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Lejal V, Cerisier N, Rouquié D, Taboureau O. Assessment of Drug-Induced Liver Injury through Cell Morphology and Gene Expression Analysis. Chem Res Toxicol 2023; 36:1456-1470. [PMID: 37652439 PMCID: PMC10523580 DOI: 10.1021/acs.chemrestox.2c00381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Indexed: 09/02/2023]
Abstract
Drug-induced liver injury (DILI) is a significant concern in drug development, often leading to drug withdrawal. Although many studies aim to identify biomarkers and gene/pathway signatures related to liver toxicity and aim to predict DILI compounds, this remains a challenge in drug discovery. With a strong development of high-content screening/imaging (HCS/HCI) for phenotypic screening, we explored the morphological cell perturbations induced by DILI compounds. In the first step, cell morphological signatures were associated with two datasets of DILI chemicals (DILIRank and eTox). The mechanisms of action were then analyzed for chemicals having transcriptomics data and sharing similar morphological perturbations. Signaling pathways associated with liver toxicity (cell cycle, cell growth, apoptosis, ...) were then captured, and a hypothetical relation between cell morphological perturbations and gene deregulation was illustrated within our analysis. Finally, using the cell morphological signatures, machine learning approaches were developed to predict chemicals with a potential risk of DILI. Some models showed relevant performance with validation set balanced accuracies between 0.645 and 0.739. Overall, our findings demonstrate the utility of combining HCI with transcriptomics data to identify the morphological and gene expression signatures related to DILI chemicals. Moreover, our protocol could be extended to other toxicity end points, offering a promising avenue for comprehensive toxicity assessment in drug discovery.
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Affiliation(s)
- Vanille Lejal
- Université
Paris Cité, Inserm U1133, CNRS
UMR 8251, 75013, Paris, France
| | - Natacha Cerisier
- Université
Paris Cité, Inserm U1133, CNRS
UMR 8251, 75013, Paris, France
| | - David Rouquié
- Bayer
SAS, Bayer Crop Science, 355 rue Dostoïevski, CS 90153, 06906 Valbonne, Sophia-Antipolis, France
- Université
Côte d’Azur 3IA Interdisciplinary Institute in Artificial Intelligence, 06103 Nice Cedex, France
| | - Olivier Taboureau
- Université
Paris Cité, Inserm U1133, CNRS
UMR 8251, 75013, Paris, France
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2
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Straková P, Bednář P, Kotouček J, Holoubek J, Fořtová A, Svoboda P, Štefánik M, Huvarová I, Šimečková P, Mašek J, Gvozdev DA, Mikhnovets IE, Chistov AA, Nikitin TD, Krasilnikov MS, Ustinov AV, Alferova VA, Korshun VA, Růžek D, Eyer L. Antiviral activity of singlet oxygen-photogenerating perylene compounds against SARS-CoV-2: Interaction with the viral envelope and photodynamic virion inactivation. Virus Res 2023; 334:199158. [PMID: 37339718 PMCID: PMC10307035 DOI: 10.1016/j.virusres.2023.199158] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/09/2023] [Accepted: 06/18/2023] [Indexed: 06/22/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has prompted great interest in novel broad-spectrum antivirals, including perylene-related compounds. In the present study, we performed a structure-activity relationship analysis of a series of perylene derivatives, which comprised a large planar perylene residue, and structurally divergent polar groups connected to the perylene core by a rigid ethynyl or thiophene linker. Most of the tested compounds did not exhibit significant cytotoxicity towards multiple cell types susceptible to SARS-CoV-2 infection, and did not change the expressions of cellular stress-related genes under normal light conditions. These compounds showed nanomolar or sub-micromolar dose-dependent anti-SARS-CoV-2 activity, and also suppressed the in vitro replication of feline coronavirus (FCoV), also termed feline infectious peritonitis virus (FIPV). Perylene compounds exhibited high affinity for liposomal and cellular membranes, and efficiently intercalated into the envelopes of SARS-CoV-2 virions, thereby blocking the viral-cell fusion machinery. Furthermore, the studied compounds were demonstrated to be potent photosensitizers, generating reactive oxygen species (ROS), and their anti-SARS-CoV-2 activities were considerably enhanced after irradiation with blue light. Our results indicated that photosensitization is the major mechanism underlying the anti-SARS-CoV-2 activity of perylene derivatives, with these compounds completely losing their antiviral potency under red light. Overall, perylene-based compounds are broad-spectrum antivirals against multiple enveloped viruses, with antiviral action based on light-induced photochemical damage (ROS-mediated, likely singlet oxygen-mediated), causing impairment of viral membrane rheology.
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Affiliation(s)
- Petra Straková
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, CZ-621 00 Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-370 05 České Budějovice, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Petr Bednář
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, CZ-621 00 Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-370 05 České Budějovice, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, CZ-37005, Czech Republic
| | - Jan Kotouček
- Department of Pharmacology and Toxicology, Veterinary Research Institute, CZ-621 00 Brno, Czech Republic
| | - Jiří Holoubek
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, CZ-621 00 Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-370 05 České Budějovice, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Andrea Fořtová
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, CZ-621 00 Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Pavel Svoboda
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, CZ-621 00 Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-370 05 České Budějovice, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic; Department of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, CZ-612 42 Brno, Czech Republic
| | - Michal Štefánik
- Department of Chemistry and Biochemistry, Mendel University in Brno, CZ-61300 Brno, Czech Republic
| | - Ivana Huvarová
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, CZ-621 00 Brno, Czech Republic
| | - Pavlína Šimečková
- Department of Pharmacology and Toxicology, Veterinary Research Institute, CZ-621 00 Brno, Czech Republic
| | - Josef Mašek
- Department of Pharmacology and Toxicology, Veterinary Research Institute, CZ-621 00 Brno, Czech Republic
| | - Daniil A Gvozdev
- Department of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Igor E Mikhnovets
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Alexey A Chistov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Timofei D Nikitin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Maxim S Krasilnikov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Alexey V Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Vera A Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Daniel Růžek
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, CZ-621 00 Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-370 05 České Budějovice, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic
| | - Luděk Eyer
- Laboratory of Emerging Viral Diseases, Veterinary Research Institute, CZ-621 00 Brno, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, CZ-370 05 České Budějovice, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-62500 Brno, Czech Republic.
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3
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Wang X, Li W, Feng X, Li J, Liu GE, Fang L, Yu Y. Harnessing male germline epigenomics for the genetic improvement in cattle. J Anim Sci Biotechnol 2023; 14:76. [PMID: 37277852 PMCID: PMC10242889 DOI: 10.1186/s40104-023-00874-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/02/2023] [Indexed: 06/07/2023] Open
Abstract
Sperm is essential for successful artificial insemination in dairy cattle, and its quality can be influenced by both epigenetic modification and epigenetic inheritance. The bovine germline differentiation is characterized by epigenetic reprogramming, while intergenerational and transgenerational epigenetic inheritance can influence the offspring's development through the transmission of epigenetic features to the offspring via the germline. Therefore, the selection of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers. We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.
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Affiliation(s)
- Xiao Wang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Konge Larsen ApS, Kongens Lyngby, 2800, Denmark
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Wenlong Li
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xia Feng
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianbing Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Ying Yu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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4
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Wu S, Ellison C, Naciff J, Karb M, Obringer C, Yan G, Shan Y, Smith A, Wang X, Daston GP. Structure-activity relationship read-across and transcriptomics for branched carboxylic acids. Toxicol Sci 2023; 191:343-356. [PMID: 36583546 DOI: 10.1093/toxsci/kfac139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The purpose of this study was to use chemical similarity evaluations, transcriptional profiling, in vitro toxicokinetic data, and physiologically based pharmacokinetic (PBPK) models to support read-across for a series of branched carboxylic acids using valproic acid (VPA), a known developmental toxicant, as a comparator. The chemicals included 2-propylpentanoic acid (VPA), 2-ethylbutanoic acid, 2-ethylhexanoic acid (EHA), 2-methylnonanoic acid, 2-hexyldecanoic acid, 2-propylnonanoic acid (PNA), dipentyl acetic acid or 2-pentylheptanoic acid, octanoic acid (a straight chain alkyl acid), and 2-ethylhexanol. Transcriptomics was evaluated in 4 cell types (A549, HepG2, MCF7, and iCell cardiomyocytes) 6 h after exposure to 3 concentrations of the compounds, using the L1000 platform. The transcriptional profiling data indicate that 2- or 3-carbon alkyl substituents at the alpha position of the carboxylic acid (EHA and PNA) elicit a transcriptional profile similar to the one elicited by VPA. The transcriptional profile is different for the other chemicals tested, which provides support for limiting read-across from VPA to much shorter and longer acids. Molecular docking models for histone deacetylases, the putative target of VPA, provide a possible mechanistic explanation for the activity cliff elucidated by transcriptomics. In vitro toxicokinetic data were utilized in a PBPK model to estimate internal dosimetry. The PBPK modeling data show that as the branched chain increases, predicted plasma Cmax decreases. This work demonstrates how transcriptomics and other mode of action-based methods can improve read-across.
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Affiliation(s)
- Shengde Wu
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Corie Ellison
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Jorge Naciff
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Michael Karb
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Cindy Obringer
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Gang Yan
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Yuqing Shan
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Alex Smith
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - Xiaohong Wang
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
| | - George P Daston
- Global Product Stewardship, The Procter and Gamble Company, Mason, Ohio 45040, USA
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Naciff JM, Shan YK, Wang X, Daston GP. Article title: Transcriptional profiling efficacy to define biological activity similarity for cosmetic ingredients' safety assessment based on next-generation read-across. FRONTIERS IN TOXICOLOGY 2022; 4:1082222. [PMID: 36618549 PMCID: PMC9811170 DOI: 10.3389/ftox.2022.1082222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The objective of this work was to use transcriptional profiling to assess the biological activity of structurally related chemicals to define their biological similarity and with that, substantiate the validity of a read-across approach usable in risk assessment. Two case studies are presented, one with 4 short alkyl chain parabens: methyl (MP), ethyl (EP), butyl (BP), and propylparaben (PP), as well as their main metabolite, p-hydroxybenzoic acid (pHBA) with the assumption that propylparaben was the target chemical; and a second one with caffeine and its main metabolites theophylline, theobromine and paraxanthine where CA was the target chemical. The comprehensive transcriptional response of MCF7, HepG2, A549 and ICell cardiomyocytes was evaluated (TempO-Seq) after exposure to vehicle-control, each paraben or pHBA, CA or its metabolites, at 3 non-cytotoxic concentrations, for 6 h. Differentially expressed genes (FDR ≥0.05, and fold change ±1.2≥) were identified for each chemical, at each concentration, and used to determine similarities. Each of the chemicals is able to elicit changes in the expression of a number of genes, as compared to controls. Importantly, the transcriptional profile elicited by each of the parabens shares a high degree of similarity across the group. The highest number of genes commonly affected was between butylparaben and PP. The transcriptional profile of the parabens is similar to the one elicited by estrogen receptor agonists, with BP being the closest structural and biological analogue for PP. In the CA case, the transcriptional profile elicited of all four methylxanthines had a high degree of similarity across the cell types, with CA and theophylline being the most active. The most robust response was obtained in the cardiomyocytes with the highest transcriptional profile similarity between CA and TP. The transcriptional profile of the methylxanthines is similar to the one elicited by inhibitors of phosphatidylinositol 3-kinase as well as other kinase inhibitors. Overall, our results support the approach of incorporating transcriptional profiling in well-designed in vitro tests as one robust stream of data to support biological similarity driven read-across procedures and strengthening the traditional structure-based approaches useful in risk assessment.
