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Reynolds JI, Choi J, Johnson BP. Crowdsourcing AOP development: Leveraging the thesis literature review to identify knowledge gaps and facilitate research translation. Curr Res Toxicol 2024; 7:100191. [PMID: 39205829 PMCID: PMC11350270 DOI: 10.1016/j.crtox.2024.100191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/26/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Chemical risk assessment still primarily relies on extrapolation of data from high-confidence in vivo studies. Emerging 21st Century Toxicology tools and approaches have potential to figure more prominently in chemical risk assessment, but many challenges in translating this research into assessments remain. One of these tools, the Adverse Outcome Pathway (AOP) Wiki provides a framework to map and evaluate adverse chemical dynamics, that is the biochemical and physiological effects that occur after chemical exposure. The AOP-guided targeted review of relevant literature, described here, shares similarities with a doctoral thesis or literature review but forces critical evaluation of each step in a pathway including those of central dogma. Additionally, it provides valuable translational regulatory relevance. Data gaps identified through this process can be targeted areas of study in the thesis itself to increase translational relevance. One of the challenges with this tool is that many AOPs are under- or undeveloped. To help fill this need, a concerted effort by subject matter experts to speed the development of AOPs supported under the Organization for Economic Cooperation and Development (OECD) framework would benefit this translational problem. As a case study, we present our experience developing AOP 460: Antagonism of Smoothened receptor leading to orofacial clefting (OECD AOP workplan project 1.101) as part of a graduate literature review. AOP development offers clear benefits to the regulatory and academic communities and increased dissemination of AOPs replete with the most current state of scientific knowledge will promote research translation and increased risk assessment capabilities.
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Affiliation(s)
- Jacob I. Reynolds
- Department of Biomedical Engineering, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Judy Choi
- Department of Pesticides Safety, Unit Toxicology of Active Substances and their Metabolites, German Federal Institute for Risk Assessment, 10589 Berlin, Germany
| | - Brian P. Johnson
- Department of Biomedical Engineering, Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
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Sahoo AK, Chivukula N, Ramesh K, Singha J, Marigoudar SR, Sharma KV, Samal A. An integrative data-centric approach to derivation and characterization of an adverse outcome pathway network for cadmium-induced toxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170968. [PMID: 38367714 DOI: 10.1016/j.scitotenv.2024.170968] [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: 12/20/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 02/19/2024]
Abstract
Cadmium is a prominent toxic heavy metal that contaminates both terrestrial and aquatic environments. Owing to its high biological half-life and low excretion rates, cadmium causes a variety of adverse biological outcomes. Adverse outcome pathway (AOP) networks were envisioned to systematically capture toxicological information to enable risk assessment and chemical regulation. Here, we leveraged AOP-Wiki and integrated heterogeneous data from four other exposome-relevant resources to build the first AOP network relevant for inorganic cadmium-induced toxicity. From AOP-Wiki, we filtered 309 high confidence AOPs, identified 312 key events (KEs) associated with inorganic cadmium from five exposome-relevant databases using a data-centric approach, and thereafter, curated 30 cadmium relevant AOPs (cadmium-AOPs). By constructing the undirected AOP network, we identified a large connected component of 18 cadmium-AOPs. Further, we analyzed the directed network of 59 KEs and 82 key event relationships (KERs) in the largest component using graph-theoretic approaches. Subsequently, we mined published literature using artificial intelligence-based tools to provide auxiliary evidence of cadmium association for all KEs in the largest component. Finally, we performed case studies to verify the rationality of cadmium-induced toxicity in humans and aquatic species. Overall, cadmium-AOP network constructed in this study will aid ongoing research in systems toxicology and chemical exposome.
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Affiliation(s)
- Ajaya Kumar Sahoo
- The Institute of Mathematical Sciences (IMSc), Chennai, India; Homi Bhabha National Institute (HBNI), Mumbai, India
| | - Nikhil Chivukula
- The Institute of Mathematical Sciences (IMSc), Chennai, India; Homi Bhabha National Institute (HBNI), Mumbai, India
| | | | - Jasmine Singha
- National Centre for Coastal Research, Ministry of Earth Sciences, Government of India, Pallikaranai, Chennai, India
| | | | - Krishna Venkatarama Sharma
- National Centre for Coastal Research, Ministry of Earth Sciences, Government of India, Pallikaranai, Chennai, India
| | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai, India; Homi Bhabha National Institute (HBNI), Mumbai, India.
