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Eriksson ANM, Dubiel J, Alcaraz AJ, Doering JA, Wiseman S. Far from Their Origins: A Transcriptomic Investigation on How 2,4-Di-tert-butyl-6-(5-chloro-2H-benzotriazol-2-yl) Phenol Affects Rainbow Trout Alevins. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 38923588 DOI: 10.1002/etc.5943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/08/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Benzotriazole ultraviolet stabilizers (BUVSs) are a group of widely used chemicals added to a variety of consumer (e.g., plastics) and industrial (e.g., metal coating) goods. Although detected globally as an environmentally persistent pollutant, BUVSs have received relatively little toxicological attention and only recently have been acknowledged to affect development and the endocrine system in vivo. In our previous study, altered behavior, indicative of potential neurotoxicity, was observed among rainbow trout alevins (day 14 posthatching) that were microinjected as embryos with a single environmentally relevant dose of 2,4-di-tert-butyl-6-(5-chloro-2H-benzotriazol-2-yl) phenol (UV-327). In the present follow-up study, we performed whole-transcriptome profiling (RNA sequencing) of newly hatched alevins from the same batch. The primary aim was to identify biomarkers related to behavior and neurology. Dose-specifically, 1 to 176 differentially expressed genes (DEGs) were identified. In the group presenting altered behavior (273.4 ng g-1), 176 DEGs were identified, yet only a fraction was related to neurological functions, including water, calcium, and potassium homeostasis; acetylcholine transmission and signaling; as well insulin and energy metabolism. The second objective was to estimate the transcriptomic point of departure (tPOD) and assess if point estimate(s) are protective of altered behavior. A tPOD was established at 35 to 94 ng UV-327 g-1 egg, making this tPOD protective of behavioral alterations. Holistically, these transcriptomic alterations provide a foundation for future research on how BUVSs can influence rainbow trout alevin development, while providing support to the hypothesis that UV-327 can influence neurogenesis and subsequent behavioral endpoints. The exact structural and functional changes caused by embryonic exposure to UV-327 remain enigmatic and will require extensive investigation before being deciphered and understood toxicologically. Environ Toxicol Chem 2024;00:1-12. © 2024 The Author(s). Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Andreas N M Eriksson
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Justin Dubiel
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Alper James Alcaraz
- National Institute of Environmental Health Sciences, Bethesda, Maryland, USA
| | - Jon A Doering
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Steve Wiseman
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
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2
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Gasque-Belz L, Park B, Siciliano S, Hogan N, Weber L, Campbell P, Peters R, Hanson M, Hecker M. Characterization of Adverse Outcomes from Legacy-Contaminated Groundwater Exposure to Early Life Stages of Fathead Minnow. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2024:10.1007/s00244-024-01069-7. [PMID: 38871949 DOI: 10.1007/s00244-024-01069-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
Complex mixtures of chemicals present in groundwater at legacy-contaminated industrial sites can pose significant risks to adjacent surface waters. The combination of short-term molecular and chronic apical effect assessments is a promising approach to characterize the potential hazard of such complex mixtures. The objectives of this study were to: (1) assess the apical effects (survival, growth, development, and liver histopathology) after chronic exposure of early life stages (ELSs) of fathead minnows (FHM; Pimephales promelas) to contaminated groundwater from a legacy-contaminated pesticide manufacturing and packaging plant, and (2) identify possible molecular mechanisms responsible for these effects by comparing results to mechanistic outcomes previously determined by a short-term reduced transcriptome assay (EcoToxChips). This study revealed a significant increase in mortality and prevalence of spinal curvatures, as well as a significant reduction in the length of FHMs exposed to the groundwater mixtures in a concentration-dependent manner. There was an increasing trend in the prevalence of edema in FHMs, though not significantly different from controls. Additionally, no histopathological effects were observed in the liver of FHMs exposed to the groundwater mixtures. Short-term molecular outcomes determined in a parallel study were found to be informative of chronic apical outcomes, including cardiotoxicity, spinal deformities, and liver toxicity. Overall, the results observed in this study demonstrated that short-term transcriptomics analyses could support the hazard assessment of complex contaminated sites.
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Affiliation(s)
- Laura Gasque-Belz
- Environment and Geography, University of Manitoba, Winnipeg, MB, Canada
| | - Bradley Park
- Environment and Geography, University of Manitoba, Winnipeg, MB, Canada
| | - Steven Siciliano
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Natacha Hogan
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Lynn Weber
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Rachel Peters
- Federated Co-Operatives Limited, Saskatoon, SK, Canada
| | - Mark Hanson
- Environment and Geography, University of Manitoba, Winnipeg, MB, Canada
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, Canada.
- School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, Canada.
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3
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Barutcu AR, Black MB, Samuel R, Slattery S, McMullen PD, Nong A. Integrating gene expression and splicing dynamics across dose-response oxidative modulators. Front Genet 2024; 15:1389095. [PMID: 38846964 PMCID: PMC11155298 DOI: 10.3389/fgene.2024.1389095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/06/2024] [Indexed: 06/09/2024] Open
Abstract
Toxicological risk assessment increasingly utilizes transcriptomics to derive point of departure (POD) and modes of action (MOA) for chemicals. One essential biological process that allows a single gene to generate several different RNA isoforms is called alternative splicing. To comprehensively assess the role of splicing dysregulation in toxicological evaluation and elucidate its potential as a complementary endpoint, we performed RNA-seq on A549 cells treated with five oxidative stress modulators across a wide dose range. Differential gene expression (DGE) showed limited pathway enrichment except at high concentrations. However, alternative splicing analysis revealed variable intron retention events affecting diverse pathways for all chemicals in the absence of significant expression changes. For instance, diazinon elicited negligible gene expression changes but progressive increase in the number of intron retention events, suggesting splicing alterations precede expression responses. Benchmark dose modeling of intron retention data highlighted relevant pathways overlooked by expression analysis. Systematic integration of splicing datasets should be a useful addition to the toxicogenomic toolkit. Combining both modalities paint a more complete picture of transcriptomic dose-responses. Overall, evaluating intron retention dynamics afforded by toxicogenomics may provide biomarkers that can enhance chemical risk assessment and regulatory decision making. This work highlights splicing-aware toxicogenomics as a possible additional tool for examining cellular responses.
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4
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Costa E, Johnson KJ, Walker CA, O’Brien JM. Transcriptomic point of departure determination: a comparison of distribution-based and gene set-based approaches. Front Genet 2024; 15:1374791. [PMID: 38784034 PMCID: PMC11112360 DOI: 10.3389/fgene.2024.1374791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
A key step in assessing the potential human and environmental health risks of industrial and agricultural chemicals is to determine the toxicity point of departure (POD), which is the highest dose level that causes no adverse effect. Transcriptomic POD (tPOD) values have been suggested to accurately estimate toxicity POD values. One step in the most common approach for tPOD determination involves mapping genes to annotated gene sets, a process that might lead to substantial information loss particularly in species with poor gene annotation. Alternatively, methods that calculate tPOD values directly from the distribution of individual gene POD values omit this mapping step. Using rat transcriptome data for 79 molecules obtained from Open TG-GATEs (Toxicogenomics Project Genomics Assisted Toxicity Evaluation System), the hypothesis was tested that methods based on the distribution of all individual gene POD values will give a similar tPOD value to that obtained via the gene set-based method. Gene set-based tPOD values using four different gene set structures were compared to tPOD values from five different individual gene distribution methods. Results revealed a high tPOD concordance for all methods tested, especially for molecules with at least 300 dose-responsive probesets: for 90% of those molecules, the tPOD values from all methods were within 4-fold of each other. In addition, random gene sets based upon the structure of biological knowledge-derived gene sets produced tPOD values with a median absolute fold change of 1.3-1.4 when compared to the original biological knowledge-derived gene set counterparts, suggesting that little biological information is used in the gene set-based tPOD generation approach. These findings indicate using individual gene distributions to calculate a tPOD is a viable and parsimonious alternative to using gene sets. Importantly, individual gene distribution-based tPOD methods do not require knowledge of biological organization and can be applied to any species including those with poorly annotated gene sets.
