1
|
Martens M, Stierum R, Schymanski EL, Evelo CT, Aalizadeh R, Aladjov H, Arturi K, Audouze K, Babica P, Berka K, Bessems J, Blaha L, Bolton EE, Cases M, Damalas DΕ, Dave K, Dilger M, Exner T, Geerke DP, Grafström R, Gray A, Hancock JM, Hollert H, Jeliazkova N, Jennen D, Jourdan F, Kahlem P, Klanova J, Kleinjans J, Kondic T, Kone B, Lynch I, Maran U, Martinez Cuesta S, Ménager H, Neumann S, Nymark P, Oberacher H, Ramirez N, Remy S, Rocca-Serra P, Salek RM, Sallach B, Sansone SA, Sanz F, Sarimveis H, Sarntivijai S, Schulze T, Slobodnik J, Spjuth O, Tedds J, Thomaidis N, Weber RJ, van Westen GJ, Wheelock CE, Williams AJ, Witters H, Zdrazil B, Županič A, Willighagen EL. ELIXIR and Toxicology: a community in development. F1000Res 2023; 10:ELIXIR-1129. [PMID: 37842337 PMCID: PMC10568213 DOI: 10.12688/f1000research.74502.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-specific predictive models. Traditionally, toxicology has strong links with other fields such as biology, chemistry, pharmacology and medicine. With the rise of synthetic and new engineered materials, alongside ongoing prioritisation needs in chemical risk assessment for existing chemicals, early predictive evaluations are becoming of utmost importance to both scientific and regulatory purposes. ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. To coordinate the linkage of various life science efforts around modern predictive toxicology, the establishment of a new ELIXIR Community is seen as instrumental. In the past few years, joint efforts, building on incidental overlap, have been piloted in the context of ELIXIR. For example, the EU-ToxRisk, diXa, HeCaToS, transQST, and the nanotoxicology community have worked with the ELIXIR TeSS, Bioschemas, and Compute Platforms and activities. In 2018, a core group of interested parties wrote a proposal, outlining a sketch of what this new ELIXIR Toxicology Community would look like. A recent workshop (held September 30th to October 1st, 2020) extended this into an ELIXIR Toxicology roadmap and a shortlist of limited investment-high gain collaborations to give body to this new community. This Whitepaper outlines the results of these efforts and defines our vision of the ELIXIR Toxicology Community and how it complements other ELIXIR activities.
Collapse
Affiliation(s)
- Marvin Martens
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
| | - Rob Stierum
- Risk Analysis for Products In Development (RAPID), Netherlands Organisation for applied scientific research TNO, Utrecht, 3584 CB, The Netherlands
| | - Emma L. Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, 6229 EN, The Netherlands
| | - Reza Aalizadeh
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Hristo Aladjov
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
| | - Kasia Arturi
- Department Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, 8600, Switzerland
| | | | - Pavel Babica
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Karel Berka
- Department of Physical Chemistry, Palacky University Olomouc, Olomouc, 77146, Czech Republic
| | | | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Evan E. Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Dimitrios Ε. Damalas
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Kirtan Dave
- School of Science, GSFC University, Gujarat, 391750, India
| | - Marco Dilger
- Forschungs- und Beratungsinstitut Gefahrstoffe (FoBiG) GmbH, Freiburg im Breisgau, 79106, Germany
| | | | - Daan P. Geerke
- AIMMS Division of Molecular Toxicology, Vrije Universiteit, Amsterdam, 1081 HZ, The Netherlands
| | - Roland Grafström
- Department of Toxicology, Misvik Biology, Turku, 20520, Finland
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, 17177, Sweden
| | - Alasdair Gray
- Department of Computer Science, Heriot-Watt University, Edinburgh, UK
| | | | - Henner Hollert
- Department Evolutionary Ecology & Environmental Toxicology (E3T), Goethe-University, Frankfurt, D-60438, Germany
| | | | - Danyel Jennen
- Department of Toxicogenomics, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Fabien Jourdan
- MetaboHUB, French metabolomics infrastructure in Metabolomics and Fluxomics, Toulouse, France
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, Toulouse, France
| | - Pascal Kahlem
- Scientific Network Management SL, Barcelona, 08015, Spain
| | - Jana Klanova
- RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Todor Kondic
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Boï Kone
- Faculty of Pharmacy, Malaria Research and Training Center, Bamako, BP:1805, Mali
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Tartu, 50411, Estonia
| | | | - Hervé Ménager
- Institut Français de Bioinformatique, Evry, F-91000, France
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, F-75015, France
| | - Steffen Neumann
- Research group Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Halle, 06120, Germany
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, 17177, Sweden
| | - Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Medical University of Innsbruck, Innsbruck, A-6020, Austria
| | - Noelia Ramirez
- Institut d'Investigacio Sanitaria Pere Virgili-Universitat Rovira i Virgili, Tarragona, 43007, Spain
| | | | - Philippe Rocca-Serra
- Data Readiness Group, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Reza M. Salek
- International Agency for Research on Cancer, World Health Organisation, Lyon, 69372, France
| | - Brett Sallach
- Department of Environment and Geography, University of York, UK, York, YO10 5NG, UK
| | | | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, 08003, Spain
| | | | | | - Tobias Schulze
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, 04318, Germany
| | | | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Uppsala, SE-75124, Sweden
| | - Jonathan Tedds
- ELIXIR Hub, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Nikolaos Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece
| | - Ralf J.M. Weber
- School of Biosciences, University of Birmingham, UK, Birmingham, B15 2TT, UK
| | - Gerard J.P. van Westen
- Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research, Leiden, 2333 CC, The Netherlands
| | - Craig E. Wheelock
- Department of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm SE-141-86, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Antony J. Williams
- Center for Computational Toxicology and Exposure, United States Environmental Protection Agency, Research Triangle Park, NC 27711, USA
| | | | - Barbara Zdrazil
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, 1090, Austria
| | - Anže Županič
- Department Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Egon L. Willighagen
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, 6229 ER, The Netherlands
| |
Collapse
|
2
|
Tan H, Gao P, Luo Y, Gou X, Xia P, Wang P, Yan L, Zhang S, Guo J, Zhang X, Yu H, Shi W. Are New Phthalate Ester Substitutes Safer than Traditional DBP and DiBP? Comparative Endocrine-Disrupting Analyses on Zebrafish Using In Vivo, Transcriptome, and In Silico Approaches. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13744-13756. [PMID: 37677100 DOI: 10.1021/acs.est.3c03282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Although previous studies have confirmed the association between phthalate esters (PAEs) exposure and endocrine disorders in humans, few studies to date have systematically assessed the threats of new PAE alternatives to endocrine disruptions. Herein, zebrafish embryos were continuously exposed to two PAEs [di-n-butyl phthalate (DBP) and diisobutyl phthalate (DiBP)], two structurally related alternatives [diiononyl phthalate (DINP) and diisononyl hexahydrophthalate (DINCH)], and two non-PAE substitutes [dipropylene glycol dibenzoate (DGD) and glyceryl triacetate (GTA)], and the endocrine-disrupting effects were investigated during the early stages (8-48 hpf). For five endogenous hormones, including progesterone, testosterone, 17β-estradiol, triiodothyronine (T3), and cortisol, the tested chemicals disturbed the contents of at least one hormone at environmentally relevant concentrations (≤3.9 μM), except DINCH and GTA. Then, the concentration-dependent reduced zebrafish transcriptome analysis was performed. Thyroid hormone (TH)- and androgen/estrogen-regulated adverse outcome pathways (AOPs) were the two types of biological pathways most sensitive to PAE exposure. Notably, six compounds disrupted four TH-mediated AOPs, from the inhibition of deiodinases (molecular initiating event, MIE), a decrease in T3 levels (key event, KE), to mortality (adverse outcome, AO) with the quantitatively linear relationships between MIE-KE (|r| = 0.96, p = 0.002), KE-AO (|r| = 0.88, p = 0.02), and MIE-AO (|r| = 0.89, p = 0.02). Multiple structural analyses showed that benzoic acid is the critical toxicogenic fragment. Our data will facilitate the screening and development of green alternatives.
Collapse
Affiliation(s)
- Haoyue Tan
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
- Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Pan Gao
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Yiwen Luo
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Xiao Gou
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Pu Xia
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Pingping Wang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Lu Yan
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Shaoqing Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Jing Guo
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
- Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
- Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
- Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| | - Wei Shi
- State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing 210023, Jiangsu, China
- Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, Jiangsu, China
| |
Collapse
|
3
|
Saarimäki LA, Fratello M, Pavel A, Korpilähde S, Leppänen J, Serra A, Greco D. A curated gene and biological system annotation of adverse outcome pathways related to human health. Sci Data 2023; 10:409. [PMID: 37355733 PMCID: PMC10290716 DOI: 10.1038/s41597-023-02321-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/20/2023] [Indexed: 06/26/2023] Open
Abstract
Adverse outcome pathways (AOPs) are emerging as a central framework in modern toxicology and other fields in biomedicine. They serve as an extension of pathway-based concepts by depicting biological mechanisms as causally linked sequences of key events (KEs) from a molecular initiating event (MIE) to an adverse outcome. AOPs guide the use and development of new approach methodologies (NAMs) aimed at reducing animal experimentation. While AOPs model the systemic mechanisms at various levels of biological organisation, toxicogenomics provides the means to study the molecular mechanisms of chemical exposures. Systematic integration of these two concepts would improve the application of AOP-based knowledge while also supporting the interpretation of complex omics data. Hence, we established this link through rigorous curation of molecular annotations for the KEs of human relevant AOPs. We further expanded and consolidated the annotations of the biological context of KEs. These curated annotations pave the way to embed AOPs in molecular data interpretation, facilitating the emergence of new knowledge in biomedicine.
Collapse
Affiliation(s)
- Laura Aliisa Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Michele Fratello
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alisa Pavel
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Seela Korpilähde
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jenni Leppänen
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Angela Serra
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
- Institute for Advanced Study, Tampere University, Tampere, Finland
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
4
|
Gou X, Ma C, Ji H, Yan L, Wang P, Wang Z, Lin Y, Chatterjee N, Yu H, Zhang X. Prediction of zebrafish embryonic developmental toxicity by integrating omics with adverse outcome pathway. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130958. [PMID: 36860045 DOI: 10.1016/j.jhazmat.2023.130958] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/09/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
New approach methodologies (NAMs), especially omics-based high-throughput bioassays have been developed rapidly, providing rich mechanistic information such as molecular initiation events (MIEs) and (sub)cellular key events (KEs) in adverse outcome pathways (AOPs). However, how to apply the knowledge of MIEs/KEs to predict adverse outcomes (AOs) induced by chemicals represents a new challenge for computational toxicology. Here, an integrated method named ScoreAOP was developed and evaluated to predict chemicals' developmental toxicity for zebrafish embryos by integrating four related AOPs and dose-dependent reduced zebrafish transcriptome (RZT). The rules of ScoreAOP included 1) sensitivity of responsive KEs demonstrated by point of departure of KEs (PODKE), 2) evidence reliability and 3) distance between KEs and AOs. Moreover, eleven chemicals with different modes of action (MoAs) were tested to evaluate ScoreAOP. Results showed that eight of the eleven chemicals caused developmental toxicity at tested concentration in apical tests. All the tested chemicals' developmental defects were predicted using ScoreAOP, whereas eight out of the eleven chemicals predicted by ScoreMIE which was developed to score MIEs disturbed by chemicals based on in vitro bioassays data. Finally, in terms of mechanism explanation, ScoreAOP clustered chemicals with different MoAs while ScoreMIE failed, and ScoreAOP revealed the activation of aryl hydrocarbon receptor (AhR) plays a significant role in dysfunction of cardiovascular system, resulting in zebrafish developmental defects and mortality. In conclusion, ScoreAOP represents a promising approach to apply mechanism information obtained from omics to predict AOs induced by chemicals.
Collapse
Affiliation(s)
- Xiao Gou
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Cong Ma
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Huimin Ji
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Lu Yan
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Pingping Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Zhihao Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Yishan Lin
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Nivedita Chatterjee
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing 210023, China.
| |
Collapse
|
5
|
Keshavan S, Bannuscher A, Drasler B, Barosova H, Petri-Fink A, Rothen-Rutishauser B. Comparing species-different responses in pulmonary fibrosis research: Current understanding of in vitro lung cell models and nanomaterials. Eur J Pharm Sci 2023; 183:106387. [PMID: 36652970 DOI: 10.1016/j.ejps.2023.106387] [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: 08/12/2022] [Revised: 12/16/2022] [Accepted: 01/14/2023] [Indexed: 01/16/2023]
Abstract
Pulmonary fibrosis (PF) is a chronic, irreversible lung disease that is typically fatal and characterized by an abnormal fibrotic response. As a result, vast areas of the lungs are gradually affected, and gas exchange is impaired, making it one of the world's leading causes of death. This can be attributed to a lack of understanding of the onset and progression of the disease, as well as a poor understanding of the mechanism of adverse responses to various factors, such as exposure to allergens, nanomaterials, environmental pollutants, etc. So far, the most frequently used preclinical evaluation paradigm for PF is still animal testing. Nonetheless, there is an urgent need to understand the factors that induce PF and find novel therapeutic targets for PF in humans. In this regard, robust and realistic in vitro fibrosis models are required to understand the mechanism of adverse responses. Over the years, several in vitro and ex vivo models have been developed with the goal of mimicking the biological barriers of the lung as closely as possible. This review summarizes recent progress towards the development of experimental models suitable for predicting fibrotic responses, with an emphasis on cell culture methods, nanomaterials, and a comparison of results from studies using cells from various species.
Collapse
Affiliation(s)
- Sandeep Keshavan
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, Fribourg CH-1700, Switzerland
| | - Anne Bannuscher
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, Fribourg CH-1700, Switzerland
| | - Barbara Drasler
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, Fribourg CH-1700, Switzerland
| | - Hana Barosova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, Prague 14220, Czech Republic
| | - Alke Petri-Fink
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, Fribourg CH-1700, Switzerland; Chemistry Department, University of Fribourg, Chemin du Musée 9, Fribourg 1700, Switzerland
| | | |
Collapse
|
6
|
Saarimäki LA, Morikka J, Pavel A, Korpilähde S, del Giudice G, Federico A, Fratello M, Serra A, Greco D. Toxicogenomics Data for Chemical Safety Assessment and Development of New Approach Methodologies: An Adverse Outcome Pathway-Based Approach. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203984. [PMID: 36479815 PMCID: PMC9839874 DOI: 10.1002/advs.202203984] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/09/2022] [Indexed: 05/25/2023]
Abstract
Mechanistic toxicology provides a powerful approach to inform on the safety of chemicals and the development of safe-by-design compounds. Although toxicogenomics supports mechanistic evaluation of chemical exposures, its implementation into the regulatory framework is hindered by uncertainties in the analysis and interpretation of such data. The use of mechanistic evidence through the adverse outcome pathway (AOP) concept is promoted for the development of new approach methodologies (NAMs) that can reduce animal experimentation. However, to unleash the full potential of AOPs and build confidence into toxicogenomics, robust associations between AOPs and patterns of molecular alteration need to be established. Systematic curation of molecular events to AOPs will create the much-needed link between toxicogenomics and systemic mechanisms depicted by the AOPs. This, in turn, will introduce novel ways of benefitting from the AOPs, including predictive models and targeted assays, while also reducing the need for multiple testing strategies. Hence, a multi-step strategy to annotate AOPs is developed, and the resulting associations are applied to successfully highlight relevant adverse outcomes for chemical exposures with strong in vitro and in vivo convergence, supporting chemical grouping and other data-driven approaches. Finally, a panel of AOP-derived in vitro biomarkers for pulmonary fibrosis (PF) is identified and experimentally validated.
Collapse
Affiliation(s)
- Laura Aliisa Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Jack Morikka
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Alisa Pavel
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Seela Korpilähde
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Giusy del Giudice
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Antonio Federico
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Michele Fratello
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
| | - Angela Serra
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
- Tampere Institute for Advanced StudyTampere UniversityKalevantie 4Tampere33100Finland
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)Faculty of Medicine and Health TechnologyTampere UniversityArvo Ylpön katu 34Tampere33520Finland
- Institute of BiotechnologyUniversity of HelsinkiP.O.Box 56HelsinkiUusimaa00014Finland
| |
Collapse
|
7
|
Martens M, Kreidl F, Ehrhart F, Jean D, Mei M, Mortensen HM, Nash A, Nymark P, Evelo CT, Cerciello F. A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. Front Oncol 2022; 12:849640. [PMID: 35558518 PMCID: PMC9088009 DOI: 10.3389/fonc.2022.849640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/29/2022] [Indexed: 12/28/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a highly aggressive malignancy mainly triggered by exposure to asbestos and characterized by complex biology. A significant body of knowledge has been generated over the decades by the research community which has improved our understanding of the disease toward prevention, diagnostic opportunities and new treatments. Omics technologies are opening for additional levels of information and hypotheses. Given the growing complexity and technological spread of biological knowledge in MPM, there is an increasing need for an integrating tool that may allow scientists to access the information and analyze data in a simple and interactive way. We envisioned that a platform to capture this widespread and fast-growing body of knowledge in a machine-readable and simple visual format together with tools for automated large-scale data analysis could be an important support for the work of the general scientist in MPM and for the community to share, critically discuss, distribute and eventually advance scientific results. Toward this goal, with the support of experts in the field and informed by existing literature, we have developed the first version of a molecular pathway model of MPM in the biological pathway database WikiPathways. This provides a visual and interactive overview of interactions and connections between the most central genes, proteins and molecular pathways known to be involved or altered in MPM. Currently, 455 unique genes and 247 interactions are included, derived after stringent manual curation of an initial 39 literature references. The pathway model provides a directly employable research tool with links to common databases and repositories for the exploration and the analysis of omics data. The resource is publicly available in the WikiPathways database (Wikipathways : WP5087) and continues to be under development and curation by the community, enabling the scientists in MPM to actively participate in the prioritization of shared biological knowledge.
Collapse
Affiliation(s)
- Marvin Martens
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Franziska Kreidl
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.,Department of Bioinformatics - BiGCaT, MHeNs, Maastricht University, Maastricht, Netherlands
| | - Didier Jean
- Centre de Recherche des Cordeliers, Inserm, Sorbonne Université, Université de Paris, Functional Genomics of Solid Tumors, Paris, France
| | - Merlin Mei
- Oak Ridge Associated Universities, Research Triangle Park, Durham, NC, United States.,Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Holly M Mortensen
- Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, Durham, NC, United States
| | - Alistair Nash
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, WA, Australia
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Chris T Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands.,Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
| | - Ferdinando Cerciello
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| |
Collapse
|
8
|
Alijagic A, Engwall M, Särndahl E, Karlsson H, Hedbrant A, Andersson L, Karlsson P, Dalemo M, Scherbak N, Färnlund K, Larsson M, Persson A. Particle Safety Assessment in Additive Manufacturing: From Exposure Risks to Advanced Toxicology Testing. FRONTIERS IN TOXICOLOGY 2022; 4:836447. [PMID: 35548681 PMCID: PMC9081788 DOI: 10.3389/ftox.2022.836447] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Additive manufacturing (AM) or industrial three-dimensional (3D) printing drives a new spectrum of design and production possibilities; pushing the boundaries both in the application by production of sophisticated products as well as the development of next-generation materials. AM technologies apply a diversity of feedstocks, including plastic, metallic, and ceramic particle powders with distinct size, shape, and surface chemistry. In addition, powders are often reused, which may change the particles’ physicochemical properties and by that alter their toxic potential. The AM production technology commonly relies on a laser or electron beam to selectively melt or sinter particle powders. Large energy input on feedstock powders generates several byproducts, including varying amounts of virgin microparticles, nanoparticles, spatter, and volatile chemicals that are emitted in the working environment; throughout the production and processing phases. The micro and nanoscale size may enable particles to interact with and to cross biological barriers, which could, in turn, give rise to unexpected adverse outcomes, including inflammation, oxidative stress, activation of signaling pathways, genotoxicity, and carcinogenicity. Another important aspect of AM-associated risks is emission/leakage of mono- and oligomers due to polymer breakdown and high temperature transformation of chemicals from polymeric particles, both during production, use, and in vivo, including in target cells. These chemicals are potential inducers of direct toxicity, genotoxicity, and endocrine disruption. Nevertheless, understanding whether AM particle powders and their byproducts may exert adverse effects in humans is largely lacking and urges comprehensive safety assessment across the entire AM lifecycle—spanning from virgin and reused to airborne particles. Therefore, this review will detail: 1) brief overview of the AM feedstock powders, impact of reuse on particle physicochemical properties, main exposure pathways and protective measures in AM industry, 2) role of particle biological identity and key toxicological endpoints in the particle safety assessment, and 3) next-generation toxicology approaches in nanosafety for safety assessment in AM. Altogether, the proposed testing approach will enable a deeper understanding of existing and emerging particle and chemical safety challenges and provide a strategy for the development of cutting-edge methodologies for hazard identification and risk assessment in the AM industry.
Collapse
Affiliation(s)
- Andi Alijagic
- Man-Technology-Environment Research Center (MTM), Örebro University, Örebro, Sweden
- Inflammatory Response and Infection Susceptibility Centre (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- *Correspondence: Andi Alijagic,
| | - Magnus Engwall
- Man-Technology-Environment Research Center (MTM), Örebro University, Örebro, Sweden
| | - Eva Särndahl
- Inflammatory Response and Infection Susceptibility Centre (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Helen Karlsson
- Department of Health, Medicine and Caring Sciences, Occupational and Environmental Medicine Center in Linköping, Linköping University, Linköping, Sweden
| | - Alexander Hedbrant
- Inflammatory Response and Infection Susceptibility Centre (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Lena Andersson
- Inflammatory Response and Infection Susceptibility Centre (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Occupational and Environmental Medicine, Örebro University, Örebro, Sweden
| | - Patrik Karlsson
- Department of Mechanical Engineering, Örebro University, Örebro, Sweden
| | | | - Nikolai Scherbak
- Man-Technology-Environment Research Center (MTM), Örebro University, Örebro, Sweden
| | | | - Maria Larsson
- Man-Technology-Environment Research Center (MTM), Örebro University, Örebro, Sweden
| | - Alexander Persson
- Inflammatory Response and Infection Susceptibility Centre (iRiSC), Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| |
Collapse
|
9
|
Tirumala MG, Anchi P, Raja S, Rachamalla M, Godugu C. Novel Methods and Approaches for Safety Evaluation of Nanoparticle Formulations: A Focus Towards In Vitro Models and Adverse Outcome Pathways. Front Pharmacol 2021; 12:612659. [PMID: 34566630 PMCID: PMC8458898 DOI: 10.3389/fphar.2021.612659] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 08/05/2021] [Indexed: 12/18/2022] Open
Abstract
Nanotoxicology is an emerging field employed in the assessment of unintentional hazardous effects produced by nanoparticles (NPs) impacting human health and the environment. The nanotoxicity affects the range between induction of cellular stress and cytotoxicity. The reasons so far reported for these toxicological effects are due to their variable sizes with high surface areas, shape, charge, and physicochemical properties, which upon interaction with the biological components may influence their functioning and result in adverse outcomes (AO). Thus, understanding the risk produced by these materials now is an important safety concern for the development of nanotechnology and nanomedicine. Since the time nanotoxicology has evolved, the methods employed have been majorly relied on in vitro cell-based evaluations, while these simple methods may not predict the complexity involved in preclinical and clinical conditions concerning pharmacokinetics, organ toxicity, and toxicities evidenced through multiple cellular levels. The safety profiles of nanoscale nanomaterials and nanoformulations in the delivery of drugs and therapeutic applications are of considerable concern. In addition, the safety assessment for new nanomedicine formulas lacks regulatory standards. Though the in vivo studies are greatly needed, the end parameters used for risk assessment are not predicting the possible toxic effects produced by various nanoformulations. On the other side, due to increased restrictions on animal usage and demand for the need for high-throughput assays, there is a need for developing and exploring novel methods to evaluate NPs safety concerns. The progress made in molecular biology and the availability of several modern techniques may offer novel and innovative methods to evaluate the toxicological behavior of different NPs by using single cells, cell population, and whole organisms. This review highlights the recent novel methods developed for the evaluation of the safety impacts of NPs and attempts to solve the problems that come with risk assessment. The relevance of investigating adverse outcome pathways (AOPs) in nanotoxicology has been stressed in particular.
Collapse
Affiliation(s)
- Mounika Gayathri Tirumala
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Pratibha Anchi
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Susmitha Raja
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| | - Mahesh Rachamalla
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Chandraiah Godugu
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, India
| |
Collapse
|
10
|
More S, Bampidis V, Benford D, Bragard C, Halldorsson T, Hernández‐Jerez A, Hougaard Bennekou S, Koutsoumanis K, Lambré C, Machera K, Naegeli H, Nielsen S, Schlatter J, Schrenk D, Silano (deceased) V, Turck D, Younes M, Castenmiller J, Chaudhry Q, Cubadda F, Franz R, Gott D, Mast J, Mortensen A, Oomen AG, Weigel S, Barthelemy E, Rincon A, Tarazona J, Schoonjans R. Guidance on risk assessment of nanomaterials to be applied in the food and feed chain: human and animal health. EFSA J 2021; 19:e06768. [PMID: 34377190 PMCID: PMC8331059 DOI: 10.2903/j.efsa.2021.6768] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2021] [Indexed: 02/08/2023] Open
Abstract
The EFSA has updated the Guidance on risk assessment of the application of nanoscience and nanotechnologies in the food and feed chain, human and animal health. It covers the application areas within EFSA's remit, including novel foods, food contact materials, food/feed additives and pesticides. The updated guidance, now Scientific Committee Guidance on nano risk assessment (SC Guidance on Nano-RA), has taken account of relevant scientific studies that provide insights to physico-chemical properties, exposure assessment and hazard characterisation of nanomaterials and areas of applicability. Together with the accompanying Guidance on Technical requirements for regulated food and feed product applications to establish the presence of small particles including nanoparticles (Guidance on Particle-TR), the SC Guidance on Nano-RA specifically elaborates on physico-chemical characterisation, key parameters that should be measured, methods and techniques that can be used for characterisation of nanomaterials and their determination in complex matrices. The SC Guidance on Nano-RA also details aspects relating to exposure assessment and hazard identification and characterisation. In particular, nanospecific considerations relating to in vitro/in vivo toxicological studies are discussed and a tiered framework for toxicological testing is outlined. Furthermore, in vitro degradation, toxicokinetics, genotoxicity, local and systemic toxicity as well as general issues relating to testing of nanomaterials are described. Depending on the initial tier results, additional studies may be needed to investigate reproductive and developmental toxicity, chronic toxicity and carcinogenicity, immunotoxicity and allergenicity, neurotoxicity, effects on gut microbiome and endocrine activity. The possible use of read-across to fill data gaps as well as the potential use of integrated testing strategies and the knowledge of modes or mechanisms of action are also discussed. The Guidance proposes approaches to risk characterisation and uncertainty analysis.
Collapse
|
11
|
Xia P, Peng Y, Fang W, Tian M, Shen Y, Ma C, Crump D, O'Brien JM, Shi W, Zhang X. Cross-Model Comparison of Transcriptomic Dose-Response of Short-Chain Chlorinated Paraffins. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8149-8158. [PMID: 34038106 DOI: 10.1021/acs.est.1c00975] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Short-chain chlorinated paraffins (SCCPs) have attracted attention because of their toxicological potential in humans and wildlife at environmentally relevant doses. However, limited information is available regarding mechanistic differences across species in terms of the biological pathways that are impacted by SCCP exposure. Here, a concentration-dependent reduced human transcriptome (RHT) approach was conducted to evaluate 15 SCCPs in HepG2 cells and compared with our previous results using a reduced zebrafish transcriptome (RZT) approach in zebrafish embryos (ZFEs). Generally, SCCPs induced a broader suite of biological pathways in ZFEs than HepG2 cells, and all of the 15 SCCPs were more potent in HepG2 cells compared to ZFEs. Despite these general differences, the transcriptional potency of SCCPs in both model systems showed a significant linear relationship (p = 0.0017, r2 = 0.57), and the average ratios of transcriptional potency for each SCCP in RZT to that in RHT were ∼100,000. C10H14Cl8 was the most potent SCCP, while C10H17Cl5 was the least potent in both ZFEs and HepG2 cells. An adverse outcome pathway network-based analysis demonstrated model-specific responses, such as xenobiotic metabolism that may be mediated by different nuclear receptor-mediated pathways between HepG2 cells (e.g., CAR and AhR activation) and ZFEs (e.g., PXR activation). Moreover, induced transcriptional changes in ZFEs associated with pathways and molecular initiating events (e.g., activation of nicotinic acetylcholine receptor) suggest that SCCPs may disrupt neural development processes. The cross-model comparison of concentration-dependent transcriptomics represents a promising approach to assess and prioritize SCCPs.
Collapse
Affiliation(s)
- Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
- National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario K1A 0H3, Canada
- Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Ying Peng
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
| | - Wendi Fang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
| | - Mingming Tian
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
| | - Yanhong Shen
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
| | - Cong Ma
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
| | - Doug Crump
- National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario K1A 0H3, Canada
| | - Jason M O'Brien
- National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario K1A 0H3, Canada
| | - Wei Shi
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, P. R. China
| |
Collapse
|
12
|
Nymark P, Sachana M, Leite SB, Sund J, Krebs CE, Sullivan K, Edwards S, Viviani L, Willett C, Landesmann B, Wittwehr C. Systematic Organization of COVID-19 Data Supported by the Adverse Outcome Pathway Framework. Front Public Health 2021; 9:638605. [PMID: 34095051 PMCID: PMC8170012 DOI: 10.3389/fpubh.2021.638605] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/19/2021] [Indexed: 12/18/2022] Open
Abstract
Adverse Outcome Pathways (AOP) provide structured frameworks for the systematic organization of research data and knowledge. The AOP framework follows a set of key principles that allow for broad application across diverse disciplines related to human health, including toxicology, pharmacology, virology and medical research. The COVID-19 pandemic engages a great number of scientists world-wide and data is increasing with exponential speed. Diligent data management strategies are employed but approaches for systematically organizing the data-derived information and knowledge are lacking. We believe AOPs can play an important role in improving interpretation and efficient application of scientific understanding of COVID-19. Here, we outline a newly initiated effort, the CIAO project (https://www.ciao-covid.net/), to streamline collaboration between scientists across the world toward development of AOPs for COVID-19, and describe the overarching aims of the effort, as well as the expected outcomes and research support that they will provide.
Collapse
Affiliation(s)
- Penny Nymark
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Magdalini Sachana
- Environment Health and Safety Division, Environment Directorate, Organisation for Economic Cooperation and Development, Paris, France
| | | | - Jukka Sund
- European Commission, Joint Research Centre, Ispra, Italy
| | - Catharine E. Krebs
- Physicians Committee for Responsible Medicine, Washington, DC, United States
| | - Kristie Sullivan
- Physicians Committee for Responsible Medicine, Washington, DC, United States
| | - Stephen Edwards
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, United States
| | - Laura Viviani
- Humane Society International, Washington, DC, United States
| | | | | | | |
Collapse
|
13
|
Nymark P, Karlsson HL, Halappanavar S, Vogel U. Adverse Outcome Pathway Development for Assessment of Lung Carcinogenicity by Nanoparticles. FRONTIERS IN TOXICOLOGY 2021; 3:653386. [PMID: 35295099 PMCID: PMC8915843 DOI: 10.3389/ftox.2021.653386] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022] Open
Abstract
Lung cancer, one of the most common and deadly forms of cancer, is in some cases associated with exposure to certain types of particles. With the rise of nanotechnology, there is concern that some engineered nanoparticles may be among such particles. In the absence of epidemiological evidence, assessment of nanoparticle carcinogenicity is currently performed on a time-consuming case-by-case basis, relying mainly on animal experiments. Non-animal alternatives exist, including a few validated cell-based methods accepted for regulatory risk assessment of nanoparticles. Furthermore, new approach methodologies (NAMs), focused on carcinogenic mechanisms and capable of handling the increasing numbers of nanoparticles, have been developed. However, such alternative methods are mainly applied as weight-of-evidence linked to generally required animal data, since challenges remain regarding interpretation of the results. These challenges may be more easily overcome by the novel Adverse Outcome Pathway (AOP) framework, which provides a basis for validation and uptake of alternative mechanism-focused methods in risk assessment. Here, we propose an AOP for lung cancer induced by nanosized foreign matter, anchored to a selection of 18 standardized methods and NAMs for in silico- and in vitro-based integrated assessment of lung carcinogenicity. The potential for further refinement of the AOP and its components is discussed in relation to available nanosafety knowledge and data. Overall, this perspective provides a basis for development of AOP-aligned alternative methods-based integrated testing strategies for assessment of nanoparticle-induced lung cancer.
Collapse
Affiliation(s)
- Penny Nymark
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
- *Correspondence: Penny Nymark
| | - Hanna L. Karlsson
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen, Denmark
- DTU Health Tech, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
14
|
Halappanavar S, Nymark P, Krug HF, Clift MJD, Rothen-Rutishauser B, Vogel U. Non-Animal Strategies for Toxicity Assessment of Nanoscale Materials: Role of Adverse Outcome Pathways in the Selection of Endpoints. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007628. [PMID: 33559363 DOI: 10.1002/smll.202007628] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Faster, cheaper, sensitive, and mechanisms-based animal alternatives are needed to address the safety assessment needs of the growing number of nanomaterials (NM) and their sophisticated property variants. Specifically, strategies that help identify and prioritize alternative schemes involving individual test models, toxicity endpoints, and assays for the assessment of adverse outcomes, as well as strategies that enable validation and refinement of these schemes for the regulatory acceptance are needed. In this review, two strategies 1) the current nanotoxicology literature review and 2) the adverse outcome pathways (AOPs) framework, a systematic process that allows the assembly of available mechanistic information concerning a toxicological response in a simple modular format, are presented. The review highlights 1) the most frequently assessed and reported ad hoc in vivo and in vitro toxicity measurements in the literature, 2) various AOPs of relevance to inhalation toxicity of NM that are presently under development, and 3) their applicability in identifying key events of toxicity for targeted in vitro assay development. Finally, using an existing AOP for lung fibrosis, the specific combinations of cell types, exposure and test systems, and assays that are experimentally supported and thus, can be used for assessing NM-induced lung fibrosis, are proposed.
Collapse
Affiliation(s)
- Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, K1A0K9, Canada
- Department of Biology, University of Ottawa, Ottawa, K1N6N5, Canada
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institute, Nobels väg 13, Stockholm, 17177, Sweden
| | - Harald F Krug
- NanoCASE GmbH, St. Gallerstr. 58, Engelburg, 9032, Switzerland
| | - Martin J D Clift
- Institute of Life Science, Swansea University Medical School, Swansea University, Singleton Park, Swansea, Wales, SA2 8PP, UK
| | | | - Ulla Vogel
- National Research Centre for the Working Environment, Lersø Parkallé 105, Copenhagen, DK-2100, Denmark
- DTU Health Tech, Technical University of Denmark, Lyngby, DK-2800 Kgs., Denmark
| |
Collapse
|
15
|
Saarimäki LA, Federico A, Lynch I, Papadiamantis AG, Tsoumanis A, Melagraki G, Afantitis A, Serra A, Greco D. Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials. Sci Data 2021; 8:49. [PMID: 33558569 PMCID: PMC7870661 DOI: 10.1038/s41597-021-00808-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/16/2020] [Indexed: 02/07/2023] Open
Abstract
Toxicogenomics (TGx) approaches are increasingly applied to gain insight into the possible toxicity mechanisms of engineered nanomaterials (ENMs). Omics data can be valuable to elucidate the mechanism of action of chemicals and to develop predictive models in toxicology. While vast amounts of transcriptomics data from ENM exposures have already been accumulated, a unified, easily accessible and reusable collection of transcriptomics data for ENMs is currently lacking. In an attempt to improve the FAIRness of already existing transcriptomics data for ENMs, we curated a collection of homogenized transcriptomics data from human, mouse and rat ENM exposures in vitro and in vivo including the physicochemical characteristics of the ENMs used in each study.
Collapse
Affiliation(s)
- Laura Aliisa Saarimäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, Birmingham, United Kingdom
| | - Anastasios G Papadiamantis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, Birmingham, United Kingdom
- NovaMechanics Ltd, P.O Box 26014 1666, Nicosia, Cyprus
| | | | | | | | - Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- BioMediTech Institute, Tampere University, Tampere, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- BioMediTech Institute, Tampere University, Tampere, Finland.
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
- Finnish Centre for Alternative Methods (FICAM), Faculty of Medicine and Heath Technology, Tampere University, Tampere, Finland.
| |
Collapse
|
16
|
Jin Y, Feng M, Ma W, Wei Y, Qi G, Luo J, Xu L, Li X, Li C, Wang Y, Li D, Chen J, Zhao Y, Hou Y, Zhao Q, Jiang L, Xie M, Zheng Y, Yu D. A toxicity pathway-oriented approach to develop adverse outcome pathway: AHR activation as a case study. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 268:115733. [PMID: 33011576 DOI: 10.1016/j.envpol.2020.115733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/03/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
With numerous new chemicals introduced into the environment everyday, identification of their potential hazards to the environment and human health is a considerable challenge. Developing adverse outcome pathway (AOP) framework is promising in helping to achieve this goal as it can bring In Vitro testing into toxicity measurement and understanding. To explore the toxic mechanism underlying environmental chemicals via the AOP approach, an integration of adequate experimental data with systems biology understanding is preferred. Here, we describe a novel method to develop reliable and sensible AOPs that relies on chemical-gene interactions, toxicity pathways, molecular regulations, phenotypes, and outcomes information obtained from comparative toxicogenomics database (CTD) and Ingenuity Pathway Analysis (IPA). Using Benzo(a)pyrene (BaP), a highly studied chemical as a stressor, we identified the pivotal IPA toxicity pathways, the molecular initiating event (MIE), and candidate key events (KEs) to structure AOPs in the liver and lung, respectively. Further, we used the corresponding CTD information of multiple typical AHR-ligands, including 2,3,7,8-tetrachlorodibenzoparadioxin (TCDD), valproic acid, quercetin, and particulate matter, to validate our AOP networks. Our approach is likely to speed up AOP development as providing a time- and cost-efficient way to collect all fragmented bioinformation in published studies. It also facilitates a better understanding of the toxic mechanism of environmental chemicals, and potentially brings new insights into the screening of critical paths in the AOP network.
Collapse
Affiliation(s)
- Yuan Jin
- School of Public Health, Qingdao University, Qingdao, China
| | - Meiyao Feng
- School of Public Health, Qingdao University, Qingdao, China
| | - Wanli Ma
- School of Public Health, Qingdao University, Qingdao, China
| | - Yanhong Wei
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Guangshuai Qi
- School of Public Health, Qingdao University, Qingdao, China
| | - Jiao Luo
- School of Public Health, Qingdao University, Qingdao, China
| | - Lin Xu
- School of Public Health, Qingdao University, Qingdao, China
| | - Xinmei Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Chuanhai Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Ying Wang
- School of Public Health, Qingdao University, Qingdao, China
| | - Daochuan Li
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jing Chen
- School of Public Health, Qingdao University, Qingdao, China
| | - Yanjie Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Yufei Hou
- School of Public Health, Qingdao University, Qingdao, China
| | - Qianwen Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Lidan Jiang
- School of Public Health, Qingdao University, Qingdao, China
| | - Mengyue Xie
- School of Public Health, Qingdao University, Qingdao, China
| | - Yuxin Zheng
- School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China.
| |
Collapse
|
17
|
Beneficial Effects of Naringenin in Cigarette Smoke-Induced Damage to the Lung Based on Bioinformatic Prediction and In Vitro Analysis. Molecules 2020; 25:molecules25204704. [PMID: 33066647 PMCID: PMC7587370 DOI: 10.3390/molecules25204704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Naringenin is found mainly in citrus fruits, and is thought to be beneficial in the prevention and control of lung diseases. This study aims to investigate the mechanisms of naringenin against the damage in the lung caused by cigarette smoke. A system bioinformatic approach was proposed to predict the mechanisms of naringenin for protecting lung health. Then, we validated this prediction in BEAS-2B cells treated with cigarette smoke extract (CSE). System bioinformatic analysis indicated that naringenin exhibits protective effects on lung through the inhibition of inflammation and suppression of oxidative stress based on a multi-pathways network, mainly including oxidative stress pathway, Nrf2 pathway, Lung fibrosis pathway, IL-3 signaling pathway, and Aryl hydrocarbon receptor pathway. The in vitro results showed that naringenin significantly attenuated CSE-induced up-regulation of IL-8 and TNF-α. CSE stimulation increased the mRNA expressions of Nrf2, HO-1, and NQO1; the levels of total protein and nuclear protein of Nrf2; and the activity of SOD on days 2 and 4; but decreased these indexes on day 6. Naringenin can balance the antioxidant system by regulating Nrf2 and its downstream genes, preliminarily validating that Nrf2 pathway is involved in the protection offered by naringenin against cigarette smoke-induced damage to the lung. It suggests that dietary naringenin shows possible potential use in the management of lung health.
Collapse
|
18
|
Davis AP, Wiegers TC, Grondin CJ, Johnson RJ, Sciaky D, Wiegers J, Mattingly CJ. Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular Disease. Toxicol Sci 2020; 177:392-404. [PMID: 32663284 PMCID: PMC7548289 DOI: 10.1093/toxsci/kfaa113] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Environmental health studies relate how exposures (eg, chemicals) affect human health and disease; however, in most cases, the molecular and biological mechanisms connecting an exposure with a disease remain unknown. To help fill in these knowledge gaps, we sought to leverage content from the public Comparative Toxicogenomics Database (CTD) to identify potential intermediary steps. In a proof-of-concept study, we systematically compute the genes, molecular mechanisms, and biological events for the environmental health association linking air pollution toxicants with 2 cardiovascular diseases (myocardial infarction and hypertension) as a test case. Our approach integrates 5 types of curated interactions in CTD to build sets of "CGPD-tetramers," computationally constructed information blocks relating a Chemical- Gene interaction with a Phenotype and Disease. This bioinformatics strategy generates 653 CGPD-tetramers for air pollution-associated myocardial infarction (involving 5 pollutants, 58 genes, and 117 phenotypes) and 701 CGPD-tetramers for air pollution-associated hypertension (involving 3 pollutants, 96 genes, and 142 phenotypes). Collectively, we identify 19 genes and 96 phenotypes shared between these 2 air pollutant-induced outcomes, and suggest important roles for oxidative stress, inflammation, immune responses, cell death, and circulatory system processes. Moreover, CGPD-tetramers can be assembled into extensive chemical-induced disease pathways involving multiple gene products and sequential biological events, and many of these computed intermediary steps are validated in the literature. Our method does not require a priori knowledge of the toxicant, interacting gene, or biological system, and can be used to analyze any environmental chemical-induced disease curated within the public CTD framework. This bioinformatics strategy links and interrelates chemicals, genes, phenotypes, and diseases to fill in knowledge gaps for environmental health studies, as demonstrated for air pollution-associated cardiovascular disease, but can be adapted by researchers for any environmentally influenced disease-of-interest.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Carolyn J Mattingly
- Department of Biological Sciences
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
| |
Collapse
|
19
|
Karatzas P, Melagraki G, Ellis LJA, Lynch I, Varsou DD, Afantitis A, Tsoumanis A, Doganis P, Sarimveis H. Development of Deep Learning Models for Predicting the Effects of Exposure to Engineered Nanomaterials on Daphnia magna. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001080. [PMID: 32548897 DOI: 10.1002/smll.202001080] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
This study presents the results of applying deep learning methodologies within the ecotoxicology field, with the objective of training predictive models that can support hazard assessment and eventually the design of safer engineered nanomaterials (ENMs). A workflow applying two different deep learning architectures on microscopic images of Daphnia magna is proposed that can automatically detect possible malformations, such as effects on the length of the tail, and the overall size, and uncommon lipid concentrations and lipid deposit shapes, which are due to direct or parental exposure to ENMs. Next, classification models assign specific objects (heart, abdomen/claw) to classes that depend on lipid densities and compare the results with controls. The models are statistically validated in terms of their prediction accuracy on external D. magna images and illustrate that deep learning technologies can be useful in the nanoinformatics field, because they can automate time-consuming manual procedures, accelerate the investigation of adverse effects of ENMs, and facilitate the process of designing safer nanostructures. It may even be possible in the future to predict impacts on subsequent generations from images of parental exposure, reducing the time and cost involved in long-term reproductive toxicity assays over multiple generations.
Collapse
Affiliation(s)
- Pantelis Karatzas
- School of Chemical Engineering, National Technical University of Athens, Athens, 15780, Greece
| | - Georgia Melagraki
- Nanoinformatics Department, NovaMechanics Ltd., Nicosia, 1065, Cyprus
| | - Laura-Jayne A Ellis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Dimitra-Danai Varsou
- School of Chemical Engineering, National Technical University of Athens, Athens, 15780, Greece
- Nanoinformatics Department, NovaMechanics Ltd., Nicosia, 1065, Cyprus
| | - Antreas Afantitis
- Nanoinformatics Department, NovaMechanics Ltd., Nicosia, 1065, Cyprus
| | - Andreas Tsoumanis
- Nanoinformatics Department, NovaMechanics Ltd., Nicosia, 1065, Cyprus
| | - Philip Doganis
- School of Chemical Engineering, National Technical University of Athens, Athens, 15780, Greece
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, Athens, 15780, Greece
| |
Collapse
|
20
|
Halappanavar S, van den Brule S, Nymark P, Gaté L, Seidel C, Valentino S, Zhernovkov V, Høgh Danielsen P, De Vizcaya A, Wolff H, Stöger T, Boyadziev A, Poulsen SS, Sørli JB, Vogel U. Adverse outcome pathways as a tool for the design of testing strategies to support the safety assessment of emerging advanced materials at the nanoscale. Part Fibre Toxicol 2020; 17:16. [PMID: 32450889 PMCID: PMC7249325 DOI: 10.1186/s12989-020-00344-4] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/02/2020] [Indexed: 12/11/2022] Open
Abstract
Toxicity testing and regulation of advanced materials at the nanoscale, i.e. nanosafety, is challenged by the growing number of nanomaterials and their property variants requiring assessment for potential human health impacts. The existing animal-reliant toxicity testing tools are onerous in terms of time and resources and are less and less in line with the international effort to reduce animal experiments. Thus, there is a need for faster, cheaper, sensitive and effective animal alternatives that are supported by mechanistic evidence. More importantly, there is an urgency for developing alternative testing strategies that help justify the strategic prioritization of testing or targeting the most apparent adverse outcomes, selection of specific endpoints and assays and identifying nanomaterials of high concern. The Adverse Outcome Pathway (AOP) framework is a systematic process that uses the available mechanistic information concerning a toxicological response and describes causal or mechanistic linkages between a molecular initiating event, a series of intermediate key events and the adverse outcome. The AOP framework provides pragmatic insights to promote the development of alternative testing strategies. This review will detail a brief overview of the AOP framework and its application to nanotoxicology, tools for developing AOPs and the role of toxicogenomics, and summarize various AOPs of relevance to inhalation toxicity of nanomaterials that are currently under various stages of development. The review also presents a network of AOPs derived from connecting all AOPs, which shows that several adverse outcomes induced by nanomaterials originate from a molecular initiating event that describes the interaction of nanomaterials with lung cells and involve similar intermediate key events. Finally, using the example of an established AOP for lung fibrosis, the review will discuss various in vitro tests available for assessing lung fibrosis and how the information can be used to support a tiered testing strategy for lung fibrosis. The AOPs and AOP network enable deeper understanding of mechanisms involved in inhalation toxicity of nanomaterials and provide a strategy for the development of alternative test methods for hazard and risk assessment of nanomaterials.
Collapse
Affiliation(s)
- Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada.
| | - Sybille van den Brule
- Louvain centre for Toxicology and Applied Pharmacology, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Toxicology, Misvik Biology, Turku, Finland
| | - Laurent Gaté
- Institut National de Recherche et de Sécurité, Vandoeuvre-lès-Nancy, France
| | - Carole Seidel
- Institut National de Recherche et de Sécurité, Vandoeuvre-lès-Nancy, France
| | - Sarah Valentino
- Institut National de Recherche et de Sécurité, Vandoeuvre-lès-Nancy, France
| | - Vadim Zhernovkov
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | | | - Andrea De Vizcaya
- Departamento de Toxicologia, CINVESTAV-IPN, Ciudad de México, Mexico
- Sabbatical leave at Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Henrik Wolff
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Tobias Stöger
- Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Lung Research (DZL), Giessen, Germany
- Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Helmholtz Zentrum München - German, Oberschleißheim, Germany
| | - Andrey Boyadziev
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Sarah Søs Poulsen
- National Research Centre for the Working Environment, Copenhagen Ø, Denmark
| | | | - Ulla Vogel
- National Research Centre for the Working Environment, Copenhagen Ø, Denmark.
- DTU Health Tech, Technical University of Denmark, Kgs. Lyngby, Denmark.
| |
Collapse
|
21
|
Tripodi IJ, Callahan TJ, Westfall JT, Meitzer NS, Dowell RD, Hunter LE. Applying knowledge-driven mechanistic inference to toxicogenomics. Toxicol In Vitro 2020; 66:104877. [PMID: 32387679 DOI: 10.1016/j.tiv.2020.104877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/13/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
When considering toxic chemicals in the environment, a mechanistic, causal explanation of toxicity may be preferred over a statistical or machine learning-based prediction by itself. Elucidating a mechanism of toxicity is, however, a costly and time-consuming process that requires the participation of specialists from a variety of fields, often relying on animal models. We present an innovative mechanistic inference framework (MechSpy), which can be used as a hypothesis generation aid to narrow the scope of mechanistic toxicology analysis. MechSpy generates hypotheses of the most likely mechanisms of toxicity, by combining a semantically-interconnected knowledge representation of human biology, toxicology and biochemistry with gene expression time series on human tissue. Using vector representations of biological entities, MechSpy seeks enrichment in a manually curated list of high-level mechanisms of toxicity, represented as biochemically- and causally-linked ontology concepts. Besides predicting the canonical mechanism of toxicity for many well-studied compounds, we experimentally validated some of our predictions for other chemicals without an established mechanism of toxicity. This mechanistic inference framework is an advantageous tool for predictive toxicology, and the first of its kind to produce a mechanistic explanation for each prediction. MechSpy can be modified to include additional mechanisms of toxicity, and is generalizable to other types of mechanisms of human biology.
Collapse
Affiliation(s)
- Ignacio J Tripodi
- University of Colorado, Computer Science / Interdisciplinary Quantitative Biology, Boulder, CO 80309, USA.
| | - Tiffany J Callahan
- University of Colorado Anschutz Medical Campus, Computational Bioscience, Denver, CO 80045, USA
| | - Jessica T Westfall
- University of Colorado, Molecular, Cellular and Developmental Biology, Boulder, CO 80309, USA
| | | | - Robin D Dowell
- University of Colorado, Molecular, Cellular and Developmental Biology / Interdisciplinary Quantitative Biology, Boulder, CO 80309, USA
| | - Lawrence E Hunter
- University of Colorado Anschutz Medical Campus, Computational Bioscience / Interdisciplinary Quantitative Biology, Denver, CO 80045, USA
| |
Collapse
|
22
|
Serra A, Fratello M, Cattelani L, Liampa I, Melagraki G, Kohonen P, Nymark P, Federico A, Kinaret PAS, Jagiello K, Ha MK, Choi JS, Sanabria N, Gulumian M, Puzyn T, Yoon TH, Sarimveis H, Grafström R, Afantitis A, Greco D. Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E708. [PMID: 32276469 PMCID: PMC7221955 DOI: 10.3390/nano10040708] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/30/2022]
Abstract
Transcriptomics data are relevant to address a number of challenges in Toxicogenomics (TGx). After careful planning of exposure conditions and data preprocessing, the TGx data can be used in predictive toxicology, where more advanced modelling techniques are applied. The large volume of molecular profiles produced by omics-based technologies allows the development and application of artificial intelligence (AI) methods in TGx. Indeed, the publicly available omics datasets are constantly increasing together with a plethora of different methods that are made available to facilitate their analysis, interpretation and the generation of accurate and stable predictive models. In this review, we present the state-of-the-art of data modelling applied to transcriptomics data in TGx. We show how the benchmark dose (BMD) analysis can be applied to TGx data. We review read across and adverse outcome pathways (AOP) modelling methodologies. We discuss how network-based approaches can be successfully employed to clarify the mechanism of action (MOA) or specific biomarkers of exposure. We also describe the main AI methodologies applied to TGx data to create predictive classification and regression models and we address current challenges. Finally, we present a short description of deep learning (DL) and data integration methodologies applied in these contexts. Modelling of TGx data represents a valuable tool for more accurate chemical safety assessment. This review is the third part of a three-article series on Transcriptomics in Toxicogenomics.
Collapse
Affiliation(s)
- Angela Serra
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (A.S.); (M.F.); (L.C.); (A.F.); (P.A.S.K.)
- BioMediTech Institute, Tampere University, FI-33014 Tampere, Finland
| | - Michele Fratello
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (A.S.); (M.F.); (L.C.); (A.F.); (P.A.S.K.)
- BioMediTech Institute, Tampere University, FI-33014 Tampere, Finland
| | - Luca Cattelani
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (A.S.); (M.F.); (L.C.); (A.F.); (P.A.S.K.)
- BioMediTech Institute, Tampere University, FI-33014 Tampere, Finland
| | - Irene Liampa
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece; (I.L.); (H.S.)
| | - Georgia Melagraki
- Nanoinformatics Department, NovaMechanics Ltd., Nicosia 1065, Cyprus; (G.M.); (A.A.)
| | - Pekka Kohonen
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; (P.K.); (P.N.); (R.G.)
- Division of Toxicology, Misvik Biology, 20520 Turku, Finland
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; (P.K.); (P.N.); (R.G.)
- Division of Toxicology, Misvik Biology, 20520 Turku, Finland
| | - Antonio Federico
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (A.S.); (M.F.); (L.C.); (A.F.); (P.A.S.K.)
- BioMediTech Institute, Tampere University, FI-33014 Tampere, Finland
| | - Pia Anneli Sofia Kinaret
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (A.S.); (M.F.); (L.C.); (A.F.); (P.A.S.K.)
- BioMediTech Institute, Tampere University, FI-33014 Tampere, Finland
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Karolina Jagiello
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland; (K.J.); (T.P.)
- University of Gdansk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - My Kieu Ha
- Center for Next Generation Cytometry, Hanyang University, Seoul 04763, Korea; (M.K.H.); (J.-S.C.); (T.-H.Y.)
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, Korea
| | - Jang-Sik Choi
- Center for Next Generation Cytometry, Hanyang University, Seoul 04763, Korea; (M.K.H.); (J.-S.C.); (T.-H.Y.)
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, Korea
| | - Natasha Sanabria
- National Institute for Occupational Health, Johannesburg 30333, South Africa; (N.S.); (M.G.)
| | - Mary Gulumian
- National Institute for Occupational Health, Johannesburg 30333, South Africa; (N.S.); (M.G.)
- Haematology and Molecular Medicine Department, School of Pathology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Tomasz Puzyn
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland; (K.J.); (T.P.)
- University of Gdansk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Tae-Hyun Yoon
- Center for Next Generation Cytometry, Hanyang University, Seoul 04763, Korea; (M.K.H.); (J.-S.C.); (T.-H.Y.)
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, Korea
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece; (I.L.); (H.S.)
| | - Roland Grafström
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden; (P.K.); (P.N.); (R.G.)
- Division of Toxicology, Misvik Biology, 20520 Turku, Finland
| | - Antreas Afantitis
- Nanoinformatics Department, NovaMechanics Ltd., Nicosia 1065, Cyprus; (G.M.); (A.A.)
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland; (A.S.); (M.F.); (L.C.); (A.F.); (P.A.S.K.)
- BioMediTech Institute, Tampere University, FI-33014 Tampere, Finland
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| |
Collapse
|
23
|
Hemmerich J, Ecker GF. In silico toxicology: From structure–activity relationships towards deep learning and adverse outcome pathways. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020; 10:e1475. [PMID: 35866138 PMCID: PMC9286356 DOI: 10.1002/wcms.1475] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/18/2022]
Abstract
In silico toxicology is an emerging field. It gains increasing importance as research is aiming to decrease the use of animal experiments as suggested in the 3R principles by Russell and Burch. In silico toxicology is a means to identify hazards of compounds before synthesis, and thus in very early stages of drug development. For chemical industries, as well as regulatory agencies it can aid in gap‐filling and guide risk minimization strategies. Techniques such as structural alerts, read‐across, quantitative structure–activity relationship, machine learning, and deep learning allow to use in silico toxicology in many cases, some even when data is scarce. Especially the concept of adverse outcome pathways puts all techniques into a broader context and can elucidate predictions by mechanistic insights. This article is categorized under:Structure and Mechanism > Computational Biochemistry and Biophysics Data Science > Chemoinformatics
Collapse
Affiliation(s)
- Jennifer Hemmerich
- Department of Pharmaceutical Chemistry University of Vienna Vienna Austria
| | - Gerhard F. Ecker
- Department of Pharmaceutical Chemistry University of Vienna Vienna Austria
| |
Collapse
|
24
|
Afantitis A, Melagraki G, Isigonis P, Tsoumanis A, Varsou DD, Valsami-Jones E, Papadiamantis A, Ellis LJA, Sarimveis H, Doganis P, Karatzas P, Tsiros P, Liampa I, Lobaskin V, Greco D, Serra A, Kinaret PAS, Saarimäki LA, Grafström R, Kohonen P, Nymark P, Willighagen E, Puzyn T, Rybinska-Fryca A, Lyubartsev A, Alstrup Jensen K, Brandenburg JG, Lofts S, Svendsen C, Harrison S, Maier D, Tamm K, Jänes J, Sikk L, Dusinska M, Longhin E, Rundén-Pran E, Mariussen E, El Yamani N, Unger W, Radnik J, Tropsha A, Cohen Y, Leszczynski J, Ogilvie Hendren C, Wiesner M, Winkler D, Suzuki N, Yoon TH, Choi JS, Sanabria N, Gulumian M, Lynch I. NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment. Comput Struct Biotechnol J 2020; 18:583-602. [PMID: 32226594 PMCID: PMC7090366 DOI: 10.1016/j.csbj.2020.02.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/18/2020] [Accepted: 02/29/2020] [Indexed: 01/26/2023] Open
Abstract
Nanotechnology has enabled the discovery of a multitude of novel materials exhibiting unique physicochemical (PChem) properties compared to their bulk analogues. These properties have led to a rapidly increasing range of commercial applications; this, however, may come at a cost, if an association to long-term health and environmental risks is discovered or even just perceived. Many nanomaterials (NMs) have not yet had their potential adverse biological effects fully assessed, due to costs and time constraints associated with the experimental assessment, frequently involving animals. Here, the available NM libraries are analyzed for their suitability for integration with novel nanoinformatics approaches and for the development of NM specific Integrated Approaches to Testing and Assessment (IATA) for human and environmental risk assessment, all within the NanoSolveIT cloud-platform. These established and well-characterized NM libraries (e.g. NanoMILE, NanoSolutions, NANoREG, NanoFASE, caLIBRAte, NanoTEST and the Nanomaterial Registry (>2000 NMs)) contain physicochemical characterization data as well as data for several relevant biological endpoints, assessed in part using harmonized Organisation for Economic Co-operation and Development (OECD) methods and test guidelines. Integration of such extensive NM information sources with the latest nanoinformatics methods will allow NanoSolveIT to model the relationships between NM structure (morphology), properties and their adverse effects and to predict the effects of other NMs for which less data is available. The project specifically addresses the needs of regulatory agencies and industry to effectively and rapidly evaluate the exposure, NM hazard and risk from nanomaterials and nano-enabled products, enabling implementation of computational 'safe-by-design' approaches to facilitate NM commercialization.
Collapse
Key Words
- (quantitative) Structure–activity relationships
- AI, Artificial Intelligence
- AOPs, Adverse Outcome Pathways
- API, Application Programming interface
- CG, coarse-grained (model)
- CNTs, carbon nanotubes
- Computational toxicology
- Engineered nanomaterials
- FAIR, Findable Accessible Inter-operable and Re-usable
- GUI, Graphical Processing Unit
- HOMO-LUMO, Highest Occupied Molecular Orbital Lowest Unoccupied Molecular Orbital
- Hazard assessment
- IATA, Integrated Approaches to Testing and Assessment
- Integrated approach for testing and assessment
- KE, key events
- MIE, molecular initiating events
- ML, machine learning
- MOA, mechanism (mode) of action
- MWCNT, multi-walled carbon nanotubes
- Machine learning
- NMs, nanomaterials
- Nanoinformatics
- OECD, Organisation for Economic Co-operation and Development
- PBPK, Physiologically Based PharmacoKinetics
- PC, Protein Corona
- PChem, Physicochemical
- PTGS, Predictive Toxicogenomics Space
- Predictive modelling
- QC, quantum-chemical
- QM, quantum-mechanical
- QSAR, quantitative structure-activity relationship
- QSPR, quantitative structure-property relationship
- RA, risk assessment
- REST, Representational State Transfer
- ROS, reactive oxygen species
- Read across
- SAR, structure-activity relationship
- SMILES, Simplified Molecular Input Line Entry System
- SOPs, standard operating procedures
- Safe-by-design
- Toxicogenomics
Collapse
Affiliation(s)
| | | | | | | | | | - Eugenia Valsami-Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, UK
| | - Anastasios Papadiamantis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, UK
| | - Laura-Jayne A. Ellis
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, UK
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Philip Doganis
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Pantelis Karatzas
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Periklis Tsiros
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Irene Liampa
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Vladimir Lobaskin
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dario Greco
- Faculty of Medicine and Health Technology, University of Tampere, FI-33014, Finland
| | - Angela Serra
- Faculty of Medicine and Health Technology, University of Tampere, FI-33014, Finland
| | | | | | - Roland Grafström
- Misvik Biology OY, Itäinen Pitkäkatu 4, 20520 Turku, Finland
- Karolinska Institute, Institute of Environmental Medicine, Nobels väg 13, 17177 Stockholm, Sweden
| | - Pekka Kohonen
- Misvik Biology OY, Itäinen Pitkäkatu 4, 20520 Turku, Finland
- Karolinska Institute, Institute of Environmental Medicine, Nobels väg 13, 17177 Stockholm, Sweden
| | - Penny Nymark
- Misvik Biology OY, Itäinen Pitkäkatu 4, 20520 Turku, Finland
- Karolinska Institute, Institute of Environmental Medicine, Nobels väg 13, 17177 Stockholm, Sweden
| | - Egon Willighagen
- Department of Bioinformatics – BiGCaT, School of Nutrition and Translational Research in Metabolism, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, the Netherlands
| | - Tomasz Puzyn
- QSAR Lab Ltd., Aleja Grunwaldzka 190/102, 80-266 Gdansk, Poland
- University of Gdansk, Faculty of Chemistry, Wita Stwosza 63, 80-308 Gdansk, Poland
| | | | - Alexander Lyubartsev
- Institutionen för material- och miljökemi, Stockholms Universitet, 106 91 Stockholm, Sweden
| | - Keld Alstrup Jensen
- The National Research Center for the Work Environment, Lersø Parkallé 105, 2100 Copenhagen, Denmark
| | - Jan Gerit Brandenburg
- Interdisciplinary Center for Scientific Computing, Heidelberg University, Germany
- Chief Digital Organization, Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Stephen Lofts
- UK Centre for Ecology and Hydrology, Library Ave, Bailrigg, Lancaster LA1 4AP, UK
| | - Claus Svendsen
- UK Centre for Ecology and Hydrology, MacLean Bldg, Benson Ln, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Samuel Harrison
- UK Centre for Ecology and Hydrology, Library Ave, Bailrigg, Lancaster LA1 4AP, UK
| | - Dieter Maier
- Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany
| | - Kaido Tamm
- Department of Chemistry, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia
| | - Jaak Jänes
- Department of Chemistry, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia
| | - Lauri Sikk
- Department of Chemistry, University of Tartu, Ülikooli 18, 50090 Tartu, Estonia
| | - Maria Dusinska
- NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Eleonora Longhin
- NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Elise Rundén-Pran
- NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Espen Mariussen
- NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Naouale El Yamani
- NILU-Norwegian Institute for Air Research, Instituttveien 18, 2002 Kjeller, Norway
| | - Wolfgang Unger
- Federal Institute for Material Testing and Research (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Jörg Radnik
- Federal Institute for Material Testing and Research (BAM), Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Alexander Tropsha
- Eschelman School of Pharmacy, University of North Carolina at Chapel Hill, 100K Beard Hall, CB# 7568, Chapel Hill, NC 27955-7568, USA
| | - Yoram Cohen
- Samueli School Of Engineering, University of California, Los Angeles, 5531 Boelter Hall, Los Angeles, CA 90095, USA
| | - Jerzy Leszczynski
- Interdisciplinary Nanotoxicity Center, Jackson State University, 1400 J. R. Lynch Street, Jackson, MS 39217, USA
| | - Christine Ogilvie Hendren
- Center for Environmental Implications of Nanotechnologies, Duke University, 121 Hudson Hall, Durham, NC 27708-0287, USA
| | - Mark Wiesner
- Center for Environmental Implications of Nanotechnologies, Duke University, 121 Hudson Hall, Durham, NC 27708-0287, USA
| | - David Winkler
- La Trobe Institute of Molecular Sciences, La Trobe University, Plenty Rd & Kingsbury Dr, Bundoora, VIC 3086, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
- CSIRO Data61, Clayton 3168, Australia
- School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Noriyuki Suzuki
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki 305-0053, Japan
| | - Tae Hyun Yoon
- Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, Republic of Korea
| | - Jang-Sik Choi
- Institute of Next Generation Material Design, Hanyang University, Seoul 04763, Republic of Korea
| | - Natasha Sanabria
- National Health Laboratory Services, 1 Modderfontein Rd, Sandringham, Johannesburg 2192, South Africa
| | - Mary Gulumian
- National Health Laboratory Services, 1 Modderfontein Rd, Sandringham, Johannesburg 2192, South Africa
- Haematology and Molecular Medicine, University of the Witwatersrand, Johannesburg, South Africa
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, B15 2TT Birmingham, UK
| |
Collapse
|
25
|
Nymark P, Bakker M, Dekkers S, Franken R, Fransman W, García-Bilbao A, Greco D, Gulumian M, Hadrup N, Halappanavar S, Hongisto V, Hougaard KS, Jensen KA, Kohonen P, Koivisto AJ, Dal Maso M, Oosterwijk T, Poikkimäki M, Rodriguez-Llopis I, Stierum R, Sørli JB, Grafström R. Toward Rigorous Materials Production: New Approach Methodologies Have Extensive Potential to Improve Current Safety Assessment Practices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1904749. [PMID: 31913582 DOI: 10.1002/smll.201904749] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Advanced material development, including at the nanoscale, comprises costly and complex challenges coupled to ensuring human and environmental safety. Governmental agencies regulating safety have announced interest toward acceptance of safety data generated under the collective term New Approach Methodologies (NAMs), as such technologies/approaches offer marked potential to progress the integration of safety testing measures during innovation from idea to product launch of nanomaterials. Divided in overall eight main categories, searchable databases for grouping and read across purposes, exposure assessment and modeling, in silico modeling of physicochemical structure and hazard data, in vitro high-throughput and high-content screening assays, dose-response assessments and modeling, analyses of biological processes and toxicity pathways, kinetics and dose extrapolation, consideration of relevant exposure levels and biomarker endpoints typify such useful NAMs. Their application generally agrees with articulated stakeholder needs for improvement of safety testing procedures. They further fit for inclusion and add value in nanomaterials risk assessment tools. Overall 37 of 50 evaluated NAMs and tiered workflows applying NAMs are recommended for considering safer-by-design innovation, including guidance to the selection of specific NAMs in the eight categories. An innovation funnel enriched with safety methods is ultimately proposed under the central aim of promoting rigorous nanomaterials innovation.
Collapse
Affiliation(s)
- Penny Nymark
- Karolinska Institutet, Institute of Environmental Medicine, Nobels väg 13, 171 77, Stockholm, Sweden
- Department of Toxicology, Misvik Biology, Karjakatu 35 B, 20520, Turku, Finland
| | - Martine Bakker
- National Institute for Public Health and the Environment, RIVM, P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Susan Dekkers
- National Institute for Public Health and the Environment, RIVM, P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - Remy Franken
- Netherlands Organisation for Applied Scientific Research, TNO, P.O. Box 96800, NL-2509 JE, The Hague, The Netherlands
| | - Wouter Fransman
- Netherlands Organisation for Applied Scientific Research, TNO, P.O. Box 96800, NL-2509 JE, The Hague, The Netherlands
| | - Amaia García-Bilbao
- GAIKER Technology Centre, Parque Tecnológico, Ed. 202, 48170, Zamudio, Bizkaia, Spain
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, Korkeakoulunkatu 6, 33720, Tampere, Finland
- Institute of Biotechnology, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland
| | - Mary Gulumian
- National Institute for Occupational Health, 25 Hospital St, Constitution Hill, 2000, Johannesburg, South Africa
- Haematology and Molecular Medicine Department, University of the Witwatersrand, 7 York Road, Parktown, 2193, Johannesburg, South Africa
| | - Niels Hadrup
- National Research Center for the Work Environment, Lersø Parkallé 105, 2100, Copenhagen, Denmark
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, 50 Colombine Driveway, Ottawa, ON, K1A 0K9, Canada
| | - Vesa Hongisto
- Department of Toxicology, Misvik Biology, Karjakatu 35 B, 20520, Turku, Finland
| | - Karin Sørig Hougaard
- National Research Center for the Work Environment, Lersø Parkallé 105, 2100, Copenhagen, Denmark
| | - Keld Alstrup Jensen
- National Research Center for the Work Environment, Lersø Parkallé 105, 2100, Copenhagen, Denmark
| | - Pekka Kohonen
- Karolinska Institutet, Institute of Environmental Medicine, Nobels väg 13, 171 77, Stockholm, Sweden
- Department of Toxicology, Misvik Biology, Karjakatu 35 B, 20520, Turku, Finland
| | - Antti Joonas Koivisto
- National Research Center for the Work Environment, Lersø Parkallé 105, 2100, Copenhagen, Denmark
| | - Miikka Dal Maso
- Aerosol Physics Laboratory, Physics Unit, Tampere University, Korkeakoulunkatu 6, 33720, Tampere, Finland
| | - Thies Oosterwijk
- Netherlands Organisation for Applied Scientific Research, TNO, P.O. Box 96800, NL-2509 JE, The Hague, The Netherlands
| | - Mikko Poikkimäki
- Aerosol Physics Laboratory, Physics Unit, Tampere University, Korkeakoulunkatu 6, 33720, Tampere, Finland
| | | | - Rob Stierum
- Netherlands Organisation for Applied Scientific Research, TNO, P.O. Box 96800, NL-2509 JE, The Hague, The Netherlands
| | - Jorid Birkelund Sørli
- National Research Center for the Work Environment, Lersø Parkallé 105, 2100, Copenhagen, Denmark
| | - Roland Grafström
- Karolinska Institutet, Institute of Environmental Medicine, Nobels väg 13, 171 77, Stockholm, Sweden
- Department of Toxicology, Misvik Biology, Karjakatu 35 B, 20520, Turku, Finland
| |
Collapse
|
26
|
Rugard M, Coumoul X, Carvaillo JC, Barouki R, Audouze K. Deciphering Adverse Outcome Pathway Network Linked to Bisphenol F Using Text Mining and Systems Toxicology Approaches. Toxicol Sci 2020; 173:32-40. [PMID: 31596483 PMCID: PMC6944215 DOI: 10.1093/toxsci/kfz214] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bisphenol F (BPF) is one of several Bisphenol A (BPA) substituents that is increasingly used in manufacturing industry leading to detectable human exposure. Whereas a large number of studies have been devoted to decipher BPA effects, much less is known about its substituents. To support decision making on BPF's safety, we have developed a new computational approach to rapidly explore the available data on its toxicological effects, combining text mining and integrative systems biology, and aiming at connecting BPF to adverse outcome pathways (AOPs). We first extracted from different databases BPF-protein associations that were expanded to protein complexes using protein-protein interaction datasets. Over-representation analysis of the protein complexes allowed to identify the most relevant biological pathways putatively targeted by BPF. Then, automatic screening of scientific abstracts from literature using the text mining tool, AOP-helpFinder, combined with data integration from various sources (AOP-wiki, CompTox, etc.) and manual curation allowed us to link BPF to AOP events. Finally, we combined all the information gathered through those analyses and built a comprehensive complex framework linking BPF to an AOP network including, as adverse outcomes, various types of cancers such as breast and thyroid malignancies. These results which integrate different types of data can support regulatory assessment of the BPA substituent, BPF, and trigger new epidemiological and experimental studies.
Collapse
Affiliation(s)
| | - Xavier Coumoul
- Université de Paris, Inserm UMR S-1124, 75006 Paris, France
| | | | - Robert Barouki
- Université de Paris, Inserm UMR S-1124, 75006 Paris, France
| | - Karine Audouze
- Université de Paris, Inserm UMR S-1124, 75006 Paris, France
| |
Collapse
|
27
|
Carvaillo JC, Barouki R, Coumoul X, Audouze K. Linking Bisphenol S to Adverse Outcome Pathways Using a Combined Text Mining and Systems Biology Approach. ENVIRONMENTAL HEALTH PERSPECTIVES 2019; 127:47005. [PMID: 30994381 PMCID: PMC6785233 DOI: 10.1289/ehp4200] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND Available toxicity data can be optimally interpreted if they are integrated using computational approaches such as systems biology modeling. Such approaches are particularly warranted in cases where regulatory decisions have to be made rapidly. OBJECTIVES The study aims at developing and applying a new integrative computational strategy to identify associations between bisphenol S (BPS), a substitute for bisphenol A (BPA), and components of adverse outcome pathways (AOPs). METHODS The proposed approach combines a text mining (TM) procedure and integrative systems biology to comprehensively analyze the scientific literature to enrich AOPs related to environmental stressors. First, to identify relevant associations between BPS and different AOP components, a list of abstracts was screened using the developed text-mining tool AOP-helpFinder, which calculates scores based on the graph theory to prioritize the findings. Then, to fill gaps between BPS, biological events, and adverse outcomes (AOs), a systems biology approach was used to integrate information from the AOP-Wiki and ToxCast databases, followed by manual curation of the relevant publications. RESULTS Links between BPS and 48 AOP key events (KEs) were identified and scored via 31 references. The main outcomes were related to reproductive health, endocrine disruption, impairments of metabolism, and obesity. We then explicitly analyzed co-mention of the terms BPS and obesity by data integration and manual curation of the full text of the publications. Several molecular and cellular pathways were identified, which allowed the proposal of a biological explanation for the association between BPS and obesity. CONCLUSIONS By analyzing dispersed information from the literature and databases, our novel approach can identify links between stressors and AOP KEs. The findings associating BPS and obesity illustrate the use of computational tools in predictive toxicology and highlight the relevance of the approach to decision makers assessing substituents to toxic chemicals. https://doi.org/10.1289/EHP4200.
Collapse
Affiliation(s)
- Jean-Charles Carvaillo
- University Paris Descartes, ComUE Sorbonne Paris Cité, Paris, France
- Institut national de la santé et de la recherche médicale (INSERM, National Institute of Health & Medical Research) UMR S-1124, Paris, France
| | - Robert Barouki
- University Paris Descartes, ComUE Sorbonne Paris Cité, Paris, France
- Institut national de la santé et de la recherche médicale (INSERM, National Institute of Health & Medical Research) UMR S-1124, Paris, France
| | - Xavier Coumoul
- University Paris Descartes, ComUE Sorbonne Paris Cité, Paris, France
- Institut national de la santé et de la recherche médicale (INSERM, National Institute of Health & Medical Research) UMR S-1124, Paris, France
| | - Karine Audouze
- University Paris Descartes, ComUE Sorbonne Paris Cité, Paris, France
- Institut national de la santé et de la recherche médicale (INSERM, National Institute of Health & Medical Research) UMR S-1124, Paris, France
- University Paris Diderot, ComUE Sorbonne Paris Cité, Paris, France
| |
Collapse
|
28
|
Oki NO, Farcal L, Abdelaziz A, Florean O, Doktorova TY, Exner T, Kohonen P, Grafström R, Hardy B. Integrated analysis of in vitro data and the adverse outcome pathway framework for prioritization and regulatory applications: An exploratory case study using publicly available data on piperonyl butoxide and liver models. Toxicol In Vitro 2019; 54:23-32. [DOI: 10.1016/j.tiv.2018.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/31/2018] [Accepted: 09/03/2018] [Indexed: 01/30/2023]
|
29
|
Niedzwiecki MM, Walker DI, Vermeulen R, Chadeau-Hyam M, Jones DP, Miller GW. The Exposome: Molecules to Populations. Annu Rev Pharmacol Toxicol 2019; 59:107-127. [PMID: 30095351 DOI: 10.1146/annurev-pharmtox-010818-021315] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Derived from the term exposure, the exposome is an omic-scale characterization of the nongenetic drivers of health and disease. With the genome, it defines the phenome of an individual. The measurement of complex environmental factors that exert pressure on our health has not kept pace with genomics and historically has not provided a similar level of resolution. Emerging technologies make it possible to obtain detailed information on drugs, toxicants, pollutants, nutrients, and physical and psychological stressors on an omic scale. These forces can also be assessed at systems and network levels, providing a framework for advances in pharmacology and toxicology. The exposome paradigm can improve the analysis of drug interactions and detection of adverse effects of drugs and toxicants and provide data on biological responses to exposures. The comprehensive model can provide data at the individual level for precision medicine, group level for clinical trials, and population level for public health.
Collapse
Affiliation(s)
- Megan M Niedzwiecki
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; ,
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; ,
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, USA
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322, USA;
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, Netherlands;
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 Utrecht, Netherlands
- MRC/PHE Centre for Environmental Health, Department of Epidemiology and Public Health, Imperial College London, W2 1PG London, United Kingdom;
| | - Marc Chadeau-Hyam
- Institute for Risk Assessment Sciences, Utrecht University, 3584 CM Utrecht, Netherlands;
- MRC/PHE Centre for Environmental Health, Department of Epidemiology and Public Health, Imperial College London, W2 1PG London, United Kingdom;
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, Georgia 30322, USA;
| | - Gary W Miller
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, USA
- Current affiliation: Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032, USA;
| |
Collapse
|
30
|
Martens M, Verbruggen T, Nymark P, Grafström R, Burgoon LD, Aladjov H, Torres Andón F, Evelo CT, Willighagen EL. Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials. Front Genet 2018; 9:661. [PMID: 30622555 PMCID: PMC6308971 DOI: 10.3389/fgene.2018.00661] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 12/04/2018] [Indexed: 01/18/2023] Open
Abstract
A paradigm shift is taking place in risk assessment to replace animal models, reduce the number of economic resources, and refine the methodologies to test the growing number of chemicals and nanomaterials. Therefore, approaches such as transcriptomics, proteomics, and metabolomics have become valuable tools in toxicological research, and are finding their way into regulatory toxicity. One promising framework to bridge the gap between the molecular-level measurements and risk assessment is the concept of adverse outcome pathways (AOPs). These pathways comprise mechanistic knowledge and connect biological events from a molecular level toward an adverse effect outcome after exposure to a chemical. However, the implementation of omics-based approaches in the AOPs and their acceptance by the risk assessment community is still a challenge. Because the existing modules in the main repository for AOPs, the AOP Knowledge Base (AOP-KB), do not currently allow the integration of omics technologies, additional tools are required for omics-based data analysis and visualization. Here we show how WikiPathways can serve as a supportive tool to make omics data interoperable with the AOP-Wiki, part of the AOP-KB. Manual matching of key events (KEs) indicated that 67% could be linked with molecular pathways. Automatic connection through linkage of identifiers between the databases showed that only 30% of AOP-Wiki chemicals were found on WikiPathways. More loose linkage through gene names in KE and Key Event Relationships descriptions gave an overlap of 70 and 71%, respectively. This shows many opportunities to create more direct connections, for example with extended ontology annotations, improving its interoperability. This interoperability allows the needed integration of omics data linked to the molecular pathways with AOPs. A new AOP Portal on WikiPathways is presented to allow the community of AOP developers to collaborate and populate the molecular pathways that underlie the KEs of AOP-Wiki. We conclude that the integration of WikiPathways and AOP-Wiki will improve risk assessment because omics data will be linked directly to KEs and therefore allow the comprehensive understanding and description of AOPs. To make this assessment reproducible and valid, major changes are needed in both WikiPathways and AOP-Wiki.
Collapse
Affiliation(s)
- Marvin Martens
- Department of Bioinformatics – BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Tim Verbruggen
- Department of Bioinformatics – BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| | - Penny Nymark
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Toxicology, Misvik Biology, Turku, Finland
| | - Roland Grafström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Toxicology, Misvik Biology, Turku, Finland
| | - Lyle D. Burgoon
- U.S. Army Engineer Research and Development Center, Vicksburg, MS, United States
| | - Hristo Aladjov
- Organisation for Economic Co-operation and Development Environment Directorate, Paris, France
| | - Fernando Torres Andón
- Laboratory of Cellular Immunology, Humanitas Clinical and Research Institute, Rozzano, Italy
- Center for Research in Molecular Medicine and Chronic Diseases, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Chris T. Evelo
- Department of Bioinformatics – BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, Netherlands
| | - Egon L. Willighagen
- Department of Bioinformatics – BiGCaT, NUTRIM, Maastricht University, Maastricht, Netherlands
| |
Collapse
|
31
|
Davis AP, Wiegers TC, Wiegers J, Johnson RJ, Sciaky D, Grondin CJ, Mattingly CJ. Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways. Toxicol Sci 2018; 165:145-156. [PMID: 29846728 PMCID: PMC6111787 DOI: 10.1093/toxsci/kfy131] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Comparative Toxicogenomics Database (CTD; http://ctdbase.org) is a public resource that manually curates the scientific literature to provide content that illuminates the molecular mechanisms by which environmental exposures affect human health. We introduce our new chemical-phenotype module that describes how chemicals can affect molecular, cellular, and physiological phenotypes. At CTD, we operationally distinguish between phenotypes and diseases, wherein a phenotype refers to a nondisease biological event: eg, decreased cell cycle arrest (phenotype) versus liver cancer (disease), increased fat cell proliferation (phenotype) versus morbid obesity (disease), etc. Chemical-phenotype interactions are expressed in a formal structured notation using controlled terms for chemicals, phenotypes, taxon, and anatomical descriptors. Combining this information with CTD's chemical-disease module allows inferences to be made between phenotypes and diseases, yielding potential insight into the predisease state. Integration of all 4 CTD modules furnishes unique opportunities for toxicologists to generate computationally predictive adverse outcome pathways, linking chemical-gene molecular initiating events with phenotypic key events, adverse diseases, and population-level health outcomes. As examples, we present 3 diverse case studies discerning the effect of vehicle emissions on altered leukocyte migration, the role of cadmium in influencing phenotypes preceding Alzheimer disease, and the connection of arsenic-induced glucose metabolic phenotypes with diabetes. To date, CTD contains over 165 000 interactions that connect more than 6400 chemicals to 3900 phenotypes for 760 anatomical terms in 215 species, from over 19 000 scientific articles. To our knowledge, this is the first comprehensive set of manually curated, literature-based, contextualized, chemical-induced, nondisease phenotype data provided to the public.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Carolyn J Mattingly
- Department of Biological Sciences
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
| |
Collapse
|
32
|
Hardy A, Benford D, Halldorsson T, Jeger MJ, Knutsen HK, More S, Naegeli H, Noteborn H, Ockleford C, Ricci A, Rychen G, Schlatter JR, Silano V, Solecki R, Turck D, Younes M, Chaudhry Q, Cubadda F, Gott D, Oomen A, Weigel S, Karamitrou M, Schoonjans R, Mortensen A. Guidance on risk assessment of the application of nanoscience and nanotechnologies in the food and feed chain: Part 1, human and animal health. EFSA J 2018; 16:e05327. [PMID: 32625968 PMCID: PMC7009542 DOI: 10.2903/j.efsa.2018.5327] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The European Food Safety Authority has produced this Guidance on human and animal health aspects (Part 1) of the risk assessment of nanoscience and nanotechnology applications in the food and feed chain. It covers the application areas within EFSA's remit, e.g. novel foods, food contact materials, food/feed additives and pesticides. The Guidance takes account of the new developments that have taken place since publication of the previous Guidance in 2011. Potential future developments are suggested in the scientific literature for nanoencapsulated delivery systems and nanocomposites in applications such as novel foods, food/feed additives, biocides, pesticides and food contact materials. Therefore, the Guidance has taken account of relevant new scientific studies that provide more insights to physicochemical properties, exposure assessment and hazard characterisation of nanomaterials. It specifically elaborates on physicochemical characterisation of nanomaterials in terms of how to establish whether a material is a nanomaterial, the key parameters that should be measured, the methods and techniques that can be used for characterisation of nanomaterials and their determination in complex matrices. It also details the aspects relating to exposure assessment and hazard identification and characterisation. In particular, nanospecific considerations relating to in vivo/in vitro toxicological studies are discussed and a tiered framework for toxicological testing is outlined. It describes in vitro degradation, toxicokinetics, genotoxicity as well as general issues relating to testing of nanomaterials. Depending on the initial tier results, studies may be needed to investigate reproductive and developmental toxicity, immunotoxicity, allergenicity, neurotoxicity, effects on gut microbiome and endocrine activity. The possible use of read‐across to fill data gaps as well as the potential use of integrated testing strategies and the knowledge of modes/mechanisms of action are also discussed. The Guidance proposes approaches to risk characterisation and uncertainty analysis, and provides recommendations for further research in this area. This publication is linked to the following EFSA Supporting Publications article: http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2018.EN-1430/full
Collapse
|
33
|
Fadeel B, Farcal L, Hardy B, Vázquez-Campos S, Hristozov D, Marcomini A, Lynch I, Valsami-Jones E, Alenius H, Savolainen K. Advanced tools for the safety assessment of nanomaterials. NATURE NANOTECHNOLOGY 2018; 13:537-543. [PMID: 29980781 DOI: 10.1038/s41565-018-0185-0] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 06/05/2018] [Indexed: 05/21/2023]
Abstract
Engineered nanomaterials (ENMs) have tremendous potential to produce beneficial technological impact in numerous sectors in society. Safety assessment is, of course, of paramount importance. However, the myriad variations of ENM properties makes the identification of specific features driving toxicity challenging. At the same time, reducing animal tests by introducing alternative and/or predictive in vitro and in silico methods has become a priority. It is important to embrace these new advances in the safety assessment of ENMs. Indeed, remarkable progress has been made in recent years with respect to mechanism-based hazard assessment of ENMs, including systems biology approaches as well as high-throughput screening platforms, and new tools are also emerging in risk assessment and risk management for humans and the environment across the whole life-cycle of nano-enabled products. Here, we highlight some of the key advances in the hazard and risk assessment of ENMs.
Collapse
Affiliation(s)
- Bengt Fadeel
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Danail Hristozov
- Department of Biology, University of Venice Ca Foscari, Venice, Italy
| | - Antonio Marcomini
- Department of Biology, University of Venice Ca Foscari, Venice, Italy
| | - Iseult Lynch
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Eugenia Valsami-Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Harri Alenius
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Kai Savolainen
- Finnish Institute of Occupational Health, Helsinki, Finland.
| |
Collapse
|