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McClure RS, Rericha Y, Waters KM, Tanguay RL. 3' RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism. Front Bioinform 2023; 3:1234218. [PMID: 37576716 PMCID: PMC10414111 DOI: 10.3389/fbinf.2023.1234218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction: The application of RNA-sequencing has led to numerous breakthroughs related to investigating gene expression levels in complex biological systems. Among these are knowledge of how organisms, such as the vertebrate model organism zebrafish (Danio rerio), respond to toxicant exposure. Recently, the development of 3' RNA-seq has allowed for the determination of gene expression levels with a fraction of the required reads compared to standard RNA-seq. While 3' RNA-seq has many advantages, a comparison to standard RNA-seq has not been performed in the context of whole organism toxicity and sparse data. Methods and results: Here, we examined samples from zebrafish exposed to perfluorobutane sulfonamide (FBSA) with either 3' or standard RNA-seq to determine the advantages of each with regards to the identification of functionally enriched pathways. We found that 3' and standard RNA-seq showed specific advantages when focusing on annotated or unannotated regions of the genome. We also found that standard RNA-seq identified more differentially expressed genes (DEGs), but that this advantage disappeared under conditions of sparse data. We also found that standard RNA-seq had a significant advantage in identifying functionally enriched pathways via analysis of DEG lists but that this advantage was minimal when identifying pathways via gene set enrichment analysis of all genes. Conclusions: These results show that each approach has experimental conditions where they may be advantageous. Our observations can help guide others in the choice of 3' RNA-seq vs standard RNA sequencing to query gene expression levels in a range of biological systems.
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Affiliation(s)
- Ryan S. McClure
- Biological Sciences Division, Pacific Northwest Laboratory, Richland, WA, United States
| | - Yvonne Rericha
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Katrina M. Waters
- Biological Sciences Division, Pacific Northwest Laboratory, Richland, WA, United States
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Robyn L. Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
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2
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Gupta SS, Singh KP, Gupta S, Dusinska M, Rahman Q. Do Carbon Nanotubes and Asbestos Fibers Exhibit Common Toxicity Mechanisms? Nanomaterials (Basel) 2022; 12:nano12101708. [PMID: 35630938 PMCID: PMC9145953 DOI: 10.3390/nano12101708] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023]
Abstract
During the last two decades several nanoscale materials were engineered for industrial and medical applications. Among them carbon nanotubes (CNTs) are the most exploited nanomaterials with global production of around 1000 tons/year. Besides several commercial benefits of CNTs, the fiber-like structures and their bio-persistency in lung tissues raise serious concerns about the possible adverse human health effects resembling those of asbestos fibers. In this review, we present a comparative analysis between CNTs and asbestos fibers using the following four parameters: (1) fibrous needle-like shape, (2) bio-persistent nature, (3) high surface to volume ratio and (4) capacity to adsorb toxicants/pollutants on the surface. We also compare mechanisms underlying the toxicity caused by certain diameters and lengths of CNTs and asbestos fibers using downstream pathways associated with altered gene expression data from both asbestos and CNT exposure. Our results suggest that indeed certain types of CNTs are emulating asbestos fiber as far as associated toxicity is concerned.
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Affiliation(s)
- Suchi Smita Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; (S.S.G.); (K.P.S.); (S.G.)
| | - Krishna P. Singh
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; (S.S.G.); (K.P.S.); (S.G.)
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; (S.S.G.); (K.P.S.); (S.G.)
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, NILU-Norwegian Institute for Air Research, 2007 Kjeller, Norway;
| | - Qamar Rahman
- Amity Institute of Biotechnology, Amity University, Lucknow 226028, India
- Correspondence:
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3
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Araújo AM, Carvalho F, Guedes de Pinho P, Carvalho M. Toxicometabolomics: Small Molecules to Answer Big Toxicological Questions. Metabolites 2021; 11:692. [PMID: 34677407 PMCID: PMC8539642 DOI: 10.3390/metabo11100692] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/17/2022] Open
Abstract
Given the high biological impact of classical and emerging toxicants, a sensitive and comprehensive assessment of the hazards and risks of these substances to organisms is urgently needed. In this sense, toxicometabolomics emerged as a new and growing field in life sciences, which use metabolomics to provide new sets of susceptibility, exposure, and/or effects biomarkers; and to characterize in detail the metabolic responses and altered biological pathways that various stressful stimuli cause in many organisms. The present review focuses on the analytical platforms and the typical workflow employed in toxicometabolomic studies, and gives an overview of recent exploratory research that applied metabolomics in various areas of toxicology.
