Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop

Roland Buesen; Brian N. Chorley; Beatriz da Silva Lima; George Daston; Lize Deferme; Timothy Ebbels; Timothy W. Gant; Amber Goetz; John Greally; Laura Gribaldo; Jörg Hackermüller; Bruno Hubesch; Danyel Jennen; Kamin Johnson; Jun Kanno; Hans Martin Kauffmann; Madeleine Laffont; Patrick McMullen; Richard Meehan; Mark Pemberton; Stefania Perdichizzi; Aldert H. Piersma; Ursula G. Sauer; Kerstin Schmidt; Hervé Seitz; Kayo Sumida; Knut E. Tollefsen; Weida Tong; Tewes Tralau; Ben van Ravenzwaay; Ralf J.M. Weber; Andrew Worth; Carole Yauk; Alan Poole

doi:10.1016/j.yrtph.2017.09.002

Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop

Roland Buesen, Brian N. Chorley, Beatriz da Silva Lima, George Daston, Lize Deferme, Timothy Ebbels, Timothy W. Gant, Amber Goetz, John Greally, Laura Gribaldo, Jörg Hackermüller, Bruno Hubesch, Danyel Jennen, Kamin Johnson, Jun Kanno, Hans Martin Kauffmann, Madeleine Laffont, Patrick McMullen, Richard Meehan, Mark PembertonStefania Perdichizzi, Aldert H. Piersma, Ursula G. Sauer, Kerstin Schmidt, Hervé Seitz, Kayo Sumida, Knut E. Tollefsen, Weida Tong, Tewes Tralau, Ben van Ravenzwaay, Ralf J.M. Weber, Andrew Worth, Carole Yauk, Alan Poole^*

^*Corresponding author for this work

HP: Toxicology

Research output: Contribution to journal › Article › peer-review

85 Citations (Scopus)

Abstract

Prevailing knowledge gaps in linking specific molecular changes to apical outcomes and methodological uncertainties in the generation, storage, processing, and interpretation of 'omics data limit the application of 'omics technologies in regulatory toxicology. Against this background, the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) convened a workshop Applying 'omics technologies in chemicals risk assessment that is reported herein. Ahead of the workshop, multi-expert teams drafted frameworks on best practices for (i) a Good-Laboratory Practice-like context for collecting, storing and curating 'omics data; (ii) the processing of 'omics data; and (iii) weight-of-evidence approaches for integrating 'omics data. The workshop participants confirmed the relevance of these Frameworks to facilitate the regulatory applicability and use of 'omics data, and the workshop discussions provided input for their further elaboration. Additionally, the key objective (iv) to establish approaches to connect 'omics perturbations to phenotypic alterations was addressed. Generally, it was considered promising to strive to link gene expression changes and pathway perturbations to the phenotype by mapping them to specific adverse outcome pathways. While further work is necessary before gene expression changes can be used to establish safe levels of substance exposure, the ECETOC workshop provided important incentives towards achieving this goal.

Original language	English
Pages (from-to)	S3-S13
Journal	Regulatory Toxicology and Pharmacology
Volume	91
DOIs	https://doi.org/10.1016/j.yrtph.2017.09.002
Publication status	Published - Dec 2017

Bibliographical note

Funding Information:
The content described in this article has been reviewed by the National Health and Environmental Research Laboratory of the U.S. Environmental Protection Agency and approved for publication. Approval does not signify that the contents necessarily reflect the views and the policies of the Agency. Mention of trade names or commercial products does not constitute endorsement or recommendation for use. The views presented in this article do not necessarily reflect current or future opinion or policy of the U.S. Food and Drug Administration. Any mention of commercial products is for clarification and not intended as an endorsement. LG and AW are staff members of the Commission. The opinions expressed are those of the authors and do not necessarily reflect the official views of the European Commission.

Publisher Copyright:
© 2017

Keywords

Adverse outcome pathway (AOP)
Differentially expressed genes
Gene expression
Good laboratory practice (GLP)
Metabolomics
Mode-of-action (MoA)
Regulatory toxicology
Transcriptomics
Weight-of-evidence (WoE)

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Buesen, R., Chorley, B. N., da Silva Lima, B., Daston, G., Deferme, L., Ebbels, T., Gant, T. W., Goetz, A., Greally, J., Gribaldo, L., Hackermüller, J., Hubesch, B., Jennen, D., Johnson, K., Kanno, J., Kauffmann, H. M., Laffont, M., McMullen, P., Meehan, R., ... Poole, A. (2017). Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop. Regulatory Toxicology and Pharmacology, 91, S3-S13. https://doi.org/10.1016/j.yrtph.2017.09.002