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6
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Lee AJ, Mould DL, Crawford J, Hu D, Powers RK, Doing G, Costello JC, Hogan DA, Greene CS. SOPHIE: Generative Neural Networks Separate Common and Specific Transcriptional Responses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:912-927. [PMID: 36216026 PMCID: PMC10025681 DOI: 10.1016/j.gpb.2022.09.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 09/09/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
Genome-wide transcriptome profiling identifies genes that are prone to differential expression (DE) across contexts, as well as genes with changes specific to the experimental manipulation. Distinguishing genes that are specifically changed in a context of interest from common differentially expressed genes (DEGs) allows more efficient prediction of which genes are specific to a given biological process under scrutiny. Currently, common DEGs or pathways can only be identified through the laborious manual curation of experiments, an inordinately time-consuming endeavor. Here we pioneer an approach, Specific cOntext Pattern Highlighting In Expression data (SOPHIE), for distinguishing between common and specific transcriptional patterns using a generative neural network to create a background set of experiments from which a null distribution of gene and pathway changes can be generated. We apply SOPHIE to diverse datasets including those from human, human cancer, and bacterial pathogen Pseudomonas aeruginosa. SOPHIE identifies common DEGs in concordance with previously described, manually and systematically determined common DEGs. Further molecular validation indicates that SOPHIE detects highly specific but low-magnitude biologically relevant transcriptional changes. SOPHIE's measure of specificity can complement log2 fold change values generated from traditional DE analyses. For example, by filtering the set of DEGs, one can identify genes that are specifically relevant to the experimental condition of interest. Consequently, these results can inform future research directions. All scripts used in these analyses are available at https://github.com/greenelab/generic-expression-patterns. Users can access https://github.com/greenelab/sophie to run SOPHIE on their own data.
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Affiliation(s)
- Alexandra J Lee
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dallas L Mould
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jake Crawford
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dongbo Hu
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rani K Powers
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Georgia Doing
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - James C Costello
- Department of Pharmacology, University of Colorado School of Medicine, Denver, CO 80045, USA
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Health AI, University of Colorado School of Medicine, Denver, CO 80045, USA; Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Denver, CO 80045, USA.
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7
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Liu A, Han N, Munoz-Muriedas J, Bender A. Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI). PLoS Comput Biol 2022; 18:e1010148. [PMID: 35687583 PMCID: PMC9292124 DOI: 10.1371/journal.pcbi.1010148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 07/18/2022] [Accepted: 04/26/2022] [Indexed: 01/10/2023] Open
Abstract
Adverse event pathogenesis is often a complex process which compromises multiple events ranging from the molecular to the phenotypic level. In toxicology, Adverse Outcome Pathways (AOPs) aim to formalize this as temporal sequences of events, in which event relationships should be supported by causal evidence according to the tailored Bradford-Hill criteria. One of the criteria is whether events are consistently observed in a certain temporal order and, in this work, we study this time concordance using the concept of “first activation” as data-driven means to generate hypotheses on potentially causal mechanisms. As a case study, we analysed liver data from repeat-dose studies in rats from the TG-GATEs database which comprises measurements across eight timepoints, ranging from 3 hours to 4 weeks post-treatment. We identified time-concordant gene expression-derived events preceding adverse histopathology, which serves as surrogate readout for Drug-Induced Liver Injury (DILI). We find known mechanisms in DILI to be time-concordant, and show further that significance, frequency and log fold change (logFC) of differential expression are metrics which can additionally prioritize events although not necessary to be mechanistically relevant. Moreover, we used the temporal order of transcription factor (TF) expression and regulon activity to identify transcriptionally regulated TFs and subsequently combined this with prior knowledge on functional interactions to derive detailed gene-regulatory mechanisms, such as reduced Hnf4a activity leading to decreased expression and activity of Cebpa. At the same time, also potentially novel events are identified such as Sox13 which is highly significantly time-concordant and shows sustained activation over time. Overall, we demonstrate how time-resolved transcriptomics can derive and support mechanistic hypotheses by quantifying time concordance and how this can be combined with prior causal knowledge, with the aim of both understanding mechanisms of toxicity, as well as potential applications to the AOP framework. We make our results available in the form of a Shiny app (https://anikaliu.shinyapps.io/dili_cascades), which allows users to query events of interest in more detail. Understanding mechanisms from systems-scale biological data is of great relevance in toxicology as well as drug discovery; however how to generate causal hypotheses instead of correlations is by no means clear. In this work, we study the conserved temporal order of events and present an automatable framework to quantify and characterize time concordance across a large set of time-series. We apply this concept to events derived from time-resolved gene expression and histopathology from the TG-GATEs in vivo liver data as a case study. We were able to recover known events involved in the pathogenesis of Drug-Induced Liver Injury (DILI), and identify potentially novel pathway and transcription factors (TFs) which precede adverse histopathology. As complementary sources of evidence for causality, we additionally show how time concordance and prior knowledge on plausible interactions between TFs can be combined to derive causal hypotheses on the TFs’ mode of regulation and interaction partners. Overall, the results derived in our case study can serve as valuable hypothesis-free starting points for the development of Adverse Outcome Pathways for DILI, and demonstrate that our approach provides a novel angle to prioritize mechanistically relevant events.
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Affiliation(s)
- Anika Liu
- Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
- Systems Modelling and Translational Biology, Data and Computational Sciences, GSK, London, United Kingdom
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (AL); (AB)
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
- Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| | - Jordi Munoz-Muriedas
- Systems Modelling and Translational Biology, Data and Computational Sciences, GSK, London, United Kingdom
- Computer-Aided Drug Design, UCB, Slough, United Kingdom
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (AL); (AB)
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Šimečková P, Pěnčíková K, Kováč O, Slavík J, Pařenicová M, Vondráček J, Machala M. In vitro profiling of toxic effects of environmental polycyclic aromatic hydrocarbons on nuclear receptor signaling, disruption of endogenous metabolism and induction of cellular stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:151967. [PMID: 34843781 DOI: 10.1016/j.scitotenv.2021.151967] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/03/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) may interact with multiple intracellular receptors and related signaling pathways. We comprehensively evaluated the toxicity profiles of six environmentally relevant PAHs differing in structure, genotoxicity and their ability to activate the aryl hydrocarbon receptor (AhR). We focused particularly on their impact on intracellular hormone-, xenobiotic- and lipid-sensing receptors, as well as on cellular stress markers, combining a battery of human reporter gene assays and qRT-PCR evaluation of endogenous gene expression in human hepatocyte-like HepaRG cells, with LC/MS-MS analysis of cellular sphingolipids. The effects of PAHs included: activation of estrogen receptor α (in case of fluoranthene (Fla), pyrene (Pyr), benz[a]anthracene (BaA), benzo[a]pyrene (BaP)), suppression of androgen receptor activity (Fla, BaA, BaP and benzo[k]fluoranthene (BkF)), enhancement of dexamethasone-induced glucocorticoid receptor activity (chrysene (Chry), BaA, and BaP), and potentiation of triiodothyronine-induced thyroid receptor α activity (all tested PAHs). PAHs also induced transcription of endogenous gene targets of constitutive androstane receptor (Fla, Pyr), or repression of target genes of pregnane X receptor and peroxisome proliferator-activated receptor α (in case of the AhR-activating PAHs - Chry, BaA, BaP, and BkF) in HepaRG cells. In the same cell model, the AhR agonists reduced the expression of glucose metabolism genes (PCK1, G6PC and PDK4), and they up-regulated levels of glucosylceramides, together with a concomitant induction of expression of UGCG, glucosylceramide synthesis enzyme. Finally, both BaP and BkF were found to induce expression of early stress and genotoxicity markers: ATF3, EGR1, GDF15, CDKN1A/p21, and GADD45A mRNAs, while BaP alone increased levels of IL-6 mRNA. Overall, whereas low-molecular-weight PAHs exerted significant effects on nuclear receptors (with CYP2B6 induction observed already at nanomolar concentrations), the AhR activation by 4-ring and 5-ring PAHs appeared to be a key mechanism underlying their impact on nuclear receptor signaling, endogenous metabolism and induction of early stress and genotoxicity markers.
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Affiliation(s)
- Pavlína Šimečková
- Department of Pharmacology and Toxicology, Veterinary Research Institute, 62100 Brno, Czech Republic
| | - Kateřina Pěnčíková
- Department of Pharmacology and Toxicology, Veterinary Research Institute, 62100 Brno, Czech Republic
| | - Ondrej Kováč
- Department of Pharmacology and Toxicology, Veterinary Research Institute, 62100 Brno, Czech Republic
| | - Josef Slavík
- Department of Pharmacology and Toxicology, Veterinary Research Institute, 62100 Brno, Czech Republic
| | - Martina Pařenicová
- Department of Pharmacology and Toxicology, Veterinary Research Institute, 62100 Brno, Czech Republic
| | - Jan Vondráček
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic
| | - Miroslav Machala
- Department of Pharmacology and Toxicology, Veterinary Research Institute, 62100 Brno, Czech Republic.
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9
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Sturm G, List M, Zhang JD. Tissue heterogeneity is prevalent in gene expression studies. NAR Genom Bioinform 2021; 3:lqab077. [PMID: 34514392 PMCID: PMC8415427 DOI: 10.1093/nargab/lqab077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/01/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Lack of reproducibility in gene expression studies is a serious issue being actively addressed by the biomedical research community. Besides established factors such as batch effects and incorrect sample annotations, we recently reported tissue heterogeneity, a consequence of unintended profiling of cells of other origins than the tissue of interest, as a source of variance. Although tissue heterogeneity exacerbates irreproducibility, its prevalence in gene expression data remains unknown. Here, we systematically analyse 2 667 publicly available gene expression datasets covering 76 576 samples. Using two independent data compendia and a reproducible, open-source software pipeline, we find a prevalence of tissue heterogeneity in gene expression data that affects between 1 and 40% of the samples, depending on the tissue type. We discover both cases of severe heterogeneity, which may be caused by mistakes in annotation or sample handling, and cases of moderate heterogeneity, which are likely caused by tissue infiltration or sample contamination. Our analysis establishes tissue heterogeneity as a widespread phenomenon in publicly available gene expression datasets, which constitutes an important source of variance that should not be ignored. Consequently, we advocate the application of quality-control methods such as BioQC to detect tissue heterogeneity prior to mining or analysing gene expression data.
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Affiliation(s)
- Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Jitao David Zhang
- Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
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10
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Trairatphisan P, de Souza TM, Kleinjans J, Jennen D, Saez-Rodriguez J. Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury. Toxicol Lett 2021; 350:40-51. [PMID: 34229068 DOI: 10.1016/j.toxlet.2021.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/19/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022]
Abstract
In recent years, network-based methods have become an attractive analytical approach for toxicogenomics studies. They can capture not only the global changes of regulatory gene networks but also the relationships between their components. Among them, a causal reasoning approach depicts the mechanisms of regulation that connect upstream regulators in signaling networks to their downstream gene targets. In this work, we applied CARNIVAL, a causal network contextualisation tool, to infer upstream signaling networks deregulated in drug-induced liver injury (DILI) from gene expression microarray data from the TG-GATEs database. We focussed on six compounds that induce observable histopathologies linked to DILI from repeated dosing experiments in rats. We compared responses in vitro and in vivo to identify potential cross-platform concordances in rats as well as network preservations between rat and human. Our results showed similarities of enriched pathways and network motifs between compounds. These pathways and motifs induced the same pathology in rats but not in humans. In particular, the causal interactions "LCK activates SOCS3, which in turn inhibits TFDP1" was commonly identified as a regulatory path among the fibrosis-inducing compounds. This potential pathology-inducing regulation illustrates the value of our approach to generate hypotheses that can be further validated experimentally.
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Affiliation(s)
- Panuwat Trairatphisan
- Heidelberg University, Faculty of Medicine, Institute of Computational Biomedicine, 69120, Heidelberg, Germany.
| | - Terezinha Maria de Souza
- Department of Toxicogenomics (TGX), GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD, Maastricht, the Netherlands.
| | - Jos Kleinjans
- Department of Toxicogenomics (TGX), GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD, Maastricht, the Netherlands.
| | - Danyel Jennen
- Department of Toxicogenomics (TGX), GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD, Maastricht, the Netherlands.
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Institute of Computational Biomedicine, 69120, Heidelberg, Germany; RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), 52074, Aachen, Germany.