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Affiliation(s)
- Ana Margarida Araújo
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Félix Carvalho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Paula Guedes de Pinho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Márcia Carvalho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
- FP-I3ID, FP-ENAS, University Fernando Pessoa, Praça 9 de Abril, 349, 4249-004 Porto, Portugal
- Faculty of Health Sciences, University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150 Porto, Portugal
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4
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McCann J, McCann T. 2018 Lush Science Prize. Altern Lab Anim 2020; 48:18S-25S. [PMID: 33106014 DOI: 10.1177/0261192920912054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The Lush Prize supports animal-free testing by awarding money prizes of up to £350,000 per year to the most effective projects and individuals who have been working towards the goal of replacing animals in product or ingredient safety testing. Since its inception in 2012, the Lush Prize has distributed almost £2 million. Prizes are awarded for developments in five strategic areas: Science; Lobbying; Training; Public Awareness; and Young Researchers. In 2015, the judges also awarded a Black Box prize for the development of the skin sensitisation Adverse Outcome Pathway and its associated in vitro assays. The Science Prize is awarded to researchers whose work the judging panel believe to have made the most significant contribution, in the preceding year, to the replacement of animal testing. This 2018 Science Background paper outlines the research projects that were presented to the Prize judges as potential candidates for the 2018 Lush Science Prize award. To obtain an overview of developments in the field of animal replacement in toxicity research, recent work by the relevant scientific institutions and projects in this area, including the OECD, CAAT, ECVAM, UK NC3Rs, US Tox21 Programme, the ToxCast programme and EU-ToxRisk, was reviewed. Recent developments in toxicity testing research were investigated by searching the relevant literature. Abstracts from conferences focusing on animal replacement in toxicity testing that were held in the preceding 12 months, were also analysed, including those from the 2017 10th World Congress on Alternatives and Animals in the Life Sciences and the 2018 Society of Toxicology annual conference.
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Zgheib E, Limonciel A, Jiang X, Wilmes A, Wink S, van de Water B, Kopp-Schneider A, Bois FY, Jennings P. Corrigendum: Investigation of Nrf2, AhR and ATF4 Activation in Toxicogenomic Databases. Front Genet 2019; 10:517. [PMID: 31231426 PMCID: PMC6558953 DOI: 10.3389/fgene.2019.00517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fgene.2018.00429.].
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Affiliation(s)
- Elias Zgheib
- Laboratoire de Biomécanique et Bio-ingénierie, Sorbonne Universités - Université de Technologie de Compiègne, Compiègne, France
| | - Alice Limonciel
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Xiaoqi Jiang
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Anja Wilmes
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Steven Wink
- Division of Drug Discovery and Safety, Leiden Cell Observatory High Content Imaging Screening Facility, Leiden Academic Center for Drug Research, Leiden University, Leiden, Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Cell Observatory High Content Imaging Screening Facility, Leiden Academic Center for Drug Research, Leiden University, Leiden, Netherlands
| | | | - Frederic Y Bois
- Models for Ecotoxicology and Toxicology Unit (DRC/VIVA/METO), Institut National de l'Environnement Industriel et des Risques, Verneuil-en-Halatte, France
| | - Paul Jennings
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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6
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Zgheib E, Limonciel A, Jiang X, Wilmes A, Wink S, van de Water B, Kopp-Schneider A, Bois FY, Jennings P. Investigation of Nrf2, AhR and ATF4 Activation in Toxicogenomic Databases. Front Genet 2018; 9:429. [PMID: 30333853 PMCID: PMC6176024 DOI: 10.3389/fgene.2018.00429] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/11/2018] [Indexed: 12/14/2022] Open
Abstract
Toxicological responses to chemical insult are largely regulated by transcriptionally activated pathways that may be independent, correlated and partially or fully overlapping. Investigating the dynamics of the interactions between stress responsive transcription factors from toxicogenomic data and defining the signature of each of them is an additional step toward a system level understanding of perturbation driven mechanisms. To this end, we investigated the segregation of the genes belonging to the three following transcriptionally regulated pathways: the AhR pathway, the Nrf2 pathway and the ATF4 pathway. Toxicogenomic datasets from three projects (carcinoGENOMICS, Predict-IV and TG-GATEs) obtained in various experimental conditions (in human and rat in vitro liver and kidney models and rat in vivo, with bolus administration and with repeated doses) were combined and consolidated where overlaps between datasets existed. A bioinformatic analysis was performed to refine pathways' signatures and to create chemical activation capacity scores to classify chemicals by their potency and selectivity of activation of each pathway. With some refinement such an approach may improve chemical safety classification and allow biological read across on a pathway level.