@article{a87e9994e4b448509c922fc2ed6d1d6d,

title = "Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop",

abstract = "Prevailing knowledge gaps in linking specific molecular changes to apical outcomes and methodological uncertainties in the generation, storage, processing, and interpretation of 'omics data limit the application of 'omics technologies in regulatory toxicology. Against this background, the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) convened a workshop Applying 'omics technologies in chemicals risk assessment that is reported herein. Ahead of the workshop, multi-expert teams drafted frameworks on best practices for (i) a Good-Laboratory Practice-like context for collecting, storing and curating 'omics data; (ii) the processing of 'omics data; and (iii) weight-of-evidence approaches for integrating 'omics data. The workshop participants confirmed the relevance of these Frameworks to facilitate the regulatory applicability and use of 'omics data, and the workshop discussions provided input for their further elaboration. Additionally, the key objective (iv) to establish approaches to connect 'omics perturbations to phenotypic alterations was addressed. Generally, it was considered promising to strive to link gene expression changes and pathway perturbations to the phenotype by mapping them to specific adverse outcome pathways. While further work is necessary before gene expression changes can be used to establish safe levels of substance exposure, the ECETOC workshop provided important incentives towards achieving this goal.",

keywords = "Adverse outcome pathway (AOP), Differentially expressed genes, Gene expression, Good laboratory practice (GLP), Metabolomics, Mode-of-action (MoA), Regulatory toxicology, Transcriptomics, Weight-of-evidence (WoE)",

author = "Roland Buesen and Chorley, {Brian N.} and {da Silva Lima}, Beatriz and George Daston and Lize Deferme and Timothy Ebbels and Gant, {Timothy W.} and Amber Goetz and John Greally and Laura Gribaldo and J{\"o}rg Hackerm{\"u}ller and Bruno Hubesch and Danyel Jennen and Kamin Johnson and Jun Kanno and Kauffmann, {Hans Martin} and Madeleine Laffont and Patrick McMullen and Richard Meehan and Mark Pemberton and Stefania Perdichizzi and Piersma, {Aldert H.} and Sauer, {Ursula G.} and Kerstin Schmidt and Herv{\'e} Seitz and Kayo Sumida and Tollefsen, {Knut E.} and Weida Tong and Tewes Tralau and {van Ravenzwaay}, Ben and Weber, {Ralf J.M.} and Andrew Worth and Carole Yauk and Alan Poole",

note = "Funding Information: The content described in this article has been reviewed by the National Health and Environmental Research Laboratory of the U.S. Environmental Protection Agency and approved for publication. Approval does not signify that the contents necessarily reflect the views and the policies of the Agency. Mention of trade names or commercial products does not constitute endorsement or recommendation for use. The views presented in this article do not necessarily reflect current or future opinion or policy of the U.S. Food and Drug Administration. Any mention of commercial products is for clarification and not intended as an endorsement. LG and AW are staff members of the Commission. The opinions expressed are those of the authors and do not necessarily reflect the official views of the European Commission. Publisher Copyright: {\textcopyright} 2017",

year = "2017",

month = dec,

doi = "10.1016/j.yrtph.2017.09.002",

language = "English",

volume = "91",

pages = "S3--S13",

journal = "Regulatory Toxicology and Pharmacology",

issn = "0273-2300",

publisher = "Elsevier",

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Buesen, R, Chorley, BN, da Silva Lima, B, Daston, G, Deferme, L, Ebbels, T, Gant, TW, Goetz, A, Greally, J, Gribaldo, L, Hackermüller, J, Hubesch, B, Jennen, D, Johnson, K, Kanno, J, Kauffmann, HM, Laffont, M, McMullen, P, Meehan, R, Pemberton, M, Perdichizzi, S, Piersma, AH, Sauer, UG, Schmidt, K, Seitz, H, Sumida, K, Tollefsen, KE, Tong, W, Tralau, T, van Ravenzwaay, B, Weber, RJM, Worth, A, Yauk, C & Poole, A 2017, 'Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop', Regulatory Toxicology and Pharmacology, vol. 91, pp. S3-S13. https://doi.org/10.1016/j.yrtph.2017.09.002

TY - JOUR

T1 - Applying 'omics technologies in chemicals risk assessment

T2 - Report of an ECETOC workshop

AU - Buesen, Roland

AU - Chorley, Brian N.

AU - da Silva Lima, Beatriz

AU - Daston, George

AU - Deferme, Lize

AU - Ebbels, Timothy

AU - Gant, Timothy W.

