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Zhao Y, Li L, Wei L, Wang Y, Han Z. Advancements and Future Prospects of CRISPR-Cas-Based Population Replacement Strategies in Insect Pest Management. INSECTS 2024; 15:653. [PMID: 39336621 PMCID: PMC11432399 DOI: 10.3390/insects15090653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/22/2024] [Accepted: 08/28/2024] [Indexed: 09/30/2024]
Abstract
Population replacement refers to the process by which a wild-type population of insect pests is replaced by a population possessing modified traits or abilities. Effective population replacement necessitates a gene drive system capable of spreading desired genes within natural populations, operating under principles akin to super-Mendelian inheritance. Consequently, releasing a small number of genetically edited insects could potentially achieve population control objectives. Currently, several gene drive approaches are under exploration, including the newly adapted CRISPR-Cas genome editing system. Multiple studies are investigating methods to engineer pests that are incapable of causing crop damage or transmitting vector-borne diseases, with several notable successful examples documented. This review summarizes the recent advancements of the CRISPR-Cas system in the realm of population replacement and provides insights into research methodologies, testing protocols, and implementation strategies for gene drive techniques. The review also discusses emerging trends and prospects for establishing genetic tools in pest management.
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Affiliation(s)
- Yu Zhao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Longfeng Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Liangzi Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yifan Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhilin Han
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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2
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Feng X, López Del Amo V, Mameli E, Lee M, Bishop AL, Perrimon N, Gantz VM. Optimized CRISPR tools and site-directed transgenesis towards gene drive development in Culex quinquefasciatus mosquitoes. Nat Commun 2021; 12:2960. [PMID: 34017003 PMCID: PMC8137705 DOI: 10.1038/s41467-021-23239-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
Culex mosquitoes are a global vector for multiple human and animal diseases, including West Nile virus, lymphatic filariasis, and avian malaria, posing a constant threat to public health, livestock, companion animals, and endangered birds. While rising insecticide resistance has threatened the control of Culex mosquitoes, advances in CRISPR genome-editing tools have fostered the development of alternative genetic strategies such as gene drive systems to fight disease vectors. However, though gene-drive technology has quickly progressed in other mosquitoes, advances have been lacking in Culex. Here, we develop a Culex-specific Cas9/gRNA expression toolkit and use site-directed homology-based transgenesis to generate and validate a Culex quinquefasciatus Cas9-expressing line. We show that gRNA scaffold variants improve transgenesis efficiency in both Culex quinquefasciatus and Drosophila melanogaster and boost gene-drive performance in the fruit fly. These findings support future technology development to control Culex mosquitoes and provide valuable insight for improving these tools in other species.
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Affiliation(s)
- Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Víctor López Del Amo
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Enzo Mameli
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University, School of Medicine, Boston, MA, USA
| | - Megan Lee
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Alena L Bishop
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- HHMI, Harvard Medical School, Boston, MA, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
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Edgington MP, Harvey‐Samuel T, Alphey L. Population-level multiplexing: A promising strategy to manage the evolution of resistance against gene drives targeting a neutral locus. Evol Appl 2020; 13:1939-1948. [PMID: 32908596 PMCID: PMC7463328 DOI: 10.1111/eva.12945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 01/30/2023] Open
Abstract
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.
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Phelps MP, Seeb LW, Seeb JE. Transforming ecology and conservation biology through genome editing. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:54-65. [PMID: 30693970 DOI: 10.1111/cobi.13292] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 12/23/2018] [Accepted: 01/24/2019] [Indexed: 06/09/2023]
Abstract
As the conservation challenges increase, new approaches are needed to help combat losses in biodiversity and slow or reverse the decline of threatened species. Genome-editing technology is changing the face of modern biology, facilitating applications that were unimaginable only a decade ago. The technology has the potential to make significant contributions to the fields of evolutionary biology, ecology, and conservation, yet the fear of unintended consequences from designer ecosystems containing engineered organisms has stifled innovation. To overcome this gap in the understanding of what genome editing is and what its capabilities are, more research is needed to translate genome-editing discoveries into tools for ecological research. Emerging and future genome-editing technologies include new clustered regularly interspaced short palindromic repeats (CRISPR) targeted sequencing and nucleic acid detection approaches as well as species genetic barcoding and somatic genome-editing technologies. These genome-editing tools have the potential to transform the environmental sciences by providing new noninvasive methods for monitoring threatened species or for enhancing critical adaptive traits. A pioneering effort by the conservation community is required to apply these technologies to real-world conservation problems.
