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Chong K, Hickey GM, Chan HM, Basu N. Exploring practices, challenges, and priorities for human health and ecological risk assessments in Indigenous communities in Canada. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2024. [PMID: 38639473 DOI: 10.1002/ieam.4927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
Indigenous peoples in Canada are disproportionately exposed to environmental contaminants and may face elevated health risks related to their unique cultural, spiritual, and economic relationships with the land, including the use of traditional food systems. However, to date, institutionalized approaches to assess risks to human and ecological health from contaminants have not been well developed or implemented with Indigenous community contexts in mind. There is regulatory interest in developing new approach methods for risk assessment, and thus an opportunity to increase their relevance to Indigenous communities in which they will be ultimately applied. Therefore, we conducted an anonymous mixed-methods survey of those involved with risk assessment in Indigenous communities in Canada to: (1) understand risk assessment practice in Indigenous communities, (2) explore challenges with conventional assessment methods and compare these across sectors, and (3) gather perspectives on the development of new approaches. In all, 38 completed survey responses were received (14% response rate). Respondents were from Indigenous community environment and health offices (21% of respondents), Indigenous governments (8%), federal and provincial governments (21%), and academia (45%). Risk communication was seen as the most challenging part of risk assessment (71% responded "difficult"), and nearly all respondents agreed that time (86%), cost (76%), and resource availability (86%) were "moderate" to "serious" problems. Few respondents (16%) had heard of "new approach methods" for risk assessment, and 76% of respondents (and 100% of community-based respondents) agreed on the need to develop improved risk assessment approaches. To modernize risk assessment, respondents recommended advancing cumulative risk assessment methods, improving risk communication, and promoting Indigenous leadership and Traditional Knowledge in assessment activities. Integr Environ Assess Manag 2024;00:1-16. © 2024 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
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Affiliation(s)
- Katherine Chong
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
- Centre for Indigenous Peoples Nutrition and Environment, McGill University, Montreal, Quebec, Canada
| | - Gordon M Hickey
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Hing Man Chan
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
- Centre for Indigenous Peoples Nutrition and Environment, McGill University, Montreal, Quebec, Canada
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2
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Bearth A, Roth N, Wilks MF, Siegrist M. Intuitive toxicology in the 21st century-Bridging the perspectives of the public and risk assessors in Europe. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2024. [PMID: 38490812 DOI: 10.1111/risa.14296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/30/2024] [Accepted: 03/02/2024] [Indexed: 03/17/2024]
Abstract
Three decades ago, several articles on the subjectivity in chemical risk judgments (i.e., labeled "intuitive toxicology") measured the divide between the public and toxicologists with different backgrounds regarding the validity of predicting health effects based on in vivo studies. Similar divides with impacts on societal discourse and chemical risk assessment practices might exist concerning alternative toxicity testing methods (i.e., in vitro and in silico). However, studies to date have focused either on the public's views of in vivo or stem cell testing or on experts' views of in vivo testing and potential alternatives (i.e., toxicologists and medical students), which do not allow for a direct investigation of potential divides. To fill this knowledge gap, we conducted two online surveys, involving members of the German-speaking public in Switzerland and European human health risk assessors, respectively. This article presents the results of these two surveys regarding the divide in the public's and risk assessors' perspectives on risk assessment based on in vivo, in vitro, and in silico testing. Particularly, the survey with the risk assessors highlights that, beyond scientific and regulatory barriers, alternatives to in vivo testing may encounter individual hurdles, such as higher uncertainty associated with them. Understanding and addressing these hurdles will be crucial to facilitate the integration of new approach methodologies into chemical risk assessment practices as well as a successful transition toward next-generation risk assessment, bringing us closer to a fit-for-purpose and more efficient regulatory landscape.