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Affiliation(s)
- Elias Zgheib
- Laboratoire de Biomécanique et Bio-ingénierie, Sorbonne Universités - Université de Technologie de Compiègne, Compiègne, France
| | - Alice Limonciel
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Xiaoqi Jiang
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Anja Wilmes
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Steven Wink
- Division of Drug Discovery and Safety, Leiden Cell Observatory High Content Imaging Screening Facility, Leiden Academic Center for Drug Research, Leiden University, Leiden, Netherlands
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Cell Observatory High Content Imaging Screening Facility, Leiden Academic Center for Drug Research, Leiden University, Leiden, Netherlands
| | | | - Frederic Y Bois
- Models for Ecotoxicology and Toxicology Unit (DRC/VIVA/METO), Institut National de l'Environnement Industriel et des Risques, Verneuil-en-Halatte, France
| | - Paul Jennings
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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7
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Souza TM, Kleinjans JCS, Jennen DGJ. Dose and Time Dependencies in Stress Pathway Responses during Chemical Exposure: Novel Insights from Gene Regulatory Networks. Front Genet 2017; 8:142. [PMID: 29085386 PMCID: PMC5649202 DOI: 10.3389/fgene.2017.00142] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/21/2017] [Indexed: 11/19/2022] Open
Abstract
Perturbation of biological networks is often observed during exposure to xenobiotics, and the identification of disturbed processes, their dynamic traits, and dose–response relationships are some of the current challenges for elucidating the mechanisms determining adverse outcomes. In this scenario, reverse engineering of gene regulatory networks (GRNs) from expression data may provide a system-level snapshot embedded within accurate molecular events. Here, we investigate the composition of GRNs inferred from groups of chemicals with two distinct outcomes, namely carcinogenicity [azathioprine (AZA) and cyclophosphamide (CYC)] and drug-induced liver injury (DILI; diclofenac, nitrofurantoin, and propylthiouracil), and a non-carcinogenic/non-DILI group (aspirin, diazepam, and omeprazole). For this, we analyzed publicly available exposed in vitro human data, taking into account dose and time dependencies. Dose–Time Network Identification (DTNI) was applied to gene sets from exposed primary human hepatocytes using four stress pathways, namely endoplasmic reticulum (ER), NF-κB, NRF2, and TP53. Inferred GRNs suggested case specificity, varying in interactions, starting nodes, and target genes across groups. DILI and carcinogenic compounds were shown to directly affect all pathway-based GRNs, while non-DILI/non-carcinogenic chemicals only affected NF-κB. NF-κB-based GRNs clearly illustrated group-specific disturbances, with the cancer-related casein kinase CSNK2A1 being a target gene only in the carcinogenic group, and opposite regulation of NF-κB subunits being observed in DILI and non-DILI/non-carcinogenic groups. Target genes in NRF2-based GRNs shared by DILI and carcinogenic compounds suggested markers of hepatotoxicity. Finally, we indicate several of these group-specific interactions as potentially novel. In summary, our reversed-engineered GRNs are capable of revealing dose dependent, chemical-specific mechanisms of action in stress-related biological networks.
