Scholarly Literature
This is a database of scholarly literature that concentrates currently on natural and engineered selfish genetic elements (gene drives). The latest are shown here.
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Bioethical issues in genome editing by CRISPR-Cas9 technology
11216F. B. Ayanoglu, A. E. Elcin and Y. M. Elcin, Turkish Journal of Biology, 44:110-120. 2020-04-02 15:13:15.
Genome editing technologies have led to fundamental changes in genetic science. Among them, CRISPR-Cas9 technology particularly stands out due to its advantages such as easy handling, high accuracy, and low cost. It has made a quick introduction in fields related to humans, animals, and the environment, while raising difficult questions, applications, concerns, and bioethical issues to be discussed. Most concerns stem from the use of CRISPR-Cas9 to genetically alter human germline cells and embryos (called germline genome editing). Germline genome editing leads to serial bioethical issues, such as the occurrence of undesirable changes in the genome, from whom and how informed consent is obtained, and the breeding of the human species (eugenics). However, the bioethical issues that CRISPR-Cas9 technology could cause in the environment, agriculture and livestock should also not be forgotten. In order for CRISPR-Cas9 to be used safely in all areas and to solve potential issues, worldwide legislation should be prepared, taking into account the opinions of both life and social scientists, policy makers, and all other stakeholders of the sectors, and CRISPR-Cas9 applications should be implemented according to such legislations. However, these controls should not restrict scientific freedom. Here, various applications of CRISPR-Cas9 technology, especially in medicine and agriculture, are described and ethical issues related to genome editing using CRISPR-Cas9 technology are discussed. The social and bioethical concerns in relation to human beings, other organisms, and the environment are addressed.
Auditing preparedness for vector control field studies
11210C. M. Collins and M. M. Quinlan, American Journal of Tropical Medicine and Hygiene, 102:707-710. 2020-04-01 14:52:00.
The value of baseline entomological data to any future area-wide release campaign relies on the application of consistent methods to produce results comparable across different times and places in a stepwise progression to larger releases. Traditionally, standard operating procedures (SOPs) and operational plans support this consistency and, thus, the validity of emergent data. When release plans include transgenic mosquitoes for vector control or other novel beneficial insects, additional factors come into play such as biosafety permits, stakeholder acceptance, and ethics approval, which require even greater coordination and thoroughness. An audit approach was developed to verify the correct use of SOPs and appropriate performance of tasks during mosquito mark, release, recapture (MRR) studies. Audit questions matched SOPs, permit terms and conditions, and other key criteria, and can be used to support subsequent “spot check” verification by field teams. An external team of auditors, however, was found to be effective for initial checks in this example before the use of a transgenic strain of laboratory mosquitoes. We recommend similar approaches for field studies using release of novel beneficial insects, to ensure useful and valid data as an outcome and to support confidence in the rigor of the step-wise process.
Engineering a minimal gene drive system for integral replacement in Drosophila melanogaster
25648A. Nash, Imperial College London, 2020-04-01 07:48:50.
Gene drives represent a powerful tool for the control of vector-borne diseases. By suppressing or replacing vector populations, laboratory studies have highlighted the potential for this group of tools to make a powerful impact on the burden of zoonotic disease. Current genetic drive systems have a number of limitations, namely their complexity, susceptibility to genetic resistance, and a high regulatory threshold. Here we suggest a novel design paradigm for the creation of replacement gene drives, which we have termed ‘Integral Replacement’. By splitting drive constructs, and integrating components into endogenous loci, we have aimed to engineer a minimal drive system, with low fitness cost, higher resilience to resistance alleles, and with greater flexibility for field testing. In so doing we have generated a model that illustrates increases in efficacy versus existing drive systems, and expanded on work performed on intronic gRNA cassettes. We subsequently were able to build prototype Integral Gene Drive (IGD) components, and demonstrate their efficacy using the model organism Drosophila melanogaster, providing evidence for an initial proof-of-principle for this novel design paradigm.
