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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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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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Jaylet T, Coustillet T, Smith NM, Viviani B, Lindeman B, Vergauwen L, Myhre O, Yarar N, Gostner JM, Monfort-Lanzas P, Jornod F, Holbech H, Coumoul X, Sarigiannis DA, Antczak P, Bal-Price A, Fritsche E, Kuchovska E, Stratidakis AK, Barouki R, Kim MJ, Taboureau O, Wojewodzic MW, Knapen D, Audouze K. Comprehensive mapping of the AOP-Wiki database: identifying biological and disease gaps. FRONTIERS IN TOXICOLOGY 2024; 6:1285768. [PMID: 38523647 PMCID: PMC10958381 DOI: 10.3389/ftox.2024.1285768] [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: 08/30/2023] [Accepted: 02/15/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction: The Adverse Outcome Pathway (AOP) concept facilitates rapid hazard assessment for human health risks. AOPs are constantly evolving, their number is growing, and they are referenced in the AOP-Wiki database, which is supported by the OECD. Here, we present a study that aims at identifying well-defined biological areas, as well as gaps within the AOP-Wiki for future research needs. It does not intend to provide a systematic and comprehensive summary of the available literature on AOPs but summarizes and maps biological knowledge and diseases represented by the already developed AOPs (with OECD endorsed status or under validation). Methods: Knowledge from the AOP-Wiki database were extracted and prepared for analysis using a multi-step procedure. An automatic mapping of the existing information on AOPs (i.e., genes/proteins and diseases) was performed using bioinformatics tools (i.e., overrepresentation analysis using Gene Ontology and DisGeNET), allowing both the classification of AOPs and the development of AOP networks (AOPN). Results: AOPs related to diseases of the genitourinary system, neoplasms and developmental anomalies are the most frequently investigated on the AOP-Wiki. An evaluation of the three priority cases (i.e., immunotoxicity and non-genotoxic carcinogenesis, endocrine and metabolic disruption, and developmental and adult neurotoxicity) of the EU-funded PARC project (Partnership for the Risk Assessment of Chemicals) are presented. These were used to highlight under- and over-represented adverse outcomes and to identify and prioritize gaps for further research. Discussion: These results contribute to a more comprehensive understanding of the adverse effects associated with the molecular events in AOPs, and aid in refining risk assessment for stressors and mitigation strategies. Moreover, the FAIRness (i.e., data which meets principles of findability, accessibility, interoperability, and reusability (FAIR)) of the AOPs appears to be an important consideration for further development.
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Affiliation(s)
- Thomas Jaylet
- Université Paris Cité, Inserm UMR-S 1124 T3S, Paris, France
| | | | - Nicola M. Smith
- Norwegian Institute of Public Health, Division of Climate and Environment, Oslo, Norway
| | - Barbara Viviani
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Birgitte Lindeman
- Norwegian Institute of Public Health, Division of Climate and Environment, Oslo, Norway
| | - Lucia Vergauwen
- Zebrafishlab, Department of Veterinary Sciences, Veterinary Physiology and Biochemistry, University of Antwerp, Wilrijk, Belgium
| | - Oddvar Myhre
- Norwegian Institute of Public Health, Division of Climate and Environment, Oslo, Norway
| | - Nurettin Yarar
- Norwegian Institute of Public Health, Division of Climate and Environment, Oslo, Norway
| | - Johanna M. Gostner
- Institute of Medical Biochemistry, Medical University of Innsbruck, Innsbruck, Austria
| | - Pablo Monfort-Lanzas
- Institute of Medical Biochemistry, Medical University of Innsbruck, Innsbruck, Austria
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Henrik Holbech
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Xavier Coumoul
- Université Paris Cité, Inserm UMR-S 1124 T3S, Paris, France
| | - Dimosthenis A. Sarigiannis
- Environmental Engineering Laboratory, Department of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
- National Hellenic Research Foundation, Athens, Greece
- Science, Technology and Society Department, Environmental Health Engineering, University School for Advanced Studies (IUSS), Pavia, Italy
| | - Philipp Antczak
- Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Anna Bal-Price
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Ellen Fritsche
- IUF-Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
- Heinrich-Heine-University, Düsseldorf, Germany
- Swiss Centre for Applied Human Toxicology, Basel, Switzerland
- DNTOX GmbH, Düsseldorf, Germany
| | - Eliska Kuchovska
- IUF-Leibniz Research Institute for Environmental Medicine, Duesseldorf, Germany
| | - Antonios K. Stratidakis
- Science, Technology and Society Department, Environmental Health Engineering, University School for Advanced Studies (IUSS), Pavia, Italy
| | - Robert Barouki
- Université Paris Cité, Inserm UMR-S 1124 T3S, Paris, France
| | - Min Ji Kim
- Inserm UMR-S 1124, Université Sorbonne Paris Nord, Bobigny, Paris, France
| | - Olivier Taboureau
- Université Paris Cité, BFA, Team CMPLI, Inserm U1133, CNRS UMR 8251, Paris, France
| | - Marcin W. Wojewodzic
- Norwegian Institute of Public Health, Division of Climate and Environment, Oslo, Norway
- Cancer Registry of Norway, NIPH, Oslo, Norway
| | - Dries Knapen
- Zebrafishlab, Department of Veterinary Sciences, Veterinary Physiology and Biochemistry, University of Antwerp, Wilrijk, Belgium
| | - Karine Audouze
- Université Paris Cité, Inserm UMR-S 1124 T3S, Paris, France
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Cui S, Gao Y, Huang Y, Shen L, Zhao Q, Pan Y, Zhuang S. Advances and applications of machine learning and deep learning in environmental ecology and health. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 335:122358. [PMID: 37567408 DOI: 10.1016/j.envpol.2023.122358] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Machine learning (ML) and deep learning (DL) possess excellent advantages in data analysis (e.g., feature extraction, clustering, classification, regression, image recognition and prediction) and risk assessment and management in environmental ecology and health (EEH). Considering the rapid growth and increasing complexity of data in EEH, it is of significance to summarize recent advances and applications of ML and DL in EEH. This review summarized the basic processes and fundamental algorithms of the ML and DL modeling, and indicated the urgent needs of ML and DL in EEH. Recent research hotspots such as environmental ecology and restoration, environmental fate of new pollutants, chemical exposures and risks, chemical hazard identification and control were highlighted. Various applications of ML and DL in EEH demonstrate their versatility and technological revolution, and present some challenges. The perspective of ML and DL in EEH were further outlined to promote the innovative analysis and cultivation of the ML-driven research paradigm.