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Mhalhel K, Arena R, Rizzo M, Piccione G, Aragona M, Levanti M, Aragona F, Arfuso F. Potential Implications of Acid-Sensing Ion Channels ASIC2 and ASIC4 in Gonadal Differentiation of Dicentrarchus labrax Subjected to Water Temperature Increase during Gonadal Development. Animals (Basel) 2024; 14:1024. [PMID: 38612263 PMCID: PMC11010900 DOI: 10.3390/ani14071024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
In this study, the expression and implication of acid-sensing ion channels 2 and 4 (ASIC2 and ASIC4) in the gonadal sex differentiation of Dicentrarchus labrax (D. labrax), subjected to increasing water temperatures during gonadal development, were evaluated. Two groups were selected: a control group (CG), in which the average water temperature was maintained at 15 °C and increased to 20 °C in 20 days until weaning; and an experimental group (EG), in which the water temperature was retained at 15 °C for 60 days; thereafter, the temperature was increased daily by 0.5 °C until it reached 20 °C up to the weaning time. Ten fish from the CG and 13 fish from the EG were sampled randomly on the 335th day after hatching (dph). A higher percentage of gonad differentiation in ovaries rather than in testes was observed in the EG compared to the CG (p = 0.01). ASIC2 and ASIC4 were detected for the first time in D. labrax ovaries by indirect immunofluorescence. Both ASIC2 and ASIC4 were expressed in previtellogenic oocytes of ovaries and in scattered cells within some testes, and were most likely intratesticular previtellogenic oocytes in both the CG and EG groups. The CG group showed a higher expression of ASIC4 than the EG cohort (p < 0.05). The results gathered in this study revealed the capacity of water temperature to influence both gonadal differentiation and growth in this gonochoristic fish species, and suggests the possible role of ASIC2 and ASIC4 in gonad differentiation and gamete development in D. labrax.
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Affiliation(s)
- Kamel Mhalhel
- Department of Veterinary Sciences, University of Messina, Viale Giovanni Palatucci SNC, 98168 Messina, Italy; (K.M.); (M.R.); (G.P.); (M.L.); (F.A.); (F.A.)
| | - Rosaria Arena
- Marine Biochemistry and Ecotoxicology Laboratory, Department of Earth and Sea Science, University of Palermo, Via Barlotta 4, 91100 Trapani, Italy;
| | - Maria Rizzo
- Department of Veterinary Sciences, University of Messina, Viale Giovanni Palatucci SNC, 98168 Messina, Italy; (K.M.); (M.R.); (G.P.); (M.L.); (F.A.); (F.A.)
| | - Giuseppe Piccione
- Department of Veterinary Sciences, University of Messina, Viale Giovanni Palatucci SNC, 98168 Messina, Italy; (K.M.); (M.R.); (G.P.); (M.L.); (F.A.); (F.A.)
| | - Marialuisa Aragona
- Department of Veterinary Sciences, University of Messina, Viale Giovanni Palatucci SNC, 98168 Messina, Italy; (K.M.); (M.R.); (G.P.); (M.L.); (F.A.); (F.A.)
| | - Maria Levanti
- Department of Veterinary Sciences, University of Messina, Viale Giovanni Palatucci SNC, 98168 Messina, Italy; (K.M.); (M.R.); (G.P.); (M.L.); (F.A.); (F.A.)
| | - Francesca Aragona
- Department of Veterinary Sciences, University of Messina, Viale Giovanni Palatucci SNC, 98168 Messina, Italy; (K.M.); (M.R.); (G.P.); (M.L.); (F.A.); (F.A.)
| | - Francesca Arfuso
- Department of Veterinary Sciences, University of Messina, Viale Giovanni Palatucci SNC, 98168 Messina, Italy; (K.M.); (M.R.); (G.P.); (M.L.); (F.A.); (F.A.)
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Zilliacus J, Draskau MK, Johansson HKL, Svingen T, Beronius A. Building an adverse outcome pathway network for estrogen-, androgen- and steroidogenesis-mediated reproductive toxicity. FRONTIERS IN TOXICOLOGY 2024; 6:1357717. [PMID: 38601197 PMCID: PMC11005472 DOI: 10.3389/ftox.2024.1357717] [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: 12/18/2023] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
Introduction: Adverse Outcome Pathways (AOPs) can support both testing and assessment of endocrine disruptors (EDs). There is, however, a need for further development of the AOP framework to improve its applicability in a regulatory context. Here we have inventoried the AOP-wiki to identify all existing AOPs related to mammalian reproductive toxicity arising from disruption to the estrogen, androgen, and steroidogenesis modalities. Core key events (KEs) shared between relevant AOPs were also identified to aid in further AOP network (AOPN) development. Methods: A systematic approach using two different methods was applied to screen and search the entire AOP-wiki library. An AOPN was visualized using Cytoscape. Manual refinement was performed to remove AOPS devoid of any KEs and/or KERs. Results: Fifty-eight AOPs relevant for mammalian reproductive toxicity were originally identified, with 42 AOPs included in the final AOPN. Several of the KEs and KE relationships (KERs) described similar events and were thus merged to optimize AOPN construction. Sixteen sub-networks related to effects on hormone levels or hormone activity, cancer outcomes, male and female reproductive systems, and overall effects on fertility and reproduction were identified within the AOPN. Twenty-six KEs and 11 KERs were identified as core blocks of knowledge in the AOPN, of which 19 core KEs are already included as parameters in current OECD and US EPA test guidelines. Discussion: The AOPN highlights knowledge gaps that can be targeted for further development of a more complete AOPN that can support the identification and assessment of EDs.