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Affiliation(s)
| | | | | | - Jason M. O’Brien
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Ottawa, ON, Canada
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5
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Rattner BA, Bean TG, Beasley VR, Berny P, Eisenreich KM, Elliott JE, Eng ML, Fuchsman PC, King MD, Mateo R, Meyer CB, O'Brien JM, Salice CJ. Wildlife ecological risk assessment in the 21st century: Promising technologies to assess toxicological effects. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2024; 20:725-748. [PMID: 37417421 DOI: 10.1002/ieam.4806] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
Despite advances in toxicity testing and the development of new approach methodologies (NAMs) for hazard assessment, the ecological risk assessment (ERA) framework for terrestrial wildlife (i.e., air-breathing amphibians, reptiles, birds, and mammals) has remained unchanged for decades. While survival, growth, and reproductive endpoints derived from whole-animal toxicity tests are central to hazard assessment, nonstandard measures of biological effects at multiple levels of biological organization (e.g., molecular, cellular, tissue, organ, organism, population, community, ecosystem) have the potential to enhance the relevance of prospective and retrospective wildlife ERAs. Other factors (e.g., indirect effects of contaminants on food supplies and infectious disease processes) are influenced by toxicants at individual, population, and community levels, and need to be factored into chemically based risk assessments to enhance the "eco" component of ERAs. Regulatory and logistical challenges often relegate such nonstandard endpoints and indirect effects to postregistration evaluations of pesticides and industrial chemicals and contaminated site evaluations. While NAMs are being developed, to date, their applications in ERAs focused on wildlife have been limited. No single magic tool or model will address all uncertainties in hazard assessment. Modernizing wildlife ERAs will likely entail combinations of laboratory- and field-derived data at multiple levels of biological organization, knowledge collection solutions (e.g., systematic review, adverse outcome pathway frameworks), and inferential methods that facilitate integrations and risk estimations focused on species, populations, interspecific extrapolations, and ecosystem services modeling, with less dependence on whole-animal data and simple hazard ratios. Integr Environ Assess Manag 2024;20:725-748. © 2023 His Majesty the King in Right of Canada and The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC). Reproduced with the permission of the Minister of Environment and Climate Change Canada. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Barnett A Rattner
- US Geological Survey, Eastern Ecological Science Center, Laurel, Maryland, USA
| | | | - Val R Beasley
- College of Veterinary Medicine, University of Illinois at Urbana, Champaign, Illinois, USA
| | | | - Karen M Eisenreich
- US Environmental Protection Agency, Washington, District of Columbia, USA
| | - John E Elliott
- Environment and Climate Change Canada, Delta, British Columbia, Canada
| | - Margaret L Eng
- Environment and Climate Change Canada, Dartmouth, Nova Scotia, Canada
| | | | - Mason D King
- Simon Fraser University, Burnaby, British Columbia, Canada
| | | | | | - Jason M O'Brien
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
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Flynn K, Le M, Hazemi M, Biales A, Bencic DC, Blackwell BR, Bush K, Flick R, Hoang JX, Martinson J, Morshead M, Rodriguez KS, Stacy E, Villeneuve DL. Comparing Transcriptomic Points of Departure to Apical Effect Concentrations For Larval Fathead Minnow Exposed to Chemicals with Four Different Modes Of Action. ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2024; 86:346-362. [PMID: 38743081 DOI: 10.1007/s00244-024-01064-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
It is postulated that below a transcriptomic-based point of departure, adverse effects are unlikely to occur, thereby providing a chemical concentration to use in screening level hazard assessment. The present study extends previous work describing a high-throughput fathead minnow assay that can provide full transcriptomic data after exposure to a test chemical. One-day post-hatch fathead minnows were exposed to ten concentrations of three representatives of four chemical modes of action: organophosphates, ecdysone receptor agonists, plant photosystem II inhibitors, and estrogen receptor agonists for 24 h. Concentration response modeling was performed on whole body gene expression data from each exposure, using measured chemical concentrations when available. Transcriptomic points of departure in larval fathead minnow were lower than apical effect concentrations across fish species but not always lower than toxic effect concentrations in other aquatic taxa like crustaceans and insects. The point of departure was highly dependent on measured chemical concentration which were often lower than the nominal concentration. Differentially expressed genes between chemicals within modes of action were compared and often showed statistically significant overlap. In addition, reproducibility between identical exposures using a positive control chemical (CuSO4) and variability associated with the transcriptomic point of departure using in silico sampling were considered. Results extend a transcriptomic-compatible fathead minnow high-throughput assay for possible use in ecological hazard screening.
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Affiliation(s)
- Kevin Flynn
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, US EPA GLTED, 6201 Congdon Blvd, Duluth, MN, 55804, USA.
| | - Michelle Le
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - Monique Hazemi
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - Adam Biales
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Cincinnati, OH, 45220, USA
| | - David C Bencic
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Cincinnati, OH, 45220, USA
| | - Brett R Blackwell
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Kendra Bush
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - Robert Flick
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Cincinnati, OH, 45220, USA
| | - John X Hoang
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - John Martinson
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Cincinnati, OH, 45220, USA
| | - Mackenzie Morshead
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - Kelvin Santana Rodriguez
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, 55804, USA
| | - Emma Stacy
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, US EPA GLTED, 6201 Congdon Blvd, Duluth, MN, 55804, USA
| | - Daniel L Villeneuve
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, US EPA GLTED, 6201 Congdon Blvd, Duluth, MN, 55804, USA
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7
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Villeneuve DL, Blackwell BR, Bush K, Harrill J, Harris F, Hazemi M, Le M, Stacy E, Flynn KM. Transcriptomics-Based Points of Departure for Daphnia magna Exposed to 18 Per- and Polyfluoroalkyl Substances. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 38450772 DOI: 10.1002/etc.5838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/08/2024] [Accepted: 01/27/2024] [Indexed: 03/08/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) represent a large group of contaminants of concern based on their widespread use, environmental persistence, and potential toxicity. Many traditional models for estimating toxicity, bioaccumulation, and other toxicological properties are not well suited for PFAS. Consequently, there is a need to generate hazard information for PFAS in an efficient and cost-effective manner. In the present study, Daphnia magna were exposed to multiple concentrations of 22 different PFAS for 24 h in a 96-well plate format. Following exposure, whole-body RNA was extracted and extracts, each representing five exposed individuals, were subjected to RNA sequencing. Following analytical measurements to verify PFAS exposure concentrations and quality control on processed cDNA libraries for sequencing, concentration-response modeling was applied to the data sets for 18 of the tested compounds, and the concentration at which a concerted molecular response occurred (transcriptomic point of departure; tPOD) was calculated. The tPODs, based on measured concentrations of PFAS, generally ranged from 0.03 to 0.58 µM (9.9-350 µg/L; interquartile range). In most cases, these concentrations were two orders of magnitude lower than similarly calculated tPODs for human cell lines exposed to PFAS. They were also lower than apical effect concentrations reported for seven PFAS for which some crustacean or invertebrate toxicity data were available, although there were a few exceptions. Despite being lower than most other available hazard benchmarks, D. magna tPODs were, on average, four orders of magnitude greater than the maximum aqueous concentrations of PFAS measured in Great Lakes tributaries. Overall, this high-throughput transcriptomics assay with D. magna holds promise as a component of a tiered hazard evaluation strategy employing new approach methodologies. Environ Toxicol Chem 2024;00:1-16. © 2024 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Daniel L Villeneuve
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, USA
| | - Brett R Blackwell
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, USA
- Bioscience Division, Biochemistry and Biotechnology Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kendra Bush
- Oak Ridge Institute for Science and Education Research Participant at US EPA, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Joshua Harrill
- Biomolecular and Computational Toxicology Division, United States Environmental Protection Agency, NC, USA
| | - Felix Harris
- Oak Ridge Institute for Science and Education Research Participant at US EPA, Biomolecular and Computational Toxicology Division, Oak Ridge, NC, USA
| | - Monique Hazemi
- Oak Ridge Institute for Science and Education Research Participant at US EPA, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Michelle Le
- Oak Ridge Institute for Science and Education Research Participant at US EPA, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Emma Stacy
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, USA
| | - Kevin M Flynn
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, MN, USA
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Ankley GT, Berninger JP, Maloney EM, Olker JH, Schaupp CM, Villeneuve DL, LaLone CA. Linking Mechanistic Effects of Pharmaceuticals and Personal Care Products to Ecologically Relevant Outcomes: A Decade of Progress. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024; 43:537-548. [PMID: 35735070 PMCID: PMC11036122 DOI: 10.1002/etc.5416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/02/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
There are insufficient toxicity data to assess the ecological risks of many pharmaceuticals and personal care products (PPCPs). While data limitations are not uncommon for contaminants of environmental concern, PPCPs are somewhat unique in that an a priori understanding of their biological activities in conjunction with measurements of molecular, biochemical, or histological responses could provide a foundation for understanding mode(s) of action and predicting potential adverse apical effects. Over the past decade significant progress has been made in the development of new approach methodologies (NAMs) to efficiently quantify these types of endpoints using computational models and pathway-based in vitro and in vivo assays. The availability of open-access knowledgebases to curate biological response (including NAM) data and sophisticated bioinformatics tools to help interpret the information also has significantly increased. Finally, advances in the development and implementation of the adverse outcome pathway framework provide the critical conceptual underpinnings needed to translate NAM data into predictions of the ecologically relevant outcomes required by risk assessors and managers. The evolution and convergence of these various data streams, tools, and concepts provides the basis for a fundamental change in how ecological risks of PPCPs can be pragmatically assessed. Environ Toxicol Chem 2024;43:537-548. © 2022 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Gerald T Ankley
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, Minnesota, USA
| | - Jason P Berninger
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, Minnesota, USA
| | - Erin M Maloney
- University of Minnesota-Duluth, Integrated Biological Sciences Program, Duluth, Minnesota, USA
| | - Jennifer H Olker
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, Minnesota, USA
| | | | - Daniel L Villeneuve
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, Minnesota, USA
| | - Carlie A LaLone
- US Environmental Protection Agency, Great Lakes Toxicology and Ecology Division, Duluth, Minnesota, USA
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Schumann P, Rivetti C, Houghton J, Campos B, Hodges G, LaLone C. Combination of computational new approach methodologies for enhancing evidence of biological pathway conservation across species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168573. [PMID: 37981146 PMCID: PMC10926110 DOI: 10.1016/j.scitotenv.2023.168573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023]
Abstract
The ability to predict which chemicals are of concern for environmental safety is dependent, in part, on the ability to extrapolate chemical effects across many species. This work investigated the complementary use of two computational new approach methodologies to support cross-species predictions of chemical susceptibility: the US Environmental Protection Agency Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool and Unilever's recently developed Genes to Pathways - Species Conservation Analysis (G2P-SCAN) tool. These stand-alone tools rely on existing biological knowledge to help understand chemical susceptibility and biological pathway conservation across species. The utility and challenges of these combined computational approaches were demonstrated using case examples focused on chemical interactions with peroxisome proliferator activated receptor alpha (PPARα), estrogen receptor 1 (ESR1), and gamma-aminobutyric acid type A receptor subunit alpha (GABRA1). Overall, the biological pathway information enhanced the weight of evidence to support cross-species susceptibility predictions. Through comparisons of relevant molecular and functional data gleaned from adverse outcome pathways (AOPs) to mapped biological pathways, it was possible to gain a toxicological context for various chemical-protein interactions. The information gained through this computational approach could ultimately inform chemical safety assessments by enhancing cross-species predictions of chemical susceptibility. It could also help fulfill a core objective of the AOP framework by potentially expanding the biologically plausible taxonomic domain of applicability of relevant AOPs.