AU - Goetz, Amber

AU - Greally, John

AU - Gribaldo, Laura

AU - Hackermüller, Jörg

AU - Hubesch, Bruno

AU - Jennen, Danyel

AU - Johnson, Kamin

AU - Kanno, Jun

AU - Kauffmann, Hans Martin

AU - Laffont, Madeleine

AU - McMullen, Patrick

AU - Meehan, Richard

AU - Pemberton, Mark

AU - Perdichizzi, Stefania

AU - Piersma, Aldert H.

AU - Sauer, Ursula G.

AU - Schmidt, Kerstin

AU - Seitz, Hervé

AU - Sumida, Kayo

AU - Tollefsen, Knut E.

AU - Tong, Weida

AU - Tralau, Tewes

AU - van Ravenzwaay, Ben

AU - Weber, Ralf J.M.

AU - Worth, Andrew

AU - Yauk, Carole

AU - Poole, Alan

N1 - Funding Information: The content described in this article has been reviewed by the National Health and Environmental Research Laboratory of the U.S. Environmental Protection Agency and approved for publication. Approval does not signify that the contents necessarily reflect the views and the policies of the Agency. Mention of trade names or commercial products does not constitute endorsement or recommendation for use. The views presented in this article do not necessarily reflect current or future opinion or policy of the U.S. Food and Drug Administration. Any mention of commercial products is for clarification and not intended as an endorsement. LG and AW are staff members of the Commission. The opinions expressed are those of the authors and do not necessarily reflect the official views of the European Commission. Publisher Copyright: © 2017

PY - 2017/12

Y1 - 2017/12

N2 - Prevailing knowledge gaps in linking specific molecular changes to apical outcomes and methodological uncertainties in the generation, storage, processing, and interpretation of 'omics data limit the application of 'omics technologies in regulatory toxicology. Against this background, the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) convened a workshop Applying 'omics technologies in chemicals risk assessment that is reported herein. Ahead of the workshop, multi-expert teams drafted frameworks on best practices for (i) a Good-Laboratory Practice-like context for collecting, storing and curating 'omics data; (ii) the processing of 'omics data; and (iii) weight-of-evidence approaches for integrating 'omics data. The workshop participants confirmed the relevance of these Frameworks to facilitate the regulatory applicability and use of 'omics data, and the workshop discussions provided input for their further elaboration. Additionally, the key objective (iv) to establish approaches to connect 'omics perturbations to phenotypic alterations was addressed. Generally, it was considered promising to strive to link gene expression changes and pathway perturbations to the phenotype by mapping them to specific adverse outcome pathways. While further work is necessary before gene expression changes can be used to establish safe levels of substance exposure, the ECETOC workshop provided important incentives towards achieving this goal.

AB - Prevailing knowledge gaps in linking specific molecular changes to apical outcomes and methodological uncertainties in the generation, storage, processing, and interpretation of 'omics data limit the application of 'omics technologies in regulatory toxicology. Against this background, the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) convened a workshop Applying 'omics technologies in chemicals risk assessment that is reported herein. Ahead of the workshop, multi-expert teams drafted frameworks on best practices for (i) a Good-Laboratory Practice-like context for collecting, storing and curating 'omics data; (ii) the processing of 'omics data; and (iii) weight-of-evidence approaches for integrating 'omics data. The workshop participants confirmed the relevance of these Frameworks to facilitate the regulatory applicability and use of 'omics data, and the workshop discussions provided input for their further elaboration. Additionally, the key objective (iv) to establish approaches to connect 'omics perturbations to phenotypic alterations was addressed. Generally, it was considered promising to strive to link gene expression changes and pathway perturbations to the phenotype by mapping them to specific adverse outcome pathways. While further work is necessary before gene expression changes can be used to establish safe levels of substance exposure, the ECETOC workshop provided important incentives towards achieving this goal.

KW - Adverse outcome pathway (AOP)

KW - Differentially expressed genes

KW - Gene expression

KW - Good laboratory practice (GLP)

KW - Metabolomics

KW - Mode-of-action (MoA)

KW - Regulatory toxicology

KW - Transcriptomics

KW - Weight-of-evidence (WoE)

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DO - 10.1016/j.yrtph.2017.09.002

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SN - 0273-2300

VL - 91

SP - S3-S13

JO - Regulatory Toxicology and Pharmacology

JF - Regulatory Toxicology and Pharmacology

ER -

Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop

Abstract

Bibliographical note

Keywords

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