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Zhang S, Champer J. Performance characteristics allow for confinement of a CRISPR toxin-antidote gene drive for population suppression in a reaction-diffusion model. Proc Biol Sci 2024; 291:20240500. [PMID: 38889790 DOI: 10.1098/rspb.2024.0500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/26/2024] [Indexed: 06/20/2024] Open
Abstract
Gene drive alleles that can bias their own inheritance could engineer populations for control of disease vectors, invasive species and agricultural pests. There are successful examples of suppression drives and confined modification drives, but developing confined suppression drives has proven more difficult. However, CRISPR-based toxin-antidote dominant embryo (TADE) suppression drive may fill this niche. It works by targeting and disrupting a haplolethal target gene in the germline with its gRNAs while rescuing this target. It also disrupts a female fertility gene by driving insertion or additional gRNAs. Here, we used a reaction-diffusion model to assess drive performance in continuous space, where outcomes can be substantially different from those in panmictic populations. We measured drive wave speed and found that moderate fitness costs or target gene disruption in the early embryo from maternally deposited nuclease can eliminate the drive's ability to form a wave of advance. We assessed the required release size, and finally we investigated migration corridor scenarios. It is often possible for the drive to suppress one population and then persist in the corridor without invading the second population, a potentially desirable outcome. Thus, even imperfect variants of TADE suppression drive may be excellent candidates for confined population suppression.
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Affiliation(s)
- Shijie Zhang
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University , Beijing 100871, People's Republic of China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University , Beijing 100871, People's Republic of China
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2
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Janzen A, Pothula R, Sychla A, Feltman NR, Smanski MJ. Predicting thresholds for population replacement gene drives. BMC Biol 2024; 22:40. [PMID: 38369493 PMCID: PMC10875781 DOI: 10.1186/s12915-024-01823-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/10/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Threshold-dependent gene drives (TDGDs) could be used to spread desirable traits through a population, and are likely to be less invasive and easier to control than threshold-independent gene drives. Engineered Genetic Incompatibility (EGI) is an extreme underdominance system previously demonstrated in Drosophila melanogaster that can function as a TDGD when EGI agents of both sexes are released into a wild-type population. RESULTS Here we use a single generation fitness assay to compare the fecundity, mating preferences, and temperature-dependent relative fitness to wild-type of two distinct genotypes of EGI agents. We find significant differences in the behavior/performance of these EGI agents that would not be predicted a priori based on their genetic design. We report a surprising temperature-dependent change in the predicted threshold for population replacement in an EGI agent that drives ectopic expression of the developmental morphogen pyramus. CONCLUSIONS The single-generation fitness assay presented here could reduce the amount of time required to estimate the threshold for TDGD strategies for which hybrid genotypes are inviable. Additionally, this work underscores the importance of empirical characterization of multiple engineered lines, as behavioral differences can arise in unique genotypes for unknown reasons.
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Affiliation(s)
- Anna Janzen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, 55455, MN, USA
- Biotechnology Institute, University of Minnesota, Saint Paul, 55108, MN, USA
| | - Ratnasri Pothula
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, 55455, MN, USA
- Biotechnology Institute, University of Minnesota, Saint Paul, 55108, MN, USA
| | - Adam Sychla
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, 55455, MN, USA
- Biotechnology Institute, University of Minnesota, Saint Paul, 55108, MN, USA
| | - Nathan R Feltman
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, 55455, MN, USA
- Biotechnology Institute, University of Minnesota, Saint Paul, 55108, MN, USA
| | - Michael J Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, 55455, MN, USA.
- Biotechnology Institute, University of Minnesota, Saint Paul, 55108, MN, USA.
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3
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Anderson MAE, Gonzalez E, Edgington MP, Ang JXD, Purusothaman DK, Shackleford L, Nevard K, Verkuijl SAN, Harvey-Samuel T, Leftwich PT, Esvelt K, Alphey L. A multiplexed, confinable CRISPR/Cas9 gene drive can propagate in caged Aedes aegypti populations. Nat Commun 2024; 15:729. [PMID: 38272895 PMCID: PMC10810878 DOI: 10.1038/s41467-024-44956-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Aedes aegypti is the main vector of several major pathogens including dengue, Zika and chikungunya viruses. Classical mosquito control strategies utilizing insecticides are threatened by rising resistance. This has stimulated interest in new genetic systems such as gene drivesHere, we test the regulatory sequences from the Ae. aegypti benign gonial cell neoplasm (bgcn) homolog to express Cas9 and a separate multiplexing sgRNA-expressing cassette inserted into the Ae. aegypti kynurenine 3-monooxygenase (kmo) gene. When combined, these two elements provide highly effective germline cutting at the kmo locus and act as a gene drive. Our target genetic element drives through a cage trial population such that carrier frequency of the element increases from 50% to up to 89% of the population despite significant fitness costs to kmo insertions. Deep sequencing suggests that the multiplexing design could mitigate resistance allele formation in our gene drive system.
