Theme (Concept) paper ‐ Application of OMICS and BIOINFORMATICS Approaches: Towards Next Generation Risk Assessment

Fabrega, Julia; Guerra, Beatriz; Heppner, Claudia; Hugas, Marta; Iacono, Giovanni; Kass, Georges; Kleiner, Juliane; Paraskevopoulos, Konstantinos

doi:10.2903/sp.efsa.2022.e200506

Cited by 7 publications

(6 citation statements)

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“…Furthermore, the comprehensive molecular characterisation and risk assessment should also comprise “Omics” (such as transcriptomics, proteomics and metabolomics) as discussed by EFSA ( EFSA et al, 2022c ).…”

Section: Discussionmentioning

confidence: 99%

“…As DNA sequencing will not always allow the identification of the associated unintended biological effects, additional methods, such as transcriptomics and metabolomics, should be used to draw reliable conclusions [see ( Kawall et al, 2020 ; EFSA et al, 2022c )]. If no unintended genetic alterations are detected that are specific to NGT processes, risk assessment may focus on the intended changes.…”

Section: Consequences For a Comprehensive Molecular Characterisation ...mentioning

confidence: 99%

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A perspective from the EU: unintended genetic changes in plants caused by NGT—their relevance for a comprehensive molecular characterisation and risk assessment

Koller,

Cieslak

2023

Front. Bioeng. Biotechnol.

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Several regions in the world are currently holding discussions in regard to the regulation of new genomic techniques (NGTs) and their application in agriculture. The European Commission, for instance, is proposing the introduction of specific regulation for NGT plants. Various questions need to be answered including e.g., the extent to which NGT-induced intended and unintended genetic modifications must be subjected to a mandatory risk assessment as part of an approval procedure. This review mostly focuses on findings in regard to unintended genetic changes that can be caused by the application of NGTs. More specifically, the review deals with the application of the nuclease CRISPR/Cas, which is currently the most important tool for developing NGT plants, and its potential to introduce double strand breaks (DSBs) at a targeted DNA sequence. For this purpose, we identified the differences in comparison to non-targeted mutagenesis methods used in conventional breeding. The review concludes that unintended genetic changes caused by NGT processes are relevant to risk assessment. Due to the technical characteristics of NGTs, the sites of the unintended changes, their genomic context and their frequency (in regard to specific sites) mean that the resulting gene combinations (intended or unintended) may be unlikely to occur with conventional methods. This, in turn, implies that the biological effects (phenotypes) can also be different and may cause risks to health and the environment. Therefore, we conclude that the assessment of intended as well as unintended genetic changes should be part of a mandatory comprehensive molecular characterisation and risk assessment of NGT plants that are meant for environmental releases or for market authorisation.

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Section: Discussionmentioning

confidence: 99%

Section: Consequences For a Comprehensive Molecular Characterisation ...mentioning

confidence: 99%

A perspective from the EU: unintended genetic changes in plants caused by NGT—their relevance for a comprehensive molecular characterisation and risk assessment

Koller,

Cieslak

2023

Front. Bioeng. Biotechnol.

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“…Here, it was suggested that to preserve the biological, genetic, and cultural services that the microbiome provides, microbial communities should be protected via the assessment of the impacts of PPPs on “diversity.” Diversity, in this case, is defined in the scientific opinion document as either phylogenetic or functional, introducing the potential for including microbial community composition within a PPP risk assessment context. This suggestion was further supported in a recent EFSA conceptual paper in which the intention to explore incorporation of the impacts of chemicals on soil bacterial communities was explicitly stated (European Food Safety Authority et al, 2022). This, therefore, indicates the possibility that changes in microbial community composition and diversity may become an endpoint in a future European PPP risk assessment.…”

Section: Introductionmentioning

confidence: 87%

Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome

Sweeney

Kaushik

Bottoms

2023

Integr Envir Assess & Manag

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There is increasing interest in further developing the plant protection product (PPP) environmental risk assessment, particularly within the European Union, to include the assessment of soil microbial community composition, as measured by metabarcoding approaches. However, to date, there has been little discussion as to how this could be implemented in a standardized, reliable, and robust manner suitable for regulatory decision‐making. Introduction of metabarcoding‐based assessments of the soil microbiome into the PPP risk assessment would represent a significant increase in the degree of complexity of the data that needs to be processed and analyzed in comparison to the existing risk assessment on in‐soil organisms. The bioinformatics procedures to process DNA sequences into community compositional data sets currently lack standardization, while little information exists on how these data should be used to generate regulatory endpoints and the ways in which these endpoints should be interpreted. Through a thorough and critical review, we explore these challenges. We conclude that currently, we do not have a sufficient degree of standardization or understanding of the required bioinformatics and data analysis procedures to consider their use in an environmental risk assessment context. However, we highlight critical knowledge gaps and the further research required to understand whether metabarcoding‐based assessments of the soil microbiome can be utilized in a statistically and ecologically relevant manner within a PPP risk assessment. Only once these challenges are addressed can we consider if and how we should use metabarcoding as a tool for regulatory decision‐making to assess and monitor ecotoxicological effects on soil microorganisms within an environmental risk assessment of PPPs. Integr Environ Assess Manag 2023;00:1–22. © 2023 SETAC

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“…One of the major hurdles is the transferability of results from, for example, in vitro cell assays to a whole organism [ 98 ]. To overcome these problems, stepwise approaches in adverse outcome pathways (AOP) are used to build a risk assessment from a variety of independent results [ 4 , 47 ]. The OECD, among others, is enabling globally harmonised principles and supports the development of the NGRA, also for microbial pesticides [ 16 , 77 ].…”

Section: Introductionmentioning

confidence: 99%

Toxicological evaluation of microbial secondary metabolites in the context of European active substance approval for plant protection products

Paege,

Feustel,

Marx-Stoelting

2024

Environ Health

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Risk assessment (RA) of microbial secondary metabolites (SM) is part of the EU approval process for microbial active substances (AS) used in plant protection products (PPP). As the number of potentially produced microbial SM may be high for a certain microbial strain and existing information on the metabolites often are low, data gaps are frequently identified during the RA. Often, RA cannot conclusively clarify the toxicological relevance of the individual substances. This work presents data and RA conclusions on four metabolites, Beauvericin, 2,3-deepoxy-2,3-didehydro-rhizoxin (DDR), Leucinostatin A and Swainsonin in detail as examples for the challenging process of RA. To overcome the problem of incomplete assessment reports, RA of microbial AS for PPP is in need of new approaches. In view of the Next Generation Risk Assessment (NGRA), the combination of literature data, omic-methods, in vitro and in silico methods combined in adverse outcome pathways (AOPs) can be used for an efficient and targeted identification and assessment of metabolites of concern (MoC).

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Theme (Concept) paper ‐ Application of OMICS and BIOINFORMATICS Approaches: Towards Next Generation Risk Assessment

Abstract: OMICS and BIOINFORMATICS Approaches for Next Generation Risk Assessmentwww.efsa.europa.eu/publications 2 EFSA Supporting publication 2022.e200506Acknowledgements: EFSA wishes to thank the following for drafting the scientific output: Also, Jaime

Cited by 7 publications

References 0 publications

A perspective from the EU: unintended genetic changes in plants caused by NGT—their relevance for a comprehensive molecular characterisation and risk assessment

A perspective from the EU: unintended genetic changes in plants caused by NGT—their relevance for a comprehensive molecular characterisation and risk assessment

Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome

Toxicological evaluation of microbial secondary metabolites in the context of European active substance approval for plant protection products

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