1
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Bianchi E, Costa E, Harrill J, Deford P, LaRocca J, Chen W, Sutake Z, Lehman A, Pappas-Garton A, Sherer E, Moreillon C, Sriram S, Dhroso A, Johnson K. Discovery Phase Agrochemical Predictive Safety Assessment Using High Content In Vitro Data to Estimate an In Vivo Toxicity Point of Departure. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39033510 DOI: 10.1021/acs.jafc.4c03094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Utilization of in vitro (cellular) techniques, like Cell Painting and transcriptomics, could provide powerful tools for agrochemical candidate sorting and selection in the discovery process. However, using these models generates challenges translating in vitro concentrations to the corresponding in vivo exposures. Physiologically based pharmacokinetic (PBPK) modeling provides a framework for quantitative in vitro to in vivo extrapolation (IVIVE). We tested whether in vivo (rat liver) transcriptomic and apical points of departure (PODs) could be accurately predicted from in vitro (rat hepatocyte or human HepaRG) transcriptomic PODs or HepaRG Cell Painting PODs using PBPK modeling. We compared two PBPK models, the ADMET predictor and the httk R package, and found httk to predict the in vivo PODs more accurately. Our findings suggest that a rat liver apical and transcriptomic POD can be estimated utilizing a combination of in vitro transcriptome-based PODs coupled with PBPK modeling for IVIVE. Thus, high content in vitro data can be translated with modest accuracy to in vivo models of ultimate regulatory importance to help select agrochemical analogs in early stage discovery program.
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Affiliation(s)
- Enrica Bianchi
- Corteva Agriscience, Indianapolis ,Indiana 46268, United States
| | | | - Joshua Harrill
- Center for Computational Toxicology and Exposure, United States Environmental Protection Agency, Research Triangle Park ,North Carolina 27709, United States
| | - Paul Deford
- Corteva Agriscience, Indianapolis ,Indiana 46268, United States
| | - Jessica LaRocca
- Corteva Agriscience, Indianapolis ,Indiana 46268, United States
| | - Wei Chen
- Corteva Agriscience, Indianapolis ,Indiana 46268, United States
| | - Zachary Sutake
- Corteva Agriscience, Indianapolis ,Indiana 46268, United States
| | - Audrey Lehman
- Corteva Agriscience, Indianapolis ,Indiana 46268, United States
| | | | - Eric Sherer
- Corteva Agriscience, Indianapolis ,Indiana 46268, United States
| | | | | | - Andi Dhroso
- Corteva Agriscience, Indianapolis ,Indiana 46268, United States
| | - Kamin Johnson
- Corteva Agriscience, Indianapolis ,Indiana 46268, United States
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2
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Kim JW, Kim HS, Kim HR, Chung KH. Next generation risk assessment of biocides (PHMG-p and CMIT/MIT)-induced pulmonary fibrosis using adverse outcome pathway-based transcriptome analysis. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:134986. [PMID: 38944992 DOI: 10.1016/j.jhazmat.2024.134986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/19/2024] [Accepted: 06/19/2024] [Indexed: 07/02/2024]
Abstract
Next-generation risk assessment (NGRA) has emerged as a promising alternative to non-animal studies owing to the increasing demand for the risk assessment of inhaled toxicants. In this study, NGRA was used to assess the inhalation risks of two biocides commonly used as humidifier disinfectants: polyhexamethylene guanidine phosphate (PHMG-p) and chloromethylisothiazolinone/methylisothiazolinone (CMIT/MIT). Human bronchial epithelial cell transcriptomic data were processed based on adverse outcome pathways and used to establish transcriptome-based points of departure (tPODs) for each biocide. tPOD values were 0.00500-0.0510 μg/cm2 and 0.0342-0.0544 μg/cm2 for PHMG-p and CMIT/MIT, respectively. tPODs may provide predictive power comparable to that of traditional animal-based PODs (aPODs). The tPOD-based NGRA determined that both PHMG-p and CMIT/MIT present a high inhalation risk. Moreover, the identified PHMG-p posed a higher risk than CMIT/MIT, and children were identified as more susceptible population compared to adults. This finding is consistent with observations from actual exposure events. Our findings suggest that NGRA with transcriptomics offers a reliable approach for risk assessment of specific humidifier disinfectant biocides, while acknowledging the limitations of current models and in vitro systems, particularly regarding uncertainties in pharmacokinetics (PK) and pharmacodynamics (PD).
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Affiliation(s)
- Jun Woo Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Hyung Sik Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea
| | - Ha Ryong Kim
- College of Pharmacy, Korea University, Sejong 30019, South Korea.
| | - Kyu Hyuck Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, South Korea.
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3
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Carpi D, Liska R, Malinowska JM, Palosaari T, Bouhifd M, Whelan M. Investigating the dependency of in vitro benchmark concentrations on exposure time in transcriptomics experiments. Toxicol In Vitro 2024; 95:105761. [PMID: 38081393 PMCID: PMC10879918 DOI: 10.1016/j.tiv.2023.105761] [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: 09/18/2023] [Revised: 11/10/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023]
Abstract
There is increasing interest to employ in vitro transcriptomics experiments in toxicological testing, for example to determine a point-of-departure (PoD) for chemical safety assessment. However current practices to derive PoD tend to utilise a single exposure time despite the importance of exposure time on the manifestation of toxicity caused by a chemical. Therefore it is important to investigate both concentration and exposure time to determine how these factors affect biological responses, and as a consequence, the derivation of PoDs. In this study, metabolically competent HepaRG cells were exposed to five known toxicants over a range of concentrations and time points for subsequent gene expression analysis, using a targeted RNA expression assay (TempO-Seq). A non-parametric factor-modelling approach was used to model the collective response of all significant genes, which exploited the interdependence of differentially expressed gene responses. This in turn allowed the determination of an isobenchmark response (isoBMR) curve for each chemical in a reproducible manner. For 2 of the 5 chemicals tested, the PoD was observed to vary by 0.5-1 log-order within the 48-h timeframe of the experiment. The approach and findings presented here clearly demonstrate the need to take both concentration and exposure time into account when designing in vitro toxicogenomics experiments to determine PoD. Doing so also provides a means to use concentration-time-response modelling as a basis to extrapolate a PoD from shorter to longer exposure durations, and to identify chemicals of concern that can cause cumulative effects over time.
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Affiliation(s)
- Donatella Carpi
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Roman Liska
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | - Taina Palosaari
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Mounir Bouhifd
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Maurice Whelan
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
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4
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Nelson GM, Carswell GK, Swartz CD, Recio L, Yauk CL, Chorley BN. Early microRNA responses in rodent liver mediated by furan exposure establish dose thresholds for later adverse outcomes. Toxicol Lett 2023; 384:105-114. [PMID: 37517673 PMCID: PMC10530563 DOI: 10.1016/j.toxlet.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
To reduce reliance on long-term in vivo studies, short-term data linking early molecular-based measurements to later adverse health effects is needed. Although transcriptional-based benchmark dose (BMDT) modeling has been used to estimate potencies and stratify chemicals based on potential to induce later-life effects, dose-responsive epigenetic alterations have not been routinely considered. Here, we evaluated the utility of microRNA (miRNA) profiling in mouse liver and blood, as well as in mouse primary hepatocytes in vitro, to indicate mechanisms of liver perturbation due to short-term exposure of the known rodent liver hepatotoxicant and carcinogen, furan. Benchmark dose modeling of miRNA measurements (BMDmiR) were compared to the referent transcriptional (BMDT) and apical (BMDA) estimates. These analyses indicate a robust dose response for 34 miRNAs to furan and involvement of p53-linked pathways in furan-mediated hepatotoxicity, supporting mRNA and apical measurements. Liver-sourced miRNAs were also altered in the blood and primary hepatocytes. Overall, these results indicate mechanistic involvement of miRNA in furan carcinogenicity and provide evidence of their potential utility as accessible biomarkers of exposure and disease.
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Affiliation(s)
- Gail M Nelson
- US Environmental Protection Agency, Research Triangle Park, NC 27709, USA
| | - Gleta K Carswell
- US Environmental Protection Agency, Research Triangle Park, NC 27709, USA
| | - Carol D Swartz
- Inotiv Co., 601 Keystone Park Drive, Suite 200, Morrisville, NC 27560, USA
| | - Leslie Recio
- ScitoVation, 100 Capitola Drive Suite 106, Durham, NC 27713, USA
| | - Carole L Yauk
- Dept. Of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Brian N Chorley
- US Environmental Protection Agency, Research Triangle Park, NC 27709, USA.
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5
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Gant TW, Auerbach SS, Von Bergen M, Bouhifd M, Botham PA, Caiment F, Currie RA, Harrill J, Johnson K, Li D, Rouquie D, van Ravenzwaay B, Sistare F, Tralau T, Viant MR, van de Laan JW, Yauk C. Applying genomics in regulatory toxicology: a report of the ECETOC workshop on omics threshold on non-adversity. Arch Toxicol 2023; 97:2291-2302. [PMID: 37296313 PMCID: PMC10322787 DOI: 10.1007/s00204-023-03522-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/11/2023] [Indexed: 06/12/2023]
Abstract
In a joint effort involving scientists from academia, industry and regulatory agencies, ECETOC's activities in Omics have led to conceptual proposals for: (1) A framework that assures data quality for reporting and inclusion of Omics data in regulatory assessments; and (2) an approach to robustly quantify these data, prior to interpretation for regulatory use. In continuation of these activities this workshop explored and identified areas of need to facilitate robust interpretation of such data in the context of deriving points of departure (POD) for risk assessment and determining an adverse change from normal variation. ECETOC was amongst the first to systematically explore the application of Omics methods, now incorporated into the group of methods known as New Approach Methodologies (NAMs), to regulatory toxicology. This support has been in the form of both projects (primarily with CEFIC/LRI) and workshops. Outputs have led to projects included in the workplan of the Extended Advisory Group on Molecular Screening and Toxicogenomics (EAGMST) group of the Organisation for Economic Co-operation and Development (OECD) and to the drafting of OECD Guidance Documents for Omics data reporting, with potentially more to follow on data transformation and interpretation. The current workshop was the last in a series of technical methods development workshops, with a sub-focus on the derivation of a POD from Omics data. Workshop presentations demonstrated that Omics data developed within robust frameworks for both scientific data generation and analysis can be used to derive a POD. The issue of noise in the data was discussed as an important consideration for identifying robust Omics changes and deriving a POD. Such variability or "noise" can comprise technical or biological variation within a dataset and should clearly be distinguished from homeostatic responses. Adverse outcome pathways (AOPs) were considered a useful framework on which to assemble Omics methods, and a number of case examples were presented in illustration of this point. What is apparent is that high dimension data will always be subject to varying processing pipelines and hence interpretation, depending on the context they are used in. Yet, they can provide valuable input for regulatory toxicology, with the pre-condition being robust methods for the collection and processing of data together with a comprehensive description how the data were interpreted, and conclusions reached.