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11
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VanderMolen KM, Naciff JM, Kennedy K, Otto-Bruc A, Shan Y, Wang X, Daston GP, Mahony C. Incorporation of in vitro techniques for botanicals dietary supplement safety assessment - Towards evaluation of developmental and reproductive toxicity (DART). Food Chem Toxicol 2020; 144:111539. [PMID: 32645467 DOI: 10.1016/j.fct.2020.111539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 12/22/2022]
Abstract
As complex mixtures, botanicals present unique challenges when assessing safe use, particularly when endpoint gaps exist that cannot be fully resolved by existing toxicological literature. Here we explore in vitro gene expression as well receptor binding and enzyme activity as alternative assays to inform on developmental and reproductive toxicity (DART) relevant modes of action, since DART data gaps are common for botanicals. Specifically, botanicals suspected to have DART effects, in addition to those with a significant history of use, were tested in these assays. Gene expression changes in a number of different cell types were analysed using the connectivity mapping approach (CMap) to identify modes of action through a functional read across approach. Taken together with ligand affinity data obtained using a set of molecular targets customised towards known DART relevant modes of action, it was possible to inform DART risk using functional analogues, potency comparisons and a margin of internal exposure approach.
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Affiliation(s)
- Karen M VanderMolen
- Procter & Gamble, Mason Business Centre, 8700 Mason - Montgomery Rd, Mason, OH, 45040, USA
| | - Jorge M Naciff
- Procter & Gamble, Mason Business Centre, 8700 Mason - Montgomery Rd, Mason, OH, 45040, USA
| | - Kevin Kennedy
- Eurofins Discovery, Bioanalytical, St Charles, MO, USA
| | | | - Yuqing Shan
- Procter & Gamble, Mason Business Centre, 8700 Mason - Montgomery Rd, Mason, OH, 45040, USA
| | - Xiaohong Wang
- Procter & Gamble, Mason Business Centre, 8700 Mason - Montgomery Rd, Mason, OH, 45040, USA
| | - George P Daston
- Procter & Gamble, Mason Business Centre, 8700 Mason - Montgomery Rd, Mason, OH, 45040, USA
| | - Catherine Mahony
- Procter & Gamble Technical Centre, Whitehall Lane, Egham, Surrey, TW20 9AW, UK.
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12
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Badillo S, Banfai B, Birzele F, Davydov II, Hutchinson L, Kam‐Thong T, Siebourg‐Polster J, Steiert B, Zhang JD. An Introduction to Machine Learning. Clin Pharmacol Ther 2020; 107:871-885. [PMID: 32128792 PMCID: PMC7189875 DOI: 10.1002/cpt.1796] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/15/2020] [Indexed: 12/16/2022]
Abstract
In the last few years, machine learning (ML) and artificial intelligence have seen a new wave of publicity fueled by the huge and ever-increasing amount of data and computational power as well as the discovery of improved learning algorithms. However, the idea of a computer learning some abstract concept from data and applying them to yet unseen situations is not new and has been around at least since the 1950s. Many of these basic principles are very familiar to the pharmacometrics and clinical pharmacology community. In this paper, we want to introduce the foundational ideas of ML to this community such that readers obtain the essential tools they need to understand publications on the topic. Although we will not go into the very details and theoretical background, we aim to point readers to relevant literature and put applications of ML in molecular biology as well as the fields of pharmacometrics and clinical pharmacology into perspective.
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Affiliation(s)
- Solveig Badillo
- Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center BaselBaselSwitzerland
| | - Balazs Banfai
- Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center BaselBaselSwitzerland
| | - Fabian Birzele
- Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center BaselBaselSwitzerland
| | - Iakov I. Davydov
- Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center BaselBaselSwitzerland
| | - Lucy Hutchinson
- Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center BaselBaselSwitzerland
| | - Tony Kam‐Thong
- Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center BaselBaselSwitzerland
| | - Juliane Siebourg‐Polster
- Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center BaselBaselSwitzerland
| | - Bernhard Steiert
- Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center BaselBaselSwitzerland
| | - Jitao David Zhang
- Pharmaceutical Sciences, Roche Pharma Research and Early Development (pRED), Roche Innovation Center BaselBaselSwitzerland
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13
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Šimečková P, Hubatka F, Kotouček J, Turánek Knötigová P, Mašek J, Slavík J, Kováč O, Neča J, Kulich P, Hrebík D, Stráská J, Pěnčíková K, Procházková J, Diviš P, Macaulay S, Mikulík R, Raška M, Machala M, Turánek J. Gadolinium labelled nanoliposomes as the platform for MRI theranostics: in vitro safety study in liver cells and macrophages. Sci Rep 2020; 10:4780. [PMID: 32179785 PMCID: PMC7075985 DOI: 10.1038/s41598-020-60284-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/18/2019] [Indexed: 12/14/2022] Open
Abstract
Gadolinium (Gd)-based contrast agents are extensively used for magnetic resonance imaging (MRI). Liposomes are potential nanocarrier-based biocompatible platforms for development of new generations of MRI diagnostics. Liposomes with Gd-complexes (Gd-lip) co-encapsulated with thrombolytic agents can serve both for imaging and treatment of various pathological states including stroke. In this study, we evaluated nanosafety of Gd-lip containing PE-DTPA chelating Gd+3 prepared by lipid film hydration method. We detected no cytotoxicity of Gd-lip in human liver cells including cancer HepG2, progenitor (non-differentiated) HepaRG, and differentiated HepaRG cells. Furthermore, no potential side effects of Gd-lip were found using a complex system including general biomarkers of toxicity, such as induction of early response genes, oxidative, heat shock and endoplasmic reticulum stress, DNA damage responses, induction of xenobiotic metabolizing enzymes, and changes in sphingolipid metabolism in differentiated HepaRG. Moreover, Gd-lip did not show pro-inflammatory effects, as assessed in an assay based on activation of inflammasome NLRP3 in a model of human macrophages, and release of eicosanoids from HepaRG cells. In conclusion, this in vitro study indicates potential in vivo safety of Gd-lip with respect to hepatotoxicity and immunopathology caused by inflammation.
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Affiliation(s)
| | | | - Jan Kotouček
- Veterinary Research Institute, Brno, Czech Republic
| | | | - Josef Mašek
- Veterinary Research Institute, Brno, Czech Republic
| | - Josef Slavík
- Veterinary Research Institute, Brno, Czech Republic
| | - Ondrej Kováč
- Veterinary Research Institute, Brno, Czech Republic
| | - Jiří Neča
- Veterinary Research Institute, Brno, Czech Republic
| | - Pavel Kulich
- Veterinary Research Institute, Brno, Czech Republic
| | - Dominik Hrebík
- Central European Institute of Technology CEITEC, Structural Virology, Masaryk University, Brno, Czech Republic
| | - Jana Stráská
- Regional Centre of Advanced Technologies and Materials, Palacký University, Olomouc, Czech Republic
| | | | | | - Pavel Diviš
- Faculty of Chemistry, Technical University, Brno, Czech Republic
| | | | - Robert Mikulík
- International Clinical Research Centre, St. Anne's University Hospital Brno, Brno, Czech Republic
- Neurology Department, St. Anne's University Hospital and Masaryk University, Brno, Czech Republic
| | - Milan Raška
- Veterinary Research Institute, Brno, Czech Republic
- Department of Immunology, Faculty of Medicine and Dentistry, Palacký University, Olomouc, Czech Republic
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14
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Zhang JD, Sach-Peltason L, Kramer C, Wang K, Ebeling M. Multiscale modelling of drug mechanism and safety. Drug Discov Today 2020; 25:519-534. [DOI: 10.1016/j.drudis.2019.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/06/2019] [Accepted: 12/23/2019] [Indexed: 12/19/2022]
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15
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Weaver RJ, Valentin JP. Today's Challenges to De-Risk and Predict Drug Safety in Human "Mind-the-Gap". Toxicol Sci 2020; 167:307-321. [PMID: 30371856 DOI: 10.1093/toxsci/kfy270] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Current gaps in drug safety sciences can result from the inability (1) to identify hazard across multiple target organs, (2) to predict and risk assess with certainty against drug safety liabilities for the major target organs, (3) to optimally manage and mitigate against drug safety liabilities, and (4) to apply principles of governance on the generation, integration, and use of experimental data. Translational safety assessment to evaluate several target-organ drug toxicities can only be partially achieved by use of current in vitro and in vivo test systems. What remains to be tackled necessitates the deployment of in vitro-human-relevant test systems to address human specific or selective forms of toxicities. Nevertheless, such models may only address in part some of the requirements in today's armament of biomedical tools essential for improving the discovery of drug candidates. Refinement of in silico tools, Target Safety Assessment and a greater understanding of mechanistic insights of toxicities might provide future opportunities to better identify drug safety liabilities. The increasing diversity of drug modalities present further challenges for nonclinical and clinical development requiring further research to develop suitable test systems and technologies. Our ability to optimally manage and mitigate safety risk will come from the greater refinement of safety margin estimates, provision and use of human-relevant safety biomarkers, and understanding of the translation from in silico, in vitro, and in vivo studies to human. An improvement of governance frameworks and standards at all levels within organizations, national, and international, can only help facilitate drug discovery and development programs.
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Affiliation(s)
| | - Jean-Pierre Valentin
- Investigative Toxicology, Development Science, UCB Biopharma SPRL, B-1420 Braine-l'Alleud, Belgium
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16
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Reyes-Caballero H, Park B, Loube J, Sanchez I, Vinayachandran V, Choi Y, Woo J, Edwards J, Brinkman MC, Sussan T, Mitzner W, Biswal S. Immune modulation by chronic exposure to waterpipe smoke and immediate-early gene regulation in murine lungs. Tob Control 2019; 29:s80-s89. [PMID: 31852817 DOI: 10.1136/tobaccocontrol-2019-054965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 08/22/2019] [Accepted: 08/24/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVE We investigated the effects of chronic waterpipe (WP) smoke on pulmonary function and immune response in a murine model using a research-grade WP and the effects of acute exposure on the regulation of immediate-early genes (IEGs). METHODS WP smoke was generated using three WP smoke puffing regimens based on the Beirut regimen. WP smoke samples generated under these puffing regimens were quantified for nicotine concentration. Mice were chronically exposed for 6 months followed by assessment of pulmonary function and airway inflammation. Transcriptomic analysis using RNAseq was conducted after acute exposure to characterise the IEG response. These biomarkers were then compared with those generated after exposure to dry smoke (without water added to the WP bowl). RESULTS We determined that nicotine composition in WP smoke ranged from 0.4 to 2.5 mg per puffing session. The lung immune response was sensitive to the incremental severity of chronic exposure, with modest decreases in airway inflammatory cells and chemokine levels compared with air-exposed controls. Pulmonary function was unmodified by chronic WP exposure. Acute WP exposure was found to activate the immune response and identified known and novel IEG as potential biomarkers of WP exposure. CONCLUSION Chronic exposure to WP smoke leads to immune suppression without significant changes to pulmonary function. Transcriptomic analysis of the lung after acute exposure to WP smoke showed activation of the immune response and revealed IEGs that are common to WP and dry smoke, as well as pools of IEGs unique to each exposure, identifying potential biomarkers specific to WP exposure.
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Affiliation(s)
- Hermes Reyes-Caballero
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Bongsoo Park
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeffrey Loube
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ian Sanchez
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vinesh Vinayachandran
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Youngshim Choi
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Juhyung Woo
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Justin Edwards
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Thomas Sussan
- Toxicology Directorate, US Army Public Health Command, Aberdeen Proving Ground, Maryland, USA
| | - Wayne Mitzner
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Shyam Biswal
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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17
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Šimečková P, Marvanová S, Kulich P, Králiková L, Neča J, Procházková J, Machala M. Screening of Cellular Stress Responses Induced by Ambient Aerosol Ultrafine Particle Fraction PM0.5 in A549 Cells. Int J Mol Sci 2019; 20:E6310. [PMID: 31847237 PMCID: PMC6940800 DOI: 10.3390/ijms20246310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/25/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022] Open
Abstract
Effects of airborne particles on the expression status of markers of cellular toxic stress and on the release of eicosanoids, linked with inflammation and oxidative damage, remain poorly characterized. Therefore, we proposed a set of various methodological approaches in order to address complexity of PM0.5-induced toxicity. For this purpose, we used a well-characterized model of A549 pulmonary epithelial cells exposed to a non-cytotoxic concentration of ambient aerosol particle fraction PM0.5 for 24 h. Electron microscopy confirmed accumulation of PM0.5 within A549 cells, yet, autophagy was not induced. Expression profiles of various cellular stress response genes that have been previously shown to be involved in early stress responses, namely unfolded protein response, DNA damage response, and in aryl hydrocarbon receptor (AhR) and p53 signaling, were analyzed. This analysis revealed induction of GREM1, EGR1, CYP1A1, CDK1A, PUMA, NOXA and GDF15 and suppression of SOX9 in response to PM0.5 exposure. Analysis of eicosanoids showed no oxidative damage and only a weak anti-inflammatory response. In conclusion, this study helps to identify novel gene markers, GREM1, EGR1, GDF15 and SOX9, that may represent a valuable tool for routine testing of PM0.5-induced in vitro toxicity in lung epithelial cells.