Development of control and sterilization technology for bluegill by genome editing
20100M. A. Madsen, Nippon Suisan Gakkaishi, 86:100-100. 2020-03-31 09:55:36.
This article is in Japanese
Male-biased adult production of the striped fruit fly, Zeugodacus scutellata, by feeding dsRNA fpecific to Transformer-2
11271M. A. Al Baki, M. Vatanparast and Y. Kim, Insects, 11:211. 2020-03-28 19:17:02.
Sterile insect release technique (SIT) is effective for eradicating quarantine insects including various tephritid fruit flies. When SIT is used for fruit flies, it is challenging to remove females from sterile males due to oviposition-associated piercing damage. This study developed a sex transition technique by feeding double-stranded RNA (dsRNA) specific to a sex-determining gene, Transformer-2 (Zs-Tra2) of the striped fruit fly, Zeugodacus scutellata. Zs-Tra2 is homologous to other fruit fly orthologs. It is highly expressed in female adults. RNA interference (RNAi) of Zs-Tra2 by injecting or feeding its specific dsRNA to larvae significantly increased male ratio. Recombinant Escherichia coli cells expressing dsRNA specific to Zs-Tra2 were prepared and used to feed larvae to suppress Zs-Tra2 gene expression levels. When these recombinant bacteria were fed to larvae during the entire feeding stage, the test population was significantly male-biased. Some females treated with such recombinant E. coli exhibited mosaic morphological characters such as the presence of male-specific abdominal setae in females. This study proposes a novel technique by feeding dsRNA specific to Transformer-2 to reduce female production during mass-rearing of tephritid males for SIT.
The value of existing regulatory frameworks for the environmental risk assessment of agricultural pest control using gene drive
8194J. Romeis, J. Collatz, D. C. M. Glandorf and M. B. Bonsall, Environmental Science & Policy, 108:19-36. 2020-03-27 20:20:04.
The application of (synthetic) gene drives is a powerful tool to control populations of insects that are agricultural pests, vectors of diseases, or a threat to biodiversity potentially leading to the local or global eradication of a species. The potential use of gene drive organisms has triggered a heated discussion regarding their environmental impacts and regulatory oversight. However, experience exists in assessing the environmental impacts of a number of established agricultural pest control methods that require the release of living organisms, that provide high levels of area-wide control and that might be irreversible. This includes classical biological control, the sterile insect technique, the incompatible insect technique that is based on the cytoplasmic incompatibility caused by Wolbachia endosymbionts, and genetically modified insects containing self-limiting traits. The different technologies are described, the regulatory practice and experience is summarized and pathways through which these control technologies could harm valued ecosystem services are presented. With a focus on the application of gene drives in agriculture, using the invasive Drosophila suzukii (Diptera: Drosophilidae) as a case study we then discuss to what extent the existing frameworks could assist the risk assessment of insects carrying gene drives. We suggest that drawing on existing practices, experiences and legislative frameworks will provide a pragmatic and proportionate approach to evaluate the environmental risks of novel solutions based on gene drive technologies.
Editorial Expression of Concern: Transgenic Aedes aegypti Mosquitoes Transfer Genes into a Natural Population
16199B. R. Evans, P. Kotsakiozi, A. L. Costa-Da-Silva, R. S. Ioshino, L. Garziera, M. C. Pedrosa, A. Malavasi, J. F. Virginio, M. L. Capurro and J. R. Powell, Scientific Reports, 10:2. 2020-03-24 15:17:41.
Shortly after publication of this Article in September 2019, the Editors were alerted to concerns regarding the interpretation of the data and some of the conclusions.
Experimental manipulation of selfish genetic elements links genes to microbial community function
11218S. D. Quistad, G. Doulcier and P. B. Rainey, Philosophical Transactions of the Royal Society B-Biological Sciences, 375:12. 2020-03-23 15:17:13.