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Affiliation(s)
- Peter Schumann
- Oak Ridge Institute for Science and Education, Duluth, MN, USA
| | - Claudia Rivetti
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Jade Houghton
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Bruno Campos
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Geoff Hodges
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire, UK
| | - Carlie LaLone
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, Duluth, MN, USA.
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10
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Tran CM, Ra JS, Rhyu DY, Kim KT. Transcriptome analysis reveals differences in developmental neurotoxicity mechanism of methyl-, ethyl-, and propyl- parabens in zebrafish embryos. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 268:115704. [PMID: 37979356 DOI: 10.1016/j.ecoenv.2023.115704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 11/20/2023]
Abstract
Studies on the comparison of developmental (neuro) toxicity of parabens are currently limited, and unharmonized concentrations between phenotypic observations and transcriptome analysis hamper the understanding of their differential molecular mechanisms. Thus, developmental toxicity testing was conducted herein using the commonly used methyl- (MtP), ethyl- (EtP), and propyl-parabens (PrP) in zebrafish embryos. With a benchmark dose of 5%, embryonic-mortality-based point-of-departure (M-POD) values of the three parabens were determined, and changes in locomotor behavior were evaluated at concentrations of 0, M-POD/50, M-POD/10, and M-POD, where transcriptome analysis was conducted to explore the underlying neurotoxicity mechanism. Higher long-chained parabens were more toxic than short-chained parabens, as determined by the M-POD values of 154.1, 72.6, and 24.2 µM for MtP, EtP, and PrP, respectively. Meanwhile, exposure to EtP resulted in hyperactivity, whereas no behavioral effect was observed with MtP and PrP. Transcriptome analysis revealed that abnormal behaviors in the EtP-exposed group were associated with distinctly enriched pathways in signaling, transport, calcium ion binding, and metal binding. In contrast, exposure to MtP and PrP mainly disrupted membranes and transmembranes, which are closely linked to abnormal embryonic development rather than neurobehavioral changes. According to the changes in the expressions of signature mRNAs, tentative transcriptome-based POD values for each paraben were determined as MtP (2.68 µM), EtP (3.85 µM), and PrP (1.4 µM). This suggests that different molecular perturbations initiated at similar concentrations determined the extent and toxicity outcome differently. Our findings provide insight into better understanding the differential developmental neurotoxicity mechanisms of parabens.
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Affiliation(s)
- Cong Minh Tran
- Department of Energy and Environmental Engineering, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Jin-Sung Ra
- Eco-testing and Risk Assessment Center, Korea Institute of Industrial Technology (KITECH), Ansan 15588, Republic of Korea
| | - Dong Young Rhyu
- Department of Biomedicine, Health & Life Convergence Sciences, BK21 FOUR, Mokpo National University, Jeonnam 58554, Republic of Korea
| | - Ki-Tae Kim
- Department of Energy and Environmental Engineering, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea; Department of Environmental Engineering, Seoul National University of Sciences and Technology, Seoul 01811, Republic of Korea.
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11
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Martin R, Hazemi M, Flynn K, Villeneuve D, Wehmas L. Short-Term Transcriptomic Points of Departure Are Consistent with Chronic Points of Departure for Three Organophosphate Pesticides across Mouse and Fathead Minnow. TOXICS 2023; 11:820. [PMID: 37888672 PMCID: PMC10611195 DOI: 10.3390/toxics11100820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023]
Abstract
New approach methods (NAMs) can reduce the need for chronic animal studies. Here, we apply benchmark dose (concentration) (BMD(C))-response modeling to transcriptomic changes in the liver of mice and in fathead minnow larvae after short-term exposures (7 days and 1 day, respectively) to several dose/concentrations of three organophosphate pesticides (OPPs): fenthion, methidathion, and parathion. The mouse liver transcriptional points of departure (TPODs) for fenthion, methidathion, and parathion were 0.009, 0.093, and 0.046 mg/Kg-bw/day, while the fathead minnow larva TPODs were 0.007, 0.115, and 0.046 mg/L, respectively. The TPODs were consistent across both species and reflected the relative potencies from traditional chronic toxicity studies with fenthion identified as the most potent. Moreover, the mouse liver TPODs were more sensitive than or within a 10-fold difference from the chronic apical points of departure (APODs) for mammals, while the fathead minnow larva TPODs were within an 18-fold difference from the chronic APODs for fish species. Short-term exposure to OPPs significantly impacted acetylcholinesterase mRNA abundance (FDR p-value <0.05, |fold change| ≥2) and canonical pathways (IPA, p-value <0.05) associated with organism death and neurological/immune dysfunctions, indicating the conservation of key events related to OPP toxicity. Together, these results build confidence in using short-term, molecular-based assays for the characterization of chemical toxicity and risk, thereby reducing reliance on chronic animal studies.
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Affiliation(s)
- Rubia Martin
- Office of Research and Development, Center for Computational Toxicology and Exposure, Chemical Characterization and Exposure Division, Oak Ridge Institute for Science and Education, U.S. Environmental Protection Agency, Durham, NC 27709, USA;
| | - Monique Hazemi
- Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Ecology Division, Oak Ridge Institute for Science and Education, U.S. Environmental Protection Agency, Duluth, MN 55804, USA;
| | - Kevin Flynn
- Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Ecology Division, U.S. Environmental Protection Agency, Duluth, MN 55804, USA; (K.F.); (D.V.)
| | - Daniel Villeneuve
- Office of Research and Development, Center for Computational Toxicology and Exposure, Great Lakes Ecology Division, U.S. Environmental Protection Agency, Duluth, MN 55804, USA; (K.F.); (D.V.)
| | - Leah Wehmas
- Office of Research and Development, Center for Computational Toxicology and Exposure, Chemical Characterization and Exposure Division, U.S. Environmental Protection Agency, Durham, NC 27709, USA
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12
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Naga D, Dimitrakopoulou S, Roberts S, Husar E, Mohr S, Booler H, Musvasva E. CSL-Tox: an open-source analytical framework for the comparison of short-term and long-term toxicity end points and assessing the need of chronic studies in drug development. Sci Rep 2023; 13:14865. [PMID: 37684321 PMCID: PMC10491674 DOI: 10.1038/s41598-023-41899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
In-vivo toxicity assessment is an important step prior to clinical development and is still the main source of data for overall risk assessment of a new molecular entity (NCE). All in-vivo studies are performed according to regulatory requirements and many efforts have been exerted to minimize these studies in accordance with the (Replacement, Reduction and Refinement) 3Rs principle. Many aspects of in-vivo toxicology packages can be optimized to reduce animal use, including the number of studies performed as well as study durations, which is the main focus of this analysis. We performed a statistical comparison of adverse findings observed in 116 short-term versus 78 long-term in-house or in-house sponsored Contract Research Organizations (CRO) studies, in order to explore the possibility of using only short-term studies as a prediction tool for the longer-term effects. All the data analyzed in this study was manually extracted from the toxicology reports (in PDF formats) to construct the dataset. Annotation of treatment related findings was one of the challenges faced during this work. A specific focus was therefore put on the summary and conclusion sections of the reports since they contain expert assessments on whether the findings were considered adverse or were attributed to other reasons. Our analysis showed a general good concordance between short-term and long-term toxicity findings for large molecules and the majority of small molecules. Less concordance was seen for certain body organs, which can be named as "target organ systems' findings". While this work supports the minimization of long-term studies, a larger-scale effort would be needed to provide more evidence. We therefore present the steps performed in this study as an open-source R workflow for the Comparison of Short-term and Long-term Toxicity studies (CSL-Tox). The dataset used in the work is provided to allow researchers to reproduce such analysis, re-evaluate the statistical tools used and promote large-scale application of this study. Important aspects of animal research reproducibility are highlighted in this work, specifically, the necessity of a reproducible adverse effects reporting system and utilization of the controlled terminologies in-vivo toxicology reports and finally the importance of open-source analytical workflows that can be assessed by other scientists in the field of preclinical toxicology.