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Affiliation(s)
- Timothy W Gant
- United Kingdom Health Security Agency, Harwell Science Campus, Didcot, Oxfordshire, United Kingdom.
- Imperial College London School of Public Health, London, United Kingdom.
| | - Scott S Auerbach
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, RTP, Durham, NC, USA
| | - Martin Von Bergen
- Department for Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | | | | | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | | | - Joshua Harrill
- Cellular and Molecular Toxicologist, Center for Computational Toxicology and Exposure (CCTE), U.S. Environmental Protection Agency, Durham, NC, USA
| | - Kamin Johnson
- Predictive Safety Center, Corteva Agriscience, Indianapolis, IN, USA
| | - Dongying Li
- National Center for Toxicological Research, U.S. Food and Drug Administration (FDA), 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - David Rouquie
- Bayer SAS, Bayer Crop Science, 355 Rue Dostoïevski, CS 90153, 06906, Valbonne Sophia-Antipolis, France
| | | | | | - Tewes Tralau
- Department of Pesticides Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Carole Yauk
- Department of Biology, University of Ottawa, Ottawa, Canada
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6
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Reardon AJF, Farmahin R, Williams A, Meier MJ, Addicks GC, Yauk CL, Matteo G, Atlas E, Harrill J, Everett LJ, Shah I, Judson R, Ramaiahgari S, Ferguson SS, Barton-Maclaren TS. From vision toward best practices: Evaluating in vitro transcriptomic points of departure for application in risk assessment using a uniform workflow. FRONTIERS IN TOXICOLOGY 2023; 5:1194895. [PMID: 37288009 PMCID: PMC10242042 DOI: 10.3389/ftox.2023.1194895] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/03/2023] [Indexed: 06/09/2023] Open
Abstract
The growing number of chemicals in the current consumer and industrial markets presents a major challenge for regulatory programs faced with the need to assess the potential risks they pose to human and ecological health. The increasing demand for hazard and risk assessment of chemicals currently exceeds the capacity to produce the toxicity data necessary for regulatory decision making, and the applied data is commonly generated using traditional approaches with animal models that have limited context in terms of human relevance. This scenario provides the opportunity to implement novel, more efficient strategies for risk assessment purposes. This study aims to increase confidence in the implementation of new approach methods in a risk assessment context by using a parallel analysis to identify data gaps in current experimental designs, reveal the limitations of common approaches deriving transcriptomic points of departure, and demonstrate the strengths in using high-throughput transcriptomics (HTTr) to derive practical endpoints. A uniform workflow was applied across six curated gene expression datasets from concentration-response studies containing 117 diverse chemicals, three cell types, and a range of exposure durations, to determine tPODs based on gene expression profiles. After benchmark concentration modeling, a range of approaches was used to determine consistent and reliable tPODs. High-throughput toxicokinetics were employed to translate in vitro tPODs (µM) to human-relevant administered equivalent doses (AEDs, mg/kg-bw/day). The tPODs from most chemicals had AEDs that were lower (i.e., more conservative) than apical PODs in the US EPA CompTox chemical dashboard, suggesting in vitro tPODs would be protective of potential effects on human health. An assessment of multiple data points for single chemicals revealed that longer exposure duration and varied cell culture systems (e.g., 3D vs. 2D) lead to a decreased tPOD value that indicated increased chemical potency. Seven chemicals were flagged as outliers when comparing the ratio of tPOD to traditional POD, thus indicating they require further assessment to better understand their hazard potential. Our findings build confidence in the use of tPODs but also reveal data gaps that must be addressed prior to their adoption to support risk assessment applications.
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Affiliation(s)
- Anthony J. F. Reardon
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada
| | - Reza Farmahin
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada
| | - Matthew J. Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada
| | - Gregory C. Addicks
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada
| | - Carole L. Yauk
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Geronimo Matteo
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Ella Atlas
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada
- Department of Biochemistry, University of Ottawa, Ottawa, ON, Canada
| | - Joshua Harrill
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Durham, NC, United States
| | - Logan J. Everett
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Durham, NC, United States
| | - Imran Shah
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Durham, NC, United States
| | - Richard Judson
- Center for Computational Toxicology and Exposure, US Environmental Protection Agency, Durham, NC, United States
| | - Sreenivasa Ramaiahgari
- Division of Translational Toxicology, Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
| | - Stephen S. Ferguson
- Division of Translational Toxicology, Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, United States
| | - Tara S. Barton-Maclaren
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada
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7
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Chauhan V, Yu J, Vuong N, Haber LT, Williams A, Auerbach SS, Beaton D, Wang Y, Stainforth R, Wilkins RC, Azzam EI, Richardson RB, Khan MGM, Jadhav A, Burtt JJ, Leblanc J, Randhawa K, Tollefsen KE, Yauk CL. Considerations for application of benchmark dose modeling in radiation research: workshop highlights. Int J Radiat Biol 2023; 99:1320-1331. [PMID: 36881459 DOI: 10.1080/09553002.2023.2181998] [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: 08/28/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND Exposure to different forms of ionizing radiation occurs in diverse occupational, medical, and environmental settings. Improving the accuracy of the estimated health risks associated with exposure is therefore, essential for protecting the public, particularly as it relates to chronic low dose exposures. A key aspect to understanding health risks is precise and accurate modeling of the dose-response relationship. Toward this vision, benchmark dose (BMD) modeling may be a suitable approach for consideration in the radiation field. BMD modeling is already extensively used for chemical hazard assessments and is considered statistically preferable to identifying low and no observed adverse effects levels. BMD modeling involves fitting mathematical models to dose-response data for a relevant biological endpoint and identifying a point of departure (the BMD, or its lower bound). Recent examples in chemical toxicology show that when applied to molecular endpoints (e.g. genotoxic and transcriptional endpoints), BMDs correlate to points of departure for more apical endpoints such as phenotypic changes (e.g. adverse effects) of interest to regulatory decisions. This use of BMD modeling may be valuable to explore in the radiation field, specifically in combination with adverse outcome pathways, and may facilitate better interpretation of relevant in vivo and in vitro dose-response data. To advance this application, a workshop was organized on June 3rd, 2022, in Ottawa, Ontario that brought together BMD experts in chemical toxicology and the radiation scientific community of researchers, regulators, and policy-makers. The workshop's objective was to introduce radiation scientists to BMD modeling and its practical application using case examples from the chemical toxicity field and demonstrate the BMDExpress software using a radiation dataset. Discussions focused on the BMD approach, the importance of experimental design, regulatory applications, its use in supporting the development of adverse outcome pathways, and specific radiation-relevant examples. CONCLUSIONS Although further deliberations are needed to advance the use of BMD modeling in the radiation field, these initial discussions and partnerships highlight some key steps to guide future undertakings related to new experimental work.
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Affiliation(s)
- Vinita Chauhan
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, Canada
| | - Jihang Yu
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
| | - Ngoc Vuong
- Radiation Protection Bureau, Health Canada, Ottawa, Canada
| | - Lynne T Haber
- Department of Environmental and Public Health Sciences, Risk Science Center, University of Cincinnati, Cincinnati, OH, USA
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Scott S Auerbach
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Danielle Beaton
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
| | - Yi Wang
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | | | - Ruth C Wilkins
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, Canada
| | - Edouard I Azzam
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
- Department of Radiology, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Richard B Richardson
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
- Medical Physics Unit, McGill University, Montreal, QC, Canada
| | | | - Ashok Jadhav
- Radiobiology and Health Branch, Canadian Nuclear Laboratories, Chalk River, Canada
| | - Julie J Burtt
- Directorate of Environmental and Radiation Protection and Assessment, Canadian Nuclear Safety Commission, Ottawa, Canada
| | - Julie Leblanc
- Directorate of Environmental and Radiation Protection and Assessment, Canadian Nuclear Safety Commission, Ottawa, Canada
| | - Kristi Randhawa
- Directorate of Environmental and Radiation Protection and Assessment, Canadian Nuclear Safety Commission, Ottawa, Canada
| | - Knut Erik Tollefsen
- Norwegian Institute for Water Research (NIVA), Oslo, Norway
- Norwegian University of Life Sciences (NMBU), Ås, Norway
- Centre for Environmental Radioactivity, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Carole L Yauk
- Department of Biology, University of Ottawa, Ottawa, Canada
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8
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Villeneuve DL, Le M, Hazemi M, Biales A, Bencic DC, Bush K, Flick R, Martinson J, Morshead M, Rodriguez KS, Vitense K, Flynn K. Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay. Curr Res Toxicol 2022; 4:100099. [PMID: 36619288 PMCID: PMC9816907 DOI: 10.1016/j.crtox.2022.100099] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/03/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Concentrations at which global gene expression profiles in cells or animals exposed to a test substance start to differ significantly from those of controls have been proposed as an alternative point of departure for use in screening level hazard assessment. The present study describes pilot testing of a high throughput compatible transcriptomics assay with larval fathead minnows. One day post hatch fathead minnows were exposed to eleven different concentrations of three metals, three selective serotonin reuptake inhibitors, and four neonicotinoid-like compounds for 24 h and concentration response modeling was applied to whole body gene expression data. Transcriptomics-based points of departure (tPODs) were consistently lower than effect concentrations reported in apical endpoint studies in fish. However, larval fathead minnow-based tPODs were not always lower than concentrations reported to elicit apical toxicity in other aquatic organisms like crustaceans or insects. Random in silico subsampling of data from the pilot assays was used to evaluate various assay design and acceptance considerations such as transcriptome coverage, number of replicate individuals to sequence per treatment, and minimum number of differentially expressed genes to produce a reliable tPOD estimate. Results showed a strong association between the total number of genes for which a concentration response relationship could be derived and the overall variability in the resulting tPOD estimates. We conclude that, for our current assay design and analysis pipeline, tPODs based on fewer than 15 differentially expressed genes are likely to be unreliable for screening and that interindividual variability in gene expression profiles appears to be a more significant driver of tPOD variability than sample size alone. Results represent initial steps toward developing high throughput transcriptomics assays for use in ecological hazard screening.