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
Can a population targeted by a CRISPR-based homing gene drive be rescued?
11269N. O. Rode, V. Courtier-Orgogozo and F. Débarre, bioRxiv, 2020.03.17.995829. 2020-03-20 19:12:23.
CRISPR-based homing gene drive is a genetic control technique aiming to modify or eradicate natural populations through the release of individuals carrying an engineered piece of DNA that can be inherited by all their progeny. Developing countermeasures is important to control the spread of gene drives, should they result in unanticipated damages. One proposed countermeasure is the introduction of individuals carrying a brake construct that targets and inactivates the drive allele but leaves the wild-type allele unaffected. Here we develop models to investigate the efficiency of such brakes. We consider a variable population size and use a combination of analytical and numerical methods to determine the conditions where a brake can prevent the extinction of a population targeted by an eradication drive. We find that a brake is not guaranteed to prevent eradication and that characteristics of both the brake and the drive affect the likelihood of recovering the wild-type population. In particular, brakes that restore fitness are more efficient than brakes that do not. Our model also suggests that threshold-dependent drives (drives that can spread only when introduced above a threshold) are more amenable to control with a brake than drives that can spread from an arbitrary low introduction frequency (threshold-independent drives). Based on our results, we provide practical recommendations and discuss safety issues.Article summary for Issue Highlights Homing gene drive is a new genetic control technology that aims to spread a genetically engineered DNA construct within natural populations even when it impairs fitness. In case of unanticipated damages, it has been proposed to stop homing gene drives by releasing individuals carrying a gene-drive brake; however, the efficiency of such brakes has been little studied. The authors develop a model to investigate the dynamics of a population targeted by a homing drive in absence or in presence of brake. The model provides insights for the design of more efficient brakes and safer gene drives.CRISPRClustered Regularly Interspaced Short Palindromic Repeats
Simulating effects of fitness and dispersal on the use of Trojan sex chromosomes for the management of invasive species
11488C. C. Day, E. L. Landguth, R. K. Simmons, W. P. Baker, A. R. Whiteley, P. M. Lukacs and A. Bearlin, Journal of Applied Ecology, 2020-03-19 20:15:27.
The use of Trojan Y chromosomes (TYC) for controlling invasive species involves manipulating the sex chromosomes of captive-raised individuals. Following release, the offspring of these individuals consist of only one sex, thereby skewing the sex ratio of the invasive population and potentially leading to eradication. Simulation models are needed that can inform managers about how to maximize the likelihood of invasive species eradication, since implementation of this novel management approach in the field is still rare. Here, we present the first spatially explicit, mechanistic simulation model of a real-world TYC program for invasive species eradication. Using a brook trout Salvelinus fontinalis system model, we investigated the effects of competitive and reproductive fitness of the captive-raised YY males, dispersal behaviour upon their release and landscape heterogeneity on eradication success. Likelihood of eradication was dependent on both the competitive and reproductive fitness of the Trojan individuals. Competitive fitness (i.e. survival) had a higher threshold for eradication, below which the invasive populations were not eradicated. Movement ecology of both the wild and YY male populations was important for eradication. Under a restricted dispersal scenario for YY males following their release, the wild population was not extirpated but maintained a stable, yet reduced, population size. Analysis of landscape configuration indicated that time to eradication of local patches increased with greater connectivity within the stream network. In addition to sex ratio distortion, density-dependent mortality resulting from outplantings made an important contribution to population decline and therefore may also affect native competitors. Synthesis and applications. The use of Trojan sex chromosomes to skew population sex ratios is a novel method for the suppression and eradication of aquatic invasive species. Results from our modelling work indicate that while eradication is possible, maximizing its likelihood requires an understanding of the fitness and movement ecology of both the wild and YY male populations of the invasive species. Both our model and the principles derived from this study related to fitness and behavioural landscape ecology can be broadly applied to other invaded species and systems.