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Affiliation(s)
- Michelle A E Anderson
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Estela Gonzalez
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- Animal and Plant Health Agency, Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Matthew P Edgington
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Joshua X D Ang
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Deepak-Kumar Purusothaman
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- MRC-University of Glasgow Centre for Virus Research, Henry Wellcome Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Lewis Shackleford
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Katherine Nevard
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
| | - Sebald A N Verkuijl
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | | | - Philip T Leftwich
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Kevin Esvelt
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0HN, UK.
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
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4
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Raban R, Marshall JM, Hay BA, Akbari OS. Manipulating the Destiny of Wild Populations Using CRISPR. Annu Rev Genet 2023; 57:361-390. [PMID: 37722684 PMCID: PMC11064769 DOI: 10.1146/annurev-genet-031623-105059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Genetic biocontrol aims to suppress or modify populations of species to protect public health, agriculture, and biodiversity. Advancements in genome engineering technologies have fueled a surge in research in this field, with one gene editing technology, CRISPR, leading the charge. This review focuses on the current state of CRISPR technologies for genetic biocontrol of pests and highlights the progress and ongoing challenges of using these approaches.
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Affiliation(s)
- Robyn Raban
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
| | - John M Marshall
- Divisions of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, California, USA
| | - Bruce A Hay
- Division of Biology and Biological Engineering (BBE), California Institute of Technology, Pasadena, California, USA
| | - Omar S Akbari
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
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5
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Hernández Elizárraga VH, Ballantyne S, O'Brien LG, Americo JA, Suhr ST, Senut MC, Minerich B, Merkes CM, Edwards TM, Klymus K, Richter CA, Waller DL, Passamaneck YJ, Rebelo MF, Gohl DM. Toward invasive mussel genetic biocontrol: Approaches, challenges, and perspectives. iScience 2023; 26:108027. [PMID: 37860763 PMCID: PMC10583111 DOI: 10.1016/j.isci.2023.108027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023] Open
Abstract
Invasive freshwater mussels, such as the zebra (Dreissena polymorpha), quagga (Dreissena rostriformis bugensis), and golden (Limnoperna fortunei) mussel have spread outside their native ranges throughout many regions of the North American, South American, and European continents in recent decades, damaging infrastructure and the environment. This review describes ongoing efforts by multiple groups to develop genetic biocontrol methods for invasive mussels. First, we provide an overview of genetic biocontrol strategies that have been applied in other invasive or pest species. Next, we summarize physical and chemical methods that are currently in use for invasive mussel control. We then describe the multidisciplinary approaches our groups are employing to develop genetic biocontrol tools for invasive mussels. Finally, we discuss the challenges and limitations of applying genetic biocontrol tools to invasive mussels. Collectively, we aim to openly share information and combine expertise to develop practical tools to enable the management of invasive freshwater mussels.
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Affiliation(s)
| | - Scott Ballantyne
- Department of Biology, University of Wisconsin River Falls, River Falls, WI, USA
| | | | | | | | | | | | - Christopher M. Merkes
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, WI, USA
| | - Thea M. Edwards
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, USA
| | - Katy Klymus
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, USA
| | - Catherine A. Richter
- U.S. Geological Survey, Columbia Environmental Research Center, Columbia, MO, USA
| | - Diane L. Waller
- U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, WI, USA
| | - Yale J. Passamaneck
- Bureau of Reclamation, Technical Service Center, Hydraulic Investigations and Laboratory Services, Ecological Research Laboratory, Denver, CO, USA
| | - Mauro F. Rebelo
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daryl M. Gohl
- University of Minnesota Genomics Center, Minneapolis, MN, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
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6
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Zhu Y, Champer J. Simulations Reveal High Efficiency and Confinement of a Population Suppression CRISPR Toxin-Antidote Gene Drive. ACS Synth Biol 2023; 12:809-819. [PMID: 36825354 DOI: 10.1021/acssynbio.2c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Though engineered gene drives hold great promise for spreading through and suppressing populations of disease vectors or invasive species, complications such as resistance alleles and spatial population structure can prevent their success. Additionally, most forms of suppression drives, such as homing drives or driving Y chromosomes, will generally spread uncontrollably between populations with even small levels of migration. The previously proposed CRISPR-based toxin-antidote system called toxin-antidote dominant embryo (TADE) suppression drive could potentially address the issues of confinement and resistance. However, it is a relatively weak form of drive compared to homing drives, which might make it particularly vulnerable to spatial population structure. In this study, we investigate TADE suppression drive using individual-based simulations in a continuous spatial landscape. We find that the drive is actually more confined than in simple models without space, even in its most efficient form with low cleavage rate in embryos from maternally deposited Cas9. Furthermore, the drive performed well in continuous space scenarios if the initial release requirements were met, suppressing the population in a timely manner without being severely affected by chasing, a phenomenon in which wild-type individuals avoid the drive by recolonizing empty areas. At higher embryo cut rates, the drive loses its ability to spread, but a single, widespread release can often still induce rapid population collapse. Thus, if TADE suppression gene drives can be successfully constructed, they may play an important role in control of disease vectors and invasive species when stringent confinement to target populations is desired.
