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

Joshua A. Harrill; Mark R. Viant; Carole L. Yauk; Magdalini Sachana; Timothy W. Gant; Scott S. Auerbach; Richard D. Beger; Mounir Bouhifd; Jason O'Brien; Lyle Burgoon; Florian Caiment; Donatella Carpi; Tao Chen; Brian N. Chorley; John Colbourne; Raffaella Corvi; Laurent Debrauwer; Claire O'Donovan; Timothy M.D. Ebbels; Drew R. Ekman; Frank Faulhammer; Laura Gribaldo; Gina M. Hilton; Stephanie P. Jones; Aniko Kende; Thomas N. Lawson; Sofia B. Leite; Pim E.G. Leonards; Mirjam Luijten; Alberto Martin; Laura Moussa; Serge Rudaz; Oliver Schmitz; Tomasz Sobanski; Volker Strauss; Monica Vaccari; Vikrant Vijay; Ralf J.M. Weber; Antony J. Williams; Andrew Williams; Russell S. Thomas; Maurice Whelan

doi:10.1016/j.yrtph.2021.105020

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

Joshua A. Harrill^*, Mark R. Viant, Carole L. Yauk, Magdalini Sachana, Timothy W. Gant, Scott S. Auerbach, Richard D. Beger, Mounir Bouhifd, Jason O'Brien, Lyle Burgoon, Florian Caiment, Donatella Carpi, Tao Chen, Brian N. Chorley, John Colbourne, Raffaella Corvi, Laurent Debrauwer, Claire O'Donovan, Timothy M.D. Ebbels, Drew R. EkmanFrank Faulhammer, Laura Gribaldo, Gina M. Hilton, Stephanie P. Jones, Aniko Kende, Thomas N. Lawson, Sofia B. Leite, Pim E.G. Leonards, Mirjam Luijten, Alberto Martin, Laura Moussa, Serge Rudaz, Oliver Schmitz, Tomasz Sobanski, Volker Strauss, Monica Vaccari, Vikrant Vijay, Ralf J.M. Weber, Antony J. Williams, Andrew Williams, Russell S. Thomas, Maurice Whelan

^*Corresponding author for this work

Biosciences

Research output: Contribution to journal › Comment/debate › peer-review

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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.

Original language	English
Article number	105020
Number of pages	6
Journal	Regulatory Toxicology and Pharmacology
Volume	125
Early online date	29 Jul 2021
DOIs	https://doi.org/10.1016/j.yrtph.2021.105020
Publication status	Published - Oct 2021

Bibliographical note

Funding Information:
TWG was supported by the National Institutes of Health Research under the Environmental Exposures and Health Protection Research Unit co-led from Imperial College London and Public Health England ( https://eeh.hpru.nihr.ac.uk/ ). ML was supported by the Dutch Ministry of Health , Welfare and Support. This work was supported in part by a European Chemicals Agency contract to Michabo Health Science (ECHA/2018/135) and by the European Chemical Industry Council (Cefic; awarded to BASF , Imperial College London , Syngenta , University of Birmingham and Vrije Universiteit Amsterdam ).

Publisher Copyright:
© 2021

Keywords

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

ASJC Scopus subject areas

Toxicology

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Harrill, J. A., Viant, M. R., Yauk, C. L., Sachana, M., Gant, T. W., Auerbach, S. S., Beger, R. D., Bouhifd, M., O'Brien, J., Burgoon, L., Caiment, F., Carpi, D., Chen, T., Chorley, B. N., Colbourne, J., Corvi, R., Debrauwer, L., O'Donovan, C., Ebbels, T. M. D., ... Whelan, M. (2021). Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology. Regulatory Toxicology and Pharmacology, 125, Article 105020. Advance online publication. https://doi.org/10.1016/j.yrtph.2021.105020

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title = "Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology",

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.",

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author = "Harrill, {Joshua A.} and Viant, {Mark R.} and Yauk, {Carole L.} and Magdalini Sachana and Gant, {Timothy W.} and Auerbach, {Scott S.} and Beger, {Richard D.} and Mounir Bouhifd and Jason O'Brien and Lyle Burgoon and Florian Caiment and Donatella Carpi and Tao Chen and Chorley, {Brian N.} and John Colbourne and Raffaella Corvi and Laurent Debrauwer and Claire O'Donovan and Ebbels, {Timothy M.D.} and Ekman, {Drew R.} and Frank Faulhammer and Laura Gribaldo and Hilton, {Gina M.} and Jones, {Stephanie P.} and Aniko Kende and Lawson, {Thomas N.} and Leite, {Sofia B.} and Leonards, {Pim E.G.} and Mirjam Luijten and Alberto Martin and Laura Moussa and Serge Rudaz and Oliver Schmitz and Tomasz Sobanski and Volker Strauss and Monica Vaccari and Vikrant Vijay and Weber, {Ralf J.M.} and Williams, {Antony J.} and Andrew Williams and Thomas, {Russell S.} and Maurice Whelan",