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Affiliation(s)
- Doha Naga
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria.
| | - Smaragda Dimitrakopoulou
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sonia Roberts
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Elisabeth Husar
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Susanne Mohr
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Helen Booler
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Eunice Musvasva
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
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13
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Cecchetto M, Peruzza L, Giubilato E, Bernardini I, Rovere GD, Marcomini A, Regoli F, Bargelloni L, Patarnello T, Semenzin E, Milan M. An innovative index to incorporate transcriptomic data into weight of evidence approaches for environmental risk assessment. ENVIRONMENTAL RESEARCH 2023; 227:115745. [PMID: 36972774 DOI: 10.1016/j.envres.2023.115745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 05/08/2023]
Abstract
The sharp decrease in the cost of RNA-sequencing and the rapid improvement in computational analysis of eco-toxicogenomic data have brought new insights into the adverse effects of chemicals on aquatic organisms. Yet, transcriptomics is generally applied qualitatively in environmental risk assessments, hampering more effective exploitation of this evidence through multidisciplinary studies. In view of this limitation, a methodology is here presented to quantitatively elaborate transcriptional data in support to environmental risk assessment. The proposed methodology makes use of results from the application of Gene Set Enrichment Analysis to recent studies investigating the response of Mytilus galloprovincialis and Ruditapes philippinarum exposed to contaminants of emerging concern. The degree of changes in gene sets and the relevance of physiological reactions are integrated in the calculation of a hazard index. The outcome is then classified according to five hazard classes (from absent to severe), providing an evaluation of whole-transcriptome effects of chemical exposure. The application to experimental and simulated datasets proved that the method can effectively discriminate different levels of altered transcriptomic responses when compared to expert judgement (Spearman correlation coefficient of 0.96). A further application to data collected in two independent studies of Salmo trutta and Xenopus tropicalis exposed to contaminants confirmed the potential extension of the methodology to other aquatic species. This methodology can serve as a proof of concept for the integration of "genomic tools" in environmental risk assessment based on multidisciplinary investigations. To this end, the proposed transcriptomic hazard index can now be incorporated into quantitative Weight of Evidence approaches and weighed, with results from other types of analysis, to elucidate the role of chemicals in adverse ecological effects.
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Affiliation(s)
- Martina Cecchetto
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, via Torino 155, 30172, Mestre-Venezia, Italy
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Elisa Giubilato
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, via Torino 155, 30172, Mestre-Venezia, Italy
| | - Ilaria Bernardini
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Antonio Marcomini
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, via Torino 155, 30172, Mestre-Venezia, Italy
| | - Francesco Regoli
- Department of Life and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, 60131, Ancona, Italy; NFBC, National Future Biodiversity Center, Palermo, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Elena Semenzin
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, via Torino 155, 30172, Mestre-Venezia, Italy.
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy; NFBC, National Future Biodiversity Center, Palermo, Italy
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14
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Tsai HHD, House JS, Wright FA, Chiu WA, Rusyn I. A tiered testing strategy based on in vitro phenotypic and transcriptomic data for selecting representative petroleum UVCBs for toxicity evaluation in vivo. Toxicol Sci 2023; 193:219-233. [PMID: 37079747 PMCID: PMC10230285 DOI: 10.1093/toxsci/kfad041] [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] [Indexed: 04/22/2023] Open
Abstract
Hazard evaluation of substances of "unknown or variable composition, complex reaction products and biological materials" (UVCBs) remains a major challenge in regulatory science because their chemical composition is difficult to ascertain. Petroleum substances are representative UVCBs and human cell-based data have been previously used to substantiate their groupings for regulatory submissions. We hypothesized that a combination of phenotypic and transcriptomic data could be integrated to make decisions as to selection of group-representative worst-case petroleum UVCBs for subsequent toxicity evaluation in vivo. We used data obtained from 141 substances from 16 manufacturing categories previously tested in 6 human cell types (induced pluripotent stem cell [iPSC]-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, and MCF7 and A375 cell lines). Benchmark doses for gene-substance combinations were calculated, and both transcriptomic and phenotype-derived points of departure (PODs) were obtained. Correlation analysis and machine learning were used to assess associations between phenotypic and transcriptional PODs and to determine the most informative cell types and assays, thus representing a cost-effective integrated testing strategy. We found that 2 cell types-iPSC-derived-hepatocytes and -cardiomyocytes-contributed the most informative and protective PODs and may be used to inform selection of representative petroleum UVCBs for further toxicity evaluation in vivo. Overall, although the use of new approach methodologies to prioritize UVCBs has not been widely adopted, our study proposes a tiered testing strategy based on iPSC-derived hepatocytes and cardiomyocytes to inform selection of representative worst-case petroleum UVCBs from each manufacturing category for further toxicity evaluation in vivo.
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Affiliation(s)
- Han-Hsuan Doris Tsai
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - John S House
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - Fred A Wright
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, USA
- Department of Biological Sciences and Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27603, USA
| | - Weihsueh A Chiu
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
| | - Ivan Rusyn
- Interdisciplinary Faculty of Toxicology, College Station, Texas 77843, USA
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas 77843, USA
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15
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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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16
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Mitchell CA, Burden N, Bonnell M, Hecker M, Hutchinson TH, Jagla M, LaLone CA, Lagadic L, Lynn SG, Shore B, Song Y, Vliet SM, Wheeler JR, Embry MR. New Approach Methodologies for the Endocrine Activity Toolbox: Environmental Assessment for Fish and Amphibians. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:757-777. [PMID: 36789969 PMCID: PMC10258674 DOI: 10.1002/etc.5584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/07/2022] [Accepted: 02/06/2023] [Indexed: 06/14/2023]
Abstract
Multiple in vivo test guidelines focusing on the estrogen, androgen, thyroid, and steroidogenesis pathways have been developed and validated for mammals, amphibians, or fish. However, these tests are resource-intensive and often use a large number of laboratory animals. Developing alternatives for in vivo tests is consistent with the replacement, reduction, and refinement principles for animal welfare considerations, which are supported by increasing mandates to move toward an "animal-free" testing paradigm worldwide. New approach methodologies (NAMs) hold great promise to identify molecular, cellular, and tissue changes that can be used to predict effects reliably and more efficiently at the individual level (and potentially on populations) while reducing the number of animals used in (eco)toxicological testing for endocrine disruption. In a collaborative effort, experts from government, academia, and industry met in 2020 to discuss the current challenges of testing for endocrine activity assessment for fish and amphibians. Continuing this cross-sector initiative, our review focuses on the current state of the science regarding the use of NAMs to identify chemical-induced endocrine effects. The present study highlights the challenges of using NAMs for safety assessment and what work is needed to reduce their uncertainties and increase their acceptance in regulatory processes. We have reviewed the current NAMs available for endocrine activity assessment including in silico, in vitro, and eleutheroembryo models. New approach methodologies can be integrated as part of a weight-of-evidence approach for hazard or risk assessment using the adverse outcome pathway framework. The development and utilization of NAMs not only allows for replacement, reduction, and refinement of animal testing but can also provide robust and fit-for-purpose methods to identify chemicals acting via endocrine mechanisms. Environ Toxicol Chem 2023;42:757-777. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
| | - Natalie Burden
- National Centre for the 3Rs (NC3Rs), London, United Kingdom
| | - Mark Bonnell
- Environment and Climate Change Canada, Ottawa, Canada
| | - Markus Hecker
- Toxicology Centre and School of the Environment & Sustainability, University of Saskatchewan, Saskatoon, Canada
| | | | | | - Carlie A. LaLone
- Office of Research and Development, Great Lakes Toxicology & Ecology Division, US Environmental Protection Agency, Duluth, Minnesota
| | - Laurent Lagadic
- Research and Development, Crop Science, Environmental Safety, Bayer, Monheim am Rhein, Germany
| | - Scott G. Lynn
- Office of Pesticide Programs, US Environmental Protection Agency, Washington, DC
| | - Bryon Shore
- Environment and Climate Change Canada, Ottawa, Canada
| | - You Song
- Norwegian Institute for Water Research, Oslo, Norway
| | - Sara M. Vliet
- Office of Research and Development, Scientific Computing and Data Curation Division, US Environmental Protection Agency, Duluth, Minnesota
| | | | - Michelle R. Embry
- The Health and Environmental Sciences Institute, Washington, DC, USA
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17
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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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18
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Song Y, Zheng K, Brede DA, Gomes T, Xie L, Kassaye Y, Salbu B, Tollefsen KE. Multiomics Point of Departure (moPOD) Modeling Supports an Adverse Outcome Pathway Network for Ionizing Radiation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3198-3205. [PMID: 36799527 PMCID: PMC9979642 DOI: 10.1021/acs.est.2c04917] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 06/07/2023]
Abstract
While adverse biological effects of acute high-dose ionizing radiation have been extensively investigated, knowledge on chronic low-dose effects is scarce. The aims of the present study were to identify hazards of low-dose ionizing radiation to Daphnia magna using multiomics dose-response modeling and to demonstrate the use of omics data to support an adverse outcome pathway (AOP) network development for ionizing radiation. Neonatal D. magna were exposed to γ radiation for 8 days. Transcriptomic analysis was performed after 4 and 8 days of exposure, whereas metabolomics and confirmative bioassays to support the omics analyses were conducted after 8 days of exposure. Benchmark doses (BMDs, 10% benchmark response) as points of departure (PODs) were estimated for both dose-responsive genes/metabolites and the enriched KEGG pathways. Relevant pathways derived using the BMD modeling and additional functional end points measured by the bioassays were overlaid with a previously published AOP network. The results showed that several molecular pathways were highly relevant to the known modes of action of γ radiation, including oxidative stress, DNA damage, mitochondrial dysfunction, protein degradation, and apoptosis. The functional assays showed increased oxidative stress and decreased mitochondrial membrane potential and ATP pool. Ranking of PODs at the pathway and functional levels showed that oxidative damage related functions had relatively low PODs, followed by DNA damage, energy metabolism, and apoptosis. These were supportive of causal events in the proposed AOP network. This approach yielded promising results and can potentially provide additional empirical evidence to support further AOP development for ionizing radiation.