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Affiliation(s)
- Yutong Zhu
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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7
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Meng J, Qiu Y, Zhang Y, Zhao H, Shi S. CMI: CRISPR/Cas9 Based Efficient Multiplexed Integration in Saccharomyces cerevisiae. ACS Synth Biol 2023; 12:1408-1414. [PMID: 36853024 DOI: 10.1021/acssynbio.2c00591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Genomic integration is the preferred method for gene expression in microbial industrial production. However, traditional homologous recombination based multiplexed integration methods often suffer from low integration efficiency and complex experimental procedures. Here, we report a CRISPR/Cas9 based multiplexed integration (CMI) system in Saccharomyces cerevisiae, which can achieve quadruple integration at an individual locus without pre-engineering the host. A fused protein, Cas9-Brex27, was used as a bait to attract Rad51 recombinase to the proximity of the double-strand breaks introduced by the CRISPR/Cas9 system. The efficiency of quadruple integration was increased to 53.9% with 40 bp homology arms (HAs) and 78% with 100 bp HAs. CMI was applied to integrate a heterologous mogrol biosynthetic pathway consisting of four genes in a one-step transformation and offered an efficient solution for multiplexed integration. This method expands the synthetic biology toolbox of S. cerevisiae.
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Affiliation(s)
- Jie Meng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yue Qiu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yueping Zhang
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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8
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Casas-Mollano JA, Zinselmeier M, Sychla A, Smanski MJ. Efficient gene activation in plants by the MoonTag programmable transcriptional activator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528671. [PMID: 36824723 PMCID: PMC9948947 DOI: 10.1101/2023.02.15.528671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
CRISPR/Cas-based transcriptional activators have been developed to induce gene expression in eukaryotic and prokaryotic organisms. The main advantages of CRISPR-Cas based systems is that they can achieve high levels of transcriptional activation and are very easy to program via pairing between the guide RNA and the DNA target strand. SunTag is a second-generation system that activates transcription by recruiting multiple copies of an activation domain (AD) to its target promoters. SunTag is a strong activator; however, in some species it is difficult to stably express. To overcome this problem, we designed MoonTag, a new activator that worked on the same basic principle as SunTag, but whose components are better tolerated when stably expressed in transgenic plants. We demonstrate that MoonTag is capable of inducing high levels of transcription in all plants tested. In Setaria, MoonTag is capable of inducing high levels of transcription of reporter genes as well as of endogenous genes. More important, MoonTag components are expressed in transgenic plants to high levels without any deleterious effects. MoonTag is also able to efficiently activate genes in eudicotyledonous species such as Arabidopsis and tomato. Finally, we show that MoonTag activation is functional across a range of temperatures, which is promising for potential field applications.
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9
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Chen J, Xu X, Champer J. Assessment of distant-site rescue elements for CRISPR toxin-antidote gene drives. Front Bioeng Biotechnol 2023; 11:1138702. [PMID: 36860883 PMCID: PMC9968759 DOI: 10.3389/fbioe.2023.1138702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/03/2023] [Indexed: 02/15/2023] Open
Abstract
Gene drive is a genetic engineering technology that can enable super-mendelian inheritance of specific alleles, allowing them to spread through a population. New gene drive types have increased flexibility, offering options for confined modification or suppression of target populations. Among the most promising are CRISPR toxin-antidote gene drives, which disrupt essential wild-type genes by targeting them with Cas9/gRNA. This results in their removal, increasing the frequency of the drive. All these drives rely on having an effective rescue element, which consists of a recoded version of the target gene. This rescue element can be at the same site as the target gene, maximizing the chance of efficient rescue, or at a distant site, which allows useful options such as easily disrupting another essential gene or increasing confinement. Previously, we developed a homing rescue drive targeting a haplolethal gene and a toxin-antidote drive targeting a haplosufficient gene. These successful drives had functional rescue elements but suboptimal drive efficiency. Here, we attempted to construct toxin-antidote drives targeting these genes with a distant-site configuration from three loci in Drosophila melanogaster. We found that additional gRNAs increased cut rates to nearly 100%. However, all distant-site rescue elements failed for both target genes. Furthermore, one rescue element with a minimally recoded sequence was used as a template for homology-directed repair for the target gene on a different chromosomal arm, resulting in the formation of functional resistance alleles. Together, these results can inform the design of future CRISPR-based toxin-antidote gene drives.
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Affiliation(s)
- Jingheng Chen
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xuejiao Xu
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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10
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Li J, Champer J. Harnessing Wolbachia cytoplasmic incompatibility alleles for confined gene drive: A modeling study. PLoS Genet 2023; 19:e1010591. [PMID: 36689491 PMCID: PMC9894560 DOI: 10.1371/journal.pgen.1010591] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/02/2023] [Accepted: 12/21/2022] [Indexed: 01/24/2023] Open
Abstract
Wolbachia are maternally-inherited bacteria, which can spread rapidly in populations by manipulating reproduction. cifA and cifB are genes found in Wolbachia phage that are responsible for cytoplasmic incompatibility, the most common type of Wolbachia reproductive interference. In this phenomenon, no viable offspring are produced when a male with both cifA and cifB (or just cifB in some systems) mates with a female lacking cifA. Utilizing this feature, we propose new types of toxin-antidote gene drives that can be constructed with only these two genes in an insect genome, instead of the whole Wolbachia bacteria. By using both mathematical and simulation models, we found that a drive containing cifA and cifB together creates a confined drive with a moderate to high introduction threshold. When introduced separately, they act as a self-limiting drive. We observed that the performance of these drives is substantially influenced by various ecological parameters and drive characteristics. Extending our models to continuous space, we found that the drive individual release distribution has a critical impact on drive persistence. Our results suggest that these new types of drives based on Wolbachia transgenes are safe and flexible candidates for genetic modification of populations.
