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Development of Proteomics Modules for the OECD Omics Reporting Framework
Citation:
Groh, K., P. Kumarathasan, S. Ayobahan, D. Degli-Esposti, V. Dumit, S. Eilebrecht, V. Engelbrecht, S. Arroyo, N. Jehmlich, P. Kukic, I. Karkossa, T. Leger, A. Salvador, J. Schmidt, K. Schubert, J. Harrill, M. Sachana, AND A. Schaffert. Development of Proteomics Modules for the OECD Omics Reporting Framework. Society of Environmental Toxicology and Chemistry (SETAC) Europe 34th Annual Meeting May 2024, Seville, SPAIN, May 05 - 09, 2024. https://doi.org/10.23645/epacomptox.25992100
Impact/Purpose:
Presentation to the Society of Environmental Toxicology and Chemistry (SETAC) Europe 34th Annual Meeting May 2024
Description:
The OECD Omics Reporting Framework (OORF) was developed to facilitate the regulatory use of omics data from laboratory-based toxicology studies, which is achieved by means of (i) increasing transparency and reproducibility, and (ii) supporting standardization and harmonization. The latter can in turn increase the efficiency of data sharing and promote its use in systematic reviews and meta-analyses. The OORF consists of a narrative guidance and reporting templates that cover the study design and data generation, processing and analysis stages. Additional modules that focus on selected application cases, such as read-across, can also be included. The first edition of OORF, released in November 2023 (see ENV-CBC-MONO(2023)41.en), focused on transcriptomics and metabolomics studies, while proteomics was not covered due to less frequent use in the past. However, since technological capabilities for proteomics analysis have greatly improved recently, the number of studies providing protein-data based insights into toxicity mechanisms and effects is expected to increase rapidly. Therefore, in order to support the application of proteomics data for regulatory purposes, this project aims to develop respective proteomics modules for inclusion in the OORF. The initial scoping, carried out by a group of international experts, prioritized the development of two proteomics-relevant Data Acquisition & Processing Reporting Modules (DAPRMs), namely (1) mass spectrometry-based proteomics (including both global and targeted acquisition, as well as label-free and label-based quantification methods), and (2) affinity proteomics. Gel-based proteomics were excluded from the scope, as this technique is rarely used for regulatory toxicology studies, if at all. In addition, the Data Analysis Reporting Modules (DARMs) currently present in the OORF will be reviewed and updated to enable their application for reporting proteomics data as well. The inclusion of proteomics-specific modules in the OORF is expected to facilitate the maturation of proteomics-based toxicity assessment methods and allow regulatory consideration of proteomics data. It thus contributes to delivering on the original vision of building a comprehensive OORF that covers the major omics data types most frequently collected in chemical toxicity studies, thus enabling an efficient and unbiased use of these data streams in chemical hazard and risk assessments performed by regulators, industry and other stakeholders. This abstract does not reflect US EPA policy.
URLs/Downloads:
DOI: Development of Proteomics Modules for the OECD Omics Reporting Framework
GROH_ET_AL_SETAC_EUROPE_2024_POSTER_PRF_V240423.PDF (PDF, NA pp, 1299.467 KB, about PDF)