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Affiliation(s)
| | | | | | | | | | | | - Miroslav Machala
- Veterinary Research Institute, Department of Chemistry and Toxicology, Hudcova 296/70, 62100 Brno, Czech Republic; (P.Š.); (S.M.); (P.K.); (L.K.); (J.N.); (J.P.)
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18
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Klaus S, Ost M. Mitochondrial uncoupling and longevity - A role for mitokines? Exp Gerontol 2019; 130:110796. [PMID: 31786315 DOI: 10.1016/j.exger.2019.110796] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022]
Abstract
Aging has been viewed both as a random process due to accumulation of molecular and cellular damage over time and as a programmed process linked to cellular pathway important for growth and maturation. These views converge on mitochondria as both the major producer of damaging reactive oxidant species (ROS) and as signaling organelles. A finite proton leak across the inner mitochondrial membrane leading to a slight uncoupling of oxidative phosphorylation and respiration is an intrinsic property of all mitochondria and according to the "uncoupling to survive" hypothesis it has evolved to protect against ROS production to minimize oxidative damage. This hypothesis is supported by evidence linking an increased endogenous, uncoupling protein (UCP1) mediated, as well as experimentally induced mitochondrial uncoupling to an increased lifespan in rodents. This is possibly due to the synergistic activation of molecular pathways linked to life extending effects of caloric restriction as well as a mitohormetic response. Mitohormesis is an adaptive stress response through mitonuclear signaling which increases stress resistance resulting in health promoting effects. Part of this response is the induction of fibroblast growth factor 21 (FGF21) and growth and differentiation factor 15 (GDF15), two stress-induced mitokines which elicit beneficial systemic metabolic effects via endocrine action.
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Affiliation(s)
- Susanne Klaus
- German Institute of Human Nutrition in Potsdam Rehbrücke, Nuthetal, Germany; University of Potsdam, Institute of Nutritional Science, Potsdam, Germany.
| | - Mario Ost
- German Institute of Human Nutrition in Potsdam Rehbrücke, Nuthetal, Germany
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19
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Schyman P, Printz RL, Estes SK, O'Brien TP, Shiota M, Wallqvist A. Assessing Chemical-Induced Liver Injury In Vivo From In Vitro Gene Expression Data in the Rat: The Case of Thioacetamide Toxicity. Front Genet 2019; 10:1233. [PMID: 31850077 PMCID: PMC6901980 DOI: 10.3389/fgene.2019.01233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 11/06/2019] [Indexed: 12/18/2022] Open
Abstract
Consumers are exposed to thousands of chemicals with potentially adverse health effects. However, these chemicals will never be tested for toxicity because of the immense resources needed for animal-based (in vivo) toxicological studies. Today, there are no viable in vitro alternatives to these types of animal studies. To develop an in vitro approach, we investigated whether we could predict in vivo organ injuries in rats with the use of RNA-seq data acquired from tissues early in the development of toxicant-induced injury, by comparing gene expression data from RNA isolated from these rat tissues with those obtained from in vitro exposure of primary liver and kidney cells. We collected RNA-seq data from the liver and kidney tissues of Sprague-Dawley rats 8 or 24 h after exposing them to vehicle (control), low (25 mg/kg), or high (100 mg/kg) doses of thioacetamide, a known liver toxicant that promotes fibrosis; we used these doses and exposure times to cause only mild toxicant-induced injury. For the in vitro study, we treated two cell types from Sprague-Dawley rats, primary hepatocytes (vehicle; low, 0.025 mM; or high, 0.125 mM dose), and renal tube epithelial cells (vehicle; low, 0.125 mM; or high, 0.500 mM) dose) with the thioacetamide metabolite, thioacetamide-S-oxide, selecting in vitro doses and exposure times to recreate the early-stage toxicant-induced injury model that we achieved in vivo. RNA-seq data were collected 9 or 24 h after application of vehicle or thioacetamide-S-oxide. We found that our modular approach for the analysis of gene expression data derived from in vivo RNA-seq strongly correlated (R2 > 0.6) with the in vitro results at two different dose levels of thioacetamide/thioacetamide-S-oxide after 24 h of exposure. The top-ranked liver injury modules in vitro correctly identified the ensuing development of liver fibrosis.
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Affiliation(s)
- Patric Schyman
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, United States.,The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc. (HJF), Bethesda, MD, United States
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Tracy P O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Anders Wallqvist
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD, United States
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20
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De Abrew KN, Shan YK, Wang X, Krailler JM, Kainkaryam RM, Lester CC, Settivari RS, LeBaron MJ, Naciff JM, Daston GP. Use of connectivity mapping to support read across: A deeper dive using data from 186 chemicals, 19 cell lines and 2 case studies. Toxicology 2019; 423:84-94. [DOI: 10.1016/j.tox.2019.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/30/2019] [Accepted: 05/19/2019] [Indexed: 01/21/2023]
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21
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Shimada K, Mitchison TJ. Unsupervised identification of disease states from high-dimensional physiological and histopathological profiles. Mol Syst Biol 2019; 15:e8636. [PMID: 30782979 PMCID: PMC6380462 DOI: 10.15252/msb.20188636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 01/14/2019] [Accepted: 01/21/2019] [Indexed: 01/22/2023] Open
Abstract
The liver and kidney in mammals play central roles in protecting the organism from xenobiotics and are at high risk of xenobiotic-induced injury. Xenobiotic-induced tissue injury has been extensively studied from both classical histopathological and biochemical perspectives. Here, we introduce a machine-learning approach to analyze toxicological response. Unsupervised characterization of physiological and histological changes in a large toxicogenomic dataset revealed nine discrete toxin-induced disease states, some of which correspond to known pathology, but others were novel. Analysis of dynamics revealed transitions between disease states at constant toxin exposure, mostly toward decreased pathology, implying induction of tolerance. Tolerance correlated with induction of known xenobiotic defense genes and decrease of novel ferroptosis sensitivity biomarkers, suggesting ferroptosis as a druggable driver of tissue pathophysiology. Lastly, mechanism of body weight decrease, a known primary marker for xenobiotic toxicity, was investigated. Combined analysis of food consumption, body weight, and molecular biomarkers indicated that organ injury promotes cachexia by whole-body signaling through Gdf15 and Igf1, suggesting strategies for therapeutic intervention that may be broadly relevant to human disease.
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Affiliation(s)
- Kenichi Shimada
- Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Timothy J Mitchison
- Laboratory of Systems Pharmacology and Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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22
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Taškova K, Fontaine JF, Mrowka R, Andrade-Navarro MA. Literature optimized integration of gene expression for organ-specific evaluation of toxicogenomics datasets. PLoS One 2019; 14:e0210467. [PMID: 30640953 PMCID: PMC6331104 DOI: 10.1371/journal.pone.0210467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/24/2018] [Indexed: 11/30/2022] Open
Abstract
The study of drug toxicity in human organs is complicated by their complex inter-relations and by the obvious difficulty to testing drug effects on biologically relevant material. Animal models and human cell cultures offer alternatives for systematic and large-scale profiling of drug effects on gene expression level, as typically found in the so-called toxicogenomics datasets. However, the complexity of these data, which includes variable drug doses, time points, and experimental setups, makes it difficult to choose and integrate the data, and to evaluate the appropriateness of one or another model system to study drug toxicity (of particular drugs) of particular human organs. Here, we define a protocol to integrate drug-wise rankings of gene expression changes in toxicogenomics data, which we apply to the TG-GATEs dataset, to prioritize genes for association to drug toxicity in liver or kidney. Contrast of the results with sets of known human genes associated to drug toxicity in the literature allows to compare different rank aggregation approaches for the task at hand. Collectively, ranks from multiple models point to genes not previously associated to toxicity, notably, the PCNA clamp associated factor (PCLAF), and genes regulated by the master regulator of the antioxidant response NFE2L2, such as NQO1 and SRXN1. In addition, comparing gene ranks from different models allowed us to evaluate striking differences in terms of toxicity-associated genes between human and rat hepatocytes or between rat liver and rat hepatocytes. We interpret these results to point to the different molecular functions associated to organ toxicity that are best described by each model. We conclude that the expected production of toxicogenomics panels with larger numbers of drugs and models, in combination with the ongoing increase of the experimental literature in organ toxicity, will lead to increasingly better associations of genes for organism toxicity.
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Affiliation(s)
| | | | - Ralf Mrowka
- Experimentelle Nephrologie, Universitätsklinikum Jena, KIM III, Jena, Germany
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23
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Souza T, Trairatphisan P, Piñero J, Furlong LI, Saez-Rodriguez J, Kleinjans J, Jennen D. Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury. Front Genet 2018; 9:527. [PMID: 30515189 PMCID: PMC6255978 DOI: 10.3389/fgene.2018.00527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/19/2018] [Indexed: 12/03/2022] Open
Abstract
In toxicogenomics, functional annotation is an important step to gain additional insights into genes with aberrant expression that drive pathophysiological mechanisms. Nevertheless, there exists a gap on annotation of these genes which often hampers the interpretation of results and limits their applicability in translational medicine. In this study, we evaluated the coverage of functional annotations of differentially expressed genes (DEGs) induced by 10 selected compounds from the TG-GATEs database identified as high- or no-risk in causing drug-induced liver injury (most-DILI or no-DILI, respectively) using in vitro human data. Functional roles of DEGs not present in the most common biological annotation databases – termed “dark genes” – were unveiled via literature mining and via the identification of shared regulatory transcription factors or signaling pathways. Our results demonstrated that there were approximately 13% of dark genes induced by these compounds in vitro and we were able to obtain additional relevant information for up to 76% of those. Using interactome data from several sources, we have uncovered genes such as LRBA, and WDR26 as highly connected in the protein network that play roles in drug response. Genes such as MALAT1, H19, and MIR29C – whose links to hepatotoxicity have been confirmed – were identified as markers for the most-DILI group and appeared as top hits across all literature-based mining methods. Furthermore, we investigated the potential impact of dark genes on liver toxicity by identifying their rat orthologs in combination with their correlation to drug-induced liver pathologies observed in vivo following chemical exposure. We identified a set of important regulatory transcription factors of dark genes for all most-DILI compounds including E2F1 and JUND with supporting evidences in literature and we found Magee1 correlated with chemically induced bile duct hyperplasia and adverse responses at 29 days in rats in vivo. In conclusion, in this study we show the potential role of these poorly annotated genes in mechanisms underlying hepatotoxicity and offer a number of computational approaches that may help to minimize current gaps in gene annotation and highlight their values as potential biomarkers in toxicological studies.
