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How Should Risk-Based Regulation Reflect Current Public Opinion?
Letter
How Should Risk-Based Regulation Reflect Current Public Opinion? Christopher John Pollock1,*
this process there have been concerns expressed about detailed elements (summarised in [2]), but the essential core has remained. The major advantage is that the evidence base is clear, comparable, and open to scrutiny, leading to decisions that are wholly concerned with the effective management of risk. Issues of public concern and choice can be addressed by traceability and labelling regulations and by the local derogation of powers to member states to ban specific GM products. These tools can be used independently of risk analysis and management, although cultivation or use of any organism where a significant additional risk was posed would not be permitted within the EU.
Risk-based regulation of novel agricultural products with public choice manifest via traceability and labelling is a more effective approach than the use of regulatory processes to reflect public concerns, which may not always Currently, the debate about NBTs revolves around whether they ‘count’ be supported by evidence. The Opinion article by Malyska et al. [1] posits that the regulatory milieu around novel agribiotech products should reflect public concerns with the technology and that this will condition discussions about the forthcoming regulation of novel breeding technologies (NBTs). However, the current regulatory framework for genetic modification (within the EU and in many other countries) was established as a risk management process, with public freedoms being promoted via traceability and labelling. Despite attempts by some nongovernmental organisations (NGOs) to shift the basis of regulation away from risk management and towards hazard identification and removal, I believe that it remains in the public interest to maintain effective risk-based regulation and to continue to separate this from delivery of choice via traceability and labelling. Risk-based regulation of genetically modified (GM) organisms to be released into the environment in the EU aims to demonstrate that the novel organism and its growth, harvesting, and processing causes no significant additional risks to human health and the environment compared with the non-GM equivalent within its system. From the beginning of
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Trends in Biotechnology, August 2016, Vol. 34, No. 8
as GM organisms and are thus subsumed into the EU regulatory framework. In my view, this is a sterile argument, since it will come down to considering the detailed wording of documents written well before the technologies were developed. We are already running into regulatory challenges because the initial assumption was that the likelihood of increased risk would be due to the genetic modification technology itself, whereas in practice it is wholly dependent on the novel phenotype within its modified cultivation and processing system. I am not aware of any compelling evidence that the technology used to generate novel phenotypes is per se a hazard that requires specific risk management. By contrast, the novel trait, and the management system within which it is employed, may generate specific risks that need to be managed. Herbicide-tolerant maize grown in an environment where overwintering grain is nonviable and where there are no wild relatives that might acquire the trait is in a radically different management and risk environment to the identical trait present in an outbreeding, overwintering temperate grass with a pool of nearby wild relatives [3]. This is equally valid whether the trait
was introduced by genetic modification (captured by the current EU regulations) or by mutation breeding (exempt from current regulations). The Malyska et al. paper [1] and other recent opinion pieces (e.g., [4]) have downplayed the significance of the debate about regulation being based on phenotype (product) rather than on process (genetic modification, NBTs, etc.). In my opinion, resolving this debate and changing the basis of regulation is crucial if we are to retain effective, evidence-based risk management processes that can cope with both the development of new technology and our increased awareness of the innate plasticity of genomes within populations [2]. The Canadian regulatory system already acknowledges the primacy of product over process and I can think of no compelling scientific reason for not extending this approach. Unfortunately, as the authors of [1] demonstrate, attempts to use risk-based regulation to reflect public or NGO concerns about specific biotechnologies will inevitably lead to a distortion of the debate and a loss of focus on the effective management of risk to human health and to the environment. Additionally, the approach founders in problems of attribution, which are likely to become more acute in the future since a number of NBTs can produce stable changes in genomes that are identical to naturally occurring mutations. By contrast, traceability and labelling regulations already deal with material that cannot be distinguished by chemical or physical tests (e.g., organic produce) and appear to have the confidence of both the buying public and many campaigning NGOs. Finally, it needs to be remembered that conventionally produced novel phenotypes and their modified management systems (e.g., winter-sown cereals) have already produced significant changes in agroecosystems. Risk-based regulation of novel products regardless of the technology used to generate them offers, in my
view, the best opportunity to manage change and improve sustainability. By contrast, the approach outlined by Malyska et al. [1] aims mainly to address current public concerns, including those that may not be supported by evidence. 1
Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
*Correspondence: [email protected] (C.J. Pollock). http://dx.doi.org/10.1016/j.tibtech.2016.05.002 References 1. Malyska, A. et al. (2016) The role of public opinion in shaping trajectories of agricultural biotechnology. Trends Biotechnol. 34, 530–534 2. Pollock, C.J. and Hails, R.S. (2014) The case for reforming the EU regulatory system for GMOs. Trends Biotechnol. 32, 63–64 3. Watrud, L.S. et al. (2004) Evidence for landscape-level, pollen-mediated gene flow from genetically modified creeping bentgrass with CP4 EPSPS as a marker. Proc. Natl. Acad. Sci. U.S.A. 101, 14533–14538 4. Kuzma, J. (2016) Reboot the debate on genetic engineering. Nature 531, 165–167
Forum
Multi-Omics of Single Cells: Strategies and Applications Christoph Bock,1,2,3,* Matthias Farlik,1 and Nathan C. Sheffield1 Most genome-wide assays provide averages across large numbers of cells, but recent technological advances promise to overcome this limitation. Pioneering single-cell assays are now available for genome, epigenome, transcriptome, proteome, and metabolome profiling. Here, we describe how these different dimensions can be combined into multi-omics assays that provide comprehensive profiles of the same cell. Sequencing-based assays yield genomewide data, but at the cost of averaging
across large cell populations and ignoring biologically relevant variability at the level of individual cells. By contrast, imagingbased methods, such as fluorescence microscopy and flow cytometry, provide single-cell resolution, but only for a handful of preselected markers.
same single cell. To obtain high-quality integrated profiles from single cells, further improvements in the efficiencies of the assays will be essential. Separate Different types of biomolecules can be biochemically extracted from the same cell lysate, separated, and independently analyzed. For example, a recent study used biotin-tagged oligo-dT adapters to pull down polyadenylated RNA, which was used for RNA-seq library preparation, while the unbound fraction was amplified and subjected to DNA sequencing [6]. This strategy critically depends on the quality of the separation because all material left in the wrong fraction is lost.
Rapid technological progress is closing this gap, giving rise to powerful assays for genome-wide profiling in single cells. Single-cell sequencing of genomes [1] and transcriptomes [2] is already well established and broadly useful, and the first methods for mapping single-cell epigenomes [3], proteomes [4], and metabolomes [5] are now becoming available. Combining several of these technologies into integrated multi-omic assays of the same single cells will yield unprecedented insights in fundamental biology and Split biomedicine. When accurate biochemical separation is not feasible, the cell lysate can be split and processed independently. For example, a Strategies In contrast to fluorescence-based live cell recent study combined RNA and protein imaging, omics methods, such as next- analysis by splitting the lysate and applygeneration sequencing and mass spec- ing multiplex quantitative PCR for reversetrometry, destroy a cell to analyze it. The transcribed RNAs to one fraction, while first generation of single-cell assays affinity-based proximity extension folselectively measured a single type of bio- lowed by quantitative PCR for the DNA molecule (such as DNA, RNA, chromatin, reporters of the antibodies was used for proteins, or metabolites) while discarding the other fraction [7]. Splitting is concepall other material. However, there is now tually inferior to biochemical separation proof-of-concept that several omics because some material will inevitably be dimensions can be analyzed in parallel lost in the wrong fraction, yet it is the most in the same cell; for example, genome/ general strategy and feasible for many transcriptome or gene/protein levels. We different assays. have identified five basic strategies for the multi-omics profiling of single cells Convert Biochemical conversion between different (Figure 1). omics dimensions makes it possible to analyze them together. For example, Combine Assays that operate on the same or similar bisulfite treatment converts DNA methylbiomolecules may be combined into a ation into DNA sequence information, single protocol. For example, sequencing which can be further combined with prior methods based on nanopores and single treatment with a GpC methyltransferase molecule, real-time (SMRT) technology to capture DNA methylation and nucleoresult in kinetic profiles that not only reflect some positioning in single cells [8]. It is the DNA sequence, but also detect DNA also possible to encode information about methylation. Similarly, carefully optimized the chromosome structure of single cells mass spectrometry assays could provide into DNA sequence information by using a proteome and metabolome data for the protocol that ligates DNA fragments that
Trends in Biotechnology, August 2016, Vol. 34, No. 8
605
How Should Risk-Based Regulation Reflect Current Public Opinion? Christopher John Pollock1,*
this process there have been concerns expressed about detailed elements (summarised in [2]), but the essential core has remained. The major advantage is that the evidence base is clear, comparable, and open to scrutiny, leading to decisions that are wholly concerned with the effective management of risk. Issues of public concern and choice can be addressed by traceability and labelling regulations and by the local derogation of powers to member states to ban specific GM products. These tools can be used independently of risk analysis and management, although cultivation or use of any organism where a significant additional risk was posed would not be permitted within the EU.
