaneously, the patterns of changes in their endogenous metabolites were different. Multivariate data analyses were carried out to recognize the spectral pattern of endogenous metabolites related to indomethacin using partial least square-discrimination analysis. In targeted profiling, a few endogenous metabolites, 2-oxoglutarate, acetate, taurine and hippurate, were selected as putative biomarkers for the gastric damage induced by indomethacin. These metabolites changed depending on the degree of GI damage, although the same dose of indomethacin (10 mg kg(-1)) was administered to rats. The results of global and targeted profiling suggest that the gastric damage induced by NSAIDs can be screened in the preclinical stage of drug development using a NMR based metabolomics approach.
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Affiliation(s)
- So Young Um
- Department of Pharmacology, National Institute of Toxicological Research, Korea Food and Drug Administration, 643 Yeonje-ri, Gangoe-myeon, Cheongwon-gun, Chungbuk, South Korea
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Thomas CE, Will Y. The impact of assay technology as applied to safety assessment in reducing compound attrition in drug discovery. Expert Opin Drug Discov 2012; 7:109-22. [DOI: 10.1517/17460441.2012.651122] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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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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Robertson DG, Ruepp SU, Stryker SA, Hnatyshyn SY, Shipkova PA, Aranibar N, Mcnaney CA, Fiehn O, Reily MD. Metabolomic and transcriptomic changes induced by overnight (16 h) fasting in male and female Sprague-Dawley rats. Chem Res Toxicol 2011; 24:481-7. [PMID: 21381695 DOI: 10.1021/tx200074f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The overnight (16-h) fast is one of the most common experimental manipulations performed in rodent studies. Despite its ubiquitous employment, a comprehensive evaluation of metabolomic and transcriptomic sequelae of fasting in conjunction with routine clinical pathology evaluation has not been undertaken. This study assessed the impact of a 16-h fast on urine and serum metabolic profiles, transcript profiles of liver, psoas muscle, and jejunum as well as on routine laboratory clinical pathology parameters. Fasting rats had an approximate 12% relative weight decrease compared to ad libitum fed animals, and urine volume was significantly increased. Fasting had no effect on hematology parameters, though several changes were evident in serum and urine clinical chemistry data. In general, metabolic changes in biofluids were modest in magnitude but broad in extent, with a majority of measured urinary metabolites and from 1/3 to 1/2 of monitored serum metabolites significantly affected. Increases in fatty acids and bile acids dominated the upregulated metabolites. Downregulated serum metabolites were dominated by diet-derived and/or gut-microflora derived metabolites. Major transcriptional changes included genes with roles in fatty acid, carbohydrate, cholesterol, and bile acid metabolism indicating decreased activity in glycolytic pathways and a shift toward increased utilization of fatty acids. Typically, several genes within these metabolic pathways, including key rate limiting genes, changed simultaneously, and those changes were frequently correlative to changes in clinical pathology parameters or metabolomic data. Importantly, up- or down-regulation of a variety of cytochrome P450s, transporters, and transferases was evident. Taken together, these data indicate profound consequences of fasting on systemic biochemistry and raise the potential for unanticipated interactions, particularly when metabolomic or transcriptomic data are primary end points.
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Affiliation(s)
- Donald G Robertson
- Applied and Investigative Metabolomics, Bristol-Myers Squibb Co., Princeton, NJ 08543, USA.
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Afshari CA, Hamadeh HK, Bushel PR. The evolution of bioinformatics in toxicology: advancing toxicogenomics. Toxicol Sci 2010; 120 Suppl 1:S225-37. [PMID: 21177775 DOI: 10.1093/toxsci/kfq373] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
As one reflects back through the past 50 years of scientific research, a significant accomplishment was the advance into the genomic era. Basic research scientists have uncovered the genetic code and the foundation of the most fundamental building blocks for the molecular activity that supports biological structure and function. Accompanying these structural and functional discoveries is the advance of techniques and technologies to probe molecular events, in time, across environmental and chemical exposures, within individuals, and across species. The field of toxicology has kept pace with advances in molecular study, and the past 50 years recognizes significant growth and explosive understanding of the impact of the compounds and environment to basic cellular and molecular machinery. The advancement of molecular techniques applied in a whole-genomic capacity to the study of toxicant effects, toxicogenomics, is no doubt a significant milestone for toxicological research. Toxicogenomics has also provided an avenue for advancing a joining of multidisciplinary sciences including engineering and informatics in traditional toxicological research. This review will cover the evolution of the field of toxicogenomics in the context of informatics integration its current promise, and limitations.