Computational and experimental performance of CRISPR homing gene drive strategies with multiplexed gRNAs
7962S. E. Champer, S. Y. Oh, C. Liu, Z. Wen, A. G. Clark, P. W. Messer and J. Champer, Science Advances, 6:eaaz0525. 2020-03-16 14:22:56.
The rapid evolution of resistance alleles poses a major obstacle for genetic manipulation of populations with CRISPR homing gene drives. One proposed solution is using multiple guide RNAs (gRNAs), allowing a drive to function even if some resistant target sites are present. Here, we develop a model of homing mechanisms parameterized by experimental studies. Our model incorporates several factors affecting drives with multiple gRNAs, including timing of cleavage, reduction in homology-directed repair efficiency due to imperfect homology, Cas9 activity saturation, gRNA activity level variance, and incomplete homology-directed repair. We find that homing drives have an optimal number of gRNAs, usually between two and eight, depending on the specific drive type and performance parameters. These results contradict the notion that resistance rates can be reduced to arbitrarily low levels by gRNA multiplexing and highlight the need for combined approaches to counter resistance evolution in CRISPR homing drives.
Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies
11201Marino, N. D., Pinilla-Redondo, R. , Csorgo, B., Bondy-Denomy, J., Nature Methods, 2020-03-16 13:52:42.
Clustered, regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes, a diverse family of prokaryotic adaptive immune systems, have emerged as a biotechnological tool and therapeutic. The discovery of protein inhibitors of CRISPR-Cas systems, called anti-CRISPR (Acr) proteins, enables the development of more controllable and precise CRISPR-Cas tools. Here we discuss applications of Acr proteins for post-translational control of CRISPR-Cas systems in prokaryotic and mammalian cells, organisms and ecosystems. This Review highlights recent discoveries and applications of anti-CRISPR (Acr) proteins that enable the regulation of CRISPR-Cas technology.
Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes
14309H. Schmidt, T. C. Collier, M. J. Hanemaaijer, P. D. Houston, Y. Lee and G. C. Lanzaro, Nature Communications, 11. 2020-03-16 12:39:04.
ere we report the results of a survey of 1280 genomes of the mosquitoes Anopheles gambiae, An. coluzzii, and Aedes aegypti in which we determine that similar to 90% of all protein-encoding CGD target genes in natural populations include at least one target site with no DRAs at a frequency of >= 1.0%.
A fly model establishes distinct mechanisms for synthetic CRISPR/Cas9 sex distorters
7973B. Fasulo, A. Meccariello, M. Morgan, C. Borufka, P. A. Papathanos and N. Windbichler, PLOS Genetics, 16:e1008647. 2020-03-13 15:02:19.
Author summary Harmful insect populations can be eliminated for a lack of females if they are made to produce mostly male offspring. There are genes that occur naturally that make males produce mostly sons and, although we don’t know exactly how they work, this appears to coincide with damage to the X-chromosome during the production of sperm. Recently, we showed in a mosquito species that such sex-biasing genes could also be constructed artificially from first principles. To better understand if this works in other species too, we designed and built male-biasing genes of two types in the fruit fly and determined what is needed to for a shift towards males. We show how different ways of cutting the X-chromosome DNA at different times with CRISPR, results in distinct outcomes and started to ask what cellular processes are involved in this. These models will help us to design such genes for the control of insect species that transmit disease or threaten crops.
Performance analysis of novel toxin-antidote CRISPR gene drive systems
7969J. Champer, I. K. Kim, S. E. Champer, A. G. Clark and P. W. Messer, BMC Biology, 18:27. 2020-03-12 14:48:01.
CRISPR gene drive systems allow the rapid spread of a genetic construct throughout a population. Such systems promise novel strategies for the management of vector-borne diseases and invasive species by suppressing a target population or modifying it with a desired trait. However, current homing-type drives have two potential shortcomings. First, they can be thwarted by the rapid evolution of resistance. Second, they lack any mechanism for confinement to a specific target population. In this study, we conduct a comprehensive performance assessment of several new types of CRISPR-based gene drive systems employing toxin-antidote (TA) principles, which should be less prone to resistance and allow for the confinement of drives to a target population due to invasion frequency thresholds.