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Affiliation(s)
- You Song
- Norwegian
Institute for Water Research (NIVA), Økernveien 94, 0579 Oslo, Norway
- Centre
for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Keke Zheng
- Centre
for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
- Faculty
of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Dag Anders Brede
- Centre
for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
- Faculty
of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Tânia Gomes
- Norwegian
Institute for Water Research (NIVA), Økernveien 94, 0579 Oslo, Norway
- Centre
for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Li Xie
- Norwegian
Institute for Water Research (NIVA), Økernveien 94, 0579 Oslo, Norway
- Centre
for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Yetneberk Kassaye
- Centre
for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
- Faculty
of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Brit Salbu
- Centre
for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
- Faculty
of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Knut Erik Tollefsen
- Norwegian
Institute for Water Research (NIVA), Økernveien 94, 0579 Oslo, Norway
- Centre
for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
- Faculty
of Environmental Sciences and Natural Resource Management (MINA), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
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19
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Morash MG, Kirzinger MW, Achenbach JC, Venkatachalam AB, Cooper JP, Ratzlaff DE, Woodland CLA, Ellis LD. The contribution of larval zebrafish transcriptomics to chemical risk assessment. Regul Toxicol Pharmacol 2023; 138:105336. [PMID: 36642323 DOI: 10.1016/j.yrtph.2023.105336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/22/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023]
Abstract
In Canada, the Canadian Environmental Protection Act (1999) requires human health and environmental risk assessments be conducted for new substances prior to their manufacture or import. While this toxicity data is historically obtained using rodents, in response to the international effort to eliminate animal testing, Health Canada is collaborating with the National Research Council (NRC) of Canada to develop a New Approach Method by refining existing NRC zebrafish models. The embryo/larval zebrafish model evaluates systemic (whole body) general toxicity which is currently unachievable with cell-based testing. The model is strengthened using behavioral, toxicokinetic and transcriptomic responses to assess non-visible indicators of toxicity following chemical exposure at sub-phenotypic concentrations. In this paper, the predictive power of zebrafish transcriptomics is demonstrated using two chemicals; Raloxifene and Resorcinol. Raloxifene exposure produced darkening of the liver and malformation of the nose/mandible, while Resorcinol exposure produced increased locomotor activity. Transcriptomic analysis correlated differentially expressed genes with the phenotypic effects and benchmark dose calculations determined that the transcriptomic Point of Departure (POD) occurred at subphenotypic concentrations. Correlating gene expression with apical (phenotypic) effects strengthens confidence in evaluation of chemical toxicity, thereby demonstrating the significant advancement that the larval zebrafish transcriptomics model represents in chemical risk assessment.
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Affiliation(s)
- Michael G Morash
- Aquatic and Crop Resource Development, National Research Council of Canada, Halifax, NS B3H 3Z1, Canada.
| | - Morgan W Kirzinger
- Aquatic and Crop Resource Development, National Research Council of Canada, Saskatoon, SK S7N 0W9, Canada.
| | - J C Achenbach
- Aquatic and Crop Resource Development, National Research Council of Canada, Halifax, NS B3H 3Z1, Canada.
| | - Ananda B Venkatachalam
- Aquatic and Crop Resource Development, National Research Council of Canada, Halifax, NS B3H 3Z1, Canada.
| | | | - Deborah E Ratzlaff
- New Substances Assessment Control Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada.
| | - Cindy L A Woodland
- New Substances Assessment Control Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada.
| | - Lee D Ellis
- Aquatic and Crop Resource Development, National Research Council of Canada, Halifax, NS B3H 3Z1, Canada.
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20
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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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21
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Ewald JD, Basu N, Crump D, Boulanger E, Head J. Characterizing Variability and Uncertainty Associated with Transcriptomic Dose-Response Modeling. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15960-15968. [PMID: 36268973 DOI: 10.1021/acs.est.2c04665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Transcriptomics dose-response analysis (TDRA) has emerged as a promising approach for integrating toxicogenomics data into a risk assessment context; however, variability and uncertainty associated with experimental design are not well understood. Here, we evaluated n = 55 RNA-seq profiles derived from Japanese quail liver tissue following exposure to chlorpyrifos (0, 0.04, 0.1, 0.2, 0.4, 1, 2, 4, 10, 20, and 40 μg/g; n = 5 replicates per group) via egg injection. The full dataset was subsampled 637 times to generate smaller datasets with different dose ranges and spacing (designs A-E) and number of replicates (n = 2-5). TDRA of the 637 datasets revealed substantial variability in the gene and pathway benchmark doses, but relative stability in overall transcriptomic point-of-departure (tPOD) values when tPODs were calculated with the "pathway" and "mode" methods. Further, we found that tPOD values were more dependent on the dose range and spacing than on the number of replicates, suggesting that optimal experimental designs should use fewer replicates (n = 2 or 3) and more dose groups to reduce uncertainty in the results. Finally, tPOD values ranged by over ten times for all surveyed experimental designs and tPOD types, suggesting that tPODs should be interpreted as order-of-magnitude estimates.
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Affiliation(s)
- Jessica D Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue H9X 3V9, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue H9X 3V9, Canada
| | - Doug Crump
- Ecotoxicology and Wildlife Health Division, National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa K1A 0H3, Canada
| | - Emily Boulanger
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue H9X 3V9, Canada
| | - Jessica Head
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue H9X 3V9, Canada
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22
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Jeon YS, Crump D, Boulanger E, Soufan O, Park B, Basu N, Hecker M, Xia J, Head JA. Hepatic Transcriptomic Responses to Ethinylestradiol in Two Life Stages of Japanese Quail. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:2769-2781. [PMID: 35975422 DOI: 10.1002/etc.5464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/29/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Chemical risk assessment for avian species typically depends on information from toxicity tests performed in adult birds. Early-life stage (ELS) toxicity tests have been proposed as an alternative, but incorporation of these data into existing frameworks will require knowledge about the similarities/differences between ELS and adult responses. The present study uses transcriptomics to assess hepatic gene expression in ELS and adult Japanese quail following exposure to ethinylestradiol (EE2). Prior to incubation, ELS quail were dosed with measured EE2 concentrations of 0.54, 6.3, and 54.2 µg/g egg weight via air cell injection. Adult quail were fed a single dose of EE2 at nominal concentrations of 0, 0.5, and 5 mg/kg body weight by gavage. Liver tissue was collected from five to six individuals per dose group at mid-incubation for ELS quail and 4 days after dosing for adults. A total of 283 and 111 differentially expressed genes (DEGs) were detected in ELS and adult quail, respectively, 16 of which were shared across life stages. Shared DEGs included estrogenic biomarkers such as vitellogenin genes and apovitellenin-1. For the dose groups that resulted in the highest number of DEGs (ELS, 6.3 µg/g; adult, 5 mg/kg), 21 and 35 Kyoto Encyclopedia of Genes and Genomes pathways were enriched, respectively. Ten of these pathways were shared between life stages, including pathways involved with signaling molecules and interaction and the endocrine system. Taken together, our results suggest conserved mechanisms of action following estrogenic exposure across two life stages, with evidence from differential expression of key biomarker genes and enriched pathways. The present study contributes to the development and evaluation of ELS tests and toxicogenomic approaches and highlights their combined potential for screening estrogenic chemicals. Environ Toxicol Chem 2022;41:2769-2781. © 2022 SETAC.
