1
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de Haas FJH, Kläy L, Débarre F, Otto SP. Modelling daisy quorum drive: A short-term bridge across engineered fitness valleys. PLoS Genet 2024; 20:e1011262. [PMID: 38753875 PMCID: PMC11135765 DOI: 10.1371/journal.pgen.1011262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/29/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
Engineered gene-drive techniques for population modification and/or suppression have the potential for tackling complex challenges, including reducing the spread of diseases and invasive species. Gene-drive systems with low threshold frequencies for invasion, such as homing-based gene drive, require initially few transgenic individuals to spread and are therefore easy to introduce. The self-propelled behavior of such drives presents a double-edged sword, however, as the low threshold can allow transgenic elements to expand beyond a target population. By contrast, systems where a high threshold frequency must be reached before alleles can spread-above a fitness valley-are less susceptible to spillover but require introduction at a high frequency. We model a proposed drive system, called "daisy quorum drive," that transitions over time from a low-threshold daisy-chain system (involving homing-based gene drive such as CRISPR-Cas9) to a high-threshold fitness-valley system (requiring a high frequency-a "quorum"-to spread). The daisy-chain construct temporarily lowers the high thresholds required for spread of the fitness-valley construct, facilitating use in a wide variety of species that are challenging to breed and release in large numbers. Because elements in the daisy chain only drive subsequent elements in the chain and not themselves and also carry deleterious alleles ("drive load"), the daisy chain is expected to exhaust itself, removing all CRISPR elements and leaving only the high-threshold fitness-valley construct, whose spread is more spatially restricted. Developing and analyzing both discrete patch and continuous space models, we explore how various attributes of daisy quorum drive affect the chance of modifying local population characteristics and the risk that transgenic elements expand beyond a target area. We also briefly explore daisy quorum drive when population suppression is the goal. We find that daisy quorum drive can provide a promising bridge between gene-drive and fitness-valley constructs, allowing spread from a low frequency in the short term and better containment in the long term, without requiring repeated introductions or persistence of CRISPR elements.
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Affiliation(s)
- Frederik J. H. de Haas
- Biodiversity Research Center, Department of Zoology, University of British Columbia, Vancouver BC, Canada
| | - Léna Kläy
- Institute of Ecology and Environmental Sciences Paris (IEES Paris), Sorbonne Université, CNRS, IRD, INRAE, Université Paris Est Creteil, Université de Paris, Paris Cedex 5, France
| | - Florence Débarre
- Institute of Ecology and Environmental Sciences Paris (IEES Paris), Sorbonne Université, CNRS, IRD, INRAE, Université Paris Est Creteil, Université de Paris, Paris Cedex 5, France
| | - Sarah P. Otto
- Biodiversity Research Center, Department of Zoology, University of British Columbia, Vancouver BC, Canada
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2
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Hou S, Chen J, Feng R, Xu X, Liang N, Champer J. A homing rescue gene drive with multiplexed gRNAs reaches high frequency in cage populations but generates functional resistance. J Genet Genomics 2024:S1673-8527(24)00070-5. [PMID: 38599514 DOI: 10.1016/j.jgg.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
CRISPR homing gene drives have considerable potential for managing populations of medically and agriculturally significant insects. They operate by Cas9 cleavage followed by homology-directed repair, copying the drive allele to the wild-type chromosome and thus increasing in frequency and spreading throughout a population. However, resistance alleles formed by end-joining repair pose a significant obstacle. To address this, we create a homing drive targeting the essential hairy gene in Drosophila melanogaster. Nonfunctional resistance alleles are recessive lethal, while drive carriers have a recoded "rescue" version of hairy. The drive inheritance rate is moderate, and multigenerational cage studies show drive spread to 96%-97% of the population. However, the drive does not reach 100% due to the formation of functional resistance alleles, despite using four gRNAs. These alleles have a large deletion but likely utilize an alternate start codon. Thus, revised designs targeting more essential regions of a gene may be necessary to avoid such functional resistance. Replacement of the rescue element's native 3' UTR with a homolog from another species increases drive inheritance by 13%-24%. This was possibly because of reduced homology between the rescue element and surrounding genomic DNA, which could also be an important design consideration for rescue gene drives.
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Affiliation(s)
- Shibo Hou
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jingheng Chen
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ruobing Feng
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xuejiao Xu
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Nan Liang
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jackson Champer
- Center for Bioinformatics, Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China.
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3
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Ma S, Ni X, Chen S, Qiao X, Xu X, Chen W, Champer J, Huang J. A small-molecule approach to restore female sterility phenotype targeted by a homing suppression gene drive in the fruit pest Drosophila suzukii. PLoS Genet 2024; 20:e1011226. [PMID: 38578788 PMCID: PMC11023630 DOI: 10.1371/journal.pgen.1011226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 04/17/2024] [Accepted: 03/15/2024] [Indexed: 04/07/2024] Open
Abstract
CRISPR-based gene drives offer promising prospects for controlling disease-transmitting vectors and agricultural pests. A significant challenge for successful suppression-type drive is the rapid evolution of resistance alleles. One approach to mitigate the development of resistance involves targeting functionally constrained regions using multiple gRNAs. In this study, we constructed a 3-gRNA homing gene drive system targeting the recessive female fertility gene Tyrosine decarboxylase 2 (Tdc2) in Drosophila suzukii, a notorious fruit pest. Our investigation revealed only a low level of homing in the germline, but feeding octopamine restored the egg-laying defects in Tdc2 mutant females, allowing easier line maintenance than for other suppression drive targets. We tested the effectiveness of a similar system in Drosophila melanogaster and constructed additional split drive systems by introducing promoter-Cas9 transgenes to improve homing efficiency. Our findings show that genetic polymorphisms in wild populations may limit the spread of gene drive alleles, and the position effect profoundly influences Cas9 activity. Furthermore, this study highlights the potential of conditionally rescuing the female infertility caused by the gene drive, offering a valuable tool for the industrial-scale production of gene drive transgenic insects.