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Affiliation(s)
- Cynthia A Afshari
- Department of Comparative Biology and Safety Sciences, Amgen Inc., Thousand Oaks, California 91320, USA.
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Toxicogenomics and cancer risk assessment: A framework for key event analysis and dose–response assessment for nongenotoxic carcinogens. Regul Toxicol Pharmacol 2010; 58:369-81. [DOI: 10.1016/j.yrtph.2010.08.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 08/01/2010] [Accepted: 08/09/2010] [Indexed: 11/20/2022]
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Abstract
Large inter-individual variability in drug response and toxicity, as well as in drug concentrations after application of the same dosage, can be of genetic, physiological, pathophysiological, or environmental origin. Absorption, distribution and metabolism of a drug and interactions with its target often are determined by genetic differences. Pharmacokinetic and pharmacodynamic variations can appear at the level of drug metabolizing enzymes (e.g., the cytochrome P450 system), drug transporters, drug targets or other biomarker genes. Pharmacogenetics or toxicogenetics can therefore be relevant in forensic toxicology. This review presents relevant aspects together with some examples from daily routines.
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Pettit S, des Etages SA, Mylecraine L, Snyder R, Fostel J, Dunn RT, Haymes K, Duval M, Stevens J, Afshari C, Vickers A. Current and future applications of toxicogenomics: Results summary of a survey from the HESI Genomics State of Science Subcommittee. ENVIRONMENTAL HEALTH PERSPECTIVES 2010; 118:992-7. [PMID: 20100679 PMCID: PMC2920921 DOI: 10.1289/ehp.0901501] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 01/25/2010] [Indexed: 05/22/2023]
Abstract
BACKGROUND In spite of the application of toxicogenomic (TGx) data to the field of toxicology for the past 10 years, the broad implementation and full impact of TGx for chemical and drug evaluation to improve decision making within organizations and by policy makers has not been achieved. OBJECTIVES The goal of the Health and Environmental Sciences Institute (HESI) Committee on the Application of Genomics to Mechanism-based Risk Assessment was to construct and summarize a multisector survey, addressing key issues and perspectives on the current and future practical uses and challenges of implementing TGx data to facilitate discussions for decision making within organizations and by policy makers. METHODS An online survey to probe the current status and future challenges facing the field of TGx for drug and chemical evaluation in experimental and nonclinical models was taken by scientists and scientific decision/policy makers actively engaged in the field of TGx within industrial, academic, and regulatory sectors of the United States, Europe, and Japan. For this survey, TGx refers specifically to the analysis of gene expression responses to evaluate xenobiotic exposure in experimental and preclinical models. RESULTS The survey results are summarized from questions covering broad areas including technology used, organizational capacity and resource allocation, experimental approaches, data storage and exchange, perceptions of benefits and hurdles, and future expectations. CONCLUSIONS The survey findings provide valuable information on the current state of the science of TGx applications and identify key areas in which TGx will have an impact as well as the key hurdles in applying TGx data to address issues. The findings serve as a public resource to facilitate discussions on the focus of future TGx efforts to ensure that a maximal benefit can be obtained from toxicogenomic studies.
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Affiliation(s)
- Syril Pettit
- ILSI Health and Environmental Sciences Institute, Washington, DC 20005, USA.
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29
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Eimon PM, Rubinstein AL. The use of in vivo zebrafish assays in drug toxicity screening. Expert Opin Drug Metab Toxicol 2010; 5:393-401. [PMID: 19368493 DOI: 10.1517/17425250902882128] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Anecdotal evidence has long suggested that zebrafish may be a good model to predict toxicity of human drugs. As summarized in this review, several groups have recently conducted systematic evaluations of zebrafish toxicity end points using large numbers of pharmacologically relevant compounds. Assays of particular interest include those for cardiotoxicity, ototoxicity, seizure liability, developmental toxicity and gastrointestinal motility. Results suggest that zebrafish assays can attain an acceptable level of predictivity, ranging from "sufficient" (65 - 75% predictivity) to "good" (75 - 85% predictivity) based on guidelines established for novel in vitro tests by the European Centre for the Validation of Alternative Methods. Further validation will probably be required to definitely establish zebrafish as a standard model for toxicity testing.