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Affiliation(s)
- Terezinha Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Panuwat Trairatphisan
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Janet Piñero
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences (DCEXS), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Barcelona, Spain
| | - Laura I Furlong
- Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences (DCEXS), Hospital del Mar Medical Research Institute (IMIM), Universitat Pompeu Fabra, Barcelona, Spain
| | - Julio Saez-Rodriguez
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, Aachen, Germany.,European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Cambridge, United Kingdom
| | - Jos Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Danyel Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
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Szebeni GJ, Balog JA, Demjén A, Alföldi R, Végi VL, Fehér LZ, Mán I, Kotogány E, Gubán B, Batár P, Hackler L, Kanizsai I, Puskás LG. Imidazo[1,2- b]pyrazole-7-carboxamides Induce Apoptosis in Human Leukemia Cells at Nanomolar Concentrations. Molecules 2018; 23:E2845. [PMID: 30388846 PMCID: PMC6278434 DOI: 10.3390/molecules23112845] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 01/14/2023] Open
Abstract
Leukemia, the malignancy of the hematopoietic system accounts for 10% of cancer cases with poor overall survival rate in adults; therefore, there is a high unmet medical need for the development of novel therapeutics. Eight imidazo[1,2-b]pyrazole-7-carboxamides have been tested for cytotoxic activity against five leukemia cell lines: Acute promyelocytic leukemia (HL-60), acute monocytic leukemia (THP-1), acute T-lymphoblastic leukemia (MOLT-4), biphenotypic B myelomonocytic leukemia (MV-4-11), and erythroleukemia (K-562) cells in vitro. Imidazo[1,2-b]pyrazole-7-carboxamides hampered the viability of all five leukemia cell lines with different potential. Optimization through structure activity relationship resulted in the following IC50 values for the most effective lead compound DU385: 16.54 nM, 27.24 nM, and 32.25 nM on HL-60, MOLT-4, MV-4-11 cells, respectively. Human primary fibroblasts were much less sensitive in the applied concentration range. Both monolayer or spheroid cultures of murine 4T1 and human MCF7 breast cancer cells were less sensitive to treatment with 1.5⁻10.8 μM IC50 values. Flow cytometry confirmed the absence of necrosis and revealed 60% late apoptotic population for MV-4-11, and 50% early apoptotic population for HL-60. MOLT-4 cells showed only about 30% of total apoptotic population. Toxicogenomic study of DU385 on the most sensitive MV-4-11 cells revealed altered expression of sixteen genes as early (6 h), midterm (12 h), and late response (24 h) genes upon treatment. Changes in ALOX5AP, TXN, and SOD1 expression suggested that DU385 causes oxidative stress, which was confirmed by depletion of cellular glutathione and mitochondrial membrane depolarization induction. Imidazo[1,2-b]pyrazole-7-carboxamides reported herein induced apoptosis in human leukemia cells at nanomolar concentrations.
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Affiliation(s)
- Gábor J Szebeni
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary.
| | - József A Balog
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - András Demjén
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Róbert Alföldi
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Vanessza L Végi
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | | | - Imola Mán
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Edit Kotogány
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
| | - Barbara Gubán
- Department of Dermatology and Allergology, University of Szeged, Korányi fasor 6, H-6720 Szeged, Hungary.
| | - Péter Batár
- Department of Hematology, Institute of Internal Medicine, University of Debrecen, Nagyerdei Körút 98, 4032 Debrecen, Hungary.
| | - László Hackler
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - Iván Kanizsai
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
| | - László G Puskás
- Laboratory of Functional Genomics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.
- Avidin Ltd., Alsó kikötő sor 11/D, H-6726 Szeged, Hungary.
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25
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Wu Y, Wang G. Machine Learning Based Toxicity Prediction: From Chemical Structural Description to Transcriptome Analysis. Int J Mol Sci 2018; 19:E2358. [PMID: 30103448 PMCID: PMC6121588 DOI: 10.3390/ijms19082358] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 02/07/2023] Open
Abstract
Toxicity prediction is very important to public health. Among its many applications, toxicity prediction is essential to reduce the cost and labor of a drug's preclinical and clinical trials, because a lot of drug evaluations (cellular, animal, and clinical) can be spared due to the predicted toxicity. In the era of Big Data and artificial intelligence, toxicity prediction can benefit from machine learning, which has been widely used in many fields such as natural language processing, speech recognition, image recognition, computational chemistry, and bioinformatics, with excellent performance. In this article, we review machine learning methods that have been applied to toxicity prediction, including deep learning, random forests, k-nearest neighbors, and support vector machines. We also discuss the input parameter to the machine learning algorithm, especially its shift from chemical structural description only to that combined with human transcriptome data analysis, which can greatly enhance prediction accuracy.
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Affiliation(s)
- Yunyi Wu
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenviroment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Guanyu Wang
- Department of Biology, Guangdong Provincial Key Laboratory of Cell Microenviroment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China.
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26
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Liu JJ, Liu S, Choo RWM, Wee SL, Xu A, Lim SC. Sex modulates the association of fibroblast growth factor 21 with end-stage renal disease in Asian people with Type 2 diabetes: a 6.3-year prospective cohort study. Diabet Med 2018; 35:880-886. [PMID: 29653030 DOI: 10.1111/dme.13641] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/03/2018] [Indexed: 01/07/2023]
Abstract
AIM To study whether plasma fibroblast growth factor 21 independently predicts the risk of end-stage renal disease in Asian people with Type 2 diabetes. METHODS In this prospective cohort study, 1700 Asian people with Type 2 diabetes were followed for a mean of 6.3 years in a regional hospital in Singapore. Incident end-stage renal disease was identified by linkage with a national renal registry. The association of baseline fibroblast growth factor 21 levels with risk of progression to end-stage renal disease was studied using survival analyses. RESULTS Participants were aged 60 ± 10 years, with an average diabetes duration of 12 years. Their estimated GFR was 73 ± 28 ml/min/1.73 m2 and 62% had albuminuria at baseline. A total of 179 incident end-stage renal disease cases were identified. Plasma fibroblast growth factor 21 interacted with sex in its association with end-stage renal disease (Pinteraction = 0.003). A 1-sd increment in fibroblast growth factor 21 (natural log-transformed) was associated with a 1.32-fold (95% CI 1.05-1.66, P = 0.02) increased hazard for end-stage renal disease in women, after adjustment for traditional risk factors including estimated GFR and albuminuria. Taking death as a competing risk did not materially change the outcome [sub-distribution hazard ratio 1.35 (95% CI 1.11-1.66, P = 0.003)]. Fibroblast growth factor 21 did not predict end-stage renal disease risk in men after adjustment for baseline estimated GFR and albuminuria [hazard ratio 1.07 (95% CI 0.89-1.28, P = 0.49)]. CONCLUSIONS Plasma fibroblast growth factor 21 level independently predicted risk of progression to end-stage renal disease in women with Type 2 diabetes. The pathophysiological relationships among FGF21, sex and renal progression warrant further study.
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Affiliation(s)
- J-J Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore
| | - S Liu
- Clinical Research Unit, Khoo Teck Puat Hospital, Singapore
| | - R W M Choo
- Geriatric Education and Research Institute, Singapore
| | - S L Wee
- Geriatric Education and Research Institute, Singapore
| | - A Xu
- Department of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - S C Lim
- Diabetes Centre, Khoo Teck Puat Hospital, Singapore
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27
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Dieckmann A, Hagedorn PH, Burki Y, Brügmann C, Berrera M, Ebeling M, Singer T, Schuler F. A Sensitive In Vitro Approach to Assess the Hybridization-Dependent Toxic Potential of High Affinity Gapmer Oligonucleotides. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 10:45-54. [PMID: 29499955 PMCID: PMC5725219 DOI: 10.1016/j.omtn.2017.11.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/10/2017] [Accepted: 11/11/2017] [Indexed: 10/29/2022]
Abstract
The successful development of high-affinity gapmer antisense oligonucleotide (ASO) therapeutics containing locked nucleic acid (LNA) or constrained ethyl (cEt) substitutions has been hampered by the risk of hepatotoxicity. Here, we present an in vitro approach using transfected mouse fibroblasts to predict the potential hepatic liabilities of LNA-modified ASOs (LNA-ASOs), validated by assessing 236 different LNA-ASOs with known hepatotoxic potential. This in vitro assay accurately reflects in vivo findings and relates hepatotoxicity to RNase H1 activity, off-target RNA downregulation, and LNA-ASO-binding affinity. We further demonstrate that the hybridization-dependent toxic potential of LNA-ASOs is also evident in different cell types from different species, which indicates probable translatability of the in vitro results to humans. Additionally, we show that the melting temperature (Tm) of LNA-ASOs maintained below a threshold level of about 55°C greatly diminished the hepatotoxic potential. In summary, we have established a sensitive in vitro screening approach for assessing the hybridization-dependent toxic potential of LNA-ASOs, enabling prioritization of candidate molecules in drug discovery and early development.
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Affiliation(s)
- Andreas Dieckmann
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland.
| | - Peter H Hagedorn
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Yvonne Burki
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Christine Brügmann
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Marco Berrera
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Martin Ebeling
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Thomas Singer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Franz Schuler
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, 4070 Basel, Switzerland
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28
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Lei T, Sun H, Kang Y, Zhu F, Liu H, Zhou W, Wang Z, Li D, Li Y, Hou T. ADMET Evaluation in Drug Discovery. 18. Reliable Prediction of Chemical-Induced Urinary Tract Toxicity by Boosting Machine Learning Approaches. Mol Pharm 2017; 14:3935-3953. [DOI: 10.1021/acs.molpharmaceut.7b00631] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Tailong Lei
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Huiyong Sun
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Yu Kang
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Feng Zhu
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Hui Liu
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Wenfang Zhou
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Zhe Wang
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Dan Li
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Youyong Li
- Institute
of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, P. R. China
| | - Tingjun Hou
- College
of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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29
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Schoen I, Koitzsch S. ATF3-Dependent Regulation of EGR1 in vitro and in vivo. ORL J Otorhinolaryngol Relat Spec 2017; 79:239-250. [PMID: 28803237 DOI: 10.1159/000478937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 06/21/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND/AIMS Activating transcription factor 3 (ATF3) and early growth response protein 1 (EGR1) are reported to interact, but their use as prognostic factors in cancer is discussed controversially. METHODS We measured ATF3 and EGR1 gene expression changes in human mini-organ cultures (MOCs) of healthy nasal epithelia, UM-SCC-22B, and FADUDD cells after acid reflux exposure. Next, ATF3 and EGR1 gene expression was analysed in tumour tissues and related to the median expression of autologous reference tissue samples. RESULTS ATF3 and EGR1 mRNA expression was significantly reduced after consecutive exposure of MOCs at pH <7.0 to artificial gastric juice (refluxate). In contrast, ATF3 mRNA was upregulated significantly within the first hour of incubation. EGR1 mRNA exhibited no significant changes. The analysed cell lines exhibited a cell line-specific alteration. In FADUDD cells, the upregulation of EGR1 was significant after refluxate exposure, but in HN-SCC 22B, no significant changes were detected. The analysis of the HNSCC samples confirmed the heterogeneous data of the literature. CONCLUSION The data maintain the hypothesis that ATF3 and EGR1 are involved in the beginning of inflammatory processes. Whether these two transcription factors act as tumour suppressors or promoters is context dependent and warrants analysis in further studies.
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Affiliation(s)
- Ilona Schoen
- Laboratory of Experimental Oncology, Department of Otolaryngology, Head and Neck Surgery, Martin Luther University Halle-Wittenberg, Halle, Germany
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30
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A review of drug-induced liver injury databases. Arch Toxicol 2017; 91:3039-3049. [DOI: 10.1007/s00204-017-2024-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/28/2017] [Indexed: 01/23/2023]
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31
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The sbv IMPROVER Systems Toxicology Computational Challenge: Identification of Human and Species-Independent Blood Response Markers as Predictors of Smoking Exposure and Cessation Status. ACTA ACUST UNITED AC 2017; 5:38-51. [PMID: 30221212 DOI: 10.1016/j.comtox.2017.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cigarette smoking entails chronic exposure to a mixture of harmful chemicals that trigger molecular changes over time, and is known to increase the risk of developing diseases. Risk assessment in the context of 21st century toxicology relies on the elucidation of mechanisms of toxicity and the identification of exposure response markers, usually from high-throughput data, using advanced computational methodologies. The sbv IMPROVER Systems Toxicology computational challenge (Fall 2015-Spring 2016) aimed to evaluate whether robust and sparse (≤40 genes) human (sub-challenge 1, SC1) and species-independent (sub-challenge 2, SC2) exposure response markers (so called gene signatures) could be extracted from human and mouse blood transcriptomics data of current (S), former (FS) and never (NS) smoke-exposed subjects as predictors of smoking and cessation status. Best-performing computational methods were identified by scoring anonymized participants' predictions. Worldwide participation resulted in 12 (SC1) and six (SC2) final submissions qualified for scoring. The results showed that blood gene expression data were informative to predict smoking exposure (i.e. discriminating smoker versus never or former smokers) status in human and across species with a high level of accuracy. By contrast, the prediction of cessation status (i.e. distinguishing FS from NS) remained challenging, as reflected by lower classification performances. Participants successfully developed inductive predictive models and extracted human and species-independent gene signatures, including genes with high consensus across teams. Post-challenge analyses highlighted "feature selection" as a key step in the process of building a classifier and confirmed the importance of testing a gene signature in independent cohorts to ensure the generalized applicability of a predictive model at a population-based level. In conclusion, the Systems Toxicology challenge demonstrated the feasibility of extracting a consistent blood-based smoke exposure response gene signature and further stressed the importance of independent and unbiased data and method evaluations to provide confidence in systems toxicology-based scientific conclusions.