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Affiliation(s)
- Jiahe Li
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- * E-mail:
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11
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Sychla A, Feltman NR, Hutchison WD, Smanski MJ. Modeling-informed Engineered Genetic Incompatibility strategies to overcome resistance in the invasive Drosophila suzukii. FRONTIERS IN INSECT SCIENCE 2022; 2:1063789. [PMID: 38468757 PMCID: PMC10926386 DOI: 10.3389/finsc.2022.1063789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/01/2022] [Indexed: 03/13/2024]
Abstract
Engineered Genetic Incompatibility (EGI) is an engineered extreme underdominance genetic system wherein hybrid animals are not viable, functioning as a synthetic speciation event. There are several strategies in which EGI could be leveraged for genetic biocontrol of pest populations. We used an agent-based model of Drosophila suzukii (Spotted Wing Drosophila) to determine how EGI would fare with high rates of endemic genetic resistance alleles. We discovered a surprising failure mode wherein field-generated females convert an incompatible male release program into a population replacement gene drive. Local suppression could still be attained in two seasons by tailoring the release strategy to take advantage of this effect, or alternatively in one season by altering the genetic design of release agents. We show in this work that data from modeling can be utilized to recognize unexpected emergent phenomena and a priori inform genetic biocontrol treatment design to increase efficacy.
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Affiliation(s)
- Adam Sychla
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN, United States
- Biotechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - Nathan R. Feltman
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN, United States
- Biotechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - William D. Hutchison
- Department of Entomology, University of Minnesota, Saint Paul, MN, United States
| | - Michael J. Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN, United States
- Biotechnology Institute, University of Minnesota, Saint Paul, MN, United States
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12
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Raban R, Gendron WAC, Akbari OS. A perspective on the expansion of the genetic technologies to support the control of neglected vector-borne diseases and conservation. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.999273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
Genetic-based technologies are emerging as promising tools to support vector population control. Vectors of human malaria and dengue have been the main focus of these development efforts, but in recent years these technologies have become more flexible and adaptable and may therefore have more wide-ranging applications. Culex quinquefasciatus, for example, is the primary vector of avian malaria in Hawaii and other tropical islands. Avian malaria has led to the extinction of numerous native bird species and many native bird species continue to be threatened as climate change is expanding the range of this mosquito. Genetic-based technologies would be ideal to support avian malaria control as they would offer alternatives to interventions that are difficult to implement in natural areas, such as larval source reduction, and limit the need for chemical insecticides, which can harm beneficial species in these natural areas. This mosquito is also an important vector of human diseases, such as West Nile and Saint Louis encephalitis viruses, so genetic-based control efforts for this species could also have a direct impact on human health. This commentary will discuss the current state of development and future needs for genetic-based technologies in lesser studied, but important disease vectors, such as C. quinquefasciatus, and make comparisons to technologies available in more studied vectors. While most current genetic control focuses on human disease, we will address the impact that these technologies could have on both disease and conservation focused vector control efforts and what is needed to prepare these technologies for evaluation in the field. The versatility of genetic-based technologies may result in the development of many important tools to control a variety of vectors that impact human, animal, and ecosystem health.
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13
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Feltman NR, Burkness EC, Ebbenga D, Hutchison WD, Smanski MJ. HUGE pipeline to measure temporal genetic variation in Drosophila suzukii populations for genetic biocontrol applications. FRONTIERS IN INSECT SCIENCE 2022; 2:981974. [PMID: 38468784 PMCID: PMC10926429 DOI: 10.3389/finsc.2022.981974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 03/13/2024]
Abstract
Understanding the fine-scale genome sequence diversity that exists within natural populations is important for developing models of species migration, temporal stability, and range expansion. For invasive species, agricultural pests, and disease vectors, sequence diversity at specific loci in the genome can impact the efficacy of next-generation genetic biocontrol strategies. Here we describe a pipeline for haplotype-resolution genetic variant discovery and quantification from thousands of Spotted Wing Drosophila (Drosophila suzukii, SWD) isolated at two field sites in the North-Central United States (Minnesota) across two seasons. We observed highly similar single nucleotide polymorphism (SNP) frequencies at each genomic location at each field site and year. This supports the hypotheses that SWD overwinters in Minnesota, is annually populated by the same source populations or a combination of both theories. Also, the stable genetic structure of SWD populations allows for the rational design of genetic biocontrol technologies for population suppression.