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Affiliation(s)
- Yeon-Seon Jeon
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Doug Crump
- Ecotoxicology and Wildlife Health Division, National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Emily Boulanger
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Othman Soufan
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
- Computer Science Department, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
| | - Bradley Park
- School of the Environment and Sustainability and Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Markus Hecker
- School of the Environment and Sustainability and Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Jessica A Head
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
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23
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Mittal K, Ewald J, Basu N. Transcriptomic Points of Departure Calculated from Rainbow Trout Gill, Liver, and Gut Cell Lines Exposed to Methylmercury and Fluoxetine. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:1982-1992. [PMID: 35622055 DOI: 10.1002/etc.5395] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Ethical and resource limitation concerns are pushing chemicals management to develop alternatives to animal testing strategies. The objective of our study was to determine whether transcriptomic point of departure (tPOD) values could be derived from studies that followed Organisation for Economic Co-operation and Development (OECD) Test No. 249 (rainbow trout gill cell line), as well as from studies on trout liver and gut cells. Gill, liver, and gut cell lines were exposed to methylmercury and fluoxetine. Concentrations causing 50% cytotoxicity (LC50) were derived, the whole transcriptome was sequenced, and gene tPOD and pathway benchmark dose (BMD) values were derived from transcriptomic dose-response analysis. Differences in LC50 and transcriptomic responses across the cell lines were noted. For methylmercury, the tPODmode values were 14.5, 20.5, and 17.8 ppb for the gill, liver, and gut cells, respectively. The most sensitive pathway (pathway BMDs in parentheses) was ferroptosis in the gill (3.1 ppb) and liver (3.5 ppb), and glutathione metabolism in the gut (6.6 ppb). For fluoxetine, the tPODmode values were 109.4, 108.4, and 97.4 ppb for the gill, liver, and gut cells, respectively. The most sensitive pathway was neurotrophin signaling in the gill (147 ppb) and dopaminergic signaling in the gut (86.3 ppb). For both chemicals, the gene tPOD and pathway BMD values were lower than cytotoxic concentrations in vitro, and within 10-fold below the in vivo LC50s. By bringing together transcriptomics and dose-response analysis with an OECD test method in three cell lines, the results help to establish an in vitro method yielding tPOD values that are hypothesized to be protective of in vivo concentrations associated with adverse outcomes, and also give insights into mechanisms of action. Environ Toxicol Chem 2022;41:1982-1992. © 2022 SETAC.
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Affiliation(s)
- Krittika Mittal
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Jessica Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
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24
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Johnson KJ, Costa E, Marshall V, Sriram S, Venkatraman A, Stebbins K, LaRocca J. A microRNA or messenger RNA point of departure estimates an apical endpoint point of departure in a rat developmental toxicity model. Birth Defects Res 2022; 114:559-576. [PMID: 35596682 PMCID: PMC9324934 DOI: 10.1002/bdr2.2046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/10/2022]
Abstract
Traditional developmental toxicity testing practice examines fetal apical endpoints to identify a point of departure (POD) for risk assessment. A potential new testing paradigm involves deriving a POD from a comprehensive analysis of molecular-level change. Here, the rat ketoconazole endocrine-mediated developmental toxicity model was used to test the hypothesis that maternal epigenomic (miRNA) and transcriptomic (mRNA) PODs are similar to fetal apical endpoint PODs. Sprague-Dawley rats were exposed from gestation day (GD) 6-21 to 0, 0.063, 0.2, 0.63, 2, 6.3, 20, or 40 mg/kg/day ketoconazole. Dam systemic, liver, and placenta PODs, along with GD 21 fetal resorption, body weight, and skeletal apical PODs were derived using BMDS software. GD 21 dam liver and placenta miRNA and mRNA PODs were obtained using three methods: a novel individual molecule POD accumulation method, a first mode method, and a gene set method. Dam apical POD values ranged from 2.0 to 38.6 mg/kg/day; the lowest value was for placenta histopathology. Fetal apical POD values were 10.9-20.3 mg/kg/day; the lowest value was for fetal resorption. Dam liver miRNA and mRNA POD values were 0.34-0.69 mg/kg/day, and placenta miRNA and mRNA POD values were 2.53-6.83 mg/kg/day. Epigenomic and transcriptomic POD values were similar across liver and placenta. Deriving a molecular POD from dam liver or placenta was protective of a fetal apical POD. These data support the conclusion that a molecular POD can be used to estimate, or be protective of, a developmental toxicity apical POD.
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Affiliation(s)
| | | | - Valerie Marshall
- Labcorp Early Development Laboratories, Inc., Greenfield, Indiana, USA
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25
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Alcaraz AJG, Baraniuk S, Mikulášek K, Park B, Lane T, Burbridge C, Ewald J, Potěšil D, Xia J, Zdráhal Z, Schneider D, Crump D, Basu N, Hogan N, Brinkmann M, Hecker M. Comparative analysis of transcriptomic points-of-departure (tPODs) and apical responses in embryo-larval fathead minnows exposed to fluoxetine. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 295:118667. [PMID: 34896397 DOI: 10.1016/j.envpol.2021.118667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/17/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Current approaches in chemical hazard assessment face significant challenges because they rely on live animal testing, which is time-consuming, expensive, and ethically questionable. These concerns serve as an impetus to develop new approach methodologies (NAMs) that do not rely on live animal tests. This study explored a molecular benchmark dose (BMD) approach using a 7-day embryo-larval fathead minnow (FHM) assay to derive transcriptomic points-of-departure (tPODs) to predict apical BMDs of fluoxetine (FLX), a highly prescribed and potent selective serotonin reuptake inhibitor frequently detected in surface waters. Fertilized FHM embryos were exposed to graded concentrations of FLX (confirmed at < LOD, 0.19, 0.74, 3.38, 10.2, 47.5 μg/L) for 32 days. Subsets of fish were subjected to omics and locomotor analyses at 7 days post-fertilization (dpf) and to histological and biometric measurements at 32 dpf. Enrichment analyses of transcriptomics and proteomics data revealed significant perturbations in gene sets associated with serotonergic and axonal functions. BMD analysis resulted in tPOD values of 0.56 μg/L (median of the 20 most sensitive gene-level BMDs), 5.0 μg/L (tenth percentile of all gene-level BMDs), 7.51 μg/L (mode of the first peak of all gene-level BMDs), and 5.66 μg/L (pathway-level BMD). These tPODs were protective of locomotor and reduced body weight effects (LOEC of 10.2 μg/L) observed in this study and were reflective of chronic apical BMDs of FLX reported in the literature. Furthermore, the distribution of gene-level BMDs followed a bimodal pattern, revealing disruption of sensitive neurotoxic pathways at low concentrations and metabolic pathway perturbations at higher concentrations. This is one of the first studies to derive protective tPODs for FLX using a short-term embryo assay at a life stage not considered to be a live animal under current legislations.
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Affiliation(s)
| | - Shaina Baraniuk
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
| | - Kamil Mikulášek
- Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Bradley Park
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada
| | - Taylor Lane
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; Department of Environment and Geography, University of York, Heslington, YO10 5NG, United Kingdom
| | - Connor Burbridge
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada
| | - Jessica Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, H9X 3V9, Canada
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, H9X 3V9, Canada
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - David Schneider
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, ON, K1A 0H3, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, H9X 3V9, Canada
| | - Natacha Hogan
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Markus Brinkmann
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, S7N 3H5, Canada
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada; School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, SK, S7N 5C8, Canada; Global Institute for Water Security, University of Saskatchewan, Saskatoon, SK, S7N 3H5, Canada.
