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      The EU-ToxRisk method documentation, data processing and chemical testing pipeline for the regulatory use of new approach methods

      research-article
      1 , 2 , 3 , 1 , 20 , 4 , 5 , 6 , 7 , 8 , 4 , 9 , 10 , 7 , 1 , 7 , 11 , 12 , 13 , 21 , 4 , 1 , 10 , 14 , 1 , 2 , 10 , 15 , 14 , 13 , 21 , 10 , 12 , 9 , 13 , 16 , 9 , 17 , 18 , 19 , 4 , 12 , 18 , 14 , 3 , 15 , 8 , 5 , 18 , 1 , 9 ,
      Archives of Toxicology
      Springer Berlin Heidelberg
      GIVIMP, In vitro toxicology, Nuclear receptor, Metadata, Data processing

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          Abstract

          Hazard assessment, based on new approach methods (NAM), requires the use of batteries of assays, where individual tests may be contributed by different laboratories. A unified strategy for such collaborative testing is presented. It details all procedures required to allow test information to be usable for integrated hazard assessment, strategic project decisions and/or for regulatory purposes. The EU-ToxRisk project developed a strategy to provide regulatorily valid data, and exemplified this using a panel of > 20 assays (with > 50 individual endpoints), each exposed to 19 well-known test compounds (e.g. rotenone, colchicine, mercury, paracetamol, rifampicine, paraquat, taxol). Examples of strategy implementation are provided for all aspects required to ensure data validity: (i) documentation of test methods in a publicly accessible database; (ii) deposition of standard operating procedures (SOP) at the European Union DB-ALM repository; (iii) test readiness scoring accoding to defined criteria; (iv) disclosure of the pipeline for data processing; (v) link of uncertainty measures and metadata to the data; (vi) definition of test chemicals, their handling and their behavior in test media; (vii) specification of the test purpose and overall evaluation plans. Moreover, data generation was exemplified by providing results from 25 reporter assays. A complete evaluation of the entire test battery will be described elsewhere. A major learning from the retrospective analysis of this large testing project was the need for thorough definitions of the above strategy aspects, ideally in form of a study pre-registration, to allow adequate interpretation of the data and to ensure overall scientific/toxicological validity.

          Electronic supplementary material

          The online version of this article (10.1007/s00204-020-02802-6) contains supplementary material, which is available to authorized users.

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          Most cited references106

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          ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology

          The U.S. Environmental Protection Agency's (EPA) ToxCast program is testing a large library of Agency-relevant chemicals using in vitro high-throughput screening (HTS) approaches to support the development of improved toxicity prediction models. Launched in 2007, Phase I of the program screened 310 chemicals, mostly pesticides, across hundreds of ToxCast assay end points. In Phase II, the ToxCast library was expanded to 1878 chemicals, culminating in the public release of screening data at the end of 2013. Subsequent expansion in Phase III has resulted in more than 3800 chemicals actively undergoing ToxCast screening, 96% of which are also being screened in the multi-Agency Tox21 project. The chemical library unpinning these efforts plays a central role in defining the scope and potential application of ToxCast HTS results. The history of the phased construction of EPA's ToxCast library is reviewed, followed by a survey of the library contents from several different vantage points. CAS Registry Numbers are used to assess ToxCast library coverage of important toxicity, regulatory, and exposure inventories. Structure-based representations of ToxCast chemicals are then used to compute physicochemical properties, substructural features, and structural alerts for toxicity and biotransformation. Cheminformatics approaches using these varied representations are applied to defining the boundaries of HTS testability, evaluating chemical diversity, and comparing the ToxCast library to potential target application inventories, such as used in EPA's Endocrine Disruption Screening Program (EDSP). Through several examples, the ToxCast chemical library is demonstrated to provide comprehensive coverage of the knowledge domains and target inventories of potential interest to EPA. Furthermore, the varied representations and approaches presented here define local chemistry domains potentially worthy of further investigation (e.g., not currently covered in the testing library or defined by toxicity "alerts") to strategically support data mining and predictive toxicology modeling moving forward.
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            Rapid, complete and large-scale generation of post-mitotic neurons from the human LUHMES cell line.

            We characterized phenotype and function of a fetal human mesencephalic cell line (LUHMES, Lund human mesencephalic) as neuronal model system. Neurodevelopmental profiling of the proliferation stage (d0, day 0) of these conditionally-immortalized cells revealed neuronal features, expressed simultaneously with some early neuroblast and stem cell markers. An optimized 2-step differentiation procedure, triggered by shut-down of the myc transgene, resulted in uniformly post-mitotic neurons within 5 days (d5). This was associated with down-regulation of some precursor markers and further up-regulation of neuronal genes. Neurite network formation involved the outgrowth of 1-2, often > 500 μm long projections. They showed dynamic growth cone behavior, as evidenced by time-lapse imaging of stably GFP-over-expressing cells. Voltage-dependent sodium channels and spontaneous electrical activity of LUHMES continuously increased from d0 to d11, while levels of synaptic markers reached their maximum on d5. The developmental expression patterns of most genes and of the dopamine uptake- and release-machinery appeared to be intrinsically predetermined, as the differentiation proceeded similarly when external factors such as dibutyryl-cAMP and glial cell derived neurotrophic factor were omitted. Only tyrosine hydroxylase required the continuous presence of cAMP. In conclusion, LUHMES are a robust neuronal model with adaptable phenotype and high value for neurodevelopmental studies, disease modeling and neuropharmacology. © 2011 The Authors. Journal of Neurochemistry © 2011 International Society for Neurochemistry.
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              Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics