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Affiliation(s)
- Nathan R. Feltman
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN, United States
- Biotechnology Institute, University of Minnesota, Saint Paul, MN, United States
| | - Eric C. Burkness
- Department of Entomology, University of Minnesota, Saint Paul, MN, United States
| | - Dominique N. Ebbenga
- Department of Entomology, University of Minnesota, Saint Paul, MN, United States
| | - William D. Hutchison
- Department of Entomology, University of Minnesota, Saint Paul, MN, United States
| | - Michael J. Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Saint Paul, MN, United States
- Biotechnology Institute, University of Minnesota, Saint Paul, MN, United States
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14
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Kojin BB, Compton A, Adelman ZN, Tu Z. Selective targeting of biting females to control mosquito-borne infectious diseases. Trends Parasitol 2022; 38:791-804. [PMID: 35952630 PMCID: PMC9372635 DOI: 10.1016/j.pt.2022.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022]
Abstract
Mosquitoes are vectors for a number of infectious diseases. Only females feed on blood to provision for their embryos and, in doing so, transmit pathogens to the associated vertebrate hosts. Therefore, sex is an important phenotype in the context of genetic control programs, both for sex separation in the rearing facilities to avoid releasing biting females and for ways to distort the sex ratio towards nonbiting males. We review recent progress in the fundamental knowledge of sex determination and sex chromosomes in mosquitoes and discuss new methods to achieve sex separation and sex ratio distortion to help control mosquito-borne infectious diseases. We conclude by suggesting a few critical areas for future research.
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Affiliation(s)
- Bianca B Kojin
- Department of Entomology and Agrilife Research, Texas A&M University, College Station, TX, USA
| | - Austin Compton
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA; Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Zach N Adelman
- Department of Entomology and Agrilife Research, Texas A&M University, College Station, TX, USA.
| | - Zhijian Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA; Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA.
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15
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Ansai S, Kitano J. Speciation and adaptation research meets genome editing. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200516. [PMID: 35634923 PMCID: PMC9149800 DOI: 10.1098/rstb.2020.0516] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/07/2022] [Indexed: 07/20/2023] Open
Abstract
Understanding the genetic basis of reproductive isolation and adaptive traits in natural populations is one of the fundamental goals in evolutionary biology. Genome editing technologies based on CRISPR-Cas systems and site-specific recombinases have enabled us to modify a targeted genomic region as desired and thus to conduct functional analyses of target loci, genes and mutations even in non-conventional model organisms. Here, we review the technical properties of genome editing techniques by classifying them into the following applications: targeted gene knock-out for investigating causative gene functions, targeted gene knock-in of marker genes for visualizing expression patterns and protein functions, precise gene replacement for identifying causative alleles and mutations, and targeted chromosomal rearrangement for investigating the functional roles of chromosomal structural variations. We describe examples of their application to demonstrate functional analysis of naturally occurring genetic variations and discuss how these technologies can be applied to speciation and adaptation research. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.
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Affiliation(s)
- Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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16
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Liu Y, Champer J. Modelling homing suppression gene drive in haplodiploid organisms. Proc Biol Sci 2022; 289:20220320. [PMID: 35414240 PMCID: PMC9006016 DOI: 10.1098/rspb.2022.0320] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/21/2022] [Indexed: 01/13/2023] Open
Abstract
Gene drives have shown great promise for suppression of pest populations. These engineered alleles can function by a variety of mechanisms, but the most common is the CRISPR homing drive, which converts wild-type alleles to drive alleles in the germline of heterozygotes. Some potential target species are haplodiploid, in which males develop from unfertilized eggs and thus have only one copy of each chromosome. This prevents drive conversion, a substantial disadvantage compared to diploids where drive conversion can take place in both sexes. Here, we study homing suppression gene drives in haplodiploids and find that a drive targeting a female fertility gene could still be successful. However, such drives are less powerful than in diploids and suffer more from functional resistance alleles. They are substantially more vulnerable to high resistance allele formation in the embryo owing to maternally deposited Cas9 and guide RNA and also to somatic cleavage activity. Examining spatial models where organisms move over a continuous landscape, we find that haplodiploid suppression drives surprisingly perform nearly as well as in diploids, possibly owing to their ability to spread further before inducing strong suppression. Together, these results indicate that gene drive can potentially be used to effectively suppress haplodiploid populations.
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Affiliation(s)
- Yiran Liu
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 People's Republic of China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 People's Republic of China
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17
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Upadhyay A, Feltman NR, Sychla A, Janzen A, Das SR, Maselko M, Smanski M. Genetically engineered insects with sex-selection and genetic incompatibility enable population suppression. eLife 2022; 11:71230. [PMID: 35108195 PMCID: PMC8860436 DOI: 10.7554/elife.71230] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 01/31/2022] [Indexed: 11/18/2022] Open
Abstract
Engineered Genetic Incompatibility (EGI) is a method to create species-like barriers to sexual reproduction. It has applications in pest control that mimic Sterile Insect Technique when only EGI males are released. This can be facilitated by introducing conditional female-lethality to EGI strains to generate a sex-sorting incompatible male system (SSIMS). Here, we demonstrate a proof of concept by combining tetracycline-controlled female lethality constructs with a pyramus-targeting EGI line in the model insect Drosophila melanogaster. We show that both functions (incompatibility and sex-sorting) are robustly maintained in the SSIMS line and that this approach is effective for population suppression in cage experiments. Further we show that SSIMS males remain competitive with wild-type males for reproduction with wild-type females, including at the level of sperm competition.