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Affiliation(s)
- Suhan Ma
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xuyang Ni
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shimin Chen
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | | | - Xuejiao Xu
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
| | - Weizhe Chen
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
- PTN program, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Center for Life Sciences, Peking University, Beijing, China
| | - Jia Huang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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4
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Li Z, You L, Hermann A, Bier E. Developmental progression of DNA double-strand break repair deciphered by a single-allele resolution mutation classifier. Nat Commun 2024; 15:2629. [PMID: 38521791 PMCID: PMC10960810 DOI: 10.1038/s41467-024-46479-2] [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: 11/13/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024] Open
Abstract
DNA double-strand breaks (DSBs) are repaired by a hierarchically regulated network of pathways. Factors influencing the choice of particular repair pathways, however remain poorly characterized. Here we develop an Integrated Classification Pipeline (ICP) to decompose and categorize CRISPR/Cas9 generated mutations on genomic target sites in complex multicellular insects. The ICP outputs graphic rank ordered classifications of mutant alleles to visualize discriminating DSB repair fingerprints generated from different target sites and alternative inheritance patterns of CRISPR components. We uncover highly reproducible lineage-specific mutation fingerprints in individual organisms and a developmental progression wherein Microhomology-Mediated End-Joining (MMEJ) or Insertion events predominate during early rapid mitotic cell cycles, switching to distinct subsets of Non-Homologous End-Joining (NHEJ) alleles, and then to Homology-Directed Repair (HDR)-based gene conversion. These repair signatures enable marker-free tracking of specific mutations in dynamic populations, including NHEJ and HDR events within the same samples, for in-depth analysis of diverse gene editing events.
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Affiliation(s)
- Zhiqian Li
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lang You
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anita Hermann
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA.
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5
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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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6
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Harris KD, Greenbaum G. Rescue by gene swamping as a gene drive deployment strategy. Cell Rep 2023; 42:113499. [PMID: 38039130 DOI: 10.1016/j.celrep.2023.113499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 10/05/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023] Open
Abstract
Gene drives are genetic constructs that can spread deleterious alleles with potential application to population suppression of harmful species. As gene drives can potentially spill over to other populations or species, control measures and fail-safe strategies must be considered. Gene drives can generate a rapid change in the population's genetic composition, leading to substantial demographic decline, processes that are expected to occur at a similar timescale during gene drive spread. We developed a gene drive model that combines evolutionary and demographic dynamics in a two-population setting. The model demonstrates how feedback between these dynamics generates additional outcomes to those generated by the evolutionary dynamics alone. We identify an outcome of particular interest where short-term suppression of the target population is followed by gene swamping and loss of the gene drive. This outcome can prevent spillover and is robust to the evolution of resistance, suggesting it may be suitable as a fail-safe strategy for gene drive deployment.
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Affiliation(s)
- Keith D Harris
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Gili Greenbaum
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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7
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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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8
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Sanz Juste S, Okamoto EM, Nguyen C, Feng X, López Del Amo V. Next-generation CRISPR gene-drive systems using Cas12a nuclease. Nat Commun 2023; 14:6388. [PMID: 37821497 PMCID: PMC10567717 DOI: 10.1038/s41467-023-42183-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023] Open
Abstract
One method for reducing the impact of vector-borne diseases is through the use of CRISPR-based gene drives, which manipulate insect populations due to their ability to rapidly propagate desired genetic traits into a target population. However, all current gene drives employ a Cas9 nuclease that is constitutively active, impeding our control over their propagation abilities and limiting the generation of alternative gene drive arrangements. Yet, other nucleases such as the temperature sensitive Cas12a have not been explored for gene drive designs in insects. To address this, we herein present a proof-of-concept gene-drive system driven by Cas12a that can be regulated via temperature modulation. Furthermore, we combined Cas9 and Cas12a to build double gene drives capable of simultaneously spreading two independent engineered alleles. The development of Cas12a-mediated gene drives provides an innovative option for designing next-generation vector control strategies to combat disease vectors and agricultural pests.
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Affiliation(s)
- Sara Sanz Juste
- Department of Epigenetics & Molecular Carcinogenesis at MD Anderson, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Emily M Okamoto
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Christina Nguyen
- University of Texas Health Science Center, School of Public Health, Department of Epidemiology, Human Genetics, and Environmental Sciences, Center for Infectious Diseases, Houston, TX, 77030, USA
| | - Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA.
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518106, China.
| | - Víctor López Del Amo
- University of Texas Health Science Center, School of Public Health, Department of Epidemiology, Human Genetics, and Environmental Sciences, Center for Infectious Diseases, Houston, TX, 77030, USA.
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9
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Frieß JL, Lalyer CR, Giese B, Simon S, Otto M. Review of gene drive modelling and implications for risk assessment of gene drive organisms. Ecol Modell 2023. [DOI: 10.1016/j.ecolmodel.2023.110285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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10
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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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11
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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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12
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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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13
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Terradas G, Bennett JB, Li Z, Marshall JM, Bier E. Genetic conversion of a split-drive into a full-drive element. Nat Commun 2023; 14:191. [PMID: 36635291 PMCID: PMC9837192 DOI: 10.1038/s41467-022-35044-4] [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: 03/18/2022] [Accepted: 11/16/2022] [Indexed: 01/13/2023] Open
Abstract
The core components of CRISPR-based gene drives, Cas9 and guide RNA (gRNA), either can be linked within a self-contained single cassette (full gene-drive, fGD) or be provided in two separate elements (split gene-drive, sGD), the latter offering greater control options. We previously engineered split systems that could be converted genetically into autonomous full drives. Here, we examine such dual systems inserted at the spo11 locus that are recoded to restore gene function and thus organismic fertility. Despite minimal differences in transmission efficiency of the sGD or fGD drive elements in single generation crosses, the reconstituted spo11 fGD cassette surprisingly exhibits slower initial drive kinetics than the unlinked sGD element in multigenerational cage studies, but then eventually catches up to achieve a similar level of final introduction. These unexpected kinetic behaviors most likely reflect differing transient fitness costs associated with individuals co-inheriting Cas9 and gRNA transgenes during the drive process.
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Affiliation(s)
- Gerard Terradas
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA.,Department of Entomology, The Center for Infectious Disease Dynamics, and the Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jared B Bennett
- Biophysics Graduate Group, Division of Biological Sciences, College of Letters and Science, University of California, Berkeley, CA, 94720, USA
| | - Zhiqian Li
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - John M Marshall
- Divisions of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA. .,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA.