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Affiliation(s)
- Angela Bearth
- Consumer Behavior, Institute for Environmental Decisions, ETH Zurich, Zurich, Switzerland
| | - Nicolas Roth
- Swiss Centre for Applied Human Toxicology, University of Basel, Basel, Switzerland
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Martin F Wilks
- Swiss Centre for Applied Human Toxicology, University of Basel, Basel, Switzerland
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Michael Siegrist
- Consumer Behavior, Institute for Environmental Decisions, ETH Zurich, Zurich, Switzerland
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3
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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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Villeneuve DL, Bush K, Hazemi M, Hoang JX, Le M, Blackwell BR, Stacy E, Flynn KM. Derivation of Transcriptomics-Based Points of Departure for 20 Per- or Polyfluoroalkyl Substances Using a Larval Fathead Minnow (Pimephales promelas) Reduced Transcriptome Assay. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 38415853 DOI: 10.1002/etc.5825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/18/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
Traditional toxicity testing has been unable to keep pace with the introduction of new chemicals into commerce. Consequently, there are limited or no toxicity data for many chemicals to which fish and wildlife may be exposed. Per- and polyfluoroalkyl substances (PFAS) are emblematic of this issue in that ecological hazards of most PFAS remain uncharacterized. The present study employed a high-throughput assay to identify the concentration at which 20 PFAS, with diverse properties, elicited a concerted gene expression response (termed a transcriptomics-based point of departure [tPOD]) in larval fathead minnows (Pimephales promelas; 5-6 days postfertilization) exposed for 24 h. Based on a reduced transcriptome approach that measured whole-body expression of 1832 genes, the median tPOD for the 20 PFAS tested was 10 µM. Longer-chain carboxylic acids (12-13 C-F); an eight-C-F dialcohol, N-alkyl sulfonamide; and telomer sulfonic acid were among the most potent PFAS, eliciting gene expression responses at concentrations <1 µM. With a few exceptions, larval fathead minnow tPODs were concordant with those based on whole-transcriptome response in human cell lines. However, larval fathead minnow tPODs were often greater than those for Daphnia magna exposed to the same PFAS. The tPODs overlapped concentrations at which other sublethal effects have been reported in fish (available for 10 PFAS). Nonetheless, fathead minnow tPODs were orders of magnitude higher than aqueous PFAS concentrations detected in tributaries of the North American Great Lakes, suggesting a substantial margin of safety. Overall, results broadly support the use of a fathead minnow larval transcriptomics assay to derive screening-level potency estimates for use in ecological risk-based prioritization. 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, Minnesota
| | - Kendra Bush
- Research Participant at Great Lakes Toxicology and Ecology Division, Oak Ridge Institute for Science and Education, Duluth, Minnesota, USA
| | - Monique Hazemi
- Research Participant at Great Lakes Toxicology and Ecology Division, Oak Ridge Institute for Science and Education, Duluth, Minnesota, USA
| | - John X Hoang
- Research Participant at Great Lakes Toxicology and Ecology Division, Oak Ridge Institute for Science and Education, Duluth, Minnesota, USA
| | - Michelle Le
- Research Participant at Great Lakes Toxicology and Ecology Division, Oak Ridge Institute for Science and Education, Duluth, Minnesota, USA
| | - Brett R Blackwell
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota
- Bioscience Division, Biochemistry and Biotechnology Group, Los Alamos National Laboratory, Los Alamos, Minnesota, USA
| | - Emma Stacy
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota
| | - Kevin M Flynn
- Great Lakes Toxicology and Ecology Division, US Environmental Protection Agency, Duluth, Minnesota
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Mittal K, Ewald J, Crump D, Head J, Hecker M, Hogan N, Xia J, Basu N. Comparing Transcriptomic Responses to Chemicals Across Six Species Using the EcoToxChip RNASeq Database. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023. [PMID: 38085106 DOI: 10.1002/etc.5803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/05/2023] [Indexed: 01/18/2024]
Abstract