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32
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Moffat JG, Vincent F, Lee JA, Eder J, Prunotto M. Opportunities and challenges in phenotypic drug discovery: an industry perspective. Nat Rev Drug Discov 2017; 16:531-543. [PMID: 28685762 DOI: 10.1038/nrd.2017.111] [Citation(s) in RCA: 496] [Impact Index Per Article: 70.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phenotypic drug discovery (PDD) approaches do not rely on knowledge of the identity of a specific drug target or a hypothesis about its role in disease, in contrast to the target-based strategies that have been widely used in the pharmaceutical industry in the past three decades. However, in recent years, there has been a resurgence in interest in PDD approaches based on their potential to address the incompletely understood complexity of diseases and their promise of delivering first-in-class drugs, as well as major advances in the tools for cell-based phenotypic screening. Nevertheless, PDD approaches also have considerable challenges, such as hit validation and target deconvolution. This article focuses on the lessons learned by researchers engaged in PDD in the pharmaceutical industry and considers the impact of 'omics' knowledge in defining a cellular disease phenotype in the era of precision medicine, introducing the concept of a chain of translatability. We particularly aim to identify features and areas in which PDD can best deliver value to drug discovery portfolios and can contribute to the identification and the development of novel medicines, and to illustrate the challenges and uncertainties that are associated with PDD in order to help set realistic expectations with regard to its benefits and costs.
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Affiliation(s)
- John G Moffat
- Biochemical &Cellular Pharmacology, Genentech, South San Francisco, California 94080, USA
| | - Fabien Vincent
- Discovery Sciences, Primary Pharmacology Group, Pfizer, Groton, Connecticut 06340, USA
| | - Jonathan A Lee
- Department of Quantitative Biology, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
| | - Jörg Eder
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Marco Prunotto
- Phenotype and Target ID, Chemical Biology, pRED, Roche, 4070 Basel, Switzerland. Present address: Office of Innovation, Immunology, Infectious Diseases &Ophthalmology (I2O), Roche Late Stage Development, 124 Grenzacherstrasse, 4070 Basel, Switzerland
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33
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Drawnel FM, Zhang JD, Küng E, Aoyama N, Benmansour F, Araujo Del Rosario A, Jensen Zoffmann S, Delobel F, Prummer M, Weibel F, Carlson C, Anson B, Iacone R, Certa U, Singer T, Ebeling M, Prunotto M. Molecular Phenotyping Combines Molecular Information, Biological Relevance, and Patient Data to Improve Productivity of Early Drug Discovery. Cell Chem Biol 2017; 24:624-634.e3. [DOI: 10.1016/j.chembiol.2017.03.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/22/2017] [Accepted: 03/24/2017] [Indexed: 12/16/2022]
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34
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Rueda-Zárate HA, Imaz-Rosshandler I, Cárdenas-Ovando RA, Castillo-Fernández JE, Noguez-Monroy J, Rangel-Escareño C. A computational toxicogenomics approach identifies a list of highly hepatotoxic compounds from a large microarray database. PLoS One 2017; 12:e0176284. [PMID: 28448553 PMCID: PMC5407788 DOI: 10.1371/journal.pone.0176284] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 04/07/2017] [Indexed: 11/18/2022] Open
Abstract
The liver and the kidney are the most common targets of chemical toxicity, due to their major metabolic and excretory functions. However, since the liver is directly involved in biotransformation, compounds in many currently and normally used drugs could affect it adversely. Most chemical compounds are already labeled according to FDA-approved labels using DILI-concern scale. Drug Induced Liver Injury (DILI) scale refers to an adverse drug reaction. Many compounds do not exhibit hepatotoxicity at early stages of development, so it is important to detect anomalies at gene expression level that could predict adverse reactions in later stages. In this study, a large collection of microarray data is used to investigate gene expression changes associated with hepatotoxicity. Using TG-GATEs a large-scale toxicogenomics database, we present a computational strategy to classify compounds by toxicity levels in human and animal models through patterns of gene expression. We combined machine learning algorithms with time series analysis to identify genes capable of classifying compounds by FDA-approved labeling as DILI-concern toxic. The goal is to define gene expression profiles capable of distinguishing the different subtypes of hepatotoxicity. The study illustrates that expression profiling can be used to classify compounds according to different hepatotoxic levels; to label those that are currently labeled as undertemined; and to determine if at the molecular level, animal models are a good proxy to predict hepatotoxicity in humans.
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Affiliation(s)
- Héctor A. Rueda-Zárate
- School of Engineering and Sciences, Tecnológico de Monterrey Mexico City, Mexico City, México
| | - Iván Imaz-Rosshandler
- Computational Genomics Lab., Instituto Nacional de Medicina Genómica, Mexico City, México
| | | | | | - Julieta Noguez-Monroy
- School of Engineering and Sciences, Tecnológico de Monterrey Mexico City, Mexico City, México
| | - Claudia Rangel-Escareño
- Computational Genomics Lab., Instituto Nacional de Medicina Genómica, Mexico City, México
- * E-mail:
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35
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Inferring Genes and Biological Functions That Are Sensitive to the Severity of Toxicity Symptoms. Int J Mol Sci 2017; 18:ijms18040755. [PMID: 28368331 PMCID: PMC5412340 DOI: 10.3390/ijms18040755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 03/23/2017] [Accepted: 03/30/2017] [Indexed: 11/16/2022] Open
Abstract
The effective development of new drugs relies on the identification of genes that are related to the symptoms of toxicity. Although many researchers have inferred toxicity markers, most have focused on discovering toxicity occurrence markers rather than toxicity severity markers. In this study, we aimed to identify gene markers that are relevant to both the occurrence and severity of toxicity symptoms. To identify gene markers for each of four targeted liver toxicity symptoms, we used microarray expression profiles and pathology data from 14,143 in vivo rat samples. The gene markers were found using sparse linear discriminant analysis (sLDA) in which symptom severity is used as a class label. To evaluate the inferred gene markers, we constructed regression models that predicted the severity of toxicity symptoms from gene expression profiles. Our cross-validated results revealed that our approach was more successful at finding gene markers sensitive to the aggravation of toxicity symptoms than conventional methods. Moreover, these markers were closely involved in some of the biological functions significantly related to toxicity severity in the four targeted symptoms.
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36
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Boess F, Lenz B, Funk J, Niederhauser U, Bassett S, Zhang JD, Singer T, Roth AB. Use of early phenotypic in vivo markers to assess human relevance of an unusual rodent non-genotoxic carcinogen in vitro. Toxicology 2017; 379:48-61. [PMID: 28174063 DOI: 10.1016/j.tox.2017.01.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 10/20/2022]
Abstract
Foci of altered hepatocytes (FAH) are considered putative, pre-neoplastic lesions that can occur spontaneously in aging rodents, but can also be induced by chemicals or drugs. Progression of FAH to hepatocellular neoplasms has been reported repeatedly but increases in foci in rodents do not necessarily lead to tumors in carcinogenicity studies and the relevance for humans often remains unclear. Here we present the case of RG3487, a molecule which induced FAH and, later on, tumors in rats. Because the molecule was negative in genotoxicity assays it was classified as a non-genotoxic carcinogen. In order to assess the potential for liver tumor formation in humans, we analyzed treatment-induced changes in vivo to establish a possible mode of action (MoA). In vivo and in vitro gene expression analysis revealed that nuclear receptor signaling was unlikely to be the relevant MoA and no other known mechanism could be established. We therefore took an approach comparing phenotypic markers, including mRNA changes, proliferation and glycogen accumulation, in vitro using cells of different species to assess the human relevance of this finding. Since the alterations observed in rats were not seen in the liver of mice or dogs in vivo, we could validate the relevance of the cell models chosen by use of hepatocytes from these species in vitro. This ultimately allowed for a cross-species comparison, which suggested that the formation of FAH and liver tumors was rat specific and unlikely to translate to human. Our work showed that phenotypic species comparison in vitro is a useful approach for assessment of the human relevance of pre-clinical findings where no known mechanism can be established.
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Affiliation(s)
- Franziska Boess
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Barbara Lenz
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Juergen Funk
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Urs Niederhauser
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Simon Bassett
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Jitao David Zhang
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Thomas Singer
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Adrian B Roth
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
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37
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Thiel C, Cordes H, Fabbri L, Aschmann HE, Baier V, Smit I, Atkinson F, Blank LM, Kuepfer L. A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations. PLoS Comput Biol 2017; 13:e1005280. [PMID: 28151932 PMCID: PMC5289425 DOI: 10.1371/journal.pcbi.1005280] [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: 10/06/2016] [Accepted: 12/03/2016] [Indexed: 11/18/2022] Open
Abstract
Drug-induced toxicity is a significant problem in clinical care. A key problem here is a general understanding of the molecular mechanisms accompanying the transition from desired drug effects to adverse events following administration of either therapeutic or toxic doses, in particular within a patient context. Here, a comparative toxicity analysis was performed for fifteen hepatotoxic drugs by evaluating toxic changes reflecting the transition from therapeutic drug responses to toxic reactions at the cellular level. By use of physiologically-based pharmacokinetic modeling, in vitro toxicity data were first contextualized to quantitatively describe time-resolved drug responses within a patient context. Comparatively studying toxic changes across the considered hepatotoxicants allowed the identification of subsets of drugs sharing similar perturbations on key cellular processes, functional classes of genes, and individual genes. The identified subsets of drugs were next analyzed with regard to drug-related characteristics and their physicochemical properties. Toxic changes were finally evaluated to predict both molecular biomarkers and potential drug-drug interactions. The results may facilitate the early diagnosis of adverse drug events in clinical application. Liver toxicity may occur at drug levels above the therapeutic range and is thus a crucial problem in clinical care. However, the cellular changes induced by drug administration of therapeutic and toxic doses in humans are still not well understood. We here coupled patient-specific drug concentration-time profiles following oral administration of therapeutic and toxic doses with in vitro drug response data to predict toxic changes that quantitatively reflect the transition from desired drug effects to undesired toxic reactions. These toxic changes were comparatively evaluated for fifteen hepatotoxic drugs to identify subsets of drugs, which show similar drug effects on key cellular processes, functional classes of genes, and individual genes, respectively. In addition, analyzing toxic changes for individual genes allowed the prediction of molecular biomarkers and potential drug-drug interactions. Our results may hence support the early diagnosis of liver toxicity in clinical care in the future and may, moreover, help to assess potential risks of drug combination therapies.