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Affiliation(s)
- Terezinha M Souza
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Jos C S Kleinjans
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
| | - Danyel G J Jennen
- Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, Netherlands
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8
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Ross JA, George BJ, Bruno M, Ge Y. Chemical-agnostic hazard prediction: statistical inference of in vitro toxicity pathways from proteomics responses to chemical mixtures. ACTA ACUST UNITED AC 2017; 2:39-44. [PMID: 30345409 DOI: 10.1016/j.comtox.2017.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Toxicity pathways have been defined as normal cellular pathways that, when sufficiently perturbed as a consequence of chemical exposure, lead to an adverse outcome. If an exposure alters one or more normal biological pathways to an extent that leads to an adverse toxicity outcome, a significant correlation must exist between the exposure, the extent of pathway alteration, and the degree of adverse outcome. Biological pathways are regulated at multiple levels, including transcriptional, post-transcriptional, post-translational, and targeted degradation, each of which can affect the levels and extents of modification of proteins involved in the pathways. Significant alterations of toxicity pathways resulting from changes in regulation at any of these levels therefore are likely to be detectable as alterations in the proteome. We hypothesize that significant correlations between exposures, adverse outcomes, and changes in the proteome have the potential to identify putative toxicity pathways, facilitating selection of candidate targets for high throughput screening, even in the absence of a priori knowledge of either the specific pathways involved or the specific agents inducing the pathway alterations. We explored this hypothesis in vitro in BEAS-2B human airway epithelial cells exposed to different concentrations of Ni2+, Cd2+, and Cr6+, alone and in defined mixtures. Levels and phosphorylation status of a variety of signaling pathway proteins and cytokines were measured after 48 hours exposure, together with cytotoxicity. Least Absolute Shrinkage and Selection Operator (LASSO) multiple regression was used to identify a subset of these proteins that constitute a putative toxicity pathway capable of predicting cytotoxicity. The putative toxicity pathway for cytotoxicity of these metals and metal mixtures identified by LASSO is composed of phospho-RPS6KB1, phospho-p53, cleaved CASP3, phospho-MAPK8, IL-10, and Hif-1α. As this approach does not depend on knowledge of the chemical composition of the mixtures, it may be generally useful for identifying sets of proteins predictive of adverse effects for a variety of mixtures, including complex environmental mixtures of unknown composition.
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Affiliation(s)
- Jeffrey A Ross
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711
| | - Barbara Jane George
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711
| | - Maribel Bruno
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711
| | - Yue Ge
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, 27711
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9
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Clewell RA, Sun B, Adeleye Y, Carmichael P, Efremenko A, McMullen PD, Pendse S, Trask OJ, White A, Andersen ME. Profiling dose-dependent activation of p53-mediated signaling pathways by chemicals with distinct mechanisms of DNA damage. Toxicol Sci 2014; 142:56-73. [PMID: 25078064 PMCID: PMC4226763 DOI: 10.1093/toxsci/kfu153] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
As part of a larger effort to provide proof-of-concept in vitro-only risk assessments, we have developed a suite of high-throughput assays for key readouts in the p53 DNA damage response toxicity pathway: double-strand break DNA damage (p-H2AX), permanent chromosomal damage (micronuclei), p53 activation, p53 transcriptional activity, and cell fate (cell cycle arrest, apoptosis, micronuclei). Dose-response studies were performed with these protein and cell fate assays, together with whole genome transcriptomics, for three prototype chemicals: etoposide, quercetin, and methyl methanesulfonate. Data were collected in a human cell line expressing wild-type p53 (HT1080) and results were confirmed in a second p53 competent cell line (HCT 116). At chemical concentrations causing similar increases in p53 protein expression, p53-mediated protein expression and cellular processes showed substantial chemical-specific differences. These chemical-specific differences in the p53 transcriptional response appear to be determined by augmentation of the p53 response by co-regulators. More importantly, dose-response data for each of the chemicals indicate that the p53 transcriptional response does not prevent micronuclei induction at low concentrations. In fact, the no observed effect levels and benchmark doses for micronuclei induction were less than or equal to those for p53-mediated gene transcription regardless of the test chemical, indicating that p53's post-translational responses may be more important than transcriptional activation in the response to low dose DNA damage. This effort demonstrates the process of defining key assays required for a pathway-based, in vitro-only risk assessment, using the p53-mediated DNA damage response pathway as a prototype.