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26
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Ekelund Ugge GMO, Jonsson A, Walstad A, Berglund O. Evaluation of transcriptional biomarkers using a high-resolution regression approach: Concentration-dependence of selected transcripts in copper-exposed freshwater mussels (Anodonta anatina). ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 90:103795. [PMID: 34971800 DOI: 10.1016/j.etap.2021.103795] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/29/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
We tested concentration-dependence of selected gene transcripts (cat, gst, hsp70, hsp90, mt and sod) for evaluation as biomarkers of chemical stress. Contrary to the common approach of factorial designs and few exposure concentrations, we used regression across a high-resolution concentration series. Specifically, freshwater mussels (Anodonta anatina) were acutely (96 h) exposed to Cu (13 nominal concentrations, measuring 0.13-1 600 µg/L), and transcripts were measured by RT-qPCR. In digestive glands, cat, hsp90 and mt decreased with water Cu (p < 0.05), but response magnitudes saturated at < 2-fold decreases. In gills, gst, hsp70, hsp90 and mt increased with water Cu (p < 0.05). While hsp70, hsp90 and mt exceeded 2-fold increases within the exposure range, high Cu concentrations were required (38-160 µg/L). Although gill responses were generally more robust compared to digestive glands, overall small response magnitudes and moderate sensitivity may set limit for potential application as general biomarkers of chemical stress.
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Affiliation(s)
- Gustaf M O Ekelund Ugge
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden; School of Bioscience, University of Skövde, Högskolevägen 3, SE-541 46 Skövde, Sweden.
| | - Annie Jonsson
- School of Bioscience, University of Skövde, Högskolevägen 3, SE-541 46 Skövde, Sweden
| | - Anders Walstad
- ALS Scandinavia Toxicon AB, Rosenhällsvägen 29, SE-261 92 Härslöv, Sweden
| | - Olof Berglund
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden
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27
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Halappanavar S, Wu D, Boyadzhiev A, Solorio-Rodriguez A, Williams A, Jariyasopit N, Saini A, Harner T. Toxicity screening of air extracts representing different source sectors in the Greater Toronto and Hamilton areas: In vitro oxidative stress, pro-inflammatory response, and toxicogenomic analysis. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2021; 872:503415. [PMID: 34798935 DOI: 10.1016/j.mrgentox.2021.503415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 09/17/2021] [Accepted: 10/01/2021] [Indexed: 01/07/2023]
Abstract
In the present study, the suitability and sensitivity of different in vitro toxicity endpoints were determined to evaluate and distinguish the specific contributions of polycyclic aromatic carbon (PAC) mixtures from various sites in Toronto (Canada), to pulmonary toxicity. Air samples were collected for two-month periods from April 2014 to March 2015 from one location, and from August 2016 to August 2017 from multiple locations reflecting different geographical areas in Toronto, and the Greater Toronto Area, with varying source emissions including background, traffic, urban, industrial and residential sites. Relative concentrations of PACs and their derivatives in these air samples were characterised. In vitro cytotoxicity, pro-inflammatory, and oxidative stress assays were employed to assess the acute pulmonary effects of urban-air-derived air pollutants. In addition, global transcriptional profiling was utilized to understand how these chemical mixtures exert their harmful effects. Lastly, the transcriptomic data and the chemical profiles for each site and season were used to relate the biological response back to individual constituents. Site-specific responses could not be derived; however, the Spring season was identified as the most responsive through benchmark concentration analysis. A combination of correlational analysis and principal component analysis revealed that nitrated and oxygenated polycyclic aromatic hydrocarbons (PAHs) drive the response at lower concentrations while specific PAHs drive the response at the highest concentration tested. Unsubstituted PAHs are the current targets for analysis as priority pollutants. The present study highlights the importance of by-products of PAH degradation in the assessment of risk. The study also demonstrates the usefulness of in vitro toxicity assays to derive meaningful data in support of risk assessment.
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Affiliation(s)
- S Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1Y 0M1, Canada.
| | - D Wu
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1Y 0M1, Canada
| | - A Boyadzhiev
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1Y 0M1, Canada
| | - A Solorio-Rodriguez
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1Y 0M1, Canada
| | - A Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1Y 0M1, Canada
| | - N Jariyasopit
- Air Quality Processes Research Section, Environment and Climate Change Canada, Toronto, ON, M3H 5T4, Canada; Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - A Saini
- Air Quality Processes Research Section, Environment and Climate Change Canada, Toronto, ON, M3H 5T4, Canada
| | - T Harner
- Air Quality Processes Research Section, Environment and Climate Change Canada, Toronto, ON, M3H 5T4, Canada
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Alcaraz AJG, Mikulášek K, Potěšil D, Park B, Shekh K, Ewald J, Burbridge C, Zdráhal Z, Schneider D, Xia J, Crump D, Basu N, Hecker M. Assessing the Toxicity of 17α-Ethinylestradiol in Rainbow Trout Using a 4-Day Transcriptomics Benchmark Dose (BMD) Embryo Assay. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10608-10618. [PMID: 34292719 DOI: 10.1021/acs.est.1c02401] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
There is an urgent demand for more efficient and ethical approaches in ecological risk assessment. Using 17α-ethinylestradiol (EE2) as a model compound, this study established an embryo benchmark dose (BMD) assay for rainbow trout (RBT; Oncorhynchus mykiss) to derive transcriptomic points-of-departure (tPODs) as an alternative to live-animal tests. Embryos were exposed to graded concentrations of EE2 (measured: 0, 1.13, 1.57, 6.22, 16.3, 55.1, and 169 ng/L) from hatch to 4 and up to 60 days post-hatch (dph) to assess molecular and apical responses, respectively. Whole proteome analyses of alevins did not show clear estrogenic effects. In contrast, transcriptomics revealed responses that were in agreement with apical effects, including excessive accumulation of intravascular and hepatic proteinaceous fluid and significant increases in mortality at 55.1 and 169 ng/L EE2 at later time points. Transcriptomic BMD analysis estimated the median of the 20th lowest geneBMD to be 0.18 ng/L, the most sensitive tPOD. Other estimates (0.78, 3.64, and 1.63 ng/L for the 10th percentile geneBMD, first peak geneBMD distribution, and median geneBMD of the most sensitive over-represented pathway, respectively) were within the same order of magnitude as empirically derived apical PODs for EE2 in the literature. This 4-day alternative RBT embryonic assay was effective in deriving tPODs that are protective of chronic effects of EE2.
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Affiliation(s)
- Alper James G Alcaraz
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5B3
| | - Kamil Mikulášek
- Central European Institute of Technology, Masaryk University, Brno CZ-625 00, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno CZ-625 00, Czech Republic
| | - Bradley Park
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5B3
| | - Kamran Shekh
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5B3
| | - Jessica Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada H9X 3V9
| | - Connor Burbridge
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 0W9
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno CZ-625 00, Czech Republic
| | - David Schneider
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 0W9
- School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5C8
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada H9X 3V9
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, Ontario, Canada K1A 0H3
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada H9X 3V9
| | - Markus Hecker
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5B3
- School of the Environment and Sustainability, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5C8
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29
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Crump D, Sharin T, Chiu S, O'Brien JM. In Vitro Screening of 21 Bisphenol A Replacement Alternatives: Compared with Bisphenol A, the Majority of Alternatives Are More Cytotoxic and Dysregulate More Genes in Avian Hepatocytes. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2021; 40:2026-2033. [PMID: 33683738 DOI: 10.1002/etc.5032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/19/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
An avian in vitro screening approach was used to determine the effects of 21 bisphenol A (BPA) alternatives. Cytotoxicity and dysregulation of genes associated with estrogen response and other toxicologically relevant pathways evoked by these alternatives were compared with BPA. Most of the BPA alternatives (15/21) were equally or more cytotoxic than BPA in chicken embryonic hepatocytes; variability in cell viability was associated with chemical structure and the log octanol-water partition coefficient (logP) values. A negative linear relationship (r 2 = 0.745; p = 0.49-07 ; n = 18) was observed between logP and the log median lethal concentration (logLC50) values. The least cytotoxic BPA alternatives elicited the greatest gene dysregulation and, overall, most of the alternatives altered more genes than BPA (measured with a custom polymerase chain reaction array). This overall approach shows promise for use as a screen for hazard-based prioritization of BPA replacement alternatives and to ideally identify those that may be less harmful and/or require additional toxicity testing. Environ Toxicol Chem 2021;40:2026-2033. © 2021 Her Majesty the Queen in Right of Canada Environmental Toxicology and Chemistry © 2021 SETAC. Reproduced with the permission of the Minister of Environment and Climate Change Canada.