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Affiliation(s)
- Michael P Phelps
- Department of Pathology, University of Washington, Box 357705, Seattle, WA, 98195, U.S.A
| | - Lisa W Seeb
- School of Aquatic and Fisheries Sciences, University of Washington, Seattle, WA, 98195, U.S.A
| | - James E Seeb
- School of Aquatic and Fisheries Sciences, University of Washington, Seattle, WA, 98195, U.S.A
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Breed MF, Harrison PA, Blyth C, Byrne M, Gaget V, Gellie NJC, Groom SVC, Hodgson R, Mills JG, Prowse TAA, Steane DA, Mohr JJ. The potential of genomics for restoring ecosystems and biodiversity. Nat Rev Genet 2019; 20:615-628. [PMID: 31300751 DOI: 10.1038/s41576-019-0152-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2019] [Indexed: 01/12/2023]
Abstract
Billions of hectares of natural ecosystems have been degraded through human actions. The global community has agreed on targets to halt and reverse these declines, and the restoration sector faces the important but arduous task of implementing programmes to meet these objectives. Existing and emerging genomics tools offer the potential to improve the odds of achieving these targets. These tools include population genomics that can improve seed sourcing, meta-omics that can improve assessment and monitoring of restoration outcomes, and genome editing that can generate novel genotypes for restoring challenging environments. We identify barriers to adopting these tools in a restoration context and emphasize that regulatory and ethical frameworks are required to guide their use.
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Affiliation(s)
- Martin F Breed
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia.
| | - Peter A Harrison
- School of Natural Sciences, Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Colette Blyth
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Western Australia, Australia
| | - Virginie Gaget
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Nicholas J C Gellie
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Scott V C Groom
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, South Australia, Australia
| | - Riley Hodgson
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Jacob G Mills
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia
| | - Thomas A A Prowse
- School of Biological Sciences and the Environment Institute, University of Adelaide, North Terrace, South Australia, Australia.,School of Mathematical Sciences, University of Adelaide, North Terrace, South Australia, Australia
| | - Dorothy A Steane
- School of Natural Sciences, Australian Research Council Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania, Australia
| | - Jakki J Mohr
- College of Business, Institute on Ecosystems, University of Montana, Missoula, MT, USA
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Abstract
Aedes mosquito-transmitted diseases, such as dengue, Zika and chikungunya, are becoming major global health emergencies while old threats, such as yellow fever, are re-emerging. Traditional control methods, which have focused on reducing mosquito populations through the application of insecticides or preventing breeding through removal of larval habitat, are largely ineffective, as evidenced by the increasing global disease burden. Here, we review novel mosquito population reduction and population modification approaches with a focus on control methods based on the release of mosquitoes, including the release of Wolbachia-infected mosquitoes and strategies to genetically modify the vector, that are currently under development and have the potential to contribute to a reversal of the current alarming disease trends.
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Affiliation(s)
- Heather A Flores
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, Australia
| | - Scott L O'Neill
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, Australia.
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Dhole S, Vella MR, Lloyd AL, Gould F. Invasion and migration of spatially self-limiting gene drives: A comparative analysis. Evol Appl 2018; 11:794-808. [PMID: 29875820 PMCID: PMC5978947 DOI: 10.1111/eva.12583] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/27/2017] [Indexed: 12/14/2022] Open
Abstract
Recent advances in research on gene drives have produced genetic constructs that could theoretically spread a desired gene (payload) into all populations of a species, with a single release in one place. This attribute has advantages, but also comes with risks and ethical concerns. There has been a call for research on gene drive systems that are spatially and/or temporally self-limiting. Here, we use a population genetics model to compare the expected characteristics of three spatially self-limiting gene drive systems: one-locus underdominance, two-locus underdominance and daisy-chain drives. We find large differences between these gene drives in the minimum release size required for successfully driving a payload into a population. The daisy-chain system is the most efficient, requiring the smallest release, followed by the two-locus underdominance system, and then the one-locus underdominance system. However, when the target population exchanges migrants with a nontarget population, the gene drives requiring smaller releases suffer from higher risks of unintended spread. For payloads that incur relatively low fitness costs (up to 30%), a simple daisy-chain drive is practically incapable of remaining localized, even with migration rates as low as 0.5% per generation. The two-locus underdominance system can achieve localized spread under a broader range of migration rates and of payload fitness costs, while the one-locus underdominance system largely remains localized. We also find differences in the extent of population alteration and in the permanence of the alteration achieved by the three gene drives. The two-locus underdominance system does not always spread the payload to fixation, even after successful drive, while the daisy-chain system can, for a small set of parameter values, achieve a temporally limited spread of the payload. These differences could affect the suitability of each gene drive for specific applications.
