Literature DB >> 34333066

Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology.

Joshua A Harrill1, Mark R Viant2, Carole L Yauk3, Magdalini Sachana4, Timothy W Gant5, Scott S Auerbach6, Richard D Beger7, Mounir Bouhifd8, Jason O'Brien9, Lyle Burgoon10, Florian Caiment11, Donatella Carpi12, Tao Chen7, Brian N Chorley13, John Colbourne14, Raffaella Corvi12, Laurent Debrauwer15, Claire O'Donovan16, Timothy M D Ebbels17, Drew R Ekman18, Frank Faulhammer19, Laura Gribaldo12, Gina M Hilton20, Stephanie P Jones9, Aniko Kende21, Thomas N Lawson22, Sofia B Leite12, Pim E G Leonards23, Mirjam Luijten24, Alberto Martin8, Laura Moussa25, Serge Rudaz26, Oliver Schmitz27, Tomasz Sobanski8, Volker Strauss19, Monica Vaccari28, Vikrant Vijay7, Ralf J M Weber14, Antony J Williams13, Andrew Williams29, Russell S Thomas13, Maurice Whelan12.   

Abstract

Omics methodologies are widely used in toxicological research to understand modes and mechanisms of toxicity. Increasingly, these methodologies are being applied to questions of regulatory interest such as molecular point-of-departure derivation and chemical grouping/read-across. Despite its value, widespread regulatory acceptance of omics data has not yet occurred. Barriers to the routine application of omics data in regulatory decision making have been: 1) lack of transparency for data processing methods used to convert raw data into an interpretable list of observations; and 2) lack of standardization in reporting to ensure that omics data, associated metadata and the methodologies used to generate results are available for review by stakeholders, including regulators. Thus, in 2017, the Organisation for Economic Co-operation and Development (OECD) Extended Advisory Group on Molecular Screening and Toxicogenomics (EAGMST) launched a project to develop guidance for the reporting of omics data aimed at fostering further regulatory use. Here, we report on the ongoing development of the first formal reporting framework describing the processing and analysis of both transcriptomic and metabolomic data for regulatory toxicology. We introduce the modular structure, content, harmonization and strategy for trialling this reporting framework prior to its publication by the OECD. Published by Elsevier Inc.

Entities:  

Keywords:  MRF; Metabolomics; Metabolomics reporting framework; OECD; QA/QC; Regulatory; TRF; Toxicology; Transcriptomics; Transcriptomics reporting framework

Mesh:

Year:  2021        PMID: 34333066      PMCID: PMC8808338          DOI: 10.1016/j.yrtph.2021.105020

Source DB:  PubMed          Journal:  Regul Toxicol Pharmacol        ISSN: 0273-2300            Impact factor:   3.598


  38 in total

1.  A Set of Six Gene Expression Biomarkers Identify Rat Liver Tumorigens in Short-term Assays.

Authors:  J Christopher Corton; Thomas Hill; Jeffrey J Sutherland; James L Stevens; John Rooney
Journal:  Toxicol Sci       Date:  2020-09-01       Impact factor: 4.849

2.  Metabolomics as read-across tool: A case study with phenoxy herbicides.

Authors:  B van Ravenzwaay; S Sperber; O Lemke; E Fabian; F Faulhammer; H Kamp; W Mellert; V Strauss; A Strigun; E Peter; M Spitzer; T Walk
Journal:  Regul Toxicol Pharmacol       Date:  2016-09-13       Impact factor: 3.271

3.  Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry.

Authors:  Warwick B Dunn; David Broadhurst; Paul Begley; Eva Zelena; Sue Francis-McIntyre; Nadine Anderson; Marie Brown; Joshau D Knowles; Antony Halsall; John N Haselden; Andrew W Nicholls; Ian D Wilson; Douglas B Kell; Royston Goodacre
Journal:  Nat Protoc       Date:  2011-06-30       Impact factor: 13.491

4.  Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity.

Authors:  Todd J Zurlinden; Katerine S Saili; Nathaniel Rush; Parth Kothiya; Richard S Judson; Keith A Houck; E Sidney Hunter; Nancy C Baker; Jessica A Palmer; Russell S Thomas; Thomas B Knudsen
Journal:  Toxicol Sci       Date:  2020-04-01       Impact factor: 4.849

5.  Use of connectivity mapping to support read across: A deeper dive using data from 186 chemicals, 19 cell lines and 2 case studies.

Authors:  K Nadira De Abrew; Yuqing K Shan; Xiaohong Wang; Jesse M Krailler; Raghunandan M Kainkaryam; Cathy C Lester; Raja S Settivari; Matthew J LeBaron; Jorge M Naciff; George P Daston
Journal:  Toxicology       Date:  2019-05-21       Impact factor: 4.221

Review 6.  Accelerating the Pace of Chemical Risk Assessment.

Authors:  Robert J Kavlock; Tina Bahadori; Tara S Barton-Maclaren; Maureen R Gwinn; Mike Rasenberg; Russell S Thomas
Journal:  Chem Res Toxicol       Date:  2018-04-06       Impact factor: 3.739

7.  Towards the development of an omics data analysis framework.

Authors:  Marcha Verheijen; Weida Tong; Leming Shi; Timothy W Gant; Bruce Seligman; Florian Caiment
Journal:  Regul Toxicol Pharmacol       Date:  2020-02-19       Impact factor: 3.271

Review 8.  A generic Transcriptomics Reporting Framework (TRF) for 'omics data processing and analysis.

Authors:  Timothy W Gant; Ursula G Sauer; Shu-Dong Zhang; Brian N Chorley; Jörg Hackermüller; Stefania Perdichizzi; Knut E Tollefsen; Ben van Ravenzwaay; Carole Yauk; Weida Tong; Alan Poole
Journal:  Regul Toxicol Pharmacol       Date:  2017-11-04       Impact factor: 3.271

9.  A Targeted Metabolomics-Based Assay Using Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Identifies Structural and Functional Cardiotoxicity Potential.

Authors:  Jessica A Palmer; Alan M Smith; Vitalina Gryshkova; Elizabeth L R Donley; Jean-Pierre Valentin; Robert E Burrier
Journal:  Toxicol Sci       Date:  2020-04-01       Impact factor: 4.849

10.  Considerations for Strategic Use of High-Throughput Transcriptomics Chemical Screening Data in Regulatory Decisions.

Authors:  Joshua Harrill; Imran Shah; R Woodrow Setzer; Derik Haggard; Scott Auerbach; Richard Judson; Russell S Thomas
Journal:  Curr Opin Toxicol       Date:  2019
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  3 in total

Review 1.  Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications.

Authors:  Daniel Desaulniers; Paule Vasseur; Abigail Jacobs; M Cecilia Aguila; Norman Ertych; Miriam N Jacobs
Journal:  Int J Mol Sci       Date:  2021-10-11       Impact factor: 5.923

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

Authors:  Elena Sostare; Thomas N Lawson; Lucy R Saunders; John K Colbourne; Ralf J M Weber; Tomasz Sobanski; Mark R Viant
Journal:  Toxicol Sci       Date:  2022-03-28       Impact factor: 4.849

3.  Mechanistic Interrogation of Cell Transformation In Vitro: The Transformics Assay as an Exemplar of Oncotransformation.

Authors:  Gelsomina Pillo; Maria Grazia Mascolo; Cristina Zanzi; Francesca Rotondo; Stefania Serra; Francesco Bortone; Sandro Grilli; Monica Vaccari; Miriam N Jacobs; Annamaria Colacci
Journal:  Int J Mol Sci       Date:  2022-07-09       Impact factor: 6.208

  3 in total

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