The EcoToxChip project includes RNA-sequencing data from experiments involving model (Japanese quail, fathead minnow, African clawed frog) and ecological (double-crested cormorant, rainbow trout, northern leopard frog) species at multiple life stages (whole embryo and adult) exposed to eight chemicals of environmental concern known to perturb a wide range of biological systems (ethinyl estradiol, hexabromocyclododecane, lead, selenomethionine, 17β trenbolone, chlorpyrifos, fluoxetine, and benzo[a]pyrene). The objectives of this short communication were to (1) present and make available this RNA-sequencing database (i.e., 724 samples from 49 experiments) under the FAIR principles (FAIR data are data which meet principles of findability, accessibility, interoperability, and reusability), while also summarizing key meta-data attributes and (2) use ExpressAnalyst (including the Seq2Fun algorithm and EcoOmicsDB) to perform a comparative transcriptomics analysis of this database focusing on baseline and differential transcriptomic changes across species-life stage-chemical combinations. The database is available in NCBI GEO under accession number GSE239776. Across all species, the number of raw reads per sample ranged between 13 and 58 million, with 30% to 79% of clean reads mapped to the "vertebrate" subgroup database in EcoOmicsDB. Principal component analyses of the reads illustrated separation across the three taxonomic groups as well as some between tissue types. The most common differentially expressed gene was CYP1A1 followed by CTSE, FAM20CL, MYC, ST1S3, RIPK4, VTG1, and VIT2. The most common enriched pathways were metabolic pathways, biosynthesis of cofactors and biosynthesis of secondary metabolites, and chemical carcinogenesis, drug metabolism, and metabolism of xenobiotics by cytochrome P450. The RNA-sequencing database in the present study may be used by the research community for multiple purposes, including, for example, cross-species investigations, in-depth analyses of a particular test compound, and transcriptomic meta-analyses. Environ Toxicol Chem 2024;00:1-6. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of 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
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Center, Ottawa, Ontario, Canada
| | - Jessica Head
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Markus Hecker
- Toxicology Center, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Natacha Hogan
- Toxicology Center, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jianguo Xia
- 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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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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7
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Magurany KA, Chang X, Clewell R, Coecke S, Haugabrooks E, Marty S. A Pragmatic Framework for the Application of New Approach Methodologies in One Health Toxicological Risk Assessment. Toxicol Sci 2023; 192:kfad012. [PMID: 36782355 PMCID: PMC10109535 DOI: 10.1093/toxsci/kfad012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Globally, industries and regulatory authorities are faced with an urgent need to assess the potential adverse effects of chemicals more efficiently by embracing new approach methodologies (NAMs). NAMs include cell and tissue methods (in vitro), structure-based/toxicokinetic models (in silico), methods that assess toxicant interactions with biological macromolecules (in chemico), and alternative models. Increasing knowledge on chemical toxicokinetics (what the body does with chemicals) and toxicodynamics (what the chemicals do with the body) obtained from in silico and in vitro systems continues to provide opportunities for modernizing chemical risk assessments. However, directly leveraging in vitro and in silico data for derivation of human health-based reference values has not received regulatory acceptance due to uncertainties in extrapolating NAM results to human populations, including metabolism, complex biological pathways, multiple exposures, interindividual susceptibility and vulnerable populations. The objective of this article is to provide a standardized pragmatic framework that applies integrated approaches with a focus on quantitative in vitro to in vivo extrapolation (QIVIVE) to extrapolate in vitro cellular exposures to human equivalent doses from which human reference values can be derived. The proposed framework intends to systematically account for the complexities in extrapolation and data interpretation to support sound human health safety decisions in diverse industrial sectors (food systems, cosmetics, industrial chemicals, pharmaceuticals etc.). Case studies of chemical entities, using new and existing data, are presented to demonstrate the utility of the proposed framework while highlighting potential sources of human population bias and uncertainty, and the importance of Good Method and Reporting Practices.