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Key Words
- BMD, Benchmark dose
- Benchmark dose
- Computational toxicology
- DEGs, Differentially expressed genes
- ECOTOX knowledgebase
- Fish
- HTTr, High throughput transcriptomics
- RIN, RNA integrity number
- RNA sequencing
- RNAseq, RNA sequencing
- SSRI, Selective serotonin reuptake inhibitor
- ToxCast, US EPA Toxicity Forecaster
- Transcriptomics-based point of departure
- cDNA, Complementary DNA
- eco-HTTr, Ecological high throughput transcriptomics
- tPOD, Transcriptomics-based point of departure
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Affiliation(s)
- Daniel L. Villeneuve
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA,Corresponding author at: U.S. EPA Great Lakes Toxicology and Ecology Division, 6201 Congdon Blvd., Duluth, MN 55804-2595, USA.
| | - Michelle Le
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, US Environmental Protection Agency Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
| | - Monique Hazemi
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, US Environmental Protection Agency Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
| | - Adam Biales
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Cincinnati, OH 45220, USA
| | - David C. Bencic
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Cincinnati, OH 45220, USA
| | - Kendra Bush
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, US Environmental Protection Agency Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
| | - Robert Flick
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Cincinnati, OH 45220, USA
| | - John Martinson
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Cincinnati, OH 45220, USA
| | - Mackenzie Morshead
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, US Environmental Protection Agency Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
| | - Kelvin Santana Rodriguez
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, US Environmental Protection Agency Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
| | - Kelsey Vitense
- US Environmental Protection Agency, Scientific Computing and Data Curation Division, Duluth, MN 55804, USA
| | - Kevin Flynn
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, MN 55804, USA
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9
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Assessing the neurotoxicity of airborne nano-scale particulate matter in human iPSC-derived neurons using a transcriptomics benchmark dose model. Toxicol Appl Pharmacol 2022; 449:116109. [DOI: 10.1016/j.taap.2022.116109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/26/2022] [Accepted: 06/02/2022] [Indexed: 11/23/2022]
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10
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Basili D, Reynolds J, Houghton J, Malcomber S, Chambers B, Liddell M, Muller I, White A, Shah I, Everett LJ, Middleton A, Bender A. Latent Variables Capture Pathway-Level Points of Departure in High-Throughput Toxicogenomic Data. Chem Res Toxicol 2022; 35:670-683. [PMID: 35333521 PMCID: PMC9019810 DOI: 10.1021/acs.chemrestox.1c00444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Estimation
of points of departure (PoDs) from high-throughput transcriptomic
data (HTTr) represents a key step in the development of next-generation
risk assessment (NGRA). Current approaches mainly rely on single key
gene targets, which are constrained by the information currently available
in the knowledge base and make interpretation challenging as scientists
need to interpret PoDs for thousands of genes or hundreds of pathways.
In this work, we aimed to address these issues by developing a computational
workflow to investigate the pathway concentration–response
relationships in a way that is not fully constrained by known biology
and also facilitates interpretation. We employed the Pathway-Level
Information ExtractoR (PLIER) to identify latent variables (LVs) describing
biological activity and then investigated in vitro LVs’ concentration–response
relationships using the ToxCast pipeline. We applied this methodology
to a published transcriptomic concentration–response data set
for 44 chemicals in MCF-7 cells and showed that our workflow can capture
known biological activity and discriminate between estrogenic and
antiestrogenic compounds as well as activity not aligning with the
existing knowledge base, which may be relevant in a risk assessment
scenario. Moreover, we were able to identify the known estrogen activity
in compounds that are not well-established ER agonists/antagonists
supporting the use of the workflow in read-across. Next, we transferred
its application to chemical compounds tested in HepG2, HepaRG, and
MCF-7 cells and showed that PoD estimates are in strong agreement
with those estimated using a recently developed Bayesian approach
(cor = 0.89) and in weak agreement with those estimated using a well-established
approach such as BMDExpress2 (cor = 0.57). These results demonstrate
the effectiveness of using PLIER in a concentration–response
scenario to investigate pathway activity in a way that is not fully
constrained by the knowledge base and to ease the biological interpretation
and support the development of an NGRA framework with the ability
to improve current risk assessment strategies for chemicals using
new approach methodologies.
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Affiliation(s)
- Danilo Basili
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.,Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Joe Reynolds
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Jade Houghton
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Sophie Malcomber
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Bryant Chambers
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Mark Liddell
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Iris Muller
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Andrew White
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Imran Shah
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Logan J Everett
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, United States
| | - Alistair Middleton
- Unilever, Safety and Environmental Assurance Centre (SEAC), Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, U.K
| | - Andreas Bender
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
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11
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ALOHA: Aggregated local extrema splines for high-throughput dose-response analysis. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 21:100196. [PMID: 35083394 PMCID: PMC8785973 DOI: 10.1016/j.comtox.2021.100196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Computational methods for genomic dose-response integrate dose-response modeling with bioinformatics tools to evaluate changes in molecular and cellular functions related to pathogenic processes. These methods use parametric models to describe each gene's dose-response, but such models may not adequately capture expression changes. Additionally, current approaches do not consider gene co-expression networks. When assessing co-expression networks, one typically does not consider the dose-response relationship, resulting in 'co-regulated' gene sets containing genes having different dose-response patterns. To avoid these limitations, we develop an analysis pipeline called Aggregated Local Extrema Splines for High-throughput Analysis (ALOHA), which computes individual genomic dose-response functions using a flexible class Bayesian shape constrained splines and clusters gene co-regulation based upon these fits. Using splines, we reduce information loss due to parametric lack-of-fit issues, and because we cluster on dose-response relationships, we better identify co-regulation clusters for genes that have co-expressed dose-response patterns from chemical exposure. The clustered pathways can then be used to estimate a dose associated with a pre-specified biological response, i.e., the benchmark dose (BMD), and approximate a point of departure dose corresponding to minimal adverse response in the whole tissue/organism. We compare our approach to current parametric methods and our biologically enriched gene sets to cluster on normalized expression data. Using this methodology, we can more effectively extract the underlying structure leading to more cohesive estimates of gene set potency.
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12
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Nault R, Saha S, Bhattacharya S, Dodson J, Sinha S, Maiti T, Zacharewski T. Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs. Nucleic Acids Res 2022; 50:e48. [PMID: 35061903 PMCID: PMC9071439 DOI: 10.1093/nar/gkac019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 12/04/2022] Open
Abstract
The application of single-cell RNA sequencing (scRNAseq) for the evaluation of chemicals, drugs, and food contaminants presents the opportunity to consider cellular heterogeneity in pharmacological and toxicological responses. Current differential gene expression analysis (DGEA) methods focus primarily on two group comparisons, not multi-group dose-response study designs used in safety assessments. To benchmark DGEA methods for dose-response scRNAseq experiments, we proposed a multiplicity corrected Bayesian testing approach and compare it against 8 other methods including two frequentist fit-for-purpose tests using simulated and experimental data. Our Bayesian test method outperformed all other tests for a broad range of accuracy metrics including control of false positive error rates. Most notable, the fit-for-purpose and standard multiple group DGEA methods were superior to the two group scRNAseq methods for dose-response study designs. Collectively, our benchmarking of DGEA methods demonstrates the importance in considering study design when determining the most appropriate test methods.
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Affiliation(s)
| | | | - Sudin Bhattacharya
- Biomedical Engineering Department, Pharmacology & Toxicology, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jack Dodson
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Samiran Sinha
- Department of Statistics, Texas A&M University, College Station, TX 77843, USA
| | - Tapabrata Maiti
- To whom correspondence should be addressed. Tel: +1 517 353 3233; Fax: +1 517 353 9334;
| | - Tim Zacharewski
- Correspondence may also be addressed to Tim Zacharewski. Tel: +1 517 355 1607; Fax: +1 517 353 9334;
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13
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Black MB, Stern A, Efremenko A, Mallick P, Moreau M, Hartman JK, McMullen PD. Biological system considerations for application of toxicogenomics in next-generation risk assessment and predictive toxicology. Toxicol In Vitro 2022; 80:105311. [PMID: 35038564 DOI: 10.1016/j.tiv.2022.105311] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 12/17/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
Abstract
There is increasing interest in using modern 'omics technologies, such as whole transcriptome sequencing, to inform decisions about human health safety and chemical toxicity hazard. High throughput methodologies using in vitro assays offer a path forward in reducing or eliminating animal testing. However, many aspects of these technologies need assessment before they will gain the trust of regulators and the public as viable alternative test methods for human health and safety. We used a high throughput whole transcriptome sequence assay (TempO-Seq) to assess the use of three widely used cancer cell lines (HepG2, MCF7, and Ishikawa cells) as in vitro systems for determination of cellular modes of action for two well studied compounds with canonical liver responses: ketoconazole and phenobarbital. We evaluated transcriptomic data to infer points of departure for use in risk analyses of compounds. Both compounds displayed shortcomings in evidence for canonical liver-related responses in any cell line, despite a strong dose response in all three. This raises questions about the competence of simple, mono-cultured cancer cell lines as appropriate surrogates for some adverse effects or toxic endpoints. Points of departure derived from benchmark doses were highly consistent across all three cell lines however, indicating the use of transcriptomic BMD analyses for such purposes would be a reliable and consistent approach.
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Affiliation(s)
- Michael B Black
- ScitoVation, 100 Capitola Drive, Suite 106, Durham, NC 27713, United States of America.
| | - Allysa Stern
- ScitoVation, 100 Capitola Drive, Suite 106, Durham, NC 27713, United States of America; Cell Microsystems, 801 Capitola Dr., Suite 10, Durham, NC 27713, United States of America
| | - Alina Efremenko
- ScitoVation, 100 Capitola Drive, Suite 106, Durham, NC 27713, United States of America
| | - Pankajini Mallick
- ScitoVation, 100 Capitola Drive, Suite 106, Durham, NC 27713, United States of America
| | - Marjory Moreau
- ScitoVation, 100 Capitola Drive, Suite 106, Durham, NC 27713, United States of America
| | - Jessica K Hartman
- ScitoVation, 100 Capitola Drive, Suite 106, Durham, NC 27713, United States of America; Cell Microsystems, 801 Capitola Dr., Suite 10, Durham, NC 27713, United States of America
| | - Patrick D McMullen
- ScitoVation, 100 Capitola Drive, Suite 106, Durham, NC 27713, United States of America
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14
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Zhang Y, Liu Z, He Q, Wu F, Xiao Y, Chen W, Jin Y, Yu D, Wang Q. Construction of Mode of Action for Cadmium-Induced Renal Tubular Dysfunction Based on a Toxicity Pathway-Oriented Approach. Front Genet 2021; 12:696892. [PMID: 34367254 PMCID: PMC8343180 DOI: 10.3389/fgene.2021.696892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/14/2021] [Indexed: 12/30/2022] Open
Abstract
Although it is recognized that cadmium (Cd) causes renal tubular dysfunction, the mechanism of Cd-induced nephrotoxicity is not yet fully understood. Mode of action (MOA) is a developing tool for chemical risk assessment. To establish the mechanistic MOA of Cd-induced renal tubular dysfunction, the Comparative Toxicogenomics Database (CTD) was used to obtain genomics data of Cd-induced nephrotoxicity, and Ingenuity® Pathway Analysis (IPA) software was applied for bioinformatics analysis. Based on the perturbed toxicity pathways during the process of Cd-induced nephrotoxicity, we established the MOA of Cd-induced renal tubular dysfunction and assessed its confidence with the tailored Bradford Hill criteria. Bioinformatics analysis showed that oxidative stress, DNA damage, cell cycle arrest, and cell death were the probable key events (KEs). Assessment of the overall MOA of Cd-induced renal tubular dysfunction indicated a moderate confidence, and there are still some evidence gaps to be filled by rational experimental designs.