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Affiliation(s)
- Christoph Thiel
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, Germany
| | - Henrik Cordes
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, Germany
| | - Lorenzo Fabbri
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, Germany
| | - Hélène Eloise Aschmann
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, Germany
| | - Vanessa Baier
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, Germany
| | - Ines Smit
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Francis Atkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lars Mathias Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, Germany
| | - Lars Kuepfer
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, Germany
- * E-mail:
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38
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Choudhury Y, Toh YC, Xing J, Qu Y, Poh J, Li H, Tan HS, Kanesvaran R, Yu H, Tan MH. Patient-specific hepatocyte-like cells derived from induced pluripotent stem cells model pazopanib-mediated hepatotoxicity. Sci Rep 2017; 7:41238. [PMID: 28120901 PMCID: PMC5264611 DOI: 10.1038/srep41238] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 12/19/2016] [Indexed: 12/18/2022] Open
Abstract
Idiosyncratic drug-induced hepatotoxicity is a major cause of liver damage and drug pipeline failure, and is difficult to study as patient-specific features are not readily incorporated in traditional hepatotoxicity testing approaches using population pooled cell sources. Here we demonstrate the use of patient-specific hepatocyte-like cells (HLCs) derived from induced pluripotent stem cells for modeling idiosyncratic hepatotoxicity to pazopanib (PZ), a tyrosine kinase inhibitor drug associated with significant hepatotoxicity of unknown mechanistic basis. In vitro cytotoxicity assays confirmed that HLCs from patients with clinically identified hepatotoxicity were more sensitive to PZ-induced toxicity than other individuals, while a prototype hepatotoxin acetaminophen was similarly toxic to all HLCs studied. Transcriptional analyses showed that PZ induces oxidative stress (OS) in HLCs in general, but in HLCs from susceptible individuals, PZ causes relative disruption of iron metabolism and higher burden of OS. Our study establishes the first patient-specific HLC-based platform for idiosyncratic hepatotoxicity testing, incorporating multiple potential causative factors and permitting the correlation of transcriptomic and cellular responses to clinical phenotypes. Establishment of patient-specific HLCs with clinical phenotypes representing population variations will be valuable for pharmaceutical drug testing.
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Affiliation(s)
- Yukti Choudhury
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore
| | - Yi Chin Toh
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore.,Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, E4 #04-08, Singapore 117583, Republic of Singapore
| | - Jiangwa Xing
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore
| | - Yinghua Qu
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore
| | - Jonathan Poh
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore
| | - Huan Li
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore
| | - Hui Shan Tan
- Division of Medical Oncology, National Cancer Centre, Singapore 169610, Republic of Singapore
| | - Ravindran Kanesvaran
- Division of Medical Oncology, National Cancer Centre, Singapore 169610, Republic of Singapore
| | - Hanry Yu
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore.,Yong Loo Lin School of Medicine and Mechanobiology Institute, National University of Singapore, Republic of Singapore.,Gastroenterology Department, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Min-Han Tan
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, Nanos #04-01, Singapore 138669, Republic of Singapore.,Division of Medical Oncology, National Cancer Centre, Singapore 169610, Republic of Singapore
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39
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Hendrickx DM, Souza T, Jennen DGJ, Kleinjans JCS. DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds. Arch Toxicol 2016; 91:2343-2352. [PMID: 28032149 PMCID: PMC5429357 DOI: 10.1007/s00204-016-1922-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 12/15/2016] [Indexed: 01/29/2023]
Abstract
Unravelling gene regulatory networks (GRNs) influenced by chemicals is a major challenge in systems toxicology. Because toxicant-induced GRNs evolve over time and dose, the analysis of global gene expression data measured at multiple time points and doses will provide insight in the adverse effects of compounds. Therefore, there is a need for mathematical methods for GRN identification from time-over-dose-dependent data. One of the current approaches for GRN inference is Time Series Network Identification (TSNI). TSNI is based on ordinary differential equations (ODE), describing the time evolution of the expression of each gene, which is assumed to be dependent on the expression of other genes and an external perturbation (i.e. chemical exposure). Here, we present Dose-Time Network Identification (DTNI), a method extending TSNI by including ODE describing how the expression of each gene evolves with dose, which is supposed to depend on the expression of other genes and the exposure time. We also adapted TSNI in order to enable inclusion of time-over-dose-dependent data from multiple compounds. Here, we show that DTNI outperforms TSNI in inferring a toxicant-induced GRN. Moreover, we show that DTNI is a suitable method to infer a GRN dose- and time-dependently induced by a group of compounds influencing a common biological process. Applying DTNI on experimental data from TG-GATEs, we demonstrate that DTNI provides in-depth information on the mode of action of compounds, in particular key events and potential molecular initiating events. Furthermore, DTNI also discloses several unknown interactions which have to be verified experimentally.
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Affiliation(s)
- Diana M Hendrickx
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands.
- , P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
| | - Terezinha Souza
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
- , P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Danyel G J Jennen
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
- , P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW-School for Oncology and Developmental Biology, Maastricht University, Universiteitssingel 40, 6229 ER, Maastricht, The Netherlands
- , P.O. Box 616, 6200 MD, Maastricht, The Netherlands
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40
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Chatterjee S, Majumder PP, Pandey P. Detecting cognizable trends of gene expression in a time series RNA-sequencing experiment: a bootstrap approach. J Genet 2016; 95:587-93. [PMID: 27659329 DOI: 10.1007/s12041-016-0681-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Study of temporal trajectory of gene expression is important. RNA sequencing is popular in genome-scale studies of transcription. Because of high expenses involved, many time-course RNA sequencing studies are challenged by inadequacy of sample sizes. This poses difficulties in conducting formal statistical tests of significance of null hypotheses. We propose a bootstrap algorithm to identify 'cognizable' 'time-trends' of gene expression. Properties of the proposed algorithm are derived using a simulation study. The proposed algorithm captured known 'time-trends' in the simulated data with a high probability of success, even when sample sizes were small (n < 10). The proposed statistical method is efficient and robust to capture 'cognizable' 'time-trends' in RNA sequencing data.
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Affiliation(s)
- Shatakshee Chatterjee
- National Institute of Biomedical Genomics, Netaji Subhas Sanatorium (T. B. Hospital), P.O.: N.S.S., Kalyani 741 251,
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41
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Rezaei Kolahchi A, Khadem Mohtaram N, Pezeshgi Modarres H, Mohammadi MH, Geraili A, Jafari P, Akbari M, Sanati-Nezhad A. Microfluidic-Based Multi-Organ Platforms for Drug Discovery. MICROMACHINES 2016; 7:E162. [PMID: 30404334 PMCID: PMC6189912 DOI: 10.3390/mi7090162] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 12/18/2022]
Abstract
Development of predictive multi-organ models before implementing costly clinical trials is central for screening the toxicity, efficacy, and side effects of new therapeutic agents. Despite significant efforts that have been recently made to develop biomimetic in vitro tissue models, the clinical application of such platforms is still far from reality. Recent advances in physiologically-based pharmacokinetic and pharmacodynamic (PBPK-PD) modeling, micro- and nanotechnology, and in silico modeling have enabled single- and multi-organ platforms for investigation of new chemical agents and tissue-tissue interactions. This review provides an overview of the principles of designing microfluidic-based organ-on-chip models for drug testing and highlights current state-of-the-art in developing predictive multi-organ models for studying the cross-talk of interconnected organs. We further discuss the challenges associated with establishing a predictive body-on-chip (BOC) model such as the scaling, cell types, the common medium, and principles of the study design for characterizing the interaction of drugs with multiple targets.
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Affiliation(s)
- Ahmad Rezaei Kolahchi
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Nima Khadem Mohtaram
- Laboratory for Innovations in MicroEngineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada.
- Division of Medical Sciences, University of Victoria, Victoria, BC V8P 5C2, Canada.
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Hassan Pezeshgi Modarres
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
| | - Mohammad Hossein Mohammadi
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Azadi Ave., Tehran 11155-9516, Iran.
| | - Armin Geraili
- Department of Chemical and Petroleum Engineering, Sharif University of Technology, Azadi Ave., Tehran 11155-9516, Iran.
| | - Parya Jafari
- Department of Electrical Engineering, Sharif University of Technology, Azadi Ave., Tehran 11155-9516, Iran.
| | - Mohsen Akbari
- Laboratory for Innovations in MicroEngineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada.
- Division of Medical Sciences, University of Victoria, Victoria, BC V8P 5C2, Canada.
| | - Amir Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory, Department of Mechanical and Manufacturing Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
- Center for Bioengineering Research and Education, Biomedical Engineering Program, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada.
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42
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Model-based contextualization of in vitro toxicity data quantitatively predicts in vivo drug response in patients. Arch Toxicol 2016; 91:865-883. [PMID: 27161439 PMCID: PMC5306109 DOI: 10.1007/s00204-016-1723-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/20/2016] [Indexed: 12/13/2022]
Abstract
Understanding central mechanisms underlying drug-induced toxicity plays a crucial role in drug development and drug safety. However, a translation of cellular in vitro findings to an actual in vivo context remains challenging. Here, physiologically based pharmacokinetic (PBPK) modeling was used for in vivo contextualization of in vitro toxicity data (PICD) to quantitatively predict in vivo drug response over time by integrating multiple levels of biological organization. Explicitly, in vitro toxicity data at the cellular level were integrated into whole-body PBPK models at the organism level by coupling in vitro drug exposure with in vivo drug concentration–time profiles simulated in the extracellular environment within the organ. PICD was exemplarily applied on the hepatotoxicant azathioprine to quantitatively predict in vivo drug response of perturbed biological pathways and cellular processes in rats and humans. The predictive accuracy of PICD was assessed by comparing in vivo drug response predicted for rats with observed in vivo measurements. To demonstrate clinical applicability of PICD, in vivo drug responses of a critical toxicity-related pathway were predicted for eight patients following acute azathioprine overdoses. Moreover, acute liver failure after multiple dosing of azathioprine was investigated in a patient case study by use of own clinical data. Simulated pharmacokinetic profiles were therefore related to in vivo drug response predicted for genes associated with observed clinical symptoms and to clinical biomarkers measured in vivo. PICD provides a generic platform to investigate drug-induced toxicity at a patient level and thus may facilitate individualized risk assessment during drug development.
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Knöspel F, Jacobs F, Freyer N, Damm G, De Bondt A, van den Wyngaert I, Snoeys J, Monshouwer M, Richter M, Strahl N, Seehofer D, Zeilinger K. In Vitro Model for Hepatotoxicity Studies Based on Primary Human Hepatocyte Cultivation in a Perfused 3D Bioreactor System. Int J Mol Sci 2016; 17:584. [PMID: 27092500 PMCID: PMC4849040 DOI: 10.3390/ijms17040584] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 03/24/2016] [Accepted: 04/12/2016] [Indexed: 01/02/2023] Open
Abstract
Accurate prediction of the potential hepatotoxic nature of new pharmaceuticals remains highly challenging. Therefore, novel in vitro models with improved external validity are needed to investigate hepatic metabolism and timely identify any toxicity of drugs in humans. In this study, we examined the effects of diclofenac, as a model substance with a known risk of hepatotoxicity in vivo, in a dynamic multi-compartment bioreactor using primary human liver cells. Biotransformation pathways of the drug and possible effects on metabolic activities, morphology and cell transcriptome were evaluated. Formation rates of diclofenac metabolites were relatively stable over the application period of seven days in bioreactors exposed to 300 µM diclofenac (300 µM bioreactors (300 µM BR)), while in bioreactors exposed to 1000 µM diclofenac (1000 µM BR) metabolite concentrations declined drastically. The biochemical data showed a significant decrease in lactate production and for the higher dose a significant increase in ammonia secretion, indicating a dose-dependent effect of diclofenac application. The microarray analyses performed revealed a stable hepatic phenotype of the cells over time and the observed transcriptional changes were in line with functional readouts of the system. In conclusion, the data highlight the suitability of the bioreactor technology for studying the hepatotoxicity of drugs in vitro.
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Affiliation(s)
- Fanny Knöspel
- Bioreactor Group, Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin 13353, Germany.
| | - Frank Jacobs
- Janssen Research & Development, Beerse 2340, Belgium.
| | - Nora Freyer
- Bioreactor Group, Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin 13353, Germany.
| | - Georg Damm
- Department for General, Visceral and Transplantation Surgery, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin 13353, Germany.
| | - An De Bondt
- Janssen Research & Development, Beerse 2340, Belgium.
| | | | - Jan Snoeys
- Janssen Research & Development, Beerse 2340, Belgium.
| | | | - Marco Richter
- Bioreactor Group, Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin 13353, Germany.
| | - Nadja Strahl
- Bioreactor Group, Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin 13353, Germany.
| | - Daniel Seehofer
- Department for General, Visceral and Transplantation Surgery, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin 13353, Germany.
| | - Katrin Zeilinger
- Bioreactor Group, Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin 13353, Germany.