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Affiliation(s)
| | | | - Rebecca Clewell
- 21st Century Tox Consulting, Chapel Hill, North Carolina 27517, USA
| | - Sandra Coecke
- European Commission Joint Research Centre, Ispra, Italy
| | - Esther Haugabrooks
- Coca-Cola Company (formerly Physicians Committee for Responsible Medicine), Atlanta, Georgia 30313, USA
| | - Sue Marty
- The Dow Chemical Company, Midland, Michigan 48667, USA
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Arslan ME, Tatar A, Yıldırım ÖÇ, Şahin İO, Ozdemir O, Sonmez E, Hacımuftuoglu A, Acikyildiz M, Geyikoğlu F, Mardinoğlu A, Türkez H. In Vitro Transcriptome Analysis of Cobalt Boride Nanoparticles on Human Pulmonary Alveolar Cells. MATERIALS (BASEL, SWITZERLAND) 2022; 15:8683. [PMID: 36500178 PMCID: PMC9740129 DOI: 10.3390/ma15238683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/24/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Nanobiotechnology influences many different areas, including the medical, food, energy, clothing, and cosmetics industries. Considering the wide usage of nanomaterials, it is necessary to investigate the toxicity potentials of specific nanosized molecules. Boron-containing nanoparticles (NPs) are attracting much interest from scientists due to their unique physicochemical properties. However, there is limited information concerning the toxicity of boron-containing NPs, including cobalt boride (Co2B) NPs. Therefore, in this study, Co2B NPs were characterized using X-ray crystallography (XRD), transmission electron microscope (TEM), scanning electron microscope (SEM), and energy-dispersive X-ray spectroscopy (EDX) techniques. Then, we performed 3-(4,5-dimethyl-thiazol-2-yl) 2,5-diphenyltetrazolium bromide (MTT), lactate dehydrogenase (LDH) release, and neutral red (NR) assays for assessing cell viability against Co2B NP exposure on cultured human pulmonary alveolar epithelial cells (HPAEpiC). In addition, whole-genome microarray analysis was carried out to reveal the global gene expression differentiation of HPAEpiC cells after Co2B NP application. The cell viability tests unveiled an IC50 value for Co2B NPs of 310.353 mg/L. The results of our microarray analysis displayed 719 gene expression differentiations (FC ≥ 2) among the analyzed 40,000 genes. The performed visualization and integrated discovery (DAVID) analysis revealed that there were interactions between various gene pathways and administration of the NPs. Based on gene ontology biological processes analysis, we found that the P53 signaling pathway, cell cycle, and cancer-affecting genes were mostly affected by the Co2B NPs. In conclusion, we suggested that Co2B NPs would be a safe and effective nanomolecule for industrial applications, particularly for medical purposes.
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Affiliation(s)
- Mehmet Enes Arslan
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum 25050, Turkey
| | - Arzu Tatar
- Department of Otorhinolaryngology, Faculty of Medicine, Ataturk University, Erzurum 25240, Turkey
| | - Özge Çağlar Yıldırım
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum 25050, Turkey
| | - İrfan Oğuz Şahin
- Department of Pediatrics, Pediatric Cardiology, Faculty of Medicine, Ondokuz Mayıs University, Samsun 55139, Turkey
| | - Ozlem Ozdemir
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum 25050, Turkey
| | - Erdal Sonmez
- Advanced Materials Research Laboratory, Department of Nanoscience & Nanoengineering, Graduate School of Natural and Applied Sciences, Ataturk University, Erzurum 25240, Turkey
| | - Ahmet Hacımuftuoglu
- Department of Medical Pharmacology, Medical Faculty, Atatürk University, Erzurum 25240, Turkey
| | - Metin Acikyildiz
- Department of Chemistry, Faculty of Science and Art, Kilis 7 Aralık University, Kilis 79000, Turkey
| | - Fatime Geyikoğlu
- Department of Biology, Faculty of Arts and Sciences, Atatürk University, Erzurum 25240, Turkey
| | - Adil Mardinoğlu
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-17121 Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London SE1 9RT, UK
| | - Hasan Türkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum 25240, Turkey
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9
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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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10
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van der Vegt R, Maguire S, Crump D, Hecker M, Basu N, Hickey GM. Chemical risk governance: Exploring stakeholder participation in Canada, the USA, and the EU. AMBIO 2022; 51:1698-1710. [PMID: 34870781 PMCID: PMC9110598 DOI: 10.1007/s13280-021-01671-2] [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: 05/04/2021] [Revised: 05/05/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Hazardous chemicals are one of the greatest environmental challenges facing our planet, testing governments in the face of economic and social development. Chemical risks are often complex systemic risks, which require particular governance processes, stakeholder participation mechanisms, and communication procedures to manage. In this article we explore how such processes, mechanisms, and procedures could offer more effective pathways for international chemical risk assessment and management. Combining document analysis with 69 key informant interviews and four focus groups with experts from across government, non-governmental organizations (NGOs) and industry in Canada, the USA and Europe (n = 24), the results highlight the importance of increasing stakeholder participation and risk communication in existing chemical risk assessment and management frameworks. Similarities and differences between the three jurisdictions are discussed with a view to inform future risk governance strategies. The contemporary insights are of relevance to decision-makers seeking to improve the effectiveness of chemical risk governance in practice.