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Affiliation(s)
- Yangchun Zhang
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ziqi Liu
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qianmei He
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Fei Wu
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yongmei Xiao
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wen Chen
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yuan Jin
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Qing Wang
- Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
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15
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Chang Y, Rager JE, Tilton SC. Linking Coregulated Gene Modules with Polycyclic Aromatic Hydrocarbon-Related Cancer Risk in the 3D Human Bronchial Epithelium. Chem Res Toxicol 2021; 34:1445-1455. [PMID: 34048650 PMCID: PMC8560124 DOI: 10.1021/acs.chemrestox.0c00333] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exposure to polycyclic aromatic hydrocarbons (PAHs) often occurs as complex chemical mixtures, which are linked to numerous adverse health outcomes in humans, with cancer as the greatest concern. The cancer risk associated with PAH exposures is commonly evaluated using the relative potency factor (RPF) approach, which estimates PAH mixture carcinogenic potential based on the sum of relative potency estimates of individual PAHs, compared to benzo[a]pyrene (BAP), a reference carcinogen. The present study evaluates molecular mechanisms related to PAH cancer risk through integration of transcriptomic and bioinformatic approaches in a 3D human bronchial epithelial cell model. Genes with significant differential expression from human bronchial epithelium exposed to PAHs were analyzed using a weighted gene coexpression network analysis (WGCNA) two-tiered approach: first to identify gene sets comodulated to RPF and second to link genes to a more comprehensive list of regulatory values, including inhalation-specific risk values. Over 3000 genes associated with processes of cell cycle regulation, inflammation, DNA damage, and cell adhesion processes were found to be comodulated with increasing RPF with pathways for cell cycle S phase and cytoskeleton actin identified as the most significantly enriched biological networks correlated to RPF. In addition, comodulated genes were linked to additional cancer-relevant risk values, including inhalation unit risks, oral cancer slope factors, and cancer hazard classifications from the World Health Organization's International Agency for Research on Cancer (IARC). These gene sets represent potential biomarkers that could be used to evaluate cancer risk associated with PAH mixtures. Among the values tested, RPF values and IARC categorizations shared the most similar responses in positively and negatively correlated gene modules. Together, we demonstrated a novel manner of integrating gene sets with chemical toxicity equivalence estimates through WGCNA to understand potential mechanisms.
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Affiliation(s)
- Yvonne Chang
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, United States
| | - Julia E. Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina, Chapel Hill, NC, United States
- Institute for Environmental Health Solutions, and Curriculum in Toxicology, The University of North Carolina, Chapel Hill, NC, United States
| | - Susan C. Tilton
- Environmental and Molecular Toxicology Department, Oregon State University, Corvallis, OR, United States
- Superfund Research Program, Oregon State University, Corvallis, OR, United States
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16
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Martínez R, Codina AE, Barata C, Tauler R, Piña B, Navarro-Martín L. Transcriptomic effects of tributyltin (TBT) in zebrafish eleutheroembryos. A functional benchmark dose analysis. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122881. [PMID: 32474318 DOI: 10.1016/j.jhazmat.2020.122881] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/03/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
Exposure to the antifouling tributyltin (TBT) has been related to imposex in mollusks and to obesogenicity, adipogenesis and masculinization in fish. To understand the underlying molecular mechanisms, we evaluated dose-response effects of TBT (1.7-56 nM) in zebrafish eleutheroembryos transcriptome exposed from 2 to 5 days post-fertilization. RNA-sequencing analysis identified 3238 differentially expressed transcripts in eleutheroembryos exposed to TBT. Benchmark dose analyses (BMD) showed that the point of departure (PoD) for transcriptomic effects (9.28 nM) was similar to the metabolomic PoD (11.5 nM) and about one order of magnitude lower than the morphometric PoD (67.9 nM) or the median lethal concentration (LC50: 93.6 nM). Functional analysis of BMD transcriptomic data identified steroid metabolism and cholesterol and vitamin D3 biosynthesis as the most sensitive pathways to TBT (<50% PoD). Conversely, transcripts related to general stress and DNA damage became affected only at doses above the PoD. Therefore, our results indicate that transcriptomes can act as early molecular indicators of pollutant exposure, and illustrates their usefulness for the mechanistic identification of the initial toxic events. As the estimated molecular PoDs are close to environmental levels, we concluded that TBT may represent a substantial risk in some natural environments.
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Affiliation(s)
- Rubén Martínez
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain; Universitat de Barcelona (UB), Barcelona, Catalunya 08007, Spain.
| | - Anna E Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
| | - Carlos Barata
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
| | - Romà Tauler
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
| | - Benjamin Piña
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
| | - Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
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17
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Lewis RW, Hill T, Corton JC. A set of six Gene expression biomarkers and their thresholds identify rat liver tumorigens in short-term assays. Toxicology 2020; 443:152547. [PMID: 32755643 PMCID: PMC10439517 DOI: 10.1016/j.tox.2020.152547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 02/01/2023]
Abstract
Traditional methods for cancer risk assessment are retrospective, resource-intensive, and not feasible for the vast majority of environmental chemicals. In earlier studies, we used a set of six biomarkers to accurately identify liver tumorigens in transcript profiles derived from chemically-treated rats using either a Toxicological Priority Index (ToxPi) approach or using derived biomarker thresholds for cancer. The biomarkers consisting of 7-113 genes are used to predict the most common liver cancer molecular initiating events: genotoxicity, cytotoxicity and activation of the xenobiotic receptors AhR, CAR, ER, and PPARα. In the present study, we apply and evaluate the performance of these methods for cancer prediction in an independent rat liver study of 44 chemicals (6 h-7d exposures) examined by Affymetrix arrays. In the first approach, ToxPi ranking of biomarker scores consistently gave the highest scores to tumorigenic chemical-dose pairs; balanced accuracies for identification of liver tumorigenic chemicals were up to 89 %. The second approach used tumorigenic thresholds derived in the present study or from our earlier study that were set at the maximum value for chemical-dose exposures without detectable liver tumor outcomes. Using these thresholds, balanced accuracies were up to 90 %. Both approaches identified all tumorigenic chemicals. Almost all of the tumorigenic chemicals activated more than one MIE. We also compared biomarker responses between two types of profiling platforms (Affymetrix full-genome array, TempO-Seq 1500+ array containing ∼2600 genes) and found that the lack of the full set of biomarker genes on the 1500+ array resulted in decreased ability to identify chemicals that activate the MIEs. Overall, these results demonstrate that predictive approaches based on the 6 biomarkers could be used in short-term assays to identify chemicals and their doses that induce liver tumors, the most common endpoint in rodent bioassays.
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Affiliation(s)
- Robert W Lewis
- Center for Computational Toxicology and Exposure, U.S. EPA, Research Triangle Park, NC, United States.
| | - Thomas Hill
- Center for Computational Toxicology and Exposure, U.S. EPA, Research Triangle Park, NC, United States; Oak Ridge Institute for Science and Education (ORISE) fellow Office of Research and Development, U.S. Environmental Protection Agency (EPA), Research Triangle Park, NC, United States.
| | - J Christopher Corton
- Center for Computational Toxicology and Exposure, U.S. EPA, Research Triangle Park, NC, United States.
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18
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Chauhan V, Adam N, Kuo B, Williams A, Yauk CL, Wilkins R, Stainforth R. Meta-analysis of transcriptomic datasets using benchmark dose modeling shows value in supporting radiation risk assessment. Int J Radiat Biol 2020; 97:31-49. [PMID: 32687419 DOI: 10.1080/09553002.2020.1798543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE Benchmark dose (BMD) modeling is used to determine the dose of a stressor at which a predefined increase in any biological effect above background occurs (e.g. 10% increase from control values). BMD analytical tools have the capacity to model transcriptional dose-response data to derive BMDs for genes, pathways and gene ontologies. We recently demonstrated the value of this approach to support various areas of radiation research using predominately 'in-house' generated datasets. MATERIALS AND METHODS As a continuation of this work, transcriptomic studies of relevance to ionizing radiation were retrieved through the Gene Expression Omnibus (GEO). The datasets were compiled and filtered, then analyzed using BMDExpress. The objective was to determine the reproducibility of BMD values in relation to pathways and genes across different exposure scenarios and compare to those derived using cytogenetic endpoints. A number of graphic visualization approaches were used to determine if BMD outputs could be correlated to parameters such as dose-rate, radiation quality and cell type. RESULTS Curated studies were diverse and derived from experiments with varied design and intent. Despite this, common genes and pathways were identified with low and high dose thresholds. The higher BMD values were associated with immune response and cell death, while transcripts with lower BMD values were generally related to the classic DNA damage response/repair processes, centered on TP53 signaling. Analysis of datasets with relatively similar dose-ranges under comparable experimental conditions showed a bi-modal distribution with a high degree of consistency in BMD values across shared genes and pathways, particularly for those below the 25th percentile of total distribution by dose. The median BMD values were noted to be approximately 0.5 Gy for genes/pathways that comprised mode 1. Furthermore, transcriptional BMD values derived from a subset of genes using in vivo and in vitro datasets were in accord to those using cytogenetic endpoints. CONCLUSION Overall, the results from this work highlight the value of the BMD methodology to derive meaningful outputs that are consistent across different models, provided the studies are conducted using a similar dose-range.