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Affiliation(s)
- Ambuj Upadhyay
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Nathan R Feltman
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, United States
| | - Adam Sychla
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, United States
| | - Anna Janzen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, United States
| | - Siba R Das
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, United States
| | | | - Michael Smanski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Saint Paul, United States
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18
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Clark M, Tepper K, Petroll K, Kumar S, Sunna A, Maselko M. Bioremediation of Industrial Pollutants by Insects Expressing a Fungal Laccase. ACS Synth Biol 2022; 11:308-316. [PMID: 34882406 DOI: 10.1021/acssynbio.1c00427] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inadequate management of household and industrial wastes poses major challenges to human and environmental health. Advances in synthetic biology may help address these challenges by engineering biological systems to perform new functions such as biomanufacturing of high-value compounds from low-value waste streams and bioremediation of industrial pollutants. The current emphasis on microbial systems for biomanufacturing, which often requires highly preprocessed inputs and sophisticated infrastructure, is not feasible for many waste streams. Furthermore, concerns about transgene biocontainment have limited the release of engineered microbes or plants for bioremediation. Engineering of animals may provide opportunities for utilizing various waste streams that are not suitable for microbial biomanufacturing while effective transgene biocontainment options should enable in situ bioremediation. Here, we engineer the model insect Drosophila melanogaster to express a functional laccase from the fungus Trametes trogii. Laccase-expressing flies reduced concentrations of the endocrine disruptor bisphenol A by more than 50% when present in their growth media. A lyophilized powder prepared from engineered adult flies retained substantial enzymatic activity, degrading more than 90% of bisphenol A and the textile dye indigo carmine in aqueous solutions. Our results demonstrate that transgenic animals may be used to bioremediate environmental contaminants in vivo and serve as novel production platforms for industrial enzymes. These results support further development of insects, and possibly other animals, as bioproduction platforms and their potential use in bioremediation.
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Affiliation(s)
- Michael Clark
- Applied BioSciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Kate Tepper
- Applied BioSciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Kerstin Petroll
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Sheemal Kumar
- Applied BioSciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Maciej Maselko
- Applied BioSciences, Macquarie University, Sydney, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane 4001 QLD, Australia
- CSIRO Health and Biosecurity, Geelong, VIC 3219, Australia
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19
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Abstract
Gene drives are an emerging technology with tremendous potential to impact public health, agriculture, and conservation. While gene drives can be described simply as selfish genetic elements (natural or engineered) that are inherited at non-Mendelian rates, upon closer inspection, engineered gene drive technology is a complex class of biotechnology that uses a diverse number of genetic features to bias rates of inheritance. As a complex technology, gene drives can be difficult to comprehend, not only for the public and stakeholders, but also to risk assessors, risk managers, and decisionmakers not familiar with gene drive literature. To address this difficulty, we describe a gene drive classification system based on 5 functional characteristics. These characteristics include a gene drive's objective, mechanism, release threshold, range, and persistence. The aggregate of the gene drive's characteristics can be described as the gene drive's architecture. Establishing a classification system to define different gene drive technologies should make them more comprehensible to the public and provide a framework to guide regulatory evaluation and decisionmaking.
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Affiliation(s)
- Justin Overcash
- Justin Overcash, PhD, is an Animal and Plant Health Inspection Service (APHIS) Science Fellow, Biotechnology Regulatory Services, Riverdale, MD
| | - Andrew Golnar
- Andrew Golnar, PhD, is an APHIS Science Fellow, Wildlife Services, Fort Collins, CO
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20
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Reid WR, Olson KE, Franz AWE. Current Effector and Gene-Drive Developments to Engineer Arbovirus-Resistant Aedes aegypti (Diptera: Culicidae) for a Sustainable Population Replacement Strategy in the Field. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1987-1996. [PMID: 33704462 PMCID: PMC8421695 DOI: 10.1093/jme/tjab030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 05/13/2023]
Abstract
Arthropod-borne viruses (arboviruses) such as dengue, Zika, and chikungunya viruses cause morbidity and mortality among human populations living in the tropical regions of the world. Conventional mosquito control efforts based on insecticide treatments and/or the use of bednets and window curtains are currently insufficient to reduce arbovirus prevalence in affected regions. Novel, genetic strategies that are being developed involve the genetic manipulation of mosquitoes for population reduction and population replacement purposes. Population replacement aims at replacing arbovirus-susceptible wild-type mosquitoes in a target region with those that carry a laboratory-engineered antiviral effector to interrupt arboviral transmission in the field. The strategy has been primarily developed for Aedes aegypti (L.), the most important urban arbovirus vector. Antiviral effectors based on long dsRNAs, miRNAs, or ribozymes destroy viral RNA genomes and need to be linked to a robust gene drive to ensure their fixation in the target population. Synthetic gene-drive concepts are based on toxin/antidote, genetic incompatibility, and selfish genetic element principles. The CRISPR/Cas9 gene editing system can be configurated as a homing endonuclease gene (HEG) and HEG-based drives became the preferred choice for mosquitoes. HEGs are highly allele and nucleotide sequence-specific and therefore sensitive to single-nucleotide polymorphisms/resistant allele formation. Current research efforts test new HEG-based gene-drive designs that promise to be less sensitive to resistant allele formation. Safety aspects in conjunction with gene drives are being addressed by developing procedures that would allow a recall or overwriting of gene-drive transgenes once they have been released.