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Affiliation(s)
- Shixuan Cui
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Yuchen Gao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yizhou Huang
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Lilai Shen
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qiming Zhao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yaru Pan
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shulin Zhuang
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China.
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Wiklund L, Caccia S, Pípal M, Nymark P, Beronius A. Development of a data-driven approach to Adverse Outcome Pathway network generation: a case study on the EATS-modalities. FRONTIERS IN TOXICOLOGY 2023; 5:1183824. [PMID: 37229356 PMCID: PMC10203404 DOI: 10.3389/ftox.2023.1183824] [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: 03/10/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Adverse Outcome Pathways (AOPs) summarize mechanistic understanding of toxicological effects and have, for example, been highlighted as a promising tool to integrate data from novel in vitro and in silico methods into chemical risk assessments. Networks based on AOPs are considered the functional implementation of AOPs, as they are more representative of complex biology. At the same time, there are currently no harmonized approaches to generate AOP networks (AOPNs). Systematic strategies to identify relevant AOPs, and methods to extract and visualize data from the AOP-Wiki, are needed. The aim of this work was to develop a structured search strategy to identify relevant AOPs in the AOP-Wiki, and an automated data-driven workflow to generate AOPNs. The approach was applied on a case study to generate an AOPN focused on the Estrogen, Androgen, Thyroid, and Steroidogenesis (EATS) modalities. A search strategy was developed a priori with search terms based on effect parameters in the ECHA/EFSA Guidance Document on Identification of Endocrine Disruptors. Furthermore, manual curation of the data was performed by screening the contents of each pathway in the AOP-Wiki, excluding irrelevant AOPs. Data were downloaded from the Wiki, and a computational workflow was utilized to automatically process, filter, and format the data for visualization. This study presents an approach to structured searches of AOPs in the AOP-Wiki coupled to an automated data-driven workflow for generating AOPNs. In addition, the case study presented here provides a map of the contents of the AOP-Wiki related to the EATS-modalities, and a basis for further research, for example, on integrating mechanistic data from novel methods and exploring mechanism-based approaches to identify endocrine disruptors (EDs). The computational approach is freely available as an R-script, and currently allows for the (re)-generation and filtering of new AOP networks based on data from the AOP-Wiki and a list of relevant AOPs used for filtering.
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Affiliation(s)
- Linus Wiklund
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sara Caccia
- Università degli Studi di Milano, Milano, Italy
| | - Marek Pípal
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Beronius
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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Hougaard KS, Svingen T. Editorial: Methods and Protocols in Developmental and Reproductive Toxicology. FRONTIERS IN TOXICOLOGY 2022; 4:948103. [PMID: 35936388 PMCID: PMC9346069 DOI: 10.3389/ftox.2022.948103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/20/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Karin Sørig Hougaard
- National Research Center for the Working Environment, Copenhagen, Denmark
- Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Terje Svingen
- National Food Institute, Technical University of Denmark, Kgs. Lyngy, Denmark
- *Correspondence: Terje Svingen,
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Svingen T, Schwartz CL, Rosenmai AK, Ramhøj L, Johansson HKL, Hass U, Draskau MK, Davidsen N, Christiansen S, Ballegaard ASR, Axelstad M. Using alternative test methods to predict endocrine disruption and reproductive adverse outcomes: do we have enough knowledge? ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 304:119242. [PMID: 35378198 DOI: 10.1016/j.envpol.2022.119242] [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: 01/20/2022] [Revised: 03/12/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are a matter of great concern. They are ubiquitous in the environment, are considered harmful to humans and wildlife, yet remain challenging to identify based on current international test guidelines and regulatory frameworks. For a compound to be identified as an EDC within the EU regulatory system, a plausible link between an endocrine mode-of-action and an adverse effect outcome in an intact organism must be established. This requires in-depth knowledge about molecular pathways regulating normal development and function in animals and humans in order to elucidate causes for disease. Although our knowledge about the role of the endocrine system in animal development and function is substantial, it remains challenging to predict endocrine-related disease outcomes in intact animals based on non-animal test data. A main reason for this is that our knowledge about mechanism-of-action are still lacking for essential causal components, coupled with the sizeable challenge of mimicking the complex multi-organ endocrine system by methodological reductionism. Herein, we highlight this challenge by drawing examples from male reproductive toxicity, which is an area that has been at the forefront of EDC research since its inception. We discuss the importance of increased focus on characterizing mechanism-of-action for EDC-induced adverse health effects. This is so we can design more robust and reliable testing strategies using non-animal test methods for predictive toxicology; both to improve chemical risk assessment in general, but also to allow for considerable reduction and replacement of animal experiments in chemicals testing of the 21st Century.
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Affiliation(s)
- Terje Svingen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark.
| | | | | | - Louise Ramhøj
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | | | - Ulla Hass
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Monica Kam Draskau
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Nichlas Davidsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Sofie Christiansen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | | | - Marta Axelstad
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
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