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Affiliation(s)
- Vinita Chauhan
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Nadine Adam
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Ruth Wilkins
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Robert Stainforth
- Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
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19
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Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. NANOMATERIALS 2020; 10:nano10040750. [PMID: 32326418 PMCID: PMC7221878 DOI: 10.3390/nano10040750] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 02/07/2023]
Abstract
The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in exposed biological systems. Transcriptomics enables the exploration of organisms' responses to environmental, chemical, and physical agents by observing the molecular alterations in more detail. Toxicogenomics integrates classical toxicology with omics assays, thus allowing the characterization of the mechanism of action (MOA) of chemical compounds, novel small molecules, and engineered nanomaterials (ENMs). Lack of standardization in data generation and analysis currently hampers the full exploitation of toxicogenomics-based evidence in risk assessment. To fill this gap, TGx methods need to take into account appropriate experimental design and possible pitfalls in the transcriptomic analyses as well as data generation and sharing that adhere to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. In this review, we summarize the recent advancements in the design and analysis of DNA microarray, RNA sequencing (RNA-Seq), and single-cell RNA-Seq (scRNA-Seq) data. We provide guidelines on exposure time, dose and complex endpoint selection, sample quality considerations and sample randomization. Furthermore, we summarize publicly available data resources and highlight applications of TGx data to understand and predict chemical toxicity potential. Additionally, we discuss the efforts to implement TGx into regulatory decision making to promote alternative methods for risk assessment and to support the 3R (reduction, refinement, and replacement) concept. This review is the first part of a three-article series on Transcriptomics in Toxicogenomics. These initial considerations on Experimental Design, Technologies, Publicly Available Data, Regulatory Aspects, are the starting point for further rigorous and reliable data preprocessing and modeling, described in the second and third part of the review series.
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20
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Wang P, Wang Z, Xia P, Zhang X. Concentration-dependent transcriptome of zebrafish embryo for environmental chemical assessment. CHEMOSPHERE 2020; 245:125632. [PMID: 31864044 DOI: 10.1016/j.chemosphere.2019.125632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Mechanistic information is essential to screen and predict the adverse effects of a large number of chemicals during early-life exposure. Concentration-dependent omics can capture the extent of perturbations of biological pathways or processes and provide information on the mechanism of toxicity. However, the application of concentration-dependent transcriptome to assess the developmental toxicity of environmental chemicals is still limited. Here, twelve chemicals representing five different modes of action (MOAs) were tested by the concentration-dependent reduced zebrafish transcriptome approach (CRZT) in combination with a phenotype-based high content screen (PHCS). The responsiveness, sensitivity and mechanistic differentiation of CRZT were validated in comparison with PHCS. First, PHCS identified 10 chemicals with obvious embryotoxicity (LD50 range: 2.11-70.68 μM), while the potencies of the biological pathways perturbed by 12 chemicals (PODpath20 range: 0.002-2.1 μM) were demonstrated by CRZT. Second, although the potency of the transcriptome perturbations was positively correlated with lethality (LD50) (R2 = 0.64, P-value < 0.05) for most tested chemicals, BbF was non-embryotoxic but was the most potent on the perturbance of biological pathways. Finally, the profiles of the perturbed biological processes and the transcriptome potency (PODpath20) captured by CRZT could effectively classify most chemicals corresponding to their known MOAs. In summary, CRZT could significantly improve testing the developmental toxicity of environmental chemicals.
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Affiliation(s)
- Pingping Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Zhihao Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, PR China.
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21
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Meier MJ, Dodge AE, Samarajeewa AD, Beaudette LA. Soil exposed to silver nanoparticles reveals significant changes in community structure and altered microbial transcriptional profiles. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113816. [PMID: 31864930 DOI: 10.1016/j.envpol.2019.113816] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/09/2019] [Accepted: 12/13/2019] [Indexed: 05/20/2023]
Abstract
Anthropogenic activities can disrupt soil ecosystems, normally resulting in reduced soil microbial health. Regulatory agencies need to determine the effects of uncharacterized substances on soil microbial health to establish the safety of these chemicals if they end up in the environment. Previous work has focused on measuring traditional ecotoxicologial endpoints within the categories of microbial biomass, activity, and community structure/diversity. Because these tests can be labor intensive, lengthy to conduct, and cannot measure changes in individual gene functions, we wanted to establish whether metatranscriptomics could be used as a more sensitive endpoint and provide a perspective on community function that is more informative than taxonomic identification of microbes alone. We spiked a freshly collected sandy loam soil (Vulcan, Alberta, Canada) with 0, 60, 145, 347, 833, and 2000 mg kg-1 of silver nanoparticles (AgNPs), a known antagonist of microorganisms due to its propensity for dissolution of toxic silver ions. Assessments performed in our previous work using traditional tests demonstrated the toxicity of AgNPs on soil microbial processes. We expanded this analysis with genomics-based tests by measuring changes in community taxonomic structure and function using 16S rDNA profiling and metatranscriptomics. In addition to identifying bacterial taxa affected by AgNPs, we found that genes involved in heavy metal resistance (e.g., the CzcA efflux pump) and other toxicity response pathways were highly upregulated in the presence of silver. Dose-response analysis using BMDExpress2 software successfully modeled many physiologically relevant genes responding to low concentrations of AgNPs. We found that the transcriptomic point of departure (BMD50) was lower than the IC50s calculated using the traditional tests in our previous work. These results suggest that dose-response modeling of metatranscriptomic gene expression is a useful tool in soil microbial health assessment. SUMMARY: Genomics-based endpoints for the assessment of soil microbial health can be used to perform quantitative dose-response modeling, and soil-based RNAseq adds functional insights.
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Affiliation(s)
- Matthew J Meier
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada.
| | - Annette E Dodge
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Ajith Dias Samarajeewa
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
| | - Lee A Beaudette
- Biological Assessment and Standardization Section, Environment and Climate Change Canada, 335 River Road, Ottawa, Ontario, K1V 1C7, Canada
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22
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Nault R, Bals B, Teymouri F, Black MB, Andersen ME, McMullen PD, Krishnan S, Kuravadi N, Paul N, Kumar S, Kannan K, Jayachandra KC, Alagappan L, Patel BD, Bogen KT, Gollapudi BB, Klaunig JE, Zacharewski TR, Bringi V. A toxicogenomic approach for the risk assessment of the food contaminant acetamide. Toxicol Appl Pharmacol 2020; 388:114872. [PMID: 31881176 PMCID: PMC7014822 DOI: 10.1016/j.taap.2019.114872] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 12/10/2019] [Accepted: 12/20/2019] [Indexed: 12/26/2022]
Abstract
Acetamide (CAS 60-35-5) is detected in common foods. Chronic rodent bioassays led to its classification as a group 2B possible human carcinogen due to the induction of liver tumors in rats. We used a toxicogenomics approach in Wistar rats gavaged daily for 7 or 28 days at doses of 300 to 1500 mg/kg/day (mkd) to determine a point of departure (POD) and investigate its mode of action (MoA). Ki67 labeling was increased at doses ≥750 mkd up to 3.3-fold representing the most sensitive apical endpoint. Differential gene expression analysis by RNA-Seq identified 1110 and 1814 differentially expressed genes in male and female rats, respectively, following 28 days of treatment. Down-regulated genes were associated with lipid metabolism while up-regulated genes included cell signaling, immune response, and cell cycle functions. Benchmark dose (BMD) modeling of the Ki67 labeling index determined the BMD10 lower confidence limit (BMDL10) as 190 mkd. Transcriptional BMD modeling revealed excellent concordance between transcriptional POD and apical endpoints. Collectively, these results indicate that acetamide is most likely acting through a mitogenic MoA, though specific key initiating molecular events could not be elucidated. A POD value of 190 mkd determined for cell proliferation is suggested for risk assessment purposes.
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Affiliation(s)
- Rance Nault
- Institute for Integrative Toxicology, Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States of America
| | - Bryan Bals
- Michigan Biotechnology Institute, Lansing, MI, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tim R Zacharewski
- Institute for Integrative Toxicology, Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States of America
| | - Venkataraman Bringi
- Chemical Engineering & Materials Science, Michigan State University, East Lansing, MI, USA.
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23
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Krewski D, Andersen ME, Tyshenko MG, Krishnan K, Hartung T, Boekelheide K, Wambaugh JF, Jones D, Whelan M, Thomas R, Yauk C, Barton-Maclaren T, Cote I. Toxicity testing in the 21st century: progress in the past decade and future perspectives. Arch Toxicol 2019; 94:1-58. [DOI: 10.1007/s00204-019-02613-4] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022]
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24
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The use of evidence from high-throughput screening and transcriptomic data in human health risk assessments. Toxicol Appl Pharmacol 2019; 380:114706. [DOI: 10.1016/j.taap.2019.114706] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 12/23/2022]
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25
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Addressing systematic inconsistencies between in vitro and in vivo transcriptomic mode of action signatures. Toxicol In Vitro 2019; 58:1-12. [DOI: 10.1016/j.tiv.2019.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/14/2019] [Accepted: 02/14/2019] [Indexed: 12/26/2022]
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26
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Martínez R, Navarro-Martín L, Luccarelli C, Codina AE, Raldúa D, Barata C, Tauler R, Piña B. Unravelling the mechanisms of PFOS toxicity by combining morphological and transcriptomic analyses in zebrafish embryos. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 674:462-471. [PMID: 31022537 DOI: 10.1016/j.scitotenv.2019.04.200] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Exposure to PFOS (perfluorooctanesulfonate) has been related to toxic effects on lipid metabolism, immunological response, and different endocrine systems. We present here a transcriptomic analysis of zebrafish embryos exposed to different concentrations of PFOS (0.03-1.0 mg/L) from 48 to 120 hpf. No major survival or morphological alterations (swimming bladder inflation, kyphosis, eye separation and size…) were observed below the 1.0 mg/L mark. Conversely, we observed significant increase in transcripts related to lipid transport and metabolism even at the lowest used concentration. In addition, we observed a general decrease on transcripts related to natural immunity and defense again infections, which adds to the recent concerns about PFOS as immunotoxicant, particularly in humans. Derived PoD (Point of Departure) values for transcriptional changes (0.011 mg/L) were about 200-fold lower than the corresponding PoD values for morphometric effects (2.53 mg/L), and close to levels observed in human blood serum or bird eggs. Our data suggest that currently applicable tolerable levels of PFOS in commercial goods should be re-evaluated, taking into account its potential effects on lipid metabolism and the immune system.
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Affiliation(s)
- Rubén Martínez
- IDAEA-CSIC, Jordi Girona, 18, 08034 Barcelona, Spain; Universitat de Barcelona (UB), Barcelona 08007, Spain.
| | | | | | - Anna E Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain.
| | | | - Carlos Barata
- IDAEA-CSIC, Jordi Girona, 18, 08034 Barcelona, Spain.
| | - Romà Tauler
- IDAEA-CSIC, Jordi Girona, 18, 08034 Barcelona, Spain.
| | - Benjamin Piña
- IDAEA-CSIC, Jordi Girona, 18, 08034 Barcelona, Spain.