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Affiliation(s)
- Sumit Dhole
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
| | - Michael R. Vella
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNCUSA
- Biomathematics Graduate ProgramDepartment of MathematicsNorth Carolina State UniversityRaleighNCUSA
| | - Alun L. Lloyd
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNCUSA
- Biomathematics Graduate ProgramDepartment of MathematicsNorth Carolina State UniversityRaleighNCUSA
| | - Fred Gould
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNCUSA
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Champer J, Liu J, Oh SY, Reeves R, Luthra A, Oakes N, Clark AG, Messer PW. Reducing resistance allele formation in CRISPR gene drive. Proc Natl Acad Sci U S A 2018; 115:5522-5527. [PMID: 29735716 PMCID: PMC6003519 DOI: 10.1073/pnas.1720354115] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CRISPR homing gene drives can convert heterozygous cells with one copy of the drive allele into homozygotes, thereby enabling super-Mendelian inheritance. Such a mechanism could be used, for example, to rapidly disseminate a genetic payload in a population, promising effective strategies for the control of vector-borne diseases. However, all CRISPR homing gene drives studied in insects thus far have produced significant quantities of resistance alleles that would limit their spread. In this study, we provide an experimental demonstration that multiplexing of guide RNAs can both significantly increase the drive conversion efficiency and reduce germline resistance rates of a CRISPR homing gene drive in Drosophila melanogaster We further show that an autosomal drive can achieve drive conversion in the male germline, with no subsequent formation of resistance alleles in embryos through paternal carryover of Cas9. Finally, we find that the nanos promoter significantly lowers somatic Cas9 expression compared with the vasa promoter, suggesting that nanos provides a superior choice in drive strategies where gene disruption in somatic cells could have fitness costs. Comparison of drive parameters among the different constructs developed in this study and a previous study suggests that, while drive conversion and germline resistance rates are similar between different genomic targets, embryo resistance rates can vary significantly. Taken together, our results mark an important step toward developing effective gene drives capable of functioning in natural populations and provide several possible avenues for further control of resistance rates.
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Affiliation(s)
- Jackson Champer
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853;
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Jingxian Liu
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Suh Yeon Oh
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Riona Reeves
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Anisha Luthra
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Nathan Oakes
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853
| | - Andrew G Clark
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Philipp W Messer
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853;
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Champer J, Reeves R, Oh SY, Liu C, Liu J, Clark AG, Messer PW. Novel CRISPR/Cas9 gene drive constructs reveal insights into mechanisms of resistance allele formation and drive efficiency in genetically diverse populations. PLoS Genet 2017; 13:e1006796. [PMID: 28727785 PMCID: PMC5518997 DOI: 10.1371/journal.pgen.1006796] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/03/2017] [Indexed: 12/17/2022] Open
Abstract
A functioning gene drive system could fundamentally change our strategies for the control of vector-borne diseases by facilitating rapid dissemination of transgenes that prevent pathogen transmission or reduce vector capacity. CRISPR/Cas9 gene drive promises such a mechanism, which works by converting cells that are heterozygous for the drive construct into homozygotes, thereby enabling super-Mendelian inheritance. Although CRISPR gene drive activity has already been demonstrated, a key obstacle for current systems is their propensity to generate resistance alleles, which cannot be converted to drive alleles. In this study, we developed two CRISPR gene drive constructs based on the nanos and vasa promoters that allowed us to illuminate the different mechanisms by which resistance alleles are formed in the model organism Drosophila melanogaster. We observed resistance allele formation at high rates both prior to fertilization in the germline and post-fertilization in the embryo due to maternally deposited Cas9. Assessment of drive activity in genetically diverse backgrounds further revealed substantial differences in conversion efficiency and resistance rates. Our results demonstrate that the evolution of resistance will likely impose a severe limitation to the effectiveness of current CRISPR gene drive approaches, especially when applied to diverse natural populations.
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Affiliation(s)
- Jackson Champer
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
- * E-mail: (JC); (PWM)
| | - Riona Reeves
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Suh Yeon Oh
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Chen Liu
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Jingxian Liu
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Andrew G. Clark
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Philipp W. Messer
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, United States of America
- * E-mail: (JC); (PWM)
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