Risk-based regulation of novel agricultural products with public choice manifest via traceability and labelling is a more effective approach than the use of regulatory processes to reflect public concerns, which may not always Currently, the debate about NBTs revolves around whether they ‘count’ be supported by evidence. The Opinion article by Malyska et al. [1] posits that the regulatory milieu around novel agribiotech products should reflect public concerns with the technology and that this will condition discussions about the forthcoming regulation of novel breeding technologies (NBTs). However, the current regulatory framework for genetic modification (within the EU and in many other countries) was established as a risk management process, with public freedoms being promoted via traceability and labelling. Despite attempts by some nongovernmental organisations (NGOs) to shift the basis of regulation away from risk management and towards hazard identification and removal, I believe that it remains in the public interest to maintain effective risk-based regulation and to continue to separate this from delivery of choice via traceability and labelling. Risk-based regulation of genetically modified (GM) organisms to be released into the environment in the EU aims to demonstrate that the novel organism and its growth, harvesting, and processing causes no significant additional risks to human health and the environment compared with the non-GM equivalent within its system. From the beginning of
604
Trends in Biotechnology, August 2016, Vol. 34, No. 8
as GM organisms and are thus subsumed into the EU regulatory framework. In my view, this is a sterile argument, since it will come down to considering the detailed wording of documents written well before the technologies were developed. We are already running into regulatory challenges because the initial assumption was that the likelihood of increased risk would be due to the genetic modification technology itself, whereas in practice it is wholly dependent on the novel phenotype within its modified cultivation and processing system. I am not aware of any compelling evidence that the technology used to generate novel phenotypes is per se a hazard that requires specific risk management. By contrast, the novel trait, and the management system within which it is employed, may generate specific risks that need to be managed. Herbicide-tolerant maize grown in an environment where overwintering grain is nonviable and where there are no wild relatives that might acquire the trait is in a radically different management and risk environment to the identical trait present in an outbreeding, overwintering temperate grass with a pool of nearby wild relatives [3]. This is equally valid whether the trait
was introduced by genetic modification (captured by the current EU regulations) or by mutation breeding (exempt from current regulations). The Malyska et al. paper [1] and other recent opinion pieces (e.g., [4]) have downplayed the significance of the debate about regulation being based on phenotype (product) rather than on process (genetic modification, NBTs, etc.). In my opinion, resolving this debate and changing the basis of regulation is crucial if we are to retain effective, evidence-based risk management processes that can cope with both the development of new technology and our increased awareness of the innate plasticity of genomes within populations [2]. The Canadian regulatory system already acknowledges the primacy of product over process and I can think of no compelling scientific reason for not extending this approach. Unfortunately, as the authors of [1] demonstrate, attempts to use risk-based regulation to reflect public or NGO concerns about specific biotechnologies will inevitably lead to a distortion of the debate and a loss of focus on the effective management of risk to human health and to the environment. Additionally, the approach founders in problems of attribution, which are likely to become more acute in the future since a number of NBTs can produce stable changes in genomes that are identical to naturally occurring mutations. By contrast, traceability and labelling regulations already deal with material that cannot be distinguished by chemical or physical tests (e.g., organic produce) and appear to have the confidence of both the buying public and many campaigning NGOs. Finally, it needs to be remembered that conventionally produced novel phenotypes and their modified management systems (e.g., winter-sown cereals) have already produced significant changes in agroecosystems. Risk-based regulation of novel products regardless of the technology used to generate them offers, in my
view, the best opportunity to manage change and improve sustainability. By contrast, the approach outlined by Malyska et al. [1] aims mainly to address current public concerns, including those that may not be supported by evidence. 1
Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