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27
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Pagé-Larivière F, Crump D, O'Brien JM. Transcriptomic points-of-departure from short-term exposure studies are protective of chronic effects for fish exposed to estrogenic chemicals. Toxicol Appl Pharmacol 2019; 378:114634. [PMID: 31226361 DOI: 10.1016/j.taap.2019.114634] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/03/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022]
Abstract
Resource limitations often require risk assessors to extrapolate chronic toxicity from acute tests using assessment factors. Transcriptomic dose-response analysis following short-term exposures may provide a more reliable and biologically-based alternative for estimating chronic toxicity. Here, we demonstrate that transcriptomic dose-response analysis in fish following short-term exposure to endocrine disrupting chemicals (EDCs) provides estimates of chronic toxicity that may be used as protective points-of-departure (POD) for risk assessment. The benchmark dose (BMD) method was used on publicly available datasets (n = 5) to determine transcriptomic PODs in fish exposed to three EDCs (bisphenol A, ethinylestradiol, and diethylstilbestrol). To test for potential bias related to data processing, our analysis compared the effect of different normalization, filtering, and BMD-grouping methods on the transcriptomic PODs. The resulting PODs were then compared to the empirically-derived chronic LOEC of each substance. Normalization and filtering methods had limited impact on the final PODs. However, we found that PODs derived from ontology- or pathway-based gene grouping methods were highly variable, whereas PODs from grouping methods that focused on the most responsive genes were more stable and provided POD estimates that were most similar to the chronic LOEC. Overall, 72% of transcriptomic PODs were within 1 order of magnitude of the chronic LOEC, regardless of data analysis method. When our recommended analysis approach was applied, the concordance improved to 100%. These results suggest that toxicogenomic dose-response analysis has the potential to be a protective decision-support tool for compounds with chronic toxicity, such as EDCs.
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Affiliation(s)
| | - Doug Crump
- National Wildlife Research Center, Environment and Climate Change Canada, Ontario, Canada
| | - Jason M O'Brien
- National Wildlife Research Center, Environment and Climate Change Canada, Ontario, Canada.
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28
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Harrill J, Shah I, Setzer RW, Haggard D, Auerbach S, Judson R, Thomas RS. Considerations for Strategic Use of High-Throughput Transcriptomics Chemical Screening Data in Regulatory Decisions. CURRENT OPINION IN TOXICOLOGY 2019; 15:64-75. [PMID: 31501805 DOI: 10.1016/j.cotox.2019.05.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, numerous organizations, including governmental regulatory agencies in the U.S. and abroad, have proposed using data from New Approach Methodologies (NAMs) for augmenting and increasing the pace of chemical assessments. NAMs are broadly defined as any technology, methodology, approach or combination thereof that can be used to provide information on chemical hazard and risk assessment that avoids the use of intact animals. High-throughput transcriptomics (HTTr) is a type of NAM that uses gene expression profiling as an endpoint for rapidly evaluating the effects of large numbers of chemicals on in vitro cell culture systems. As compared to targeted high-throughput screening (HTS) approaches that measure the effect of chemical X on target Y, HTTr is a non-targeted approach that allows researchers to more broadly characterize the integrated response of an intact biological system to chemicals that may affect a specific biological target or many biological targets under a defined set of treatment conditions (time, concentration, etc.). HTTr screening performed in concentration-response mode can provide potency estimates for the concentrations of chemicals that produce perturbations in cellular response pathways. Here, we discuss study design considerations for HTTr concentration-response screening and present a framework for the use of HTTr-based biological pathway-altering concentrations (BPACs) in a screening-level, risk-based chemical prioritization approach. The framework involves concentration-response modeling of HTTr data, mapping gene level responses to biological pathways, determination of BPACs, in vitro-to-in vivo extrapolation (IVIVE) and comparison to human exposure predictions.
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Affiliation(s)
- Joshua Harrill
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Imran Shah
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - R Woodrow Setzer
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Derik Haggard
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, USA
| | - Scott Auerbach
- National Toxicology Program, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC, USA
| | - Richard Judson
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Russell S Thomas
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
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29
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Levorato S, Rietjens IMCM, Carmichael PL, Hepburn PA. Novel approaches to derive points of departure for food chemical risk assessment. Curr Opin Food Sci 2019. [DOI: 10.1016/j.cofs.2019.02.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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30
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Dose-dependence of chemical carcinogenicity: Biological mechanisms for thresholds and implications for risk assessment. Chem Biol Interact 2019; 301:112-127. [DOI: 10.1016/j.cbi.2019.01.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/11/2019] [Accepted: 01/25/2019] [Indexed: 12/19/2022]
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31
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Farmahin R, Gannon AM, Gagné R, Rowan-Carroll A, Kuo B, Williams A, Curran I, Yauk CL. Hepatic transcriptional dose-response analysis of male and female Fischer rats exposed to hexabromocyclododecane. Food Chem Toxicol 2018; 133:110262. [PMID: 30594549 DOI: 10.1016/j.fct.2018.12.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/13/2018] [Accepted: 12/20/2018] [Indexed: 12/14/2022]
Abstract
Hexabromocyclododecane (HBCD) is a brominated flame retardant found in the environment and human tissues. The toxicological effects of HBCD exposure are not clearly understood. We employed whole-genome RNA-sequencing on liver samples from male and female Fischer rats exposed to 0, 250, 1250, and 5000 mg technical mixture of HBCD/kg diet for 28 days to gain further insight into HBCD toxicity. HBCD altered 428 and 250 gene transcripts in males and females, respectively, which were involved in metabolism of xenobiotics, oxidative stress, immune response, metabolism of glucose and lipids, circadian regulation, cell cycle, fibrotic activity, and hormonal balance. Signature analysis supported that HBCD operates through the constitutive androstane and pregnane X receptors. The median transcriptomic benchmark dose (BMD) for the lowest statistically significant pathway was within 1.5-fold of the BMD for increased liver weight, while the BMD for the lowest pathway with at least three modeled genes (minimum 5% of pathway) was similar to the lowest apical endpoint BMD. The results show how transcriptional analyses can inform mechanisms underlying chemical toxicity and the doses at which potentially adverse effects occur. This experiment is part of a larger study exploring the use of toxicogenomics and high-throughput screening for human health risk assessment.
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Affiliation(s)
- Reza Farmahin
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Anne Marie Gannon
- Regulatory Toxicology Research Division, Health Products and Food Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Rémi Gagné
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Ivan Curran
- Regulatory Toxicology Research Division, Health Products and Food Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada.
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32
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Larras F, Billoir E, Baillard V, Siberchicot A, Scholz S, Wubet T, Tarkka M, Schmitt-Jansen M, Delignette-Muller ML. DRomics: A Turnkey Tool to Support the Use of the Dose-Response Framework for Omics Data in Ecological Risk Assessment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:14461-14468. [PMID: 30444611 DOI: 10.1021/acs.est.8b04752] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Omics approaches (e.g., transcriptomics, metabolomics) are promising for ecological risk assessment (ERA) since they provide mechanistic information and early warning signals. A crucial step in the analysis of omics data is the modeling of concentration-dependency which may have different trends including monotonic (e.g., linear, exponential) or biphasic (e.g., U shape, bell shape) forms. The diversity of responses raises challenges concerning detection and modeling of significant responses and effect concentration (EC) derivation. Furthermore, handling high-throughput data sets is time-consuming and requires effective and automated processing routines. Thus, we developed an open source tool (DRomics, available as an R-package and as a web-based service) which, after elimination of molecular responses (e.g., gene expressions from microarrays) with no concentration-dependency and/or high variability, identifies the best model for concentration-response curve description. Subsequently, an EC (e.g., a benchmark dose) is estimated from each curve, and curves are classified based on their model parameters. This tool is especially dedicated to manage data obtained from an experimental design favoring a great number of tested doses rather than a great number of replicates and also to handle properly monotonic and biphasic trends. The tool finally provides restitution for a table of results that can be directly used to perform ERA approaches.