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14
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Verkuijl SAN, Gonzalez E, Li M, Ang JXD, Kandul NP, Anderson MAE, Akbari OS, Bonsall MB, Alphey L. A CRISPR endonuclease gene drive reveals distinct mechanisms of inheritance bias. Nat Commun 2022; 13:7145. [PMID: 36414618 PMCID: PMC9681865 DOI: 10.1038/s41467-022-34739-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR/Cas gene drives can bias transgene inheritance through different mechanisms. Homing drives are designed to replace a wild-type allele with a copy of a drive element on the homologous chromosome. In Aedes aegypti, the sex-determining locus is closely linked to the white gene, which was previously used as a target for a homing drive element (wGDe). Here, through an analysis using this linkage we show that in males inheritance bias of wGDe did not occur by homing, rather through increased propagation of the donor drive element. We test the same wGDe drive element with transgenes expressing Cas9 with germline regulatory elements sds3, bgcn, and nup50. We only find inheritance bias through homing, even with the identical nup50-Cas9 transgene. We propose that DNA repair outcomes may be more context dependent than anticipated and that other previously reported homing drives may, in fact, bias their inheritance through other mechanisms.
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Affiliation(s)
- Sebald A N Verkuijl
- Mathematical Ecology Research Group, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
| | - Estela Gonzalez
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ming Li
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Joshua X D Ang
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Nikolay P Kandul
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michelle A E Anderson
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Omar S Akbari
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michael B Bonsall
- Mathematical Ecology Research Group, Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
- The Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
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15
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Garrood WT, Cuber P, Willis K, Bernardini F, Page NM, Haghighat-Khah RE. Driving down malaria transmission with engineered gene drives. Front Genet 2022; 13:891218. [PMID: 36338968 PMCID: PMC9627344 DOI: 10.3389/fgene.2022.891218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 09/13/2022] [Indexed: 11/26/2022] Open
Abstract
The last century has witnessed the introduction, establishment and expansion of mosquito-borne diseases into diverse new geographic ranges. Malaria is transmitted by female Anopheles mosquitoes. Despite making great strides over the past few decades in reducing the burden of malaria, transmission is now on the rise again, in part owing to the emergence of mosquito resistance to insecticides, antimalarial drug resistance and, more recently, the challenges of the COVID-19 pandemic, which resulted in the reduced implementation efficiency of various control programs. The utility of genetically engineered gene drive mosquitoes as tools to decrease the burden of malaria by controlling the disease-transmitting mosquitoes is being evaluated. To date, there has been remarkable progress in the development of CRISPR/Cas9-based homing endonuclease designs in malaria mosquitoes due to successful proof-of-principle and multigenerational experiments. In this review, we examine the lessons learnt from the development of current CRISPR/Cas9-based homing endonuclease gene drives, providing a framework for the development of gene drive systems for the targeted control of wild malaria-transmitting mosquito populations that overcome challenges such as with evolving drive-resistance. We also discuss the additional substantial works required to progress the development of gene drive systems from scientific discovery to further study and subsequent field application in endemic settings.
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Affiliation(s)
- William T. Garrood
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Piotr Cuber
- Department of Molecular Biology, Core Research Laboratories, Natural History Museum, London, United Kingdom
| | - Katie Willis
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Federica Bernardini
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Nicole M. Page
- Department of Life Sciences, Imperial College London, London, United Kingdom
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16
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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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17
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Verkuijl SAN, Anderson MAE, Alphey L, Bonsall MB. Daisy-chain gene drives: The role of low cut-rate, resistance mutations, and maternal deposition. PLoS Genet 2022; 18:e1010370. [PMID: 36121880 PMCID: PMC9521892 DOI: 10.1371/journal.pgen.1010370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 09/29/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022] Open
Abstract
The introgression of genetic traits through gene drive may serve as a powerful and widely applicable method of biological control. However, for many applications, a self-perpetuating gene drive that can spread beyond the specific target population may be undesirable and preclude use. Daisy-chain gene drives have been proposed as a means of tuning the invasiveness of a gene drive, allowing it to spread efficiently into the target population, but be self-limiting beyond that. Daisy-chain gene drives are made up of multiple independent drive elements, where each element, except one, biases the inheritance of another, forming a chain. Under ideal inheritance biasing conditions, the released drive elements remain linked in the same configuration, generating copies of most of their elements except for the last remaining link in the chain. Through mathematical modelling of populations connected by migration, we have evaluated the effect of resistance alleles, different fitness costs, reduction in the cut-rate, and maternal deposition on two alternative daisy-chain gene drive designs. We find that the self-limiting nature of daisy-chain gene drives makes their spread highly dependent on the efficiency and fidelity of the inheritance biasing mechanism. In particular, reductions in the cut-rate and the formation of non-lethal resistance alleles can cause drive elements to lose their linked configuration. This severely reduces the invasiveness of the drives and allows for phantom cutting, where an upstream drive element cuts a downstream target locus despite the corresponding drive element being absent, creating and biasing the inheritance of additional resistance alleles. This phantom cutting can be mitigated by an alternative indirect daisy-chain design. We further find that while dominant fitness costs and maternal deposition reduce daisy-chain invasiveness, if overcome with an increased release frequency, they can reduce the spread of the drive into a neighbouring population.
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Affiliation(s)
- Sebald A. N. Verkuijl
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
| | | | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
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18
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Melesse Vergara M, Labbé J, Tannous J. Reflection on the Challenges, Accomplishments, and New Frontiers of Gene Drives. BIODESIGN RESEARCH 2022; 2022:9853416. [PMID: 37850135 PMCID: PMC10521683 DOI: 10.34133/2022/9853416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/19/2022] [Indexed: 10/19/2023] Open
Abstract
Ongoing pest and disease outbreaks pose a serious threat to human, crop, and animal lives, emphasizing the need for constant genetic discoveries that could serve as mitigation strategies. Gene drives are genetic engineering approaches discovered decades ago that may allow quick, super-Mendelian dissemination of genetic modifications in wild populations, offering hopes for medicine, agriculture, and ecology in combating diseases. Following its first discovery, several naturally occurring selfish genetic elements were identified and several gene drive mechanisms that could attain relatively high threshold population replacement have been proposed. This review provides a comprehensive overview of the recent advances in gene drive research with a particular emphasis on CRISPR-Cas gene drives, the technology that has revolutionized the process of genome engineering. Herein, we discuss the benefits and caveats of this technology and place it within the context of natural gene drives discovered to date and various synthetic drives engineered. Later, we elaborate on the strategies for designing synthetic drive systems to address resistance issues and prevent them from altering the entire wild populations. Lastly, we highlight the major applications of synthetic CRISPR-based gene drives in different living organisms, including plants, animals, and microorganisms.