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Affiliation(s)
- Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, Ontario, Canada
| | - Tasnia Sharin
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, Ontario, Canada
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Suzanne Chiu
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, Ontario, Canada
| | - Jason M O'Brien
- Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa, Ontario, Canada
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Ewald J, Soufan O, Xia J, Basu N. FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data. Bioinformatics 2021; 37:1035-1036. [PMID: 32761065 PMCID: PMC8128449 DOI: 10.1093/bioinformatics/btaa700] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/07/2020] [Accepted: 07/28/2020] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION Transcriptomics dose-response analysis is a promising new approach method for toxicity testing. While international regulatory agencies have spent substantial effort establishing a standardized statistical approach, existing software that follows this approach is computationally inefficient and must be locally installed. RESULTS FastBMD is a web-based tool that implements standardized methods for transcriptomics benchmark dose-response analysis in R. It is >60 times faster than the current leading software, supports transcriptomics data from 13 species, and offers a comprehensive analytical pipeline that goes from processing and normalization of raw gene expression values to interactive exploration of pathway-level benchmark dose results. AVAILABILITY AND IMPLEMENTATION FastBMD is freely available at www.fastbmd.ca. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jessica Ewald
- Department of Natural Resource Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Othman Soufan
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada
| | - Niladri Basu
- Department of Natural Resource Sciences, McGill University, Montreal, QC H9X 3V9, Canada
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Forner-Piquer I, Faucherre A, Byram J, Blaquiere M, de Bock F, Gamet-Payrastre L, Ellero-Simatos S, Audinat E, Jopling C, Marchi N. Differential impact of dose-range glyphosate on locomotor behavior, neuronal activity, glio-cerebrovascular structures, and transcript regulations in zebrafish larvae. CHEMOSPHERE 2021; 267:128986. [PMID: 33359984 DOI: 10.1016/j.chemosphere.2020.128986] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/05/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
The presence of glyphosate represents a debated ecotoxicological and health risk factor. Here, zebrafish larvae were exposed, from 1.5 to 120 h post-fertilization, to a broad concentration range (0.05-10.000 μg/L) of glyphosate to explore its impact on the brain. We evaluated morphology, tracked locomotor behavior and neurophysiological parameters, examined neuro-glio-vascular cell structures, and outlined transcriptomic outcomes by RNA sequencing. At the concentration range tested, glyphosate did not elicit gross morphological changes. Behavioral analysis revealed a significant decrease in locomotor activity following the exposure to 1000 μg/L glyphosate or higher. In parallel, midbrain electrophysiological recordings indicated abnormal, and variable, spike activity in zebrafish larvae exposed to 1000 μg/L glyphosate. Next, we asked whether the observed neurophysiological outcome could be secondary to brain structural modifications. We used transgenic zebrafish and in vivo 2-photon microscopy to examine, at the cellular level, the effects of the behavior-modifying concentration of 1000 μg/L, comparing to low 0.1 μg/L, and control. We ruled out the presence of cerebrovascular and neuronal malformations. However, microglia morphological modifications were visible at the two glyphosate concentrations, specifically the presence of amoeboid cells suggestive of activation. Lastly, RNAseq analysis showed the deregulation of transcript families implicated in neuronal physiology, synaptic transmission, and inflammation, as evaluated at the two selected glyphosate concentrations. In zebrafish larvae, behavioral and neurophysiological defects occur after the exposure to high glyphosate concentrations while cellular and transcript signatures can be detected in response to low dose. The prospective applicability to ecotoxicology and the possible extension to brain-health vulnerability are critically discussed.
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Affiliation(s)
- Isabel Forner-Piquer
- Cerebrovascular and Glia Research, Institute for Functional Genomics (University of Montpellier - UMR 5203 CNRS - U 1191 INSERM), 141 rue de la Cardonille, 34094, Montpellier, France
| | - Adèle Faucherre
- Molecular mechanisms of regeneration, Institute for Functional Genomics (University of Montpellier - UMR 5203 CNRS - U 1191 INSERM LabEx ICST), 141 rue de la Cardonille, 34094, Montpellier, France
| | - Julia Byram
- Cerebrovascular and Glia Research, Institute for Functional Genomics (University of Montpellier - UMR 5203 CNRS - U 1191 INSERM), 141 rue de la Cardonille, 34094, Montpellier, France
| | - Marine Blaquiere
- Cerebrovascular and Glia Research, Institute for Functional Genomics (University of Montpellier - UMR 5203 CNRS - U 1191 INSERM), 141 rue de la Cardonille, 34094, Montpellier, France
| | - Frederic de Bock
- Cerebrovascular and Glia Research, Institute for Functional Genomics (University of Montpellier - UMR 5203 CNRS - U 1191 INSERM), 141 rue de la Cardonille, 34094, Montpellier, France
| | - Laurence Gamet-Payrastre
- Toxalim, Research Centre in Food Toxicology (Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS), 180 Chemin de tournefeuille, 31300, Toulouse, France
| | - Sandrine Ellero-Simatos
- Toxalim, Research Centre in Food Toxicology (Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS), 180 Chemin de tournefeuille, 31300, Toulouse, France
| | - Etienne Audinat
- Cerebrovascular and Glia Research, Institute for Functional Genomics (University of Montpellier - UMR 5203 CNRS - U 1191 INSERM), 141 rue de la Cardonille, 34094, Montpellier, France
| | - Chris Jopling
- Molecular mechanisms of regeneration, Institute for Functional Genomics (University of Montpellier - UMR 5203 CNRS - U 1191 INSERM LabEx ICST), 141 rue de la Cardonille, 34094, Montpellier, France.
| | - Nicola Marchi
- Cerebrovascular and Glia Research, Institute for Functional Genomics (University of Montpellier - UMR 5203 CNRS - U 1191 INSERM), 141 rue de la Cardonille, 34094, Montpellier, France.
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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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Serra A, Fratello M, del Giudice G, Saarimäki LA, Paci M, Federico A, Greco D. TinderMIX: Time-dose integrated modelling of toxicogenomics data. Gigascience 2020; 9:giaa055. [PMID: 32449777 PMCID: PMC7247400 DOI: 10.1093/gigascience/giaa055] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/22/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Omics technologies have been widely applied in toxicology studies to investigate the effects of different substances on exposed biological systems. A classical toxicogenomic study consists in testing the effects of a compound at different dose levels and different time points. The main challenge consists in identifying the gene alteration patterns that are correlated to doses and time points. The majority of existing methods for toxicogenomics data analysis allow the study of the molecular alteration after the exposure (or treatment) at each time point individually. However, this kind of analysis cannot identify dynamic (time-dependent) events of dose responsiveness. RESULTS We propose TinderMIX, an approach that simultaneously models the effects of time and dose on the transcriptome to investigate the course of molecular alterations exerted in response to the exposure. Starting from gene log fold-change, TinderMIX fits different integrated time and dose models to each gene, selects the optimal one, and computes its time and dose effect map; then a user-selected threshold is applied to identify the responsive area on each map and verify whether the gene shows a dynamic (time-dependent) and dose-dependent response; eventually, responsive genes are labelled according to the integrated time and dose point of departure. CONCLUSIONS To showcase the TinderMIX method, we analysed 2 drugs from the Open TG-GATEs dataset, namely, cyclosporin A and thioacetamide. We first identified the dynamic dose-dependent mechanism of action of each drug and compared them. Our analysis highlights that different time- and dose-integrated point of departure recapitulates the toxicity potential of the compounds as well as their dynamic dose-dependent mechanism of action.
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Affiliation(s)
- Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- BioMediTech Institute, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
| | - Michele Fratello
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- BioMediTech Institute, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
| | - Giusy del Giudice
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- BioMediTech Institute, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
| | - Laura Aliisa Saarimäki
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- BioMediTech Institute, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
| | - Michelangelo Paci
- BioMediTech Institute, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- BioMediTech Institute, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- BioMediTech Institute, Tampere University, Arvo Ylpön katu 34, 33520, Tampere, Finland
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5, 00014, Helsinki, Finland
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Ewald JD, Soufan O, Crump D, Hecker M, Xia J, Basu N. EcoToxModules: Custom Gene Sets to Organize and Analyze Toxicogenomics Data from Ecological Species. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4376-4387. [PMID: 32106671 DOI: 10.1021/acs.est.9b06607] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Traditional results from toxicogenomics studies are complex lists of significantly impacted genes or gene sets, which are challenging to synthesize down to actionable results with a clear interpretation. Here, we defined two sets of 21 custom gene sets, called the functional and statistical EcoToxModules, in fathead minnow (Pimephales promelas) to (1) re-cast predefined molecular pathways into a toxicological framework and (2) provide a data-driven, unsupervised grouping of genes impacted by exposure to environmental contaminants. The functional EcoToxModules were identified by re-organizing KEGG pathways into biological processes that are more relevant to ecotoxicology based on the input from expert scientists and regulators. The statistical EcoToxModules were identified using co-expression analysis of publicly available microarray data (n = 303 profiles) measured in livers of fathead minnows after exposure to 38 different conditions. Potential applications of the EcoToxModules were demonstrated with two case studies that represent exposure to a pure chemical and to environmental wastewater samples. In comparisons to differential expression and gene set analysis, we found that EcoToxModule responses were consistent with these traditional results. Additionally, they were easier to visualize and quantitatively compare across different conditions, which facilitated drawing conclusions about the relative toxicity of the exposures within each case study.
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Affiliation(s)
- Jessica D Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue H9X 3V9, Canada
| | - Othman Soufan
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue H9X 3V9, Canada
| | - Doug Crump
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, National Wildlife Research Centre, Ottawa K1A 0H3, Canada
| | - Markus Hecker
- School of the Environment & Sustainability and Toxicology Centre, University of Saskatchewan, Saskatoon S7N 5B3, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue H9X 3V9, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue H9X 3V9, Canada
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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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