Toward Precision Toxicology: New Approach Methodologies for Chemical Safety

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Stakeholder-driven priorities document published by SAG

We will take advantage of our first kickoff meeting to elaborate the report to highlight SAG roles in developing longterm project applications and bring their own sectors and organisations priorities in line with the overall PrecisionTox goal and Project objectives

Protocols for routine and higher-throughput processing of experimental samples for multi-omics analysis

Written Standard Operating Protocols will be written that are version controlled and that provide a stepbystep set of instructions on how to conduct automated and highthroughput extractions for RNA and metabolite analysis for each of the NSOs and human cell lines A detailed description on how to incorporate a beadbased tissue and cell homogeniser and stateoftheart liquid handling robotics will be included

First loaded database and associated schema

First version of the central database for the PrecisionTox project will be created for the purposes of managing all of the data produced by or used by the consortium This database will allow fast and relevant queries by defining links between chemicals genesproteins phenotypes and all of the associated information that can be obtained from existing external sources In addition to simple textbased queries it will offer sequence eg BLAST and chemoinformatics eg Open Babel RDKit CDK searches

Project website

We will first explore alternatives for web frameworks, consult graphic designers and launch the website with content by M3. The website will include a presentation of the project objectives and partners, a repository for open access peer reviewed publication (subject to dissemination permissions from the Project), newsletters, links to partners websites, regular updates regarding the project developments and activities (events, webinars), and will embed videos, podcasts, articles and press releases.

Data Management Plan

Written Data Management Plan DMP that incorporates the outputs of the WPs following H2020 project guidelines defining a strategy that ensures findability accessibility interoperability and reusability of all digital asset ensuring FAIRness in all phases of the data life cycle ie data generation curation storage processing handling metadata and dissemination of and access to the project data The report will document the data format specifications terminologies and data repositories vetted by the community and relevant to the project A first initial plan will be formulated at month 12 and the final version of the PrecisionTox Data Management Plan will be made available at month 36

Publications

Zebrafish regulatory genomic resources for disease modelling and regeneration

Auteurs: Ada Jimenez Gonzalez; Damir Baranasic; Ferenc Müller
Publié dans: Disease Models & Mechanisms, Numéro Volume 16, Numéro 8, 2023, ISSN 1754-8411
Éditeur: Company of Biologists
DOI: 10.1242/dmm.050280

Reactivity of Acrylamides Causes Cytotoxicity and Activates Oxidative Stress Response

Auteurs: Julia Huchthausen, Beate I. Escher*, Nico Grasse, Maria König, Stephan Beil, and Luise Henneberger
Publié dans: Chemical Research in Toxicology, Numéro Volume 36, 2023, Page(s) 1374-1385, ISSN 0893-228X
Éditeur: American Chemical Society
DOI: 10.1021/acs.chemrestox.3c00115

Assessment of Chemical Toxicity in Adult <em>Drosophila Melanogaster</em>

Auteurs: Jessica M. Holsopple; Shannon R. Smoot; Ellen M. Popodi; John K. Colbourne; Joseph R. Shaw; Brian Oliver; Thomas C. Kaufman; Jason M. Tennessen
Publié dans: JoVE, Numéro 193, 2023, ISSN 1940-087X
Éditeur: MYJoVE Corporation
DOI: 10.3791/65029

ELIXIR and Toxicology: a community in development

Auteurs: Marvin Martens; Rob Stierum; Emma L. Schymanski; Chris T. Evelo; Reza Aalizadeh; Hristo Aladjov; Kasia Arturi; Karine Audouze; Pavel Babica; Karel Berka; Jos Bessems; Ludek Blaha; Evan E Bolton; Montserrat Cases; Dimitrios Damalas; Kirtan Dave; Marco Dilger; Thomas Exner; Daan P. Geerke; Roland C. Grafström; Alasdair J. G. Gray; John M. Hancock; Henner Hollert; Nina Jeliazkova; Danyel Jennen; Fab
Publié dans: F1000Research, Numéro 1, 2021, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.74502.1