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Affiliation(s)
| | - Jesse Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Invaio Sciences, Cambridge, MA 02138USA
| | - Joanna Tannous
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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19
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A nickase Cas9 gene-drive system promotes super-Mendelian inheritance in Drosophila. Cell Rep 2022; 39:110843. [PMID: 35613590 PMCID: PMC9190248 DOI: 10.1016/j.celrep.2022.110843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/07/2022] [Accepted: 04/28/2022] [Indexed: 01/01/2023] Open
Abstract
CRISPR-based gene-drives have been proposed for managing insect populations, including disease-transmitting mosquitoes, due to their ability to bias their inheritance toward super-Mendelian rates (>50%). Current technologies use a Cas9 that introduces DNA double-strand breaks into the opposing wild-type allele to replace it with a copy of the gene-drive allele via DNA homology-directed repair. However, the use of different Cas9 versions is unexplored, and alternative approaches could increase the available toolkit for gene-drive designs. Here, we report a gene-drive that relies on Cas9 nickases that generate staggered paired nicks in DNA to propagate the engineered gene-drive cassette. We show that generating 5′ overhangs in the system yields efficient allelic conversion. The nickase gene-drive arrangement produces large, stereotyped deletions that are advantageous to eliminate viable animals carrying small mutations when targeting essential genes. Our nickase approach should expand the repertoire for gene-drive arrangements aimed at applications in mosquitoes and beyond. Gene-drives using wild-type Cas9 offer solutions to fight vector-borne diseases, yet alternative strategies are needed to increase the available toolkit. López Del Amo et al. describe a nickase-based gene-drive system that promotes super-Mendelian inheritance of an engineered cassette in the Drosophila germ line, providing alternative designs for CRISPR-based gene-drive.
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20
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Nash A, Capriotti P, Hoermann A, Papathanos PA, Windbichler N. Intronic gRNAs for the Construction of Minimal Gene Drive Systems. Front Bioeng Biotechnol 2022; 10:857460. [PMID: 35646834 PMCID: PMC9133698 DOI: 10.3389/fbioe.2022.857460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Gene drives are promising tools for the genetic control of insect vector or pest populations. CRISPR-based gene drives are generally highly complex synthetic constructs consisting of multiple transgenes and their respective regulatory elements. This complicates the generation of new gene drives and the testing of the behavior of their constituent functional modules. Here, we explored the minimal genetic components needed to constitute autonomous gene drives in Drosophila melanogaster. We first designed intronic gRNAs that can be located directly within coding transgene sequences and tested their functions in cell lines. We then integrated a Cas9 open reading frame hosting such an intronic gRNA within the Drosophila rcd-1r locus that drives the expression in the male and female germlines. We showed that upon removal of the fluorescent transformation marker, the rcd-1rd allele supports efficient gene drive. We assessed the propensity of this driver, designed to be neutral with regards to fitness and host gene function, to propagate in caged fly populations. Because of their simplicity, such integral gene drives could enable the modularization of drive and effector functions. We also discussed the possible biosafety implications of minimal and possibly recoded gene drives.
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Affiliation(s)
- Alexander Nash
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Paolo Capriotti
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Astrid Hoermann
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Phillipos Aris Papathanos
- Department of Entomology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, London, United Kingdom
- *Correspondence: Nikolai Windbichler,
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21
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Propagation of seminal toxins through binary expression gene drives could suppress populations. Sci Rep 2022; 12:6332. [PMID: 35428855 PMCID: PMC9012762 DOI: 10.1038/s41598-022-10327-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/05/2022] [Indexed: 11/25/2022] Open
Abstract
Gene drives can be highly effective in controlling a target population by disrupting a female fertility gene. To spread across a population, these drives require that disrupted alleles be largely recessive so as not to impose too high of a fitness penalty. We argue that this restriction may be relaxed by using a double gene drive design to spread a split binary expression system. One drive carries a dominant lethal/toxic effector alone and the other a transactivator factor, without which the effector will not act. Only after the drives reach sufficiently high frequencies would individuals have the chance to inherit both system components and the effector be expressed. We explore through mathematical modeling the potential of this design to spread dominant lethal/toxic alleles and suppress populations. We show that this system could be implemented to spread engineered seminal proteins designed to kill females, making it highly effective against polyandrous populations.
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22
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Verkuijl SAN, Ang JXD, Alphey L, Bonsall MB, Anderson MAE. The Challenges in Developing Efficient and Robust Synthetic Homing Endonuclease Gene Drives. Front Bioeng Biotechnol 2022; 10:856981. [PMID: 35419354 PMCID: PMC8996256 DOI: 10.3389/fbioe.2022.856981] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Making discrete and precise genetic changes to wild populations has been proposed as a means of addressing some of the world's most pressing ecological and public health challenges caused by insect pests. Technologies that would allow this, such as synthetic gene drives, have been under development for many decades. Recently, a new generation of programmable nucleases has dramatically accelerated technological development. CRISPR-Cas9 has improved the efficiency of genetic engineering and has been used as the principal effector nuclease in different gene drive inheritance biasing mechanisms. Of these nuclease-based gene drives, homing endonuclease gene drives have been the subject of the bulk of research efforts (particularly in insects), with many different iterations having been developed upon similar core designs. We chart the history of homing gene drive development, highlighting the emergence of challenges such as unintended repair outcomes, "leaky" expression, and parental deposition. We conclude by discussing the progress made in developing strategies to increase the efficiency of homing endonuclease gene drives and mitigate or prevent unintended outcomes.
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Affiliation(s)
- Sebald A. N. Verkuijl
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Joshua X. D. Ang
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Pirbright, United Kingdom
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23
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Wang GH, Du J, Chu CY, Madhav M, Hughes GL, Champer J. Symbionts and gene drive: two strategies to combat vector-borne disease. Trends Genet 2022; 38:708-723. [PMID: 35314082 DOI: 10.1016/j.tig.2022.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 01/26/2023]
Abstract
Mosquitoes bring global health problems by transmitting parasites and viruses such as malaria and dengue. Unfortunately, current insecticide-based control strategies are only moderately effective because of high cost and resistance. Thus, scalable, sustainable, and cost-effective strategies are needed for mosquito-borne disease control. Symbiont-based and genome engineering-based approaches provide new tools that show promise for meeting these criteria, enabling modification or suppression approaches. Symbiotic bacteria like Wolbachia are maternally inherited and manipulate mosquito host reproduction to enhance their vertical transmission. Genome engineering-based gene drive methods, in which mosquitoes are genetically altered to spread drive alleles throughout wild populations, are also proving to be a potentially powerful approach in the laboratory. Here, we review the latest developments in both symbionts and gene drive-based methods. We describe some notable similarities, as well as distinctions and obstacles, relating to these promising technologies.