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Affiliation(s)
- Rebecca A Clewell
- The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709
| | - Bin Sun
- The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709
| | - Yeyejide Adeleye
- Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Paul Carmichael
- Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Alina Efremenko
- The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709
| | - Patrick D McMullen
- The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709
| | - Salil Pendse
- The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709
| | - O J Trask
- The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709
| | - Andy White
- Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Melvin E Andersen
- The Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709
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10
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Bhattacharya S, Shoda LKM, Zhang Q, Woods CG, Howell BA, Siler SQ, Woodhead JL, Yang Y, McMullen P, Watkins PB, Andersen ME. Modeling drug- and chemical-induced hepatotoxicity with systems biology approaches. Front Physiol 2012; 3:462. [PMID: 23248599 PMCID: PMC3522076 DOI: 10.3389/fphys.2012.00462] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 11/21/2012] [Indexed: 12/22/2022] Open
Abstract
We provide an overview of computational systems biology approaches as applied to the study of chemical- and drug-induced toxicity. The concept of “toxicity pathways” is described in the context of the 2007 US National Academies of Science report, “Toxicity testing in the 21st Century: A Vision and A Strategy.” Pathway mapping and modeling based on network biology concepts are a key component of the vision laid out in this report for a more biologically based analysis of dose-response behavior and the safety of chemicals and drugs. We focus on toxicity of the liver (hepatotoxicity) – a complex phenotypic response with contributions from a number of different cell types and biological processes. We describe three case studies of complementary multi-scale computational modeling approaches to understand perturbation of toxicity pathways in the human liver as a result of exposure to environmental contaminants and specific drugs. One approach involves development of a spatial, multicellular “virtual tissue” model of the liver lobule that combines molecular circuits in individual hepatocytes with cell–cell interactions and blood-mediated transport of toxicants through hepatic sinusoids, to enable quantitative, mechanistic prediction of hepatic dose-response for activation of the aryl hydrocarbon receptor toxicity pathway. Simultaneously, methods are being developing to extract quantitative maps of intracellular signaling and transcriptional regulatory networks perturbed by environmental contaminants, using a combination of gene expression and genome-wide protein-DNA interaction data. A predictive physiological model (DILIsym™) to understand drug-induced liver injury (DILI), the most common adverse event leading to termination of clinical development programs and regulatory actions on drugs, is also described. The model initially focuses on reactive metabolite-induced DILI in response to administration of acetaminophen, and spans multiple biological scales.
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Affiliation(s)
- Sudin Bhattacharya
- Institute for Chemical Safety Sciences, The Hamner Institutes for Health Sciences Research Triangle Park, NC, USA
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11
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Abstract
Traditional toxicity testing using animal models is slow, low capacity, expensive and assesses a limited number of endpoints. Such approaches are inadequate to deal with the increasingly large number of compounds found in the environment for which there are no toxicity data. Mechanism-centered high-throughput testing represents an alternative approach to meet this pressing need but is limited by our current understanding of toxicity pathways. Functional toxicogenomics, the global study of the biological function of genes on the modulation of the toxic effect of a compound, can play an important role in identifying the essential cellular components and pathways involved in toxicity response. The combination of the identification of fundamental toxicity pathways and mechanism-centered targeted assays represents an integrated approach to advance molecular toxicology to meet the challenges of toxicity testing in the 21st century.
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Affiliation(s)
- Matthew North
- Department of Nutritional Science and Toxicology, University of California Berkeley, Berkeley, California 94720, USA; E-Mail:
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