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Affiliation(s)
- William R Reid
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Ken E Olson
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Alexander W E Franz
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
- Corresponding author, e-mail:
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21
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Devos Y, Mumford JD, Bonsall MB, Glandorf DCM, Quemada HD. Risk management recommendations for environmental releases of gene drive modified insects. Biotechnol Adv 2021; 54:107807. [PMID: 34314837 DOI: 10.1016/j.biotechadv.2021.107807] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/01/2021] [Accepted: 07/21/2021] [Indexed: 12/18/2022]
Abstract
The ability to engineer gene drives (genetic elements that bias their own inheritance) has sparked enthusiasm and concerns. Engineered gene drives could potentially be used to address long-standing challenges in the control of insect disease vectors, agricultural pests and invasive species, or help to rescue endangered species. However, risk concerns and uncertainty associated with potential environmental release of gene drive modified insects (GDMIs) have led some stakeholders to call for a global moratorium on such releases or the application of other strict precautionary measures to mitigate perceived risk assessment and risk management challenges. Instead, we provide recommendations that may help to improve the relevance of risk assessment and risk management frameworks for environmental releases of GDMIs. These recommendations include: (1) developing additional and more practical risk assessment guidance to ensure appropriate levels of safety; (2) making policy goals and regulatory decision-making criteria operational for use in risk assessment so that what constitutes harm is clearly defined; (3) ensuring a more dynamic interplay between risk assessment and risk management to manage uncertainty through closely interlinked pre-release modelling and post-release monitoring; (4) considering potential risks against potential benefits, and comparing them with those of alternative actions to account for a wider (management) context; and (5) implementing a modular, phased approach to authorisations for incremental acceptance and management of risks and uncertainty. Along with providing stakeholder engagement opportunities in the risk analysis process, the recommendations proposed may enable risk managers to make choices that are more proportionate and adaptive to potential risks, uncertainty and benefits of GDMI applications, and socially robust.
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Affiliation(s)
- Yann Devos
- Scientific Committee and Emerging Risk (SCER) Unit, European Food Safety Authority (EFSA), Parma, Italy.
| | - John D Mumford
- Centre for Environmental Policy, Imperial College London, Ascot, United Kingdom
| | | | - Debora C M Glandorf
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Hector D Quemada
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, United States
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22
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Buchman A, Shriner I, Yang T, Liu J, Antoshechkin I, Marshall JM, Perry MW, Akbari OS. Engineered reproductively isolated species drive reversible population replacement. Nat Commun 2021; 12:3281. [PMID: 34078888 DOI: 10.1101/2020.08.09.242982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 04/23/2021] [Indexed: 05/27/2023] Open
Abstract
Engineered reproductive species barriers are useful for impeding gene flow and driving desirable genes into wild populations in a reversible threshold-dependent manner. However, methods to generate synthetic barriers are lacking in advanced eukaryotes. Here, to overcome this challenge, we engineer SPECIES (Synthetic Postzygotic barriers Exploiting CRISPR-based Incompatibilities for Engineering Species), an engineered genetic incompatibility approach, to generate postzygotic reproductive barriers. Using this approach, we create multiple reproductively isolated SPECIES and demonstrate their reproductive isolation and threshold-dependent gene drive capabilities in D. melanogaster. Given the near-universal functionality of CRISPR tools, this approach should be portable to many species, including insect disease vectors in which confinable gene drives could be of great practical utility.
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Affiliation(s)
- Anna Buchman
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Isaiah Shriner
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Ting Yang
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering (BBE), California Institute of Technology, Pasadena, CA, USA
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Michael W Perry
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA.
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23
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Buchman A, Shriner I, Yang T, Liu J, Antoshechkin I, Marshall JM, Perry MW, Akbari OS. Engineered reproductively isolated species drive reversible population replacement. Nat Commun 2021; 12:3281. [PMID: 34078888 PMCID: PMC8173020 DOI: 10.1038/s41467-021-23531-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 04/23/2021] [Indexed: 01/09/2023] Open
Abstract
Engineered reproductive species barriers are useful for impeding gene flow and driving desirable genes into wild populations in a reversible threshold-dependent manner. However, methods to generate synthetic barriers are lacking in advanced eukaryotes. Here, to overcome this challenge, we engineer SPECIES (Synthetic Postzygotic barriers Exploiting CRISPR-based Incompatibilities for Engineering Species), an engineered genetic incompatibility approach, to generate postzygotic reproductive barriers. Using this approach, we create multiple reproductively isolated SPECIES and demonstrate their reproductive isolation and threshold-dependent gene drive capabilities in D. melanogaster. Given the near-universal functionality of CRISPR tools, this approach should be portable to many species, including insect disease vectors in which confinable gene drives could be of great practical utility.