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Thompson K. Toxicogenomics and studies of genomic effects of dietary components. JOURNAL OF NUTRIGENETICS AND NUTRIGENOMICS 2010; 3:251-8. [PMID: 21474956 DOI: 10.1159/000324361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Karol Thompson
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
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Wills Q, Mitchell C. Toxicogenomics in drug discovery and development -- making an impact. Altern Lab Anim 2009; 37 Suppl 1:33-7. [PMID: 19807202 DOI: 10.1177/026119290903701s11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
As a branch of pharmacogenomics aimed at predicting drug safety concerns, toxicogenomics drew much excitement with the emergence of technologies such as gene expression microarrays. A few years down the line, the evidence is scant that current approaches to toxicogenomics are really making an impact in areas such as preclinical toxicology. It has been argued that there needs to be a re-focus of application toward high-throughput approaches which combine the best of tissue and genomic modelling. This commentary gives a brief introduction to in vitro toxicogenomics, drawn from the perspectives of the specialist toxicogenomics company, SimuGen.
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Ruden DM, Chen L, Possidente D, Possidente B, Rasouli P, Wang L, Lu X, Garfinkel MD, Hirsch HVB, Page GP. Genetical toxicogenomics in Drosophila identifies master-modulatory loci that are regulated by developmental exposure to lead. Neurotoxicology 2009; 30:898-914. [PMID: 19737576 DOI: 10.1016/j.neuro.2009.08.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 08/17/2009] [Accepted: 08/27/2009] [Indexed: 12/20/2022]
Abstract
The genetics of gene expression in recombinant inbred lines (RILs) can be mapped as expression quantitative trait loci (eQTLs). So-called "genetical genomics" studies have identified locally acting eQTLs (cis-eQTLs) for genes that show differences in steady-state RNA levels. These studies have also identified distantly acting master-modulatory trans-eQTLs that regulate tens or hundreds of transcripts (hotspots or transbands). We expand on these studies by performing genetical genomics experiments in two environments in order to identify trans-eQTL that might be regulated by developmental exposure to the neurotoxin lead. Flies from each of 75 RIL were raised from eggs to adults on either control food (made with 250 microM sodium acetate), or lead-treated food (made with 250 microM lead acetate, PbAc). RNA expression analyses of whole adult male flies (5-10 days old) were performed with Affymetrix DrosII whole genome arrays (18,952 probesets). Among the 1389 genes with cis-eQTL, there were 405 genes unique to control flies and 544 genes unique to lead-treated ones (440 genes had the same cis-eQTLs in both samples). There are 2396 genes with trans-eQTL which mapped to 12 major transbands with greater than 95 genes. Permutation analyses of the strain labels but not the expression data suggests that the total number of eQTL and the number of transbands are more important criteria for validation than the size of the transband. Two transbands, one located on the 2nd chromosome and one on the 3rd chromosome, co-regulate 33 lead-induced genes, many of which are involved in neurodevelopmental processes. For these 33 genes, rather than allelic variation at one locus exerting differential effects in two environments, we found that variation at two different loci are required for optimal effects on lead-induced expression.
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Affiliation(s)
- Douglas M Ruden
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201-2654, USA.
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Kapitulnik J, Pelkonen O, Gundert-Remy U, Dahl SG, Boobis AR. Effects of pharmaceuticals and other active chemicals at biological targets: mechanisms, interactions, and integration into PB-PK/PD models. Expert Opin Ther Targets 2009; 13:867-87. [DOI: 10.1517/14728220903018965] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Fabre N, Anglade I, Vericat JA. Application of toxicogenomic tools in the drug research and development process. Toxicol Lett 2009; 186:13-7. [PMID: 19373985 DOI: 10.1016/j.toxlet.2009.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The cost for the development of new active and safe drugs is higher than ever and continues to increase. At the same time, both the pharmaceutical industry and the Regulatory Authorities are, despite the increasing effort to develop safer drugs, concerned by the risk of unexpected side effects observed in the late steps of the development of new drugs, either in late clinical development or after marketing approval. Then, the early knowledge of any potential toxic effect of a new drug is a key issue to allow adequate decision making. This means that current approaches based on the determination of the No-Adverse-Effect-Level and the Human-Equivalent-Dose are far from being perfect, and fail mainly to detect toxic phenomena of low intensity and/or low frequency. To improve the predictability of the existing experimental models, Toxicogenomics could be included into the in vitro candidate-selection steps and/or during the regulatory preclinical (or clinical) studies. In this communication, the authors present an example of the use of Toxicogenomic data to support decision making when selecting a new candidate to regulatory development. The authors also present a second example of integration of Toxicogenomics with the animal regulatory studies within the preclinical development of a new drug.