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Affiliation(s)
- R.G. van der Vegt
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Macdonald-Stewart Building, Sainte-Anne-de-Bellevue, QC H9X 3V9 Canada
| | - Steven Maguire
- The University of Sydney Business School, Room 4228 Abercrombie Building (H70), Sydney, NSW 2006 Australia
- Department of Chemistry, Faculty of Science, McGill University, Montreal, QC Canada
| | - Doug Crump
- National Wildlife Research Centre, Environment and Climate Change Canada, Carleton University, 1125 Colonel By Drive, Raven Road, Ottawa, ON K1A 0H3 Canada
| | - Markus Hecker
- School of the Environment and Sustainability, University of Saskatchewan, Saskatchewan, SK Canada
- Toxicology Center, University of Saskatchewan, Saskatchewan, SK Canada
| | - Niladri Basu
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Macdonald-Stewart Building, Sainte-Anne-de-Bellevue, QC H9X 3V9 Canada
| | - Gordon M. Hickey
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Macdonald-Stewart Building, Sainte-Anne-de-Bellevue, QC H9X 3V9 Canada
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11
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Wang Y, Wang S, Jing H, Zhang T, Song N, Xu S. CircRNA-IGLL1/miR-15a/RNF43 axis mediates ammonia-induced autophagy in broilers jejunum via Wnt/β-catenin pathway. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118332. [PMID: 34637826 DOI: 10.1016/j.envpol.2021.118332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/30/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
With the continued increase of global ammonia emission, the damage to human or animal caused by ammonia pollution has attracted wide attention. The noncoding RNAs have been reported to regulate a variety of biological processes under different environmental stimulation via ceRNA (competing endogenous RNA) networks. Autophagy is a hallmark of tissue damage from air pollution. However, the specific role of circular RNAs (circRNAs) in the injury of intestinal tissue caused by autophagy remains unclear. Here, we established 42-days old ammonia-exposed broiler models and observed that autophagy flux in broiler jejunum was activated under ammonia exposure. Meanwhile, a total of eight significantly dysregulated expressed circRNAs were obtained and a circRNAs-miRNAs-genes interaction networks were constructed by bioinformatics analysis. Furthermore, an axis named circRNA-IGLL1/miR-15a/RNF43 was predicted to participate in the excessive autophagy by targeting RNF43. The target relationship was proved by dual-luciferase reporter assay in vitro. Mechanistically, downregulated circRNA-IGLL1 could suppress the expression of RNF43 in ammonia-exposed jejunum and the Wnt/β-catenin pathway was activated. Inhibition of miR-15a reversed autophagy caused by downregulated circRNA-IGLL1. CircRNA-IGLL1 could competitively bind miR-15a to regulate RNF43 expression, thus modulating the occurrence of autophagy. Taken together, our results showed that circRNA-IGLL1/miR-15a/RNF43 axis is involved in ammonia-induced intestinal autophagy in broilers.
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Affiliation(s)
- Yue Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China
| | - Shengchen Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China
| | - Hongyuan Jing
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China
| | - Tianyi Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China
| | - Nuan Song
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China
| | - Shiwen Xu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China; Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, PR China.