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Affiliation(s)
- Johanna Zilliacus
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Monica K. Draskau
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Terje Svingen
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Beronius
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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Bernhard A, Poulsen R, Brun Hansen AM, Hansen M. Toxicometabolomics as a tool for next generation environmental risk assessment. EFSA J 2023; 21:e211005. [PMID: 38047121 PMCID: PMC10687767 DOI: 10.2903/j.efsa.2023.e211005] [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] [Indexed: 12/05/2023] Open
Abstract
Traditionally applied methodology in environmental risk assessment (ERA) has fallen out of step with technological advancements and regulatory requirements, challenging effectiveness and accuracy of the assessments. Extensive efforts have been focused towards a transition to a more data-driven and mechanistically-based next generation risk assessment. Metabolomics can produce detailed and comprehensive molecular insight into affected biochemical processes. Combining metabolomics with environmental toxicology can help to understand the mechanisms and/or modes of action underlying toxicity of environmental pollutants and inform adverse outcome pathways, as well as facilitate identification of biomarkers to quantify effects and/or exposure. This Technical Report describes the activities and work performed within the frame of the European Food Risk Assessment Fellowship Programme (EU-FORA), implemented at the section 'Environmental Chemistry and Toxicology' at the Department of Environmental Science at Aarhus University in Denmark with synergies to an ongoing H2020 RIA project 'EndocRine Guideline Optimisation' (ERGO). In accordance with the 'training by doing' principles of the EU-FORA, the fellowship project combined the exploration of the status of scientific discussion on methodology in ERA through literature study with hands-on training, using the metabolomics analysis pipeline established at Aarhus University. For the hands-on training, an amphibian metamorphosis assay (OECD test no.231) was used as a proof-of-concept toxicometabolomics study case. Both a targeted biomarker - and an untargeted metabolomics approach was applied.
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Affiliation(s)
| | - Rikke Poulsen
- Section of Environmental Chemistry and Toxicology, Department of Environmental ScienceAarhus UniversityDenmark
| | - Anna M Brun Hansen
- Section of Environmental Chemistry and Toxicology, Department of Environmental ScienceAarhus UniversityDenmark
| | - Martin Hansen
- Section of Environmental Chemistry and Toxicology, Department of Environmental ScienceAarhus UniversityDenmark
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Vliet SM, Markey KJ, Lynn SG, Adetona A, Fallacara D, Ceger P, Choksi N, Karmaus AL, Watson A, Ewans A, Daniel AB, Hamm J, Vitense K, Wolf KA, Thomas A, LaLone CA. Weight of evidence for cross-species conservation of androgen receptor-based biological activity. Toxicol Sci 2023; 193:131-145. [PMID: 37071731 PMCID: PMC10796108 DOI: 10.1093/toxsci/kfad038] [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: 04/20/2023] Open
Abstract
The U.S. Environmental Protection Agency's Endocrine Disruptor Screening Program (EDSP) is tasked with assessing chemicals for their potential to perturb endocrine pathways, including those controlled by androgen receptor (AR). To address challenges associated with traditional testing strategies, EDSP is considering in vitro high-throughput screening assays to screen and prioritize chemicals more efficiently. The ability of these assays to accurately reflect chemical interactions in nonmammalian species remains uncertain. Therefore, a goal of the EDSP is to evaluate how broadly results can be extrapolated across taxa. To assess the cross-species conservation of AR-modulated pathways, computational analyses and systematic literature review approaches were used to conduct a comprehensive analysis of existing in silico, in vitro, and in vivo data. First, molecular target conservation was assessed across 585 diverse species based on the structural similarity of ARs. These results indicate that ARs are conserved across vertebrates and are predicted to share similarly susceptibility to chemicals that interact with the human AR. Systematic analysis of over 5000 published manuscripts was used to compile in vitro and in vivo cross-species toxicity data. Assessment of in vitro data indicates conservation of responses occurs across vertebrate ARs, with potential differences in sensitivity. Similarly, in vivo data indicate strong conservation of the AR signaling pathways across vertebrate species, although sensitivity may vary. Overall, this study demonstrates a framework for utilizing bioinformatics and existing data to build weight of evidence for cross-species extrapolation and provides a technical basis for extrapolating hAR-based data to prioritize hazard in nonmammalian vertebrate species.
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Affiliation(s)
- Sara M.F. Vliet
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Scientific Computing and Data Curation Division, Duluth, MN, USA
| | - Kristan J. Markey
- U.S. Environmental Protection Agency, Office of Pesticide Programs, Endocrine Disrupter Screening Program, Washington, DC, USA
| | - Scott G. Lynn
- U.S. Environmental Protection Agency, Office of Pesticide Programs, Endocrine Disrupter Screening Program, Washington, DC, USA
| | | | | | | | | | | | | | | | | | | | - Kelsey Vitense
- U.S. Environmental Protection Agency, Office of Research and Development, Center for Computational Toxicology and Exposure, Scientific Computing and Data Curation Division, Duluth, MN, USA
| | | | - Amy Thomas
- Battelle Memorial Institute, Columbus, OH, USA
| | - Carlie A. 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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