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Affiliation(s)
- Guan-Hong Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jie Du
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chen Yi Chu
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Mukund Madhav
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Grant L Hughes
- Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Jackson Champer
- Center for Bioinformatics, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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24
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Xu X, Harvey-Samuel T, Siddiqui HA, Ang JXD, Anderson ME, Reitmayer CM, Lovett E, Leftwich PT, You M, Alphey L. Toward a CRISPR-Cas9-based Gene Drive in the Diamondback Moth Plutella xylostella. CRISPR J 2022; 5:224-236. [PMID: 35285719 DOI: 10.1089/crispr.2021.0129] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Promising to provide powerful genetic control tools, gene drives have been constructed in multiple dipteran insects, yeast, and mice for the purposes of population elimination or modification. However, it remains unclear whether these techniques can be applied to lepidopterans. Here, we used endogenous regulatory elements to drive Cas9 and single guide RNA (sgRNA) expression in the diamondback moth (DBM), Plutella xylostella, and test the first split gene drive system in a lepidopteran. The DBM is an economically important global agriculture pest of cruciferous crops and has developed severe resistance to various insecticides, making it a prime candidate for such novel control strategy development. A very high level of somatic editing was observed in Cas9/sgRNA transheterozygotes, although no significant homing was revealed in the subsequent generation. Although heritable Cas9-medated germline cleavage as well as maternal and paternal Cas9 deposition were observed, rates were far lower than for somatic cleavage events, indicating robust somatic but limited germline activity of Cas9/sgRNA under the control of selected regulatory elements. Our results provide valuable experience, paving the way for future construction of gene drives or other Cas9-based genetic control strategies in DBM and other lepidopterans.
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Affiliation(s)
- Xuejiao Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, P.R. China.,School of Life Sciences, Peking University, Beijing, P.R. China
| | - Tim Harvey-Samuel
- Arthropod Genetics Group, The Pirbright Institute, Woking, Pirbright, United Kingdom
| | - Hamid Anees Siddiqui
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Joshua Xin De Ang
- Arthropod Genetics Group, The Pirbright Institute, Woking, Pirbright, United Kingdom
| | | | - Christine M Reitmayer
- Arthropod Genetics Group, The Pirbright Institute, Woking, Pirbright, United Kingdom
| | - Erica Lovett
- Arthropod Genetics Group, The Pirbright Institute, Woking, Pirbright, United Kingdom
| | - Philip T Leftwich
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, P.R. China
| | - Luke Alphey
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, P.R. China.,Arthropod Genetics Group, The Pirbright Institute, Woking, Pirbright, United Kingdom
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25
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Cook F, Bull JJ, Gomulkiewicz R. Gene drive escape from resistance depends on mechanism and ecology. Evol Appl 2022; 15:721-734. [PMID: 35603023 PMCID: PMC9108321 DOI: 10.1111/eva.13358] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 11/26/2022] Open
Abstract
Gene drives can potentially be used to suppress pest populations, and the advent of CRISPR technology has made it feasible to engineer them in many species, especially insects. What remains largely unknown for implementations is whether antidrive resistance will evolve to block the population suppression. An especially serious threat to some kinds of drive is mutations in the CRISPR cleavage sequence that block the action of CRISPR, but designs have been proposed to avoid this type of resistance. Various types of resistance at loci away from the cleavage site remain a possibility, which is the focus here. It is known that modest‐effect suppression drives can essentially “outrun” unlinked resistance even when that resistance is present from the start. We demonstrate here how the risk of evolving (unlinked) resistance can be further reduced without compromising overall suppression by introducing multiple suppression drives or by designing drives with specific ecological effects. However, we show that even modest‐effect suppression drives remain vulnerable to the evolution of extreme levels of inbreeding, which halt the spread of the drive without actually interfering with its mechanism. The landscape of resistance evolution against suppression drives is therefore complex, but avenues exist for enhancing gene drive success.
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Affiliation(s)
- Forest Cook
- School of Electrical Engineering & Computer Science Washington State University Pullman WA 99164 USA
| | - James J. Bull
- Dept of Biological Sciences University of Idaho Moscow ID 83843 USA
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26
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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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27
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Kaduskar B, Kushwah RBS, Auradkar A, Guichard A, Li M, Bennett JB, Julio AHF, Marshall JM, Montell C, Bier E. Reversing insecticide resistance with allelic-drive in Drosophila melanogaster. Nat Commun 2022; 13:291. [PMID: 35022402 PMCID: PMC8755802 DOI: 10.1038/s41467-021-27654-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/02/2021] [Indexed: 12/27/2022] Open
Abstract
A recurring target-site mutation identified in various pests and disease vectors alters the voltage gated sodium channel (vgsc) gene (often referred to as knockdown resistance or kdr) to confer resistance to commonly used insecticides, pyrethroids and DDT. The ubiquity of kdr mutations poses a major global threat to the continued use of insecticides as a means for vector control. In this study, we generate common kdr mutations in isogenic laboratory Drosophila strains using CRISPR/Cas9 editing. We identify differential sensitivities to permethrin and DDT versus deltamethrin among these mutants as well as contrasting physiological consequences of two different kdr mutations. Importantly, we apply a CRISPR-based allelic-drive to replace a resistant kdr mutation with a susceptible wild-type counterpart in population cages. This successful proof-of-principle opens-up numerous possibilities including targeted reversion of insecticide-resistant populations to a native susceptible state or replacement of malaria transmitting mosquitoes with those bearing naturally occurring parasite resistant alleles. Insecticide resistance (IR) poses a major global health challenge. Here, the authors generate common IR mutations in laboratory Drosophila strains and use a CRISPR-based allelic-drive to replace an IR allele with a susceptible wild-type counterpart, providing a potent new tool for vector control.
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Affiliation(s)
- Bhagyashree Kaduskar
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India.,Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Raja Babu Singh Kushwah
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India.,Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Annabel Guichard
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Menglin Li
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Jared B Bennett
- Biophysics Graduate Group, Division of Biological Sciences, College of Letters and Science, University of California, Berkeley, CA, 94720, USA
| | | | - John M Marshall
- Division of Biostatistics and Epidemiology - School of Public Health, University of California, Berkeley, CA, 94720, USA.,Innovative Genomics Institute, Berkeley, CA, 94720, USA
| | - Craig Montell
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA. .,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA.