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Affiliation(s)
- Floriane Larras
- Helmholtz-Centre for Environmental Research UFZ , Department of Bioanalytical Ecotoxicology , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Elise Billoir
- Université de Lorraine , CNRS, UMR 7360, LIEC, Laboratoire Interdisciplinaire des Environnements Continentaux , 57070 Metz , France
| | - Vincent Baillard
- Université de Lorraine , CNRS, UMR 7360, LIEC, Laboratoire Interdisciplinaire des Environnements Continentaux , 57070 Metz , France
| | - Aurélie Siberchicot
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup , UMR 5558, Laboratoire de Biométrie et Biologie Evolutive , 69622 Villeurbanne , France
| | - Stefan Scholz
- Helmholtz-Centre for Environmental Research UFZ , Department of Bioanalytical Ecotoxicology , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Tesfaye Wubet
- Department of Community Ecology , Helmholtz-Centre for Environmental Research-UFZ , Theodor-Lieser-Straße 4 , 06120 Halle , Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Deutscher Platz 5e , 04103 Leipzig , Germany
| | - Mika Tarkka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Deutscher Platz 5e , 04103 Leipzig , Germany
- Department of Soil Ecology , Helmholtz-Centre for Environmental Research-UFZ , Theodor-Lieser-Straße 4 , 06120 Halle , Germany
| | - Mechthild Schmitt-Jansen
- Helmholtz-Centre for Environmental Research UFZ , Department of Bioanalytical Ecotoxicology , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Marie-Laure Delignette-Muller
- Université de Lyon, Université Lyon 1, CNRS, VetAgro Sup , UMR 5558, Laboratoire de Biométrie et Biologie Evolutive , 69622 Villeurbanne , France
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Qutob SS, Chauhan V, Kuo B, Williams A, Yauk CL, McNamee JP, Gollapudi B. The application of transcriptional benchmark dose modeling for deriving thresholds of effects associated with solar-simulated ultraviolet radiation exposure. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:502-515. [PMID: 29761935 PMCID: PMC6099464 DOI: 10.1002/em.22196] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 03/02/2018] [Accepted: 03/16/2018] [Indexed: 06/08/2023]
Abstract
Considerable data has been generated to elucidate the transcriptional response of cells to ultraviolet radiation (UVR) exposure providing a mechanistic understanding of UVR-induced cellular responses. However, using these data to support standards development has been challenging. In this study, we apply benchmark dose (BMD) modeling of transcriptional data to derive thresholds of gene responsiveness following exposure to solar-simulated UVR. Human epidermal keratinocytes were exposed to three doses (10, 20, 150 kJ/m2 ) of solar simulated UVR and assessed for gene expression changes 6 and 24 hr postexposure. The dose-response curves for genes with p-fit values (≥ 0.1) were used to derive BMD values for genes and pathways. Gene BMDs were bi-modally distributed, with a peak at ∼16 kJ/m2 and ∼108 kJ/m2 UVR exposure. Genes/pathways within Mode 1 were involved in cell signaling and DNA damage response, while genes/pathways in the higher Mode 2 were associated with immune response and cancer development. The median value of each Mode coincides with the current human exposure limits for UVR and for the minimal erythemal dose, respectively. Such concordance implies that the use of transcriptional BMD data may represent a promising new approach for deriving thresholds of actinic effects. Environ. Mol. Mutagen. 59:502-515, 2018. © 2018 The Authors Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Sami S. Qutob
- Consumer and Clinical Radiation Protection BureauHealth CanadaOttawaOntarioK1A 1C1Canada
| | - Vinita Chauhan
- Consumer and Clinical Radiation Protection BureauHealth CanadaOttawaOntarioK1A 1C1Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Health CanadaOttawaOntarioCanada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health CanadaOttawaOntarioCanada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Health CanadaOttawaOntarioCanada
| | - James P. McNamee
- Consumer and Clinical Radiation Protection BureauHealth CanadaOttawaOntarioK1A 1C1Canada
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Integration of the TGx-28.65 genomic biomarker with the flow cytometry micronucleus test to assess the genotoxicity of disperse orange and 1,2,4-benzenetriol in human TK6 cells. Mutat Res 2017; 806:51-62. [PMID: 29017062 DOI: 10.1016/j.mrfmmm.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/21/2017] [Accepted: 09/10/2017] [Indexed: 12/13/2022]
Abstract
In vitro gene expression signatures to predict toxicological responses can provide mechanistic context for regulatory testing. We previously developed the TGx-28.65 genomic biomarker from a database of gene expression profiles derived from human TK6 cells exposed to 28 well-known compounds. The biomarker comprises 65 genes that can classify chemicals as DNA damaging or non-DNA damaging. In this study, we applied the TGx-28.65 genomic biomarker in parallel with the in vitro micronucleus (MN) assay to determine if two chemicals of regulatory interest at Health Canada, disperse orange (DO: the orange azo dye 3-[[4-[(4-Nitrophenyl)azo]phenyl] benzylamino]propanenitrile) and 1,2,4-benzenetriol (BT: a metabolite of benzene) are genotoxic or non-genotoxic. Both chemicals caused dose-dependent declines in relative survival and increases in apoptosis. A strong significant increase in MN induction was observed for all concentrations of BT; the top two concentrations of DO also caused a statistically significant increase in MN, but these increases were <2-fold above controls. TGx-28.65 analysis classified BT as genotoxic at all three concentrations and DO as genotoxic at the mid and high concentrations. Thus, although DO only caused a small increase in MN, this response was sufficient to induce a cellular DNA damage response. Benchmark dose modeling confirmed that BT is much more potent than DO. The results strongly suggest that follow-up work is required to assess whether DO and BT are also genotoxic in vivo. This is particularly important for DO, which may require metabolic activation by bacterial gut flora to fully induce its genotoxic potential. Our previously published data and this proof of concept study suggest that the TGx-28.65 genomic biomarker has the potential to add significant value to existing approaches used to assess genotoxicity.
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35
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Transcriptional profiling of male F344 rats suggests the involvement of calcium signaling in the mode of action of acrylamide-induced thyroid cancer. Food Chem Toxicol 2017; 107:186-200. [DOI: 10.1016/j.fct.2017.06.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 12/21/2022]
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36
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Recio L, Friedman M, Marroni D, Maynor T, Chepelev NL. Impact of Acrylamide on Calcium Signaling and Cytoskeletal Filaments in Testes From F344 Rat. Int J Toxicol 2017; 36:124-132. [PMID: 28403741 DOI: 10.1177/1091581817697696] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acrylamide (AA) at high exposure levels is neurotoxic, induces testicular toxicity, and increases dominant lethal mutations in rats. RNA-sequencing in testes was used to identify differentially expressed genes (DEG), explore AA-induced pathway perturbations that could contribute to AA-induced testicular toxicity and then used to derive a benchmark dose (BMD). Male F344/DuCrl rats were administered 0.0, 0.5, 1.5, 3.0, 6.0, or 12.0 mg AA/kg bw/d in drinking water for 5, 15, or 31 days. The experimental design used exposure levels that spanned and exceeded the exposure levels used in the rat dominant lethal, 2-generation reproductive toxicology, and cancer bioassays. The time of sample collection was based on previous studies that developed gene expression-based BMD. At 12.0 mg/kg, there were 38, 33, and 65 DEG ( P value <.005; fold change >1.5) in the testes after 5, 15, or 31 days of exposure, respectively. At 31 days, there was a dose-dependent increase in the number of DEG, and at 12.0 mg/kg/d the top three functional clusters affected by AA exposure were actin filament organization, response to calcium ion, and regulation of cell proliferation. The BMD lower 95% confidence limit using DEG ranged from 1.8 to 6.8 mg/kg compared to a no-observed-adverse-effect-level of 2.0 mg/kg/d for male reproductive toxicity. These results are consistent with the known effects of AA on calcium signaling and cytoskeletal actin filaments leading to neurotoxicity and suggest that AA can cause rat dominant lethal mutations by these same mechanisms leading to impaired chromosome segregation during cell division.
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Affiliation(s)
- Leslie Recio
- 1 Integrated Laboratory Systems Inc, Research Triangle Park, NC, USA
| | - Marvin Friedman
- 2 SNF SAS, rue Adrienne Bolland, ZAC de Milieux, Andrézieux, Rhône-Alpes, France
| | - Dennis Marroni
- 2 SNF SAS, rue Adrienne Bolland, ZAC de Milieux, Andrézieux, Rhône-Alpes, France
| | - Timothy Maynor
- 1 Integrated Laboratory Systems Inc, Research Triangle Park, NC, USA
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Farmahin R, Williams A, Kuo B, Chepelev NL, Thomas RS, Barton-Maclaren TS, Curran IH, Nong A, Wade MG, Yauk CL. Recommended approaches in the application of toxicogenomics to derive points of departure for chemical risk assessment. Arch Toxicol 2016; 91:2045-2065. [PMID: 27928627 PMCID: PMC5399047 DOI: 10.1007/s00204-016-1886-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/02/2016] [Indexed: 12/15/2022]
Abstract
There is increasing interest in the use of quantitative transcriptomic data to determine benchmark dose (BMD) and estimate a point of departure (POD) for human health risk assessment. Although studies have shown that transcriptional PODs correlate with those derived from apical endpoint changes, there is no consensus on the process used to derive a transcriptional POD. Specifically, the subsets of informative genes that produce BMDs that best approximate the doses at which adverse apical effects occur have not been defined. To determine the best way to select predictive groups of genes, we used published microarray data from dose–response studies on six chemicals in rats exposed orally for 5, 14, 28, and 90 days. We evaluated eight approaches for selecting genes for POD derivation and three previously proposed approaches (the lowest pathway BMD, and the mean and median BMD of all genes). The relationship between transcriptional BMDs derived using these 11 approaches and PODs derived from apical data that might be used in chemical risk assessment was examined. Transcriptional BMD values for all 11 approaches were remarkably aligned with corresponding apical PODs, with the vast majority of toxicogenomics PODs being within tenfold of those derived from apical endpoints. We identified at least four approaches that produce BMDs that are effective estimates of apical PODs across multiple sampling time points. Our results support that a variety of approaches can be used to derive reproducible transcriptional PODs that are consistent with PODs produced from traditional methods for chemical risk assessment.
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Affiliation(s)
- Reza Farmahin
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Nikolai L Chepelev
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Russell S Thomas
- National Center for Computational Toxicology, United States Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Tara S Barton-Maclaren
- Existing Substances Risk Assessment Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Ivan H Curran
- Toxicology Research Division, Health Products and Food Branch, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Andy Nong
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Michael G Wade
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada.
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38
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Chauhan V, Kuo B, McNamee JP, Wilkins RC, Yauk CL. Transcriptional benchmark dose modeling: Exploring how advances in chemical risk assessment may be applied to the radiation field. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:589-604. [PMID: 27601323 DOI: 10.1002/em.22043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/05/2016] [Indexed: 06/06/2023]
Abstract
Recent advances in "-omics" technologies have simplified capacity to concurrently assess expression profiles of thousands of targets in a cellular system. However, compilation and analysis of "omics" data in support of human health protection remains a challenge. Benchmark dose (BMD) modeling is currently being employed in chemical risk assessment to estimate acceptable levels of exposure. Although typically applied to conventional endpoints, newer software has enabled this application to be extended to transcriptomic datasets. BMD analytical tools now have the capacity to model transcriptional dose-response data to derive meaningful BMD values for genes, pathways and gene ontologies. In this report, radiation data obtained from the Gene Expression Omnibus (GEO) were analyzed to generate BMD values for transcriptional responses. The datasets comprised microarray analyses of human blood gamma-irradiated ex vivo (0-20 Gy) and human-derived cell lines exposed to alpha particle radiation (0.5-1.5 Gy). The distributions of BMDs for statistically significant genes and pathways in response to radiation exposure were examined and compared across studies. BMD modeling could identify pathway/gene sensitivities across wide radiation dose ranges, experimental conditions (time-points, cell types) and radiation qualities. BMD analysis offered a new approach to examine transcriptional data. The results were shown to provide information on transcriptional thresholds of effects to support refined risk assessments for low dose ionizing radiation exposures, derive gene-based values for relative biological effectiveness and identify pathways involved in radiation sensitivities across cell types which may extend to applications a clinical setting. Environ. Mol. Mutagen. 57:589-604, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Vinita Chauhan
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada.