Stakeholder workshop “Problem formulation for the environmental risk assessment of gene drive modified insects” (15 May 2019, Brussels)
8192European Food Safety, A., Devos, Y., Gallani, B. & Firbank, L. G, A. European Food Safety, Y. Devos, B. Gallani and L. G. Firbank, 17:1819E. 2020-03-09 20:12:26.
Recent advances in molecular and synthetic biology are enabling the engineering of gene drives that spread genes of interest through interbreeding populations at a frequency greater than the rate expected by simple Mendelian inheritance. At present, insects represent the most likely cases of gene drive modified organisms for deliberate release into the environment. Through an open workshop, the European Food Safety Authority (EFSA) aimed to engage with stakeholders to discuss potential environmental risks associated with the deliberate release into the environment of gene drive modified insects. Workshop participants were invited to contribute to an example problem formulation to: (1) identify relevant broad protection goals and make them operational for use in environmental risk assessment; (2) formally devise examples of plausible pathways to harm that describe how the deployment of gene drive modified insects could be harmful; (3) formulate example risk hypotheses about the likelihood and severity of such events; (4) identify possible information that would be useful to test these risk hypotheses; and (5) identify how to acquire new data for hypothesis testing when existing information is deemed insufficient for regulatory decision-making. The problem formulation exercise was run for two hypothetical case studies (i.e. self-sustaining low threshold gene drives to control disease-spreading mosquitoes (Aedes albopictus, the Asian tiger mosquito) and agricultural pests (Drosophila suzukii, the spotted-wing Drosophila)). Points raised by the workshop participants reveal different often contrasting opinions/perspectives toward gene drive and their risk assessment. Overall, there was agreement that the problem formulation process is fit-for-purpose for the environmental risk assessment of gene drive modified insects, but it was acknowledged that practical challenges may be encountered. Points raised by the workshop participants, on defining protection goals, formulating specific pathways to harm and on structuring risks, have been considered by EFSA's Panel on genetically modified organisms during its deliberations.
Toward the definition of efficacy and safety criteria for advancing gene drive-modified mosquitoes to field testing
7971S. L. James, J. M. Marshall, G. K. Christophides, F. O. Okumu and T. Nolan, Vector Borne and Zoonotic Diseases, 20:237. 2020-03-09 14:54:00.
Mosquitoes containing gene drive systems are being developed as complementary tools to prevent transmission of malaria and other mosquito-borne diseases. As with any new tool, decision makers and other stakeholders will need to balance risks (safety) and benefits (efficacy) when considering the rationale for testing and deploying gene drive-modified mosquito products. Developers will benefit from standards for judging whether an investigational gene drive product meets acceptability criteria for advancing to field trials. Such standards may be formalized as preferred product characteristics and target product profiles, which describe the desired attributes of the product category and of a particular product, respectively. This report summarizes discussions from two scientific workshops aimed at identifying efficacy and safety characteristics that must be minimally met for an investigational gene drive-modified mosquito product to be deemed viable to move from contained testing to field release and the data that will be needed to support an application for first field release.
Population-level multiplexing: A promising strategy to manage the evolution of resistance against gene drives targeting a neutral locus
11212M. P. Edgington, T. Harvey-Samuel and L. Alphey, Evolutionary Applications, 10. 2020-03-06 14:52:40.