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Affiliation(s)
- Anna Buchman
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Isaiah Shriner
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Ting Yang
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering (BBE), California Institute of Technology, Pasadena, CA, USA
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Michael W Perry
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, San Diego, CA, USA.
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24
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Hay BA, Oberhofer G, Guo M. Engineering the Composition and Fate of Wild Populations with Gene Drive. ANNUAL REVIEW OF ENTOMOLOGY 2021; 66:407-434. [PMID: 33035437 DOI: 10.1146/annurev-ento-020117-043154] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Insects play important roles as predators, prey, pollinators, recyclers, hosts, parasitoids, and sources of economically important products. They can also destroy crops; wound animals; and serve as vectors for plant, animal, and human diseases. Gene drive-a process by which genes, gene complexes, or chromosomes encoding specific traits are made to spread through wild populations, even if these traits result in a fitness cost to carriers-provides new opportunities for altering populations to benefit humanity and the environment in ways that are species specific and sustainable. Gene drive can be used to alter the genetic composition of an existing population, referred to as population modification or replacement, or to bring about population suppression or elimination. We describe technologies under consideration, progress that has been made, and remaining technological hurdles, particularly with respect to evolutionary stability and our ability to control the spread and ultimate fate of genes introduced into populations.
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Affiliation(s)
- Bruce A Hay
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA; ,
- St. John's College, University of Cambridge, Cambridge CB2 1TP, United Kingdom
| | - Georg Oberhofer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA; ,
| | - Ming Guo
- Departments of Neurology and Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA;
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25
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Naegeli H, Bresson J, Dalmay T, Dewhurst IC, Epstein MM, Guerche P, Hejatko J, Moreno FJ, Mullins E, Nogué F, Rostoks N, Sánchez Serrano JJ, Savoini G, Veromann E, Veronesi F, Bonsall MB, Mumford J, Wimmer EA, Devos Y, Paraskevopoulos K, Firbank LG. Adequacy and sufficiency evaluation of existing EFSA guidelines for the molecular characterisation, environmental risk assessment and post-market environmental monitoring of genetically modified insects containing engineered gene drives. EFSA J 2020; 18:e06297. [PMID: 33209154 PMCID: PMC7658669 DOI: 10.2903/j.efsa.2020.6297] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Advances in molecular and synthetic biology are enabling the engineering of gene drives in insects for disease vector/pest control. Engineered gene drives (that bias their own inheritance) can be designed either to suppress interbreeding target populations or modify them with a new genotype. Depending on the engineered gene drive system, theoretically, a genetic modification of interest could spread through target populations and persist indefinitely, or be restricted in its spread or persistence. While research on engineered gene drives and their applications in insects is advancing at a fast pace, it will take several years for technological developments to move to practical applications for deliberate release into the environment. Some gene drive modified insects (GDMIs) have been tested experimentally in the laboratory, but none has been assessed in small-scale confined field trials or in open release trials as yet. There is concern that the deliberate release of GDMIs in the environment may have possible irreversible and unintended consequences. As a proactive measure, the European Food Safety Authority (EFSA) has been requested by the European Commission to review whether its previously published guidelines for the risk assessment of genetically modified animals (EFSA, 2012 and 2013), including insects (GMIs), are adequate and sufficient for GDMIs, primarily disease vectors, agricultural pests and invasive species, for deliberate release into the environment. Under this mandate, EFSA was not requested to develop risk assessment guidelines for GDMIs. In this Scientific Opinion, the Panel on Genetically Modified Organisms (GMO) concludes that EFSA's guidelines are adequate, but insufficient for the molecular characterisation (MC), environmental risk assessment (ERA) and post-market environmental monitoring (PMEM) of GDMIs. While the MC,ERA and PMEM of GDMIs can build on the existing risk assessment framework for GMIs that do not contain engineered gene drives, there are specific areas where further guidance is needed for GDMIs.
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26
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Casas-Mollano JA, Zinselmeier MH, Erickson SE, Smanski MJ. CRISPR-Cas Activators for Engineering Gene Expression in Higher Eukaryotes. CRISPR J 2020; 3:350-364. [PMID: 33095045 PMCID: PMC7580621 DOI: 10.1089/crispr.2020.0064] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CRISPR-Cas-based transcriptional activators allow genetic engineers to specifically induce expression of one or many target genes in trans. Here we review the many design variations of these versatile tools and compare their effectiveness in different eukaryotic systems. Lastly, we highlight several applications of programmable transcriptional activation to interrogate and engineer complex biological processes.
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Affiliation(s)
- J. Armando Casas-Mollano
- Department of Biochemistry, Molecular Biology, and Biophysics, BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA; and Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
| | - Matthew H. Zinselmeier
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
| | - Samuel E. Erickson
- Department of Biochemistry, Molecular Biology, and Biophysics, BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA; and Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
| | - Michael J. Smanski
- Department of Biochemistry, Molecular Biology, and Biophysics, BioTechnology Institute, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA; and Cell Biology, and Development, University of Minnesota, Twin-Cities, Saint Paul, Minnesota, USA
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