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28
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Fölsz O, Lin CC, Task D, Riabinina O, Potter CJ. The Q-system: A Versatile Repressible Binary Expression System. Methods Mol Biol 2022; 2540:35-78. [PMID: 35980572 DOI: 10.1007/978-1-0716-2541-5_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] [Indexed: 06/15/2023]
Abstract
Binary expression systems are useful genetic tools for experimentally labeling or manipulating the function of defined cells. The Q-system is a repressible binary expression system that consists of a transcription factor QF (and the recently improved QF2/QF2w), the inhibitor QS, a QUAS-geneX effector, and a drug that inhibits QS (quinic acid). The Q-system can be used alone or in combination with other binary expression systems, such as GAL4/UAS and LexA/LexAop. In this review chapter, we discuss the past, present, and future of the Q-system for applications in Drosophila and other organisms. We discuss the in vivo application of the Q-system for transgenic labeling, the modular nature of QF that allows chimeric or split transcriptional activators to be developed, its temporal control by quinic acid, new methods to generate QF2 reagents, intersectional expression labeling, and its recent adoption into many emerging experimental species.
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Affiliation(s)
- Orsolya Fölsz
- Department of Biosciences, Durham University, Durham, UK
| | - Chun-Chieh Lin
- Department of Pathology and Laboratory Medicine, Giesel School of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Darya Task
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | | | - Christopher J Potter
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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29
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Abstract
Gene drives are selfish genetic elements that are transmitted to progeny at super-Mendelian (>50%) frequencies. Recently developed CRISPR-Cas9-based gene-drive systems are highly efficient in laboratory settings, offering the potential to reduce the prevalence of vector-borne diseases, crop pests and non-native invasive species. However, concerns have been raised regarding the potential unintended impacts of gene-drive systems. This Review summarizes the phenomenal progress in this field, focusing on optimal design features for full-drive elements (drives with linked Cas9 and guide RNA components) that either suppress target mosquito populations or modify them to prevent pathogen transmission, allelic drives for updating genetic elements, mitigating strategies including trans-complementing split-drives and genetic neutralizing elements, and the adaptation of drive technology to other organisms. These scientific advances, combined with ethical and social considerations, will facilitate the transparent and responsible advancement of these technologies towards field implementation.
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Affiliation(s)
- Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, USA.
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30
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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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31
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Lalyer CR, Sigsgaard L, Giese B. Ecological vulnerability analysis for suppression of Drosophila suzukii by gene drives. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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32
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Terradas G, Hermann A, James AA, McGinnis W, Bier E. High-resolution in situ analysis of Cas9 germline transcript distributions in gene-drive Anopheles mosquitoes. G3-GENES GENOMES GENETICS 2021; 12:6428532. [PMID: 34791161 PMCID: PMC8728002 DOI: 10.1093/g3journal/jkab369] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/14/2021] [Indexed: 11/12/2022]
Abstract
Gene drives are programmable genetic elements that can spread beneficial traits into wild populations to aid in vector-borne pathogen control. Two different drives have been developed for population modification of mosquito vectors. The Reckh drive (vasa-Cas9) in Anopheles stephensi displays efficient allelic conversion through males but generates frequent drive-resistant mutant alleles when passed through females. In contrast, the AgNos-Cd1 drive (nos-Cas9) in An. gambiae achieves almost complete allelic conversion through both genders. Here, we examined the subcellular localization of RNA transcripts in the mosquito germline. In both transgenic lines, Cas9 is strictly co-expressed with endogenous genes in stem and pre-meiotic cells of the testes, where both drives display highly efficient conversion. However, we observed distinct co-localization patterns for the two drives in female reproductive tissues. These studies suggest potential determinants underlying efficient drive through the female germline. We also evaluated expression patterns of alternative germline genes for future gene-drive designs.
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Affiliation(s)
- Gerard Terradas
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anita Hermann
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anthony A James
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, 92697, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA
| | - William McGinnis
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
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33
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Kandul NP, Belikoff EJ, Liu J, Buchman A, Li F, Yamamoto A, Yang T, Shriner I, Scott MJ, Akbari OS. Genetically Encoded CRISPR Components Yield Efficient Gene Editing in the Invasive Pest Drosophila suzukii. CRISPR J 2021; 4:739-751. [PMID: 34661429 DOI: 10.1089/crispr.2021.0032] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Originally from Asia, Drosophila suzukii Matsumura is a global pest of economically important soft-skinned fruits. Also commonly known as spotted wing drosophila, it is largely controlled through repeated applications of broad-spectrum insecticides by which resistance has been observed in the field. There is a pressing need for a better understanding of D. suzukii biology and for developing alternative environmentally friendly methods of control. The RNA-guided Cas9 nuclease has revolutionized functional genomics and is an integral component of several recently developed genetic strategies for population control of insects. Here, we describe genetically modified strains that encode three different terminators and four different promoters to express Cas9 robustly in both the soma and/or germline of D. suzukii. The Cas9 strains were rigorously evaluated through genetic crossing to transgenic strains that encode single-guide RNAs targeting the conserved X-linked yellow body and white eye genes. We find that several Cas9/gRNA strains display remarkably high editing capacity. Going forward, these tools will be instrumental for evaluating gene function in D. suzukii and may even provide tools useful for the development of new genetic strategies for control of this invasive species.
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Affiliation(s)
- Nikolay P Kandul
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
| | - Esther J Belikoff
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
| | - Anna Buchman
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
| | - Fang Li
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Akihiko Yamamoto
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Ting Yang
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
| | - Isaiah Shriner
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
| | - Maxwell J Scott
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, USA; and North Carolina State University, Raleigh, North Carolina, USA
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34
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Faber NR, Meiborg AB, Mcfarlane GR, Gorjanc G, Harpur BA. A gene drive does not spread easily in populations of the honey bee parasite Varroa destructor. APIDOLOGIE 2021; 52:1112-1127. [PMID: 35068598 PMCID: PMC8755698 DOI: 10.1007/s13592-021-00891-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/04/2021] [Accepted: 08/19/2021] [Indexed: 05/29/2023]
Abstract
UNLABELLED Varroa mites (Varroa destructor) are the most significant threat to beekeeping worldwide. They are directly or indirectly responsible for millions of colony losses each year. Beekeepers are somewhat able to control varroa populations through the use of physical and chemical treatments. However, these methods range in effectiveness, can harm honey bees, can be physically demanding on the beekeeper, and do not always provide complete protection from varroa. More importantly, in some populations varroa mites have developed resistance to available acaricides. Overcoming the varroa mite problem will require novel and targeted treatment options. Here, we explore the potential of gene drive technology to control varroa. We show that spreading a neutral gene drive in varroa is possible but requires specific colony-level management practices to overcome the challenges of both inbreeding and haplodiploidy. Furthermore, continued treatment with acaricides is necessary to give a gene drive time to fix in the varroa population. Unfortunately, a gene drive that impacts female or male fertility does not spread in varroa. Therefore, we suggest that the most promising way forward is to use a gene drive which carries a toxin precursor or removes acaricide resistance alleles. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13592-021-00891-5.