CRISPR-based gene drives bias inheritance in their favour by inducing double-stranded breaks (DSBs) at wild-type homologous loci and using the drive transgene as a repair template-converting drive heterozygotes into homozygotes. Recent studies have shown that alternate end-joining repair mechanisms produce cut-resistant alleles that rapidly induce drive failure. Multiplexing-simultaneously targeting multiple sites at the wild-type locus-is commonly assumed to overcome this issue since resistance would need to develop at all target sites for the system to fail. This may work for some population suppression drives targeting essential (e.g. viability or fertility) genes if careful design can ensure cut-resistant alleles themselves have low fitness. However, here, models are used to demonstrate that this approach will be ineffective when targeting neutral loci. We then go on to compare the performance of four alternative population-level multiplexing approaches with standard individual-level multiplexing. Two of these approaches have mechanisms preventing them from becoming linked, thus avoiding multiple simultaneous DSBs and giving a large improvement. Releasing multiple unlinked drives gives a modest improvement, while releasing multiple drives that may become linked over time produces a decrease in performance under the conditions tested here. Based on performance and technical feasibility, we then take one approach forward for further investigation, demonstrating its robustness to different performance parameters and its potential for controlling very large target populations.
A unifying approach to gene drive
7957P. Verma, R. Reeves and C. S. Gokhale, bioRxiv, 2020.02.28.970103. 2020-03-03 13:53:12.
Synthetic gene drive technologies aim to spread transgenic constructs into wild populations even when they impose organismal fitness disadvantages. The properties of gene drive constructs are diverse and depend on their molecular construction, and differential selection pressure they impose in the varied ecological situations they encounter. The extraordinary diversity of conceivable drive mechanisms and the range of selective parameters they may encounter makes it very difficult to convey their relative predicted properties. The sheer number of published manuscripts in this field, experimental and theoretical, is a testament to the possibilities presented by this technology. We evaluate and condense the essential synthetic drive mechanisms from a variety of studies and present a unified mathematical paradigm (and a user-friendly tool DrMxR - Drive Mixer) describing the properties of a wide variety of single construct gene drives (non-suppression). Within this common framework, we have been able to recapitulate key published results derived using bespoke modelling frameworks. Because a unified framework is employed, it is also possible to seamlessly explore the consequences of combining multiple drive approaches within a single construct. We provide a method for analytically assessing the measure of invasiveness of a drive construct. As opposed to typical studies of synthetic drives, we explore the resilience of such drives in a spatially explicit manner advancing the connection between realistic spatial dynamics and typical well-mixed populations. Besides a scientific advance, our results and the tools provided an intuitive and objective way for regulators, scientists and NGOs to evaluate the properties and robustness of proposed and future gene drive approaches.
Public health concerns over gene-drive mosquitoes: will future use of gene-drive snails for schistosomiasis control gain increased level of community acceptance?
7950D. O. Famakinde, Pathogens and Global Health, 2020-02-26 20:49:43.
With the advent of CRISPR (clustered regularly interspaced short palindromic repeat)-based gene drive, present genetic research in schistosomiasis vector control envisages the breeding and release of transgenic schistosome-resistant (TSR) snail vectors to curb the spread of the disease. Although this approach is still in its infancy, studies focussing on production of genetically modified (GM) mosquitoes (including gene-drive mosquitoes) are well advanced and set the pace for other transgenic vector research. Unfortunately, as with other GM mosquitoes, open field release of gene-drive mosquitoes is currently challenged in part by some concerns such as gene drive failure and increased transmission potential for other mosquito-borne diseases among others, which might have adverse effects on human wellbeing. Therefore, not only should we learn from the GM mosquito protocols, frameworks and guidelines but also appraise the applicability of its current hurdles to other transgenic vector systems, such as the TSR snail approach. Placing these issues in a coherent comparative perspective, I argue that although the use of TSR snails may face similar technical, democratic and diplomatic challenges, some of the concerns over gene-drive mosquitoes may not apply to gene-drive snails, proposing a theory that community consent will be no harder and possibly easier to obtain for TSR snails than the experience with GM mosquitoes. In the future, these observations may help public health practitioners and policy makers in effective communication with communities on issues regarding the use of TSR snails to interrupt schistosomiasis transmission, especially in sub-Saharan Africa.
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