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Sutherland JJ, Jolly RA, Goldstein KM, Stevens JL. Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes. PLoS Comput Biol 2016; 12:e1004847. [PMID: 27028627 PMCID: PMC4814051 DOI: 10.1371/journal.pcbi.1004847] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/03/2016] [Indexed: 12/13/2022] Open
Abstract
The effect of drugs, disease and other perturbations on mRNA levels are studied using gene expression microarrays or RNA-seq, with the goal of understanding molecular effects arising from the perturbation. Previous comparisons of reproducibility across laboratories have been limited in scale and focused on a single model. The use of model systems, such as cultured primary cells or cancer cell lines, assumes that mechanistic insights derived from the models would have been observed via in vivo studies. We examined the concordance of compound-induced transcriptional changes using data from several sources: rat liver and rat primary hepatocytes (RPH) from Drug Matrix (DM) and open TG-GATEs (TG), human primary hepatocytes (HPH) from TG, and mouse liver / HepG2 results from the Gene Expression Omnibus (GEO) repository. Gene expression changes for treatments were normalized to controls and analyzed with three methods: 1) gene level for 9071 high expression genes in rat liver, 2) gene set analysis (GSA) using canonical pathways and gene ontology sets, 3) weighted gene co-expression network analysis (WGCNA). Co-expression networks performed better than genes or GSA when comparing treatment effects within rat liver and rat vs. mouse liver. Genes and modules performed similarly at Connectivity Map-style analyses, where success at identifying similar treatments among a collection of reference profiles is the goal. Comparisons between rat liver and RPH, and those between RPH, HPH and HepG2 cells reveal lower concordance for all methods. We observe that the baseline state of untreated cultured cells relative to untreated rat liver shows striking similarity with toxicant-exposed cells in vivo, indicating that gross systems level perturbation in the underlying networks in culture may contribute to the low concordance. Gene expression studies in model systems are widely used for understanding the mechanism of drugs and other perturbations in biological systems. Other researchers have examined the reproducibility of microarray studies between laboratories, or comparing microarrays and/or RNA sequencing. However, no large scale studies have compared results from protocols which differ in minor details, or results generated in vivo vs. in vitro culture systems thought to serve as useful models. The rat liver is by far the most extensively studied model evaluating effects of drugs and other perturbations, and existing data allowed us to assess the level of concordance between rat liver and rat primary hepatocytes cultured in collagen-coated plates (i.e. “flat” culture) for hundreds of drugs. We found that the mouse liver serves as a better model of the rat liver than do rat primary hepatocytes, even after allowing for differences due to pharmacokinetics. The low concordance observed between rat liver and rat hepatocytes suggests that validating the utility of ‘omics data generated on emerging cell culture approaches (e.g. “organ-on-a-chip”, 3D-printed tissues) using rat cells and comparison to the rat liver may be necessary in order to gain confidence these approaches substantially improve on traditional culture models of human cells.
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Affiliation(s)
- Jeffrey J. Sutherland
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
- * E-mail: (JJS); (JLS)
| | - Robert A. Jolly
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - Keith M. Goldstein
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
| | - James L. Stevens
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
- * E-mail: (JJS); (JLS)
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De Abrew KN, Kainkaryam RM, Shan YK, Overmann GJ, Settivari RS, Wang X, Xu J, Adams RL, Tiesman JP, Carney EW, Naciff JM, Daston GP. Grouping 34 Chemicals Based on Mode of Action Using Connectivity Mapping. Toxicol Sci 2016; 151:447-61. [DOI: 10.1093/toxsci/kfw058] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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46
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El-Hachem N, Grossmann P, Blanchet-Cohen A, Bateman AR, Bouchard N, Archambault J, Aerts HJ, Haibe-Kains B. Characterization of Conserved Toxicogenomic Responses in Chemically Exposed Hepatocytes across Species and Platforms. ENVIRONMENTAL HEALTH PERSPECTIVES 2016; 124:313-20. [PMID: 26173225 PMCID: PMC4786983 DOI: 10.1289/ehp.1409157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 07/09/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND Genome-wide expression profiling is increasingly being used to identify transcriptional changes induced by drugs and environmental stressors. In this context, the Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system (TG-GATEs) project generated transcriptional profiles from rat liver samples and human/rat cultured primary hepatocytes exposed to more than 100 different chemicals. OBJECTIVES To assess the capacity of the cell culture models to recapitulate pathways induced by chemicals in vivo, we leveraged the TG-GATEs data set to compare the early transcriptional responses observed in the liver of rats treated with a large set of chemicals with those of cultured rat and human primary hepatocytes challenged with the same compounds in vitro. METHODS We developed a new pathway-based computational pipeline that efficiently combines gene set enrichment analysis (GSEA) using pathways from the Reactome database with biclustering to identify common modules of pathways that are modulated by several chemicals in vivo and in vitro across species. RESULTS We found that some chemicals induced conserved patterns of early transcriptional responses in in vitro and in vivo settings, and across human and rat genomes. These responses involved pathways of cell survival, inflammation, xenobiotic metabolism, oxidative stress, and apoptosis. Moreover, our results support the transforming growth factor beta receptor (TGF-βR) signaling pathway as a candidate biomarker associated with exposure to environmental toxicants in primary human hepatocytes. CONCLUSIONS Our integrative analysis of toxicogenomics data provides a comprehensive overview of biochemical perturbations affected by a large panel of chemicals. Furthermore, we show that the early toxicological response occurring in animals is recapitulated in human and rat primary hepatocyte cultures at the molecular level, indicating that these models reproduce key pathways in response to chemical stress. These findings expand our understanding and interpretation of toxicogenomics data from human hepatocytes exposed to environmental toxicants.
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Affiliation(s)
- Nehme El-Hachem
- Integrative systems biology, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montréal, Quebec, Canada
| | - Patrick Grossmann
- Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Alain R. Bateman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Nicolas Bouchard
- Department of Medicine, University of Montreal, Montréal, Quebec, Canada
- Molecular Biology of Neural Development, Institut de Recherches Cliniques de Montréal, Montreal, Canada
| | - Jacques Archambault
- Laboratory of Molecular Virology, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada
| | - Hugo J.W.L. Aerts
- Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Address correspondence to B. Haibe-Kains, Princess Margaret Cancer Centre, University Health Network, 101 College St., Toronto, ON, M5G 1L7, Canada. Telephone: 1 (416) 581-7628. E-mail: , or to H.J.W.L. Aerts, Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA. E-mail:
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada
- Address correspondence to B. Haibe-Kains, Princess Margaret Cancer Centre, University Health Network, 101 College St., Toronto, ON, M5G 1L7, Canada. Telephone: 1 (416) 581-7628. E-mail: , or to H.J.W.L. Aerts, Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA. E-mail:
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47
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Precision multidimensional assay for high-throughput microRNA drug discovery. Nat Commun 2016; 7:10709. [PMID: 26880188 PMCID: PMC4757758 DOI: 10.1038/ncomms10709] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/12/2016] [Indexed: 12/16/2022] Open
Abstract
Development of drug discovery assays that combine high content with throughput is challenging. Information-processing gene networks can address this challenge by integrating multiple potential targets of drug candidates' activities into a small number of informative readouts, reporting simultaneously on specific and non-specific effects. Here we show a family of networks implementing this concept in a cell-based drug discovery assay for miRNA drug targets. The networks comprise multiple modules reporting on specific effects towards an intended miRNA target, together with non-specific effects on gene expression, off-target miRNAs and RNA interference pathway. We validate the assays using known perturbations of on- and off-target miRNAs, and evaluate an ∼700 compound library in an automated screen with a follow-up on specific and non-specific hits. We further customize and validate assays for additional drug targets and non-specific inputs. Our study offers a novel framework for precision drug discovery assays applicable to diverse target families. Progress in drug discovery can be hampered by a limited exploration of chemical space and the difficulty in assessing the full range of drug candidates' effects on living cells. Here the authors describe a cell-based assay to distinguish between off-target and specific effects of candidate compounds targeting micro RNAs.
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48
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Ippolito DL, AbdulHameed MDM, Tawa GJ, Baer CE, Permenter MG, McDyre BC, Dennis WE, Boyle MH, Hobbs CA, Streicker MA, Snowden BS, Lewis JA, Wallqvist A, Stallings JD. Gene Expression Patterns Associated With Histopathology in Toxic Liver Fibrosis. Toxicol Sci 2015; 149:67-88. [DOI: 10.1093/toxsci/kfv214] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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49
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Kim H, Kim JH, Kim SY, Jo D, Park HJ, Kim J, Jung S, Kim HS, Lee K. Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PLoS One 2015; 10:e0136698. [PMID: 26335687 PMCID: PMC4559398 DOI: 10.1371/journal.pone.0136698] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/05/2015] [Indexed: 11/19/2022] Open
Abstract
Undesirable toxicity is one of the main reasons for withdrawing drugs from the market or eliminating them as candidates in clinical trials. Although numerous studies have attempted to identify biomarkers capable of predicting pharmacotoxicity, few have attempted to discover robust biomarkers that are coherent across various species and experimental settings. To identify such biomarkers, we conducted meta-analyses of massive gene expression profiles for 6,567 in vivo rat samples and 453 compounds. After applying rigorous feature reduction procedures, our analyses identified 18 genes to be related with toxicity upon comparisons of untreated versus treated and innocuous versus toxic specimens of kidney, liver and heart tissue. We then independently validated these genes in human cell lines. In doing so, we found several of these genes to be coherently regulated in both in vivo rat specimens and in human cell lines. Specifically, mRNA expression of neuronal regeneration-related protein was robustly down-regulated in both liver and kidney cells, while mRNA expression of cathepsin D was commonly up-regulated in liver cells after exposure to toxic concentrations of chemical compounds. Use of these novel toxicity biomarkers may enhance the efficiency of screening for safe lead compounds in early-phase drug development prior to animal testing.
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Affiliation(s)
- Hyosil Kim
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Ju-Hwa Kim
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - So Youn Kim
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
| | - Deokyeon Jo
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
| | - Ho Jun Park
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
| | - Jihyun Kim
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
| | - Sungwon Jung
- Department of Genome Medicine and Science, School of Medicine, Gachon University, Incheon, Korea
- * E-mail: (HSK); (SJ)
| | - Hyun Seok Kim
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
- * E-mail: (HSK); (SJ)
| | - KiYoung Lee
- Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Korea
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50
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Goldring C, Norris A, Kitteringham N, Aleo MD, Antoine DJ, Heslop J, Howell BA, Ingelman-Sundberg M, Kia R, Kamalian L, Koerber S, Martinou JC, Mercer A, Moggs J, Naisbitt DJ, Powell C, Sidaway J, Sison-Young R, Snoeys J, van de Water B, Watkins PB, Weaver RJ, Wolf A, Zhang F, Park BK. Mechanism-Based Markers of Drug-Induced Liver Injury to Improve the Physiological Relevance and Predictivity of In Vitro Models. ACTA ACUST UNITED AC 2015. [DOI: 10.1089/aivt.2015.0001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chris Goldring
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Alan Norris
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Neil Kitteringham
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael D. Aleo
- Drug Safety Research & Development, Pfizer R&D, Groton, Connecticut
| | - Daniel J. Antoine
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - James Heslop
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Brett A. Howell
- The Hamner-UNC Institute for Drug Safety Sciences, Research Triangle Park, North Carolina
| | | | - Richard Kia
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Laleh Kamalian
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sarah Koerber
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | | | - Amy Mercer
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Jonathan Moggs
- Discovery and Investigative Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dean J. Naisbitt
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Christopher Powell
- Safety Assessment, GSK David Jack Research Centre, Hertfordshire, United Kingdom
| | - James Sidaway
- Molecular Toxicology and Safety Pharmacology, Global Safety Assessment UK, Innovative Medicines, AstraZeneca R&D, Macclesfield, United Kingdom
| | - Rowena Sison-Young
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Jan Snoeys
- Pharmacokinetics Dynamics and Metabolism, Janssen Research and Development, Beerse, Belgium
| | - Bob van de Water
- Division of Toxicology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Paul B. Watkins
- The Hamner-UNC Institute for Drug Safety Sciences, Research Triangle Park, North Carolina
| | | | - Armin Wolf
- Discovery and Investigative Safety, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Fang Zhang
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - B. Kevin Park
- MRC Centre for Drug Safety Science, Department of Clinical and Molecular Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
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