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Affiliation(s)
- Nicky R. Faber
- HighlanderLab, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG United Kingdom
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Adriaan B. Meiborg
- HighlanderLab, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG United Kingdom
| | - Gus R. Mcfarlane
- Burdon Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG United Kingdom
| | - Gregor Gorjanc
- HighlanderLab, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG United Kingdom
| | - Brock A. Harpur
- Department of Entomology, Purdue University, West Lafayette, IN 47907 USA
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35
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Fuchs S, Garrood WT, Beber A, Hammond A, Galizi R, Gribble M, Morselli G, Hui TYJ, Willis K, Kranjc N, Burt A, Crisanti A, Nolan T. Resistance to a CRISPR-based gene drive at an evolutionarily conserved site is revealed by mimicking genotype fixation. PLoS Genet 2021; 17:e1009740. [PMID: 34610011 PMCID: PMC8519452 DOI: 10.1371/journal.pgen.1009740] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/15/2021] [Accepted: 09/24/2021] [Indexed: 01/06/2023] Open
Abstract
CRISPR-based homing gene drives can be designed to disrupt essential genes whilst biasing their own inheritance, leading to suppression of mosquito populations in the laboratory. This class of gene drives relies on CRISPR-Cas9 cleavage of a target sequence and copying ('homing') therein of the gene drive element from the homologous chromosome. However, target site mutations that are resistant to cleavage yet maintain the function of the essential gene are expected to be strongly selected for. Targeting functionally constrained regions where mutations are not easily tolerated should lower the probability of resistance. Evolutionary conservation at the sequence level is often a reliable indicator of functional constraint, though the actual level of underlying constraint between one conserved sequence and another can vary widely. Here we generated a novel adult lethal gene drive (ALGD) in the malaria vector Anopheles gambiae, targeting an ultra-conserved target site in a haplosufficient essential gene (AGAP029113) required during mosquito development, which fulfils many of the criteria for the target of a population suppression gene drive. We then designed a selection regime to experimentally assess the likelihood of generation and subsequent selection of gene drive resistant mutations at its target site. We simulated, in a caged population, a scenario where the gene drive was approaching fixation, where selection for resistance is expected to be strongest. Continuous sampling of the target locus revealed that a single, restorative, in-frame nucleotide substitution was selected. Our findings show that ultra-conservation alone need not be predictive of a site that is refractory to target site resistance. Our strategy to evaluate resistance in vivo could help to validate candidate gene drive targets for their resilience to resistance and help to improve predictions of the invasion dynamics of gene drives in field populations.
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Affiliation(s)
- Silke Fuchs
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - William T. Garrood
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Anna Beber
- Department of Biology, University of Padua, Padua, Italy
| | - Andrew Hammond
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, United States of America
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, Staffordshire, United Kingdom
| | - Matthew Gribble
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Giulia Morselli
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tin-Yu J. Hui
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Katie Willis
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Andrea Crisanti
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Molecular Medicine, University of Padua, Padua, Italy
- * E-mail: (AC); (TN)
| | - Tony Nolan
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- * E-mail: (AC); (TN)
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36
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Bier E, Nizet V. Driving to Safety: CRISPR-Based Genetic Approaches to Reducing Antibiotic Resistance. Trends Genet 2021; 37:745-757. [PMID: 33745750 DOI: 10.1016/j.tig.2021.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Bacterial resistance to antibiotics has reached critical levels, skyrocketing in hospitals and the environment and posing a major threat to global public health. The complex and challenging problem of reducing antibiotic resistance (AR) requires a network of both societal and science-based solutions to preserve the most lifesaving pharmaceutical intervention known to medicine. In addition to developing new classes of antibiotics, it is essential to safeguard the clinical efficacy of existing drugs. In this review, we examine the potential application of novel CRISPR-based genetic approaches to reducing AR in both environmental and clinical settings and prolonging the utility of vital antibiotics.
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Affiliation(s)
- Ethan Bier
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA.
| | - Victor Nizet
- Tata Institute for Genetics and Society, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0349, USA; Collaborative to Halt Antibiotic-Resistant Microbes, Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA; Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0687, USA
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37
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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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38
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Wang GH, Gamez S, Raban RR, Marshall JM, Alphey L, Li M, Rasgon JL, Akbari OS. Combating mosquito-borne diseases using genetic control technologies. Nat Commun 2021; 12:4388. [PMID: 34282149 PMCID: PMC8290041 DOI: 10.1038/s41467-021-24654-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/30/2021] [Indexed: 01/03/2023] Open
Abstract
Mosquito-borne diseases, such as dengue and malaria, pose significant global health burdens. Unfortunately, current control methods based on insecticides and environmental maintenance have fallen short of eliminating the disease burden. Scalable, deployable, genetic-based solutions are sought to reduce the transmission risk of these diseases. Pathogen-blocking Wolbachia bacteria, or genome engineering-based mosquito control strategies including gene drives have been developed to address these problems, both requiring the release of modified mosquitoes into the environment. Here, we review the latest developments, notable similarities, and critical distinctions between these promising technologies and discuss their future applications for mosquito-borne disease control.
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Affiliation(s)
- Guan-Hong Wang
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Stephanie Gamez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA
| | - Robyn R Raban
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, 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
| | - Luke Alphey
- Arthropod Genetics, The Pirbright Institute, Pirbright, UK
| | - Ming Li
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA
| | - Jason L Rasgon
- Department of Entomology, The Pennsylvania State University, University Park, PA, USA
- The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA, USA.