*Correspondence: [email protected] (C.J. Pollock). http://dx.doi.org/10.1016/j.tibtech.2016.05.002 References 1. Malyska, A. et al. (2016) The role of public opinion in shaping trajectories of agricultural biotechnology. Trends Biotechnol. 34, 530–534 2. Pollock, C.J. and Hails, R.S. (2014) The case for reforming the EU regulatory system for GMOs. Trends Biotechnol. 32, 63–64 3. Watrud, L.S. et al. (2004) Evidence for landscape-level, pollen-mediated gene flow from genetically modified creeping bentgrass with CP4 EPSPS as a marker. Proc. Natl. Acad. Sci. U.S.A. 101, 14533–14538 4. Kuzma, J. (2016) Reboot the debate on genetic engineering. Nature 531, 165–167
Forum
Multi-Omics of Single Cells: Strategies and Applications Christoph Bock,1,2,3,* Matthias Farlik,1 and Nathan C. Sheffield1 Most genome-wide assays provide averages across large numbers of cells, but recent technological advances promise to overcome this limitation. Pioneering single-cell assays are now available for genome, epigenome, transcriptome, proteome, and metabolome profiling. Here, we describe how these different dimensions can be combined into multi-omics assays that provide comprehensive profiles of the same cell. Sequencing-based assays yield genomewide data, but at the cost of averaging
across large cell populations and ignoring biologically relevant variability at the level of individual cells. By contrast, imagingbased methods, such as fluorescence microscopy and flow cytometry, provide single-cell resolution, but only for a handful of preselected markers.
same single cell. To obtain high-quality integrated profiles from single cells, further improvements in the efficiencies of the assays will be essential. Separate Different types of biomolecules can be biochemically extracted from the same cell lysate, separated, and independently analyzed. For example, a recent study used biotin-tagged oligo-dT adapters to pull down polyadenylated RNA, which was used for RNA-seq library preparation, while the unbound fraction was amplified and subjected to DNA sequencing [6]. This strategy critically depends on the quality of the separation because all material left in the wrong fraction is lost.
Rapid technological progress is closing this gap, giving rise to powerful assays for genome-wide profiling in single cells. Single-cell sequencing of genomes [1] and transcriptomes [2] is already well established and broadly useful, and the first methods for mapping single-cell epigenomes [3], proteomes [4], and metabolomes [5] are now becoming available. Combining several of these technologies into integrated multi-omic assays of the same single cells will yield unprecedented insights in fundamental biology and Split biomedicine. When accurate biochemical separation is not feasible, the cell lysate can be split and processed independently. For example, a Strategies In contrast to fluorescence-based live cell recent study combined RNA and protein imaging, omics methods, such as next- analysis by splitting the lysate and applygeneration sequencing and mass spec- ing multiplex quantitative PCR for reversetrometry, destroy a cell to analyze it. The transcribed RNAs to one fraction, while first generation of single-cell assays affinity-based proximity extension folselectively measured a single type of bio- lowed by quantitative PCR for the DNA molecule (such as DNA, RNA, chromatin, reporters of the antibodies was used for proteins, or metabolites) while discarding the other fraction [7]. Splitting is concepall other material. However, there is now tually inferior to biochemical separation proof-of-concept that several omics because some material will inevitably be dimensions can be analyzed in parallel lost in the wrong fraction, yet it is the most in the same cell; for example, genome/ general strategy and feasible for many transcriptome or gene/protein levels. We different assays. have identified five basic strategies for the multi-omics profiling of single cells Convert Biochemical conversion between different (Figure 1). omics dimensions makes it possible to analyze them together. For example, Combine Assays that operate on the same or similar bisulfite treatment converts DNA methylbiomolecules may be combined into a ation into DNA sequence information, single protocol. For example, sequencing which can be further combined with prior methods based on nanopores and single treatment with a GpC methyltransferase molecule, real-time (SMRT) technology to capture DNA methylation and nucleoresult in kinetic profiles that not only reflect some positioning in single cells [8]. It is the DNA sequence, but also detect DNA also possible to encode information about methylation. Similarly, carefully optimized the chromosome structure of single cells mass spectrometry assays could provide into DNA sequence information by using a proteome and metabolome data for the protocol that ligates DNA fragments that
Trends in Biotechnology, August 2016, Vol. 34, No. 8
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