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                Author and article information

                Contributors
                marcel.leist@uni-konstanz.de
                Journal
                Arch Toxicol
                Arch. Toxicol
                Archives of Toxicology
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                0340-5761
                1432-0738
                6 July 2020
                6 July 2020
                2020
                : 94
                : 7
                : 2435-2461
                Affiliations
                [1 ]GRID grid.9811.1, ISNI 0000 0001 0658 7699, In Vitro Toxicology and Biomedicine, Department Inaugurated by the Doerenkamp-Zbinden Foundation, , University of Konstanz, ; Universitaetsstr. 10, 78457 Konstanz, Germany
                [2 ]GRID grid.9811.1, ISNI 0000 0001 0658 7699, Konstanz Research School Chemical Biology, , University of Konstanz, ; 78457 Konstanz, Germany
                [3 ]GRID grid.450522.4, ISNI 0000 0004 0646 8536, BioDetection Systems BV, ; Science Park 406, 1098 XH Amsterdam, The Netherlands
                [4 ]GRID grid.419241.b, ISNI 0000 0001 2285 956X, Leibniz-Institut für Arbeitsforschung an der TU Dortmund, Leibniz Research Center for Working Environment and Human Factors (IfADo), ; Ardeystraße 67, 44139 Dortmund, Germany
                [5 ]GRID grid.10419.3d, ISNI 0000000089452978, Leiden University Medical Center, ; P.O. Box 9600, 2300 RC Leiden, The Netherlands
                [6 ]GRID grid.5132.5, ISNI 0000 0001 2312 1970, Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research, , Leiden University, ; Einsteinweg 55, 2333 CC Leiden, The Netherlands
                [7 ]Edelweiss Connect GmbH, Technology Park Basel, Hochbergerstrasse 60C, 4057 Basel, Switzerland
                [8 ]GRID grid.7700.0, ISNI 0000 0001 2190 4373, Aquatic Ecology and Toxicology Group, Center for Organismal Studies, , University of Heidelberg, ; Im Neuenheimer Feld 504, 69120 Heidelberg, Germany
                [9 ]GRID grid.9811.1, ISNI 0000 0001 0658 7699, CAAT Europe, , University of Konstanz, ; Steinbeis SU-1866, 78457 Konstanz, Germany
                [10 ]GRID grid.424211.0, ISNI 0000 0004 0483 8097, BioTalentum Ltd., ; Aulich Lajos str. 26, Gödöllő, 2100 Hungary
                [11 ]Simcyp Division, Certara UK Limited, Level 2-Acero, 1 Concourse Way, Sheffield, S1 2BJ UK
                [12 ]InSphero AG, Wagistrasse 27, 8952 Schlieren, Switzerland
                [13 ]GRID grid.4714.6, ISNI 0000 0004 1937 0626, Unit of Toxicology Sciences, Swedish Toxicology Sciences Research Center (Swetox), , Karolinska Institutet, ; Forskargatan 20, 151 36 Södertälje, Sweden
                [14 ]GRID grid.12380.38, ISNI 0000 0004 1754 9227, Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, , Vrije Universiteit Amsterdam, ; De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
                [15 ]GRID grid.5596.f, ISNI 0000 0001 0668 7884, Department of Development and Regeneration, Stem Cell Biology and Embryology, Stem Cell Institute Leuven, , KU Leuven, ; O&N IV Herestraat 49, 3000 Leuven, Belgium
                [16 ]GRID grid.5612.0, ISNI 0000 0001 2172 2676, Department of Experimental and Health Sciences, Research Programme on Biomedical Informatics (GRIB), Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), , Universitat Pompeu Fabra, ; 08003 Barcelona, Spain
                [17 ]GRID grid.225360.0, ISNI 0000 0000 9709 7726, European Molecular Biology Laboratory, , European Bioinformatics Institute (EMBL-EBI), ; Wellcome Genome Campus, Cambridge, UK
                [18 ]GRID grid.5132.5, ISNI 0000 0001 2312 1970, Leiden Academic Center for Drug Research, LACDR/Toxicology, , Leiden University, ; PO Box 9500, 2300 RA Leiden, The Netherlands
                [19 ]GRID grid.5596.f, ISNI 0000 0001 0668 7884, Switch Laboratory, Department of Cellular and Molecular Medicine, VIB‐KU Leuven Center for Brain and Disease Research, , KU Leuven, ; Herestraat 49, 3000 Leuven, Belgium
                [20 ]trenzyme GmbH, Byk-Gulden-Str. 2, 78467 Konstanz, Germany
                [21 ]GRID grid.10548.38, ISNI 0000 0004 1936 9377, Department of Biochemistry and Biophysics, , Stockholm University, ; 10691 Stockholm, Sweden
                Author information
                http://orcid.org/0000-0002-0276-4747
                Article
                2802
                10.1007/s00204-020-02802-6
                7367925
                32632539
                a7516df3-0f4e-4814-8918-86485ce1d8ee
                © The Author(s) 2020

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 28 January 2020
                : 3 June 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100010663, H2020 European Research Council;
                Award ID: 681002
                Categories
                In Vitro Systems
                Custom metadata
                © Springer-Verlag GmbH Germany, part of Springer Nature 2020

                Toxicology
                givimp,in vitro toxicology,nuclear receptor,metadata,data processing
                Toxicology
                givimp, in vitro toxicology, nuclear receptor, metadata, data processing

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