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada
| | - James P McNamee
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Ruth C Wilkins
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, ON, Canada
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Webster AF, Lambert IB, Yauk CL. Toxicogenomics Case Study: Furan. TOXICOGENOMICS IN PREDICTIVE CARCINOGENICITY 2016. [DOI: 10.1039/9781782624059-00390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Development of pragmatic methodologies for human health risk assessment is required to address current regulatory challenges. We applied three toxicogenomic approaches—quantitative, predictive, and mechanistic—to a case study in mice exposed for 3 weeks to the hepatocarcinogen furan. We modeled the dose response of a variety of transcriptional endpoints and found that they produced benchmark doses similar to the furan-dependent cancer benchmark doses. Meta-analyses showed strong similarity between furan-dependent gene expression changes and those associated with several hepatic pathologies. Molecular pathways facilitated the development of a molecular mode of action for furan-induced hepatocellular carcinogenicity. Finally, we compared transcriptomic profiles derived from formalin-fixed and paraffin-embedded (FFPE) samples with those from high-quality frozen samples to evaluate whether archival samples are a viable option for toxicogenomic studies. The advantage of using FFPE tissues is that they are very well characterized (phenotypically); the disadvantage is that formalin degrades biomacromolecules, including RNA. We found that FFPE samples can be used for toxicogenomics using a ribo-depletion RNA-seq protocol. Our case study demonstrates the utility of toxicogenomics data to human health risk assessment, the potential of archival FFPE tissue samples, and identifies viable strategies toward the reduction of animal usage in chemical testing.
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Affiliation(s)
- A. Francina Webster
- Department of Biology, Carleton University 1125 Colonel By Drive Ottawa ON Canada
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture 50 Colombine Driveway Ottawa ON Canada
| | - Iain B. Lambert
- Department of Biology, Carleton University 1125 Colonel By Drive Ottawa ON Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture 50 Colombine Driveway Ottawa ON Canada
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40
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Chepelev NL, Long AS, Bowers WJ, Gagné R, Williams A, Kuo B, Phillips DH, Arlt VM, White PA, Yauk CL. Transcriptional profiling of the mouse hippocampus supports an NMDAR-mediated neurotoxic mode of action for benzo[a]pyrene. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:350-63. [PMID: 27195522 PMCID: PMC4915531 DOI: 10.1002/em.22020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/19/2016] [Indexed: 06/05/2023]
Abstract
Benzo[a]pyrene (BaP) is a genotoxic carcinogen and a neurotoxicant. The neurotoxicity of BaP is proposed to arise from either genotoxicity leading to neuronal cell death, or perturbed expression of N-methyl-d-aspartate receptor (NMDAR) subunits. To explore these hypotheses, we profiled hippocampal gene expression of adult male Muta(™) Mouse administered 0, 1, 35, or 70 mg BaP/kg bw per day by oral gavage for 3 days. Transcriptional profiles were examined by RNA-sequencing (RNA-seq), DNA microarrays, and real-time quantitative reverse transcription polymerase chain reaction (RT-PCR). BaP-DNA adducts in the cerebellum were quantified by (32) P-post-labeling to measure genotoxicity. RNA-seq revealed altered expression of 0, 260, and 219 genes (P-value < 0.05, fold-change ≥ ± 1.5) following exposure to the low, medium, and high doses, respectively; 54 genes were confirmed by microarrays. Microarray and RT-PCR analysis showed increased expression of NMDAR subunits Grina and Grin2a. In contrast, no effects on DNA-damage response genes were observed despite comparable BaP-DNA adduct levels in the cerebellum and in the lungs and livers of mice at similar BaP doses in previous studies. The results suggest that DNA-damage response does not play a major role in BaP-induced adult neurotoxicity. Meta-analysis revealed that BaP-induced transcriptional profiles are highly correlated with those from the hippocampus of transgenic mice exhibiting similar neurotoxicity outcomes to BaP-exposed mice and rats (i.e., defects in learning and memory). Overall, we suggest that BaP-induced neurotoxicity is more likely to be a consequence of NMDAR perturbation than genotoxicity, and identify other important genes potentially mediating this adverse outcome. Environ. Mol. Mutagen. 57:350-363, 2016. © 2016 Her Majesty the Queen in Right of Canada. Environmental and Molecular Mutagenesis © 2016 Environmental Mutagen Society.
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Affiliation(s)
- Nikolai L Chepelev
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, HECSB, Health Canada, Ottawa, Ontario, Canada, K1A 0K9
| | - Alexandra S Long
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, HECSB, Health Canada, Ottawa, Ontario, Canada, K1A 0K9
| | - Wayne J Bowers
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, HECSB, Health Canada, Ottawa, Ontario, Canada, K1A 0K9
| | - Rémi Gagné
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, HECSB, Health Canada, Ottawa, Ontario, Canada, K1A 0K9
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, HECSB, Health Canada, Ottawa, Ontario, Canada, K1A 0K9
| | - Byron Kuo
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, HECSB, Health Canada, Ottawa, Ontario, Canada, K1A 0K9
| | - David H Phillips
- Analytical and Environmental Sciences Division, MRC-PHE Centre for Environment and Health, King's College London, London, SE1 9NH, United Kingdom
| | - Volker M Arlt
- Analytical and Environmental Sciences Division, MRC-PHE Centre for Environment and Health, King's College London, London, SE1 9NH, United Kingdom
| | - Paul A White
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, HECSB, Health Canada, Ottawa, Ontario, Canada, K1A 0K9
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Environmental and Radiation Health Sciences Directorate, HECSB, Health Canada, Ottawa, Ontario, Canada, K1A 0K9
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Labib S, Williams A, Yauk CL, Nikota JK, Wallin H, Vogel U, Halappanavar S. Nano-risk Science: application of toxicogenomics in an adverse outcome pathway framework for risk assessment of multi-walled carbon nanotubes. Part Fibre Toxicol 2016; 13:15. [PMID: 26979667 PMCID: PMC4792104 DOI: 10.1186/s12989-016-0125-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/01/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND A diverse class of engineered nanomaterials (ENMs) exhibiting a wide array of physical-chemical properties that are associated with toxicological effects in experimental animals is in commercial use. However, an integrated framework for human health risk assessment (HHRA) of ENMs has yet to be established. Rodent 2-year cancer bioassays, clinical chemistry, and histopathological endpoints are still considered the 'gold standard' for detecting substance-induced toxicity in animal models. However, the use of data derived from alternative toxicological tools, such as genome-wide expression profiling and in vitro high-throughput assays, are gaining acceptance by the regulatory community for hazard identification and for understanding the underlying mode-of-action. Here, we conducted a case study to evaluate the application of global gene expression data in deriving pathway-based points of departure (PODs) for multi-walled carbon nanotube (MWCNT)-induced lung fibrosis, a non-cancer endpoint of regulatory importance. METHODS Gene expression profiles from the lungs of mice exposed to three individual MWCNTs with different physical-chemical properties were used within the framework of an adverse outcome pathway (AOP) for lung fibrosis to identify key biological events linking MWCNT exposure to lung fibrosis. Significantly perturbed pathways were categorized along the key events described in the AOP. Benchmark doses (BMDs) were calculated for each perturbed pathway and were used to derive transcriptional BMDs for each MWCNT. RESULTS Similar biological pathways were perturbed by the different MWCNT types across the doses and post-exposure time points studied. The pathway BMD values showed a time-dependent trend, with lower BMDs for pathways perturbed at the earlier post-exposure time points (24 h, 3d). The transcriptional BMDs were compared to the apical BMDs derived by the National Institute for Occupational Safety and Health (NIOSH) using alveolar septal thickness and fibrotic lesions endpoints. We found that regardless of the type of MWCNT, the BMD values for pathways associated with fibrosis were 14.0-30.4 μg/mouse, which are comparable to the BMDs derived by NIOSH for MWCNT-induced lung fibrotic lesions (21.0-27.1 μg/mouse). CONCLUSIONS The results demonstrate that transcriptomic data can be used to as an effective mechanism-based method to derive acceptable levels of exposure to nanomaterials in product development when epidemiological data are unavailable.
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Affiliation(s)
- Sarah Labib
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
| | - Jake K. Nikota
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
| | - Håkan Wallin
- National Research Centre for the Working Environment, Lerso Parkallé 105, DK-2100 Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, DK-1353 Copenhagen K, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Lerso Parkallé 105, DK-2100 Copenhagen, Denmark
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
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Kuo B, Francina Webster A, Thomas RS, Yauk CL. BMDExpress Data Viewer - a visualization tool to analyze BMDExpress datasets. J Appl Toxicol 2015; 36:1048-59. [PMID: 26671443 PMCID: PMC5064610 DOI: 10.1002/jat.3265] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/15/2015] [Accepted: 10/16/2015] [Indexed: 12/13/2022]
Abstract
Regulatory agencies increasingly apply benchmark dose (BMD) modeling to determine points of departure for risk assessment. BMDExpress applies BMD modeling to transcriptomic datasets to identify transcriptional BMDs. However, graphing and analytical capabilities within BMDExpress are limited, and the analysis of output files is challenging. We developed a web‐based application, BMDExpress Data Viewer (http://apps.sciome.com:8082/BMDX_Viewer/), for visualizing and graphing BMDExpress output files. The application consists of “Summary Visualization” and “Dataset Exploratory” tools. Through analysis of transcriptomic datasets of the toxicants furan and 4,4′‐methylenebis(N,N‐dimethyl)benzenamine, we demonstrate that the “Summary Visualization Tools” can be used to examine distributions of gene and pathway BMD values, and to derive a potential point of departure value based on summary statistics. By applying filters on enrichment P‐values and minimum number of significant genes, the “Functional Enrichment Analysis” tool enables the user to select biological processes or pathways that are selectively perturbed by chemical exposure and identify the related BMD. The “Multiple Dataset Comparison” tool enables comparison of gene and pathway BMD values across multiple experiments (e.g., across timepoints or tissues). The “BMDL‐BMD Range Plotter” tool facilitates the observation of BMD trends across biological processes or pathways. Through our case studies, we demonstrate that BMDExpress Data Viewer is a useful tool to visualize, explore and analyze BMDExpress output files. Visualizing the data in this manner enables rapid assessment of data quality, model fit, doses of peak activity, most sensitive pathway perturbations and other metrics that will be useful in applying toxicogenomics in risk assessment. © 2015 Her Majesty the Queen in Right of Canada. Journal of Applied Toxicology published by John Wiley & Sons, Ltd. We developed BMDExpress Data Viewer, which contains two collections of tools, “Summary Visualization Tools” and “Dataset Exploratory Tools,” to visualize and analyze BMDExpress output files. Through two case studies, we demonstrate the capabilities of graphically examining transcriptomic dose–response datasets in a risk assessment context by comparing and observing trends in transcriptomic benchmark doses (BMDs) for biological processes and pathways. Our results illustrate that BMDExpress Data Viewer is a useful tool to visualize, explore and analyze BMDExpress output files.
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Affiliation(s)
- Byron Kuo
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada, K1A 0K9
| | - A Francina Webster
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada, K1A 0K9.,Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, K1S 5B6, Canada
| | - Russell S Thomas
- United States Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology, Research Triangle Park, NC, 27711, USA
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada, K1A 0K9
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