note = "Funding Information: TWG was supported by the National Institutes of Health Research under the Environmental Exposures and Health Protection Research Unit co-led from Imperial College London and Public Health England ( https://eeh.hpru.nihr.ac.uk/ ). ML was supported by the Dutch Ministry of Health , Welfare and Support. This work was supported in part by a European Chemicals Agency contract to Michabo Health Science (ECHA/2018/135) and by the European Chemical Industry Council (Cefic; awarded to BASF , Imperial College London , Syngenta , University of Birmingham and Vrije Universiteit Amsterdam ). Publisher Copyright: {\textcopyright} 2021",

year = "2021",

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doi = "10.1016/j.yrtph.2021.105020",

language = "English",

volume = "125",

journal = "Regulatory Toxicology and Pharmacology",

issn = "0273-2300",

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Harrill, JA, Viant, MR, Yauk, CL, Sachana, M, Gant, TW, Auerbach, SS, Beger, RD, Bouhifd, M, O'Brien, J, Burgoon, L, Caiment, F, Carpi, D, Chen, T, Chorley, BN, Colbourne, J, Corvi, R, Debrauwer, L, O'Donovan, C, Ebbels, TMD, Ekman, DR, Faulhammer, F, Gribaldo, L, Hilton, GM, Jones, SP, Kende, A, Lawson, TN, Leite, SB, Leonards, PEG, Luijten, M, Martin, A, Moussa, L, Rudaz, S, Schmitz, O, Sobanski, T, Strauss, V, Vaccari, M, Vijay, V, Weber, RJM, Williams, AJ, Williams, A, Thomas, RS & Whelan, M 2021, 'Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology', Regulatory Toxicology and Pharmacology, vol. 125, 105020. https://doi.org/10.1016/j.yrtph.2021.105020

TY - JOUR

T1 - Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology

AU - Harrill, Joshua A.

AU - Viant, Mark R.

AU - Yauk, Carole L.

AU - Sachana, Magdalini

AU - Gant, Timothy W.

AU - Auerbach, Scott S.

AU - Beger, Richard D.

AU - Bouhifd, Mounir

AU - O'Brien, Jason

AU - Burgoon, Lyle

AU - Caiment, Florian

AU - Carpi, Donatella

AU - Chen, Tao

AU - Chorley, Brian N.

AU - Colbourne, John

AU - Corvi, Raffaella

AU - Debrauwer, Laurent

AU - O'Donovan, Claire

AU - Ebbels, Timothy M.D.

AU - Ekman, Drew R.

AU - Faulhammer, Frank

AU - Gribaldo, Laura

AU - Hilton, Gina M.

AU - Jones, Stephanie P.

AU - Kende, Aniko

AU - Lawson, Thomas N.

AU - Leite, Sofia B.

AU - Leonards, Pim E.G.

AU - Luijten, Mirjam

AU - Martin, Alberto

AU - Moussa, Laura

AU - Rudaz, Serge

AU - Schmitz, Oliver

AU - Sobanski, Tomasz

AU - Strauss, Volker

AU - Vaccari, Monica

AU - Vijay, Vikrant

AU - Weber, Ralf J.M.

AU - Williams, Antony J.

AU - Williams, Andrew

AU - Thomas, Russell S.

AU - Whelan, Maurice

N1 - Funding Information: TWG was supported by the National Institutes of Health Research under the Environmental Exposures and Health Protection Research Unit co-led from Imperial College London and Public Health England ( https://eeh.hpru.nihr.ac.uk/ ). ML was supported by the Dutch Ministry of Health , Welfare and Support. This work was supported in part by a European Chemicals Agency contract to Michabo Health Science (ECHA/2018/135) and by the European Chemical Industry Council (Cefic; awarded to BASF , Imperial College London , Syngenta , University of Birmingham and Vrije Universiteit Amsterdam ). Publisher Copyright: © 2021

PY - 2021/10

Y1 - 2021/10

N2 - 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.

AB - 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.

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KW - Metabolomics reporting framework

KW - MRF

KW - OECD

KW - QA/QC

KW - Regulatory

KW - Toxicology

KW - Transcriptomics

KW - Transcriptomics reporting framework

KW - TRF

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U2 - 10.1016/j.yrtph.2021.105020

DO - 10.1016/j.yrtph.2021.105020

M3 - Comment/debate

AN - SCOPUS:85111958766

SN - 0273-2300

VL - 125

JO - Regulatory Toxicology and Pharmacology

JF - Regulatory Toxicology and Pharmacology

M1 - 105020

ER -

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

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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