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12
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Soufan O, Ewald J, Zhou G, Hacariz O, Boulanger E, Alcaraz AJ, Hickey G, Maguire S, Pain G, Hogan N, Hecker M, Crump D, Head J, Basu N, Xia J. EcoToxXplorer: Leveraging Design Thinking to Develop a Standardized Web-Based Transcriptomics Analytics Platform for Diverse Users. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:21-29. [PMID: 34762316 DOI: 10.1002/etc.5251] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Othman Soufan
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
- Department of Computer Science, Saint Francis Xavier University, Antigonish, Nova Scotia, Canada
| | - Jessica Ewald
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Guangyan Zhou
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Orcun Hacariz
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Emily Boulanger
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Alper James Alcaraz
- Toxicology Center, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Gordon Hickey
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Steve Maguire
- The University of Sydney Business School & Sydney Nano Institute, University of Sydney, Sydney, Australia
- Department of Chemistry, Faculty of Science, McGill University, Montreal, Quebec, Canada
| | - Guillaume Pain
- Faculty of Administrative Sciences, Université Laval, Quebec City, Quebec, Canada
| | - Natacha Hogan
- Toxicology Center, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Markus Hecker
- Toxicology Center, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Doug Crump
- Environment and Climate Change Canada, National Wildlife Research Centre, Carleton University, Ottawa, Ontario, Canada
| | - Jessica Head
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
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13
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Gorzalczany SB, Rodriguez Basso AG. Strategies to apply 3Rs in preclinical testing. Pharmacol Res Perspect 2021; 9:e00863. [PMID: 34609088 PMCID: PMC8491455 DOI: 10.1002/prp2.863] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
Animal experimentation has been fundamental in biological and biomedical research. To guarantee the maximum quality, efficacy and/or safety of products intended for the use in humans in vivo testing is necessary; however, for over 60 years, alternative methods have been developed in response to the necessity to reduce the number of animals used in experimentation, to guarantee their welfare; resorting to animal models only when strictly necessary. The three Rs (Replacement, Reduction, and Refinement), seek to ensure the rational and respectful use of laboratory animals and maintain an adequate projection in terms of bioethical considerations. This article describes different approaches to apply 3Rs in preclinical experimentation for either research or regulatory purposes.
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Affiliation(s)
- Susana B. Gorzalczany
- Universidad de Buenos AiresFacultad de Farmacia y Bioquímica, Pharmacology DepartmentBuenos AiresArgentina
| | - Angeles G. Rodriguez Basso
- Universidad de Buenos AiresFacultad de Farmacia y Bioquímica, Pharmacology DepartmentBuenos AiresArgentina
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14
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Ebner JN. Trends in the Application of "Omics" to Ecotoxicology and Stress Ecology. Genes (Basel) 2021; 12:1481. [PMID: 34680873 PMCID: PMC8535992 DOI: 10.3390/genes12101481] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/12/2021] [Accepted: 09/16/2021] [Indexed: 02/08/2023] Open
Abstract
Our ability to predict and assess how environmental changes such as pollution and climate change affect components of the Earth's biome is of paramount importance. This need positioned the fields of ecotoxicology and stress ecology at the center of environmental monitoring efforts. Advances in these interdisciplinary fields depend not only on conceptual leaps but also on technological advances and data integration. High-throughput "omics" technologies enabled the measurement of molecular changes at virtually all levels of an organism's biological organization and thus continue to influence how the impacts of stressors are understood. This bibliometric review describes literature trends (2000-2020) that indicate that more different stressors than species are studied each year but that only a few stressors have been studied in more than two phyla. At the same time, the molecular responses of a diverse set of non-model species have been investigated, but cross-species comparisons are still rare. While transcriptomics studies dominated until 2016, a shift towards proteomics and multiomics studies is apparent. There is now a wealth of data at functional omics levels from many phylogenetically diverse species. This review, therefore, addresses the question of how to integrate omics information across species.
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Affiliation(s)
- Joshua Niklas Ebner
- Spring Ecology Research Group, Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
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