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Auteurs: Damir Baranasic; Matthias Hörtenhuber; Piotr J. Balwierz; Tobias Zehnder; Abdul Kadir Mukarram; Chirag Nepal; Csilla Várnai; Yavor Hadzhiev; Ada Jimenez-Gonzalez; Nan Li; Joseph Wragg; Fabio M. D’Orazio; Dorde Relic; Mikhail Pachkov; Noelia Díaz; Benjamín Hernández-Rodríguez; Zelin Chen; Marcus Stoiber; Michaël Dong; Irene Stevens; Samuel E. Ross; Anne Eagle; Ryan Martin; Oluwapelumi Obas
Publié dans: Nature Genetics, Numéro Volume 54, 2022, Page(s) 1037-1050, ISSN 1061-4036
Éditeur: Nature Publishing Group
DOI: 10.1038/s41588-022-01089-w

Toxicity by descent: A comparative approach for chemical hazard assessment

Auteurs: John K. Colbourne, Joseph R. Shaw, Elena Sostare, Claudia Rivetti, Romain Derelle, Rosemary Barnett, Bruno Campos, Carlie LaLone, Mark R. Viant, Geoff Hodges,
Publié dans: Environmental Advances, Numéro Volume 9, 2022, ISSN 2666-7657
Éditeur: Elsevier BV
DOI: 10.1016/j.envadv.2022.100287

Modernizing persistence–bioaccumulation–toxicity (PBT) assessment with high throughput animal-free methods

Auteurs: Escher, Beate I; Altenburger, Rolf; Blüher, Matthias; Colbourne, John K; Ebinghaus, Ralf; Fantke, Peter; Hein, Michaela; Köck, Wolfgang; Kümmerer, Klaus; Leipold, Sina; Li, Xiaojing; Scheringer, Martin; Scholz, Stefan; Schloter, Michael; Schweizer, Pia-Johanna; Tal, Tamara; Tetko, Igor; Traidl-Hoffmann, Claudia; Wick, Lukas Y; Fenner, Kathrin
Publié dans: Archives of Toxicology, Numéro Volume 97, 2023, Page(s) 1267-1283, ISSN 0340-5761
Éditeur: Springer Verlag
DOI: 10.1007/s00204-023-03485-5

Precision toxicology: new approach methodologies for chemical safety

Auteurs: Aleksandra Cavoski, John Colbourne, Laura Holden, Robert Lee
Publié dans: Bio-Science Law Review, Numéro Volume 19, Numéro 3, 2024, Page(s) 101-107, ISSN 1365-8867
Éditeur: Lawtext Publishing Ltd

The Precision Toxicology initiative

Auteurs: The PrecisionTox Consortium
Publié dans: Toxicology Letters, Numéro Volume 383, 2023, Page(s) 33-42, ISSN 0378-4274
Éditeur: Elsevier BV
DOI: 10.1016/j.toxlet.2023.05.004

Knowledge-Driven Approaches to Create the MTox700+ Metabolite Panel for Predicting Toxicity

Auteurs: Elena Sostare, Thomas N Lawson, Lucy R Saunders, John K Colbourne, Ralf J M Weber, Tomasz Sobanski, Mark R Viant
Publié dans: Toxicological Sciences, Numéro Volume 186, Numéro 2, 2022, Page(s) 208-220, ISSN 1096-6080
Éditeur: Oxford University Press
DOI: 10.1093/toxsci/kfac007

The hologenome of <i>Daphnia magna</i> reveals possible DNA methylation and microbiome-mediated evolution of the host genome

Auteurs: Anurag Chaturvedi; Xiaojing Li; Vignesh Dhandapani; Hollie Marshall; Stephen Kissane; Maria Cuenca-Cambronero; Giovanni Asole; Ferriol Calvet; Marina Ruiz-Romero; Paolo Marangio; Roderic Guigó; Daria Rago; Leda Mirbahai; Niamh Eastwood; John K Colbourne; Jiarui Zhou; Eamonn Mallon; Luisa Orsini
Publié dans: Nucleic Acids Research, Numéro Volume 51, Numéro 18, 2023, Page(s) 9785-9803, ISSN 1096-6080
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad685

Reviewing science-based decisions: CWS Powder Coatings GmbH v European Commission

Auteurs: Aleksandra Cavoski, Laura Holden, Robert Lee
Publié dans: Environmental Liability - Law, Policy and Practice, Numéro Volume 28, Numéro 1, 2023, Page(s) 16-22, ISSN 0966-2030
Éditeur: Lawtext Publishing Ltd

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