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39
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Devos Y, Mumford JD, Bonsall MB, Camargo AM, Firbank LG, Glandorf DCM, Nogué F, Paraskevopoulos K, Wimmer EA. Potential use of gene drive modified insects against disease vectors, agricultural pests and invasive species poses new challenges for risk assessment. Crit Rev Biotechnol 2021; 42:254-270. [PMID: 34167401 DOI: 10.1080/07388551.2021.1933891] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Potential future application of engineered gene drives (GDs), which bias their own inheritance and can spread genetic modifications in wild target populations, has sparked both enthusiasm and concern. Engineered GDs in insects could potentially be used to address long-standing challenges in control of disease vectors, agricultural pests and invasive species, or help to rescue endangered species, and thus provide important public benefits. However, there are concerns that the deliberate environmental release of GD modified insects may pose different or new harms to animal and human health and the wider environment, and raise novel challenges for risk assessment. Risk assessors, risk managers, developers, potential applicants and other stakeholders at many levels are currently discussing whether there is a need to develop new or additional risk assessment guidance for the environmental release of GD modified organisms, including insects. Developing new or additional guidance that is useful and practical is a challenge, especially at an international level, as risk assessors, risk managers and many other stakeholders have different, often contrasting, opinions and perspectives toward the environmental release of GD modified organisms, and on the adequacy of current risk assessment frameworks for such organisms. Here, we offer recommendations to overcome some of the challenges associated with the potential future development of new or additional risk assessment guidance for GD modified insects and provide considerations on areas where further risk assessment guidance may be required.
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Affiliation(s)
- Yann Devos
- GMO Unit, European Food Safety Authority (EFSA), Parma, Italy
| | - John D Mumford
- Centre for Environmental Policy, Imperial College London, Ascot, UK
| | | | - Ana M Camargo
- GMO Unit, European Food Safety Authority (EFSA), Parma, Italy
| | | | - Debora C M Glandorf
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | | | - Ernst A Wimmer
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, GZMB, Georg August University, Göttingen, Germany
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40
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Li Z, Marcel N, Devkota S, Auradkar A, Hedrick SM, Gantz VM, Bier E. CopyCatchers are versatile active genetic elements that detect and quantify inter-homolog somatic gene conversion. Nat Commun 2021; 12:2625. [PMID: 33976171 PMCID: PMC8113449 DOI: 10.1038/s41467-021-22927-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 04/01/2021] [Indexed: 11/08/2022] Open
Abstract
CRISPR-based active genetic elements, or gene-drives, copied via homology-directed repair (HDR) in the germline, are transmitted to progeny at super-Mendelian frequencies. Active genetic elements also can generate widespread somatic mutations, but the genetic basis for such phenotypes remains uncertain. It is generally assumed that such somatic mutations are generated by non-homologous end-joining (NHEJ), the predominant double stranded break repair pathway active in somatic cells. Here, we develop CopyCatcher systems in Drosophila to detect and quantify somatic gene conversion (SGC) events. CopyCatchers inserted into two independent genetic loci reveal unexpectedly high rates of SGC in the Drosophila eye and thoracic epidermis. Focused RNAi-based genetic screens identify several unanticipated loci altering SGC efficiency, one of which (c-MYC), when downregulated, promotes SGC mediated by both plasmid and homologous chromosome-templates in human HEK293T cells. Collectively, these studies suggest that CopyCatchers can serve as effective discovery platforms to inform potential gene therapy strategies.
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Affiliation(s)
- Zhiqian Li
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Nimi Marcel
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Stephen M Hedrick
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA, USA.
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41
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Kandul NP, Liu J, Bennett JB, Marshall JM, Akbari OS. A confinable home-and-rescue gene drive for population modification. eLife 2021; 10:e65939. [PMID: 33666174 PMCID: PMC7968924 DOI: 10.7554/elife.65939] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Homing-based gene drives, engineered using CRISPR/Cas9, have been proposed to spread desirable genes throughout populations. However, invasion of such drives can be hindered by the accumulation of resistant alleles. To limit this obstacle, we engineer a confinable population modification home-and-rescue (HomeR) drive in Drosophila targeting an essential gene. In our experiments, resistant alleles that disrupt the target gene function were recessive lethal and therefore disadvantaged. We demonstrate that HomeR can achieve an increase in frequency in population cage experiments, but that fitness costs due to the Cas9 insertion limit drive efficacy. Finally, we conduct mathematical modeling comparing HomeR to contemporary gene drive architectures for population modification over wide ranges of fitness costs, transmission rates, and release regimens. HomeR could potentially be adapted to other species, as a means for safe, confinable, modification of wild populations.
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Affiliation(s)
- Nikolay P Kandul
- Section of Cell and Developmental Biology, University of California, San DiegoSan DiegoUnited States
| | - Junru Liu
- Section of Cell and Developmental Biology, University of California, San DiegoSan DiegoUnited States
| | - Jared B Bennett
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
| | - John M Marshall
- Division of Epidemiology and Biostatistics, School of Public Health, University of California, BerkeleyBerkeleyUnited States
| | - Omar S Akbari
- Section of Cell and Developmental Biology, University of California, San DiegoSan DiegoUnited States
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42
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Willis K, Burt A. Double drives and private alleles for localised population genetic control. PLoS Genet 2021; 17:e1009333. [PMID: 33755671 PMCID: PMC8018619 DOI: 10.1371/journal.pgen.1009333] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/02/2021] [Accepted: 03/07/2021] [Indexed: 12/12/2022] Open
Abstract
Synthetic gene drive constructs could, in principle, provide the basis for highly efficient interventions to control disease vectors and other pest species. This efficiency derives in part from leveraging natural processes of dispersal and gene flow to spread the construct and its impacts from one population to another. However, sometimes (for example, with invasive species) only specific populations are in need of control, and impacts on non-target populations would be undesirable. Many gene drive designs use nucleases that recognise and cleave specific genomic sequences, and one way to restrict their spread would be to exploit sequence differences between target and non-target populations. In this paper we propose and model a series of low threshold double drive designs for population suppression, each consisting of two constructs, one imposing a reproductive load on the population and the other inserted into a differentiated locus and controlling the drive of the first. Simple deterministic, discrete-generation computer simulations are used to assess the alternative designs. We find that the simplest double drive designs are significantly more robust to pre-existing cleavage resistance at the differentiated locus than single drive designs, and that more complex designs incorporating sex ratio distortion can be more efficient still, even allowing for successful control when the differentiated locus is neutral and there is up to 50% pre-existing resistance in the target population. Similar designs can also be used for population replacement, with similar benefits. A population genomic analysis of CRISPR PAM sites in island and mainland populations of the malaria mosquito Anopheles gambiae indicates that the differentiation needed for our methods to work can exist in nature. Double drives should be considered when efficient but localised population genetic control is needed and there is some genetic differentiation between target and non-target populations.
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Affiliation(s)
- Katie Willis
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, United Kingdom
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