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Affiliation(s)
- Nicolas Fabre
- NOSCIRA SA, Department of Preclinical Development, Spain.
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An FDA perspective on the nonclinical use of the X-Omics technologies and the safety of new drugs. Toxicol Lett 2009; 186:32-5. [DOI: 10.1016/j.toxlet.2008.08.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Revised: 08/25/2008] [Accepted: 08/25/2008] [Indexed: 11/22/2022]
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Blomme EA, Yang Y, Waring JF. Use of toxicogenomics to understand mechanisms of drug-induced hepatotoxicity during drug discovery and development. Toxicol Lett 2009; 186:22-31. [DOI: 10.1016/j.toxlet.2008.09.017] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 09/10/2008] [Accepted: 09/22/2008] [Indexed: 12/26/2022]
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Omic profiling for drug safety assessment: current trends and public–private partnerships. Drug Discov Today 2009; 14:337-42. [DOI: 10.1016/j.drudis.2009.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Burczynski M. Pharmacogenomic approaches in clinical studies to identify biomarkers of safety and efficacy. Toxicol Lett 2009; 186:18-21. [DOI: 10.1016/j.toxlet.2008.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 09/29/2008] [Accepted: 10/02/2008] [Indexed: 01/19/2023]
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Hirsch HVB, Possidente D, Averill S, Despain TP, Buytkins J, Thomas V, Goebel WP, Shipp-Hilts A, Wilson D, Hollocher K, Possidente B, Lnenicka G, Ruden DM. Variations at a quantitative trait locus (QTL) affect development of behavior in lead-exposed Drosophila melanogaster. Neurotoxicology 2009; 30:305-11. [PMID: 19428504 DOI: 10.1016/j.neuro.2009.01.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 12/31/2008] [Accepted: 01/12/2009] [Indexed: 12/01/2022]
Abstract
We developed Drosophila melanogaster as a model to study correlated behavioral, neuronal and genetic effects of the neurotoxin lead, known to affect cognitive and behavioral development in children. We showed that, as in vertebrates, lead affects both synaptic development and complex behaviors (courtship, fecundity, locomotor activity) in Drosophila. By assessing differential behavioral responses to developmental lead exposure among recombinant inbred Drosophila lines (RI), derived from parental lines Oregon R and Russian 2b, we have now identified a genotype by environment interaction (GEI) for a behavioral trait affected by lead. Drosophila Activity Monitors (TriKinetics, Waltham, MA), which measure activity by counting the number of times a single fly in a small glass tube walks through an infrared beam aimed at the middle of the tube, were used to measure activity of flies, reared from eggs to 4 days of adult age on either control or lead-contaminated medium, from each of 75 RI lines. We observed a significant statistical association between the effect of lead on Average Daytime Activity (ADA) across lines and one marker locus, 30AB, on chromosome 2; we define this as a Quantitative Trait Locus (QTL) associated with behavioral effects of developmental lead exposure. When 30AB was from Russian 2b, lead significantly increased locomotor activity, whereas, when 30AB was from Oregon R, lead decreased it. 30AB contains about 125 genes among which are likely "candidate genes" for the observed lead-dependent behavioral changes. Drosophila are thus a useful, underutilized model for studying behavioral, synaptic and genetic changes following chronic exposure to lead or other neurotoxins during development.
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Affiliation(s)
- Helmut V B Hirsch
- Department of Biology, University at Albany, SUNY, Albany, NY 12222, USA.
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40
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Lord P, Nie A, McMillian M. Collaborations Lay the Critical Path to Acceptance of Genomics in Drug Safety Assessment. Genomics 2008. [DOI: 10.3109/9781420067064-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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41
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