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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.
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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
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Zhang C, Hong H, Mendrick DL, Tang Y, Cheng F. Biomarker-based drug safety assessment in the age of systems pharmacology: from foundational to regulatory science. Biomark Med 2015; 9:1241-52. [PMID: 26506997 DOI: 10.2217/bmm.15.81] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Improved biomarker-based assessment of drug safety is needed in drug discovery and development as well as regulatory evaluation. However, identifying drug safety-related biomarkers such as genes, proteins, miRNA and single-nucleotide polymorphisms remains a big challenge. The advances of 'omics' and computational technologies such as genomics, transcriptomics, metabolomics, proteomics, systems biology, network biology and systems pharmacology enable us to explore drug actions at the organ and organismal levels. Computational and experimental systems pharmacology approaches could be utilized to facilitate biomarker-based drug safety assessment for drug discovery and development and to inform better regulatory decisions. In this article, we review the current status and advances of systems pharmacology approaches for the development of predictive models to identify biomarkers for drug safety assessment.
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Affiliation(s)
- Chen Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
| | - Huixiao Hong
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Donna L Mendrick
- National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China
| | - Feixiong Cheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